Contrast transfer function correction applied to cryo-electron tomography and sub-tomogram averaging

Cryo-electron tomography together with averaging of sub-tomograms containing identical particles can reveal the structure of proteins or protein complexes in their native environment. The resolution of this technique is limited by the contrast transfer function (CTF) of the microscope. The CTF is not routinely corrected in cryo-electron tomography because of difficulties including CTF detection, due to the low signal to noise ratio, and CTF correction, since images are characterised by a spatially variant CTF. Here we simulate the effects of the CTF on the resolution of the final reconstruction, before and after CTF correction, and consider the effect of errors and approximations in defocus determination. We show that errors in defocus determination are well tolerated when correcting a series of tomograms collected at a range of defocus values. We apply methods for determining the CTF parameters in low signal to noise images of tilted specimens, for monitoring defocus changes using observed magnification changes, and for correcting the CTF prior to reconstruction. Using bacteriophage PRDI as a test sample, we demonstrate that this approach gives an improvement in the structure obtained by sub-tomogram averaging from cryo-electron tomograms.

Muscle gene electrotransfer is increased by the antioxidant tempol in mice

Electropermeabilization (EP) is an effective method of gene transfer into different tissues. During EP, reactive oxygen species (ROS) are formed, which could affect transfection efficiency. The role of generated ROS and the role of antioxidants in electrotransfer in myoblasts in vitro and in Musculus tibialis cranialis in mice were, therefore, investigated. We demonstrate in the study that during EP of C2C12 myoblasts, ROS are generated on the surface of the cells, which do not induce long-term genomic DNA damage. Plasmid DNA for transfection (pEGFP-N1), which is present outside the cells during EP, neutralizes the generated ROS. The ROS generation is proportional to the amplitude of the electric pulses and can be scavenged by antioxidants, such as vitamin C or tempol. When antioxidants were used during gene electrotransfer, the transfection efficiency of C2C12 myoblasts was statistically significantly increased 1.6-fold with tempol. Also in vivo, the transfection efficiency of M. tibialis cranialis in mice was statistically significantly increased 1.4-fold by tempol. The study indicates that ROS are generated on cells during EP and can be scavenged by antioxidants. Specifically, tempol can be used to improve gene electrotransfer into the muscle and possibly also to other tissues.

Predictors of mental health in midlife and older women : results from the Australian Healthy Aging of Women Study

Purpose: To examine the extent to which socio-demographic characteristics, modifiable lifestyle factors and health status influence the mental health of midlife and older Australian women from the Australian Healthy Aging of Women (HOW) study. Methods: Data on health status, chronic disease and modifiable lifestyle factors were collected from a random sample of 340 women aged 40-65 years, residing in Queensland, Australia in 2011. Structural equation modelling (SEM) was used to measure the effect of a range of socio-demographic characteristics (marital status, age, income), modifiable lifestyle factors (caffeine intake, alcohol consumption, exercise, physical activity, sleep), and health markers (self-reported physical health, history of chronic illness) on the latent construct, mental health. Mental health was evaluated using the Medical Outcomes Study Short Form 12 (SF-12®) and the Center for Epidemiologic Studies Depression Scale (CES-D). Results: The model was a good fit for the data (χ2 = 40.166, df =312, p 0.125, CFI = 0.976, TLI = 0.950, RMSEA = 0.030, 90% CI = 0.000-0.053); the model suggested mental health was negatively influenced by sleep disturbance (β = -0.628), sedentary lifestyle (β = -0.137), having been diagnosed with one or more chronic illnesses (β = -0.203), and poor self-reported physical health (β = - 0.161). While mental health was associated with sleep, it was not correlated with many other lifestyle factors (BMI (β = -0.050), alcohol consumption (β = 0.079), or cigarette smoking (β = 0.008)) or background socio-demographic characteristics (age (β = 0.078), or income (β = -0.039)). Conclusion: While research suggests that it is important to engage in a range health promoting behaviours to preserve good health, we found that only sleep disturbance, physical health, chronic illness and level of physical activity predicted current mental health. However, while socio-demographic characteristics and modifiable lifestyle factors seemed to have little direct impact on mental health, they probably had an indirect effect.

Environmental productivity and Kuznets curve in India

As a result of India's extremely rapid economic growth, the scale and seriousness of environmental problems are no longer in doubt. Whether pollution abatement technologies are utilized more efficiently is crucial in the analysis of environmental management because it influences the cost of alternative production and pollution abatement technologies. In this study, we use state-level industry data of sulfur dioxide, nitrogen dioxide, and suspended particular matter over the period 1991-2003. Employing recently developed productivity measurement technique, we show that overall environmental productivities decrease over time in India. Furthermore, we analyze the determinants of environmental productivities and find environmental Kuznets curve type relationship existences between environmental productivity and income. Panel analysis results show that the scale effect dominates over the technique effect. Therefore, a combined effect of income on environmental productivity is negative.

Recommendations for the categorization of germ cell mutagens

Germ cell mutagens are currently classified into three categories in the German List of MAK- and BAT-Values. These categories have been revised and extended in analogy to the new categories for carcinogenic chemicals. Germ cell mutagens produce heritable gene mutations, and heritable structural and numerical chromosome aberrations in germ cells. The original categories 1 and 2 for germ cell mutagens remained unchanged. Two new categories 3 A and 3 B are proposed for chemicals which are suspected to be germ cell mutagens. A new category 5 is proposed for germ cell mutagens with low potency which contribute negligibly to human genetic risk provided the MAK value is observed. The following categories are presented for further discussion. 1. Germ cell mutagens which have been shown to increase the mutant frequency among the progeny of exposed humans. 2. Germ cell mutagens which have been shown to increase the mutant frequency among the progeny of exposed animals. 3 A. Substances which have been shown to induce genetic damage in germ cells of humans or animals, or which are mutagenic in somatic cells and have been shown to reach the germ cells in their active forms. 3 B. Substances which are suspected of being germ cell mutagens because of their genotoxic effects in mammalian somatic cells in vivo or, in exceptional cases in the absence of in vivo data, if they are clearly mutagenic in vitro and structurally related to in vivo mutagens. 4. not applicable (Category 4 was introduced for carcinogenic substances with nongenotoxic modes of action. By definition, germ cell mutagens are genotoxic. Therefore, a Category 4 for germ cell mutagens cannot exist.) 5. Germ cell mutagens, the potency of which is considered to be so low that, provided the MAK value is observed, their contribution to genetic risk is expected not to be significant.

Cytochrome p450 1b1, a new keystone in gene-environment interactions related to human head and neck cancer?

Alcohol consumption and tobacco smoking are major causes of head and neck cancers, and regional differences point to the importance of research into gene-environment interactions. Much interest has been focused on polymorphisms of CYP1A1 and of GSTM1 and GSTT1, but a number of studies have not demonstrated significant effects. This has mostly been ascribed to small sample sizes. In general, the impact of polymorphisms of metabolic enzymes appears inconsistent, with some reports of weak-to-moderate associations, and with others of no elevation of risks. The classical cytochrome P450 isoenzyme considered for metabolic activation of polycyclic aromatic hydrocarbons (PAH) is CYP1A1. A new member of the CYP1 family, CYP1B1, was cloned in 1994, currently representing the only member of the CYP1B subfamily. A number of single nucleotide polymorphisms of the CYP1B1 gene have been reported. The amino acid substitutions Val432Leu (CYP1B1*3) and Asn453Ser (CYP1B1*4), located in the heme binding domain of CYP1B1, appear as likely candidates to be linked with biological effects. CYP1B1 activates a wide range of PAH, aromatic and heterocyclic amines. Very recently, the CYP1B1 codon 432 polymorphism (CYP1B1*3) has been identified as a susceptibility factor in smoking-related head-and-neck squamous cell cancer. The impact of this polymorphic variant of CYP1B1 on cancer risk was also reflected by an association with the frequency of somatic mutations of the p53 gene. Combined genotype analysis of CYP1B1 and the glutathione transferases GSTM1 or GSTT1 has pointed to interactive effects. This provides new molecular evidence that tobacco smoke-specific compounds relevant to head and neck carcinogenesis are metabolically activated through CYP1B1 and is consistent with a major pathogenetic relevance of PAH as ingredients of tobacco smoke.

Markers of genetic susceptibility in human environmental hygiene and toxicology : the role of selected CYP, NAT and GST genes

Inherited genetic traits co-determine the susceptibility of an individual to a toxic chemical. Special emphasis has been put on individual responses to environmental and industrial carcinogens, but other chronic diseases are of increasing interest. Polymorphisms of relevant xenobiotic metabolising enzymes may be used as toxicological susceptibility markers. A growing number of genes encoding enzymes involved in biotransformation of toxicants and in cellular defence against toxicant-induced damage to the cells has been identified and cloned, leading to increased knowledge of allelic variants of genes and genetic defects that may result in a differential susceptibility toward environmental toxicants. "Low penetrating" polymorphisms in metabolism genes tend to be much more common in the population than allelic variants of "high penetrating" cancer genes, and are therefore of considerable importance from a public health point of view. Positive associations between cancer and CYP1A1 alleles, in particular the *2C I462V allele, were found for tissues following the aerodigestive tract. Again, in most cases, the effect of the variant CYP1A1 allele becomes apparent or clearer in connection with the GSTM1 null allele. The CYP1B1 codon 432 polymorphism (CYP1B1*3) has been identified as a susceptibility factor in smoking-related head-and-neck squameous cell cancer. The impact of this polymorphic variant of CYP1B1 on cancer risk was also reflected by an association with the frequency of somatic mutations of the p53 gene. Combined genotype analysis of CYP1B1 and the glutathione transferases GSTM1 or GSTT1 has also pointed to interactive effects. Of particular interest for the industrial and environmental field is the isozyme CYP2E1. Several genotypes of this isozyme have been characterised which seem to be associated with different levels of expression of enzyme activity. The acetylator status for NAT2 can be determined by genotyping or by phenotyping. In the pathogenesis of human bladder cancer due to occupational exposure to "classical" aromatic amines (benzidine, 4-aminodiphenyl, 1-naphthylamine) acetylation by NAT2 is regarded as a detoxication step. Interestingly, the underlying European findings of a higher susceptibility of slow acetylators towards aromatic amines are in contrast to findings in Chinese workers occupationally exposed to aromatic amines which points to different mechanisms of susceptibility between European and Chinese populations. Regarding human bladder cancer, the hypothesis has been put forward that genetic polymorphism of GSTM1 might be linked with the occurrence of this tumour type. This supports the hypothesis that exposure to PAH might causally be involved in urothelial cancers. The human polymorphic GST catalysing conjugation of halomethanes, dihalomethanes, ethylene oxide and a number of other industrial compounds could be characterised as a class theta enzyme (GSTT1) by means of molecular biology. "Conjugator" and "non-conjugator" phenotypes are coincident with the presence and absence of the GSTT1 gene. There are wide variations in the frequencies of GSTT1 deletion (GSTT1 *0/0) among different ethnicities. Human phenotyping is facilitated by the GST activity towards methyl bromide or ethylene oxide in erythrocytes which is representative of the metabolic GSTT1 competence of the entire organism. Inter-individual variations in xenobiotic metabolism capacities may be due to polymorphisms of the genes coding for the enzymes themselves or of the genes coding for the receptors or transcription factors which regulate the expression of the enzymes. Also, polymorphisms in several regions of genes may cause altered ligand affinity, transactivation activity or expression levels of the receptor subsequently influencing the expression of the downstream target genes. Studies of individual susceptibility to toxicants and gene-environment interaction are now emerging as an important component of molecular epidemiology.

Troubling silences and taboo texts : constructing safer and more positive school climates for same-sex attracted high school students in Australia

This chapter offers three insights into the relationship between curriculum decision making, positive school climate, and academic achievement for same-sex attracted (SSA) students, highlighting the need for students to be offered more than heteronormative narratives and silence on issues of sexuality in the official school curriculum. The authors firstly provide a review of research and report on findings of a doctoral study (Mikulsky, 2007) explaining the impact of SSA students’ perceptions of school climate on their motivation and academic self-concept. Situating the work in the context of the Australian Curriculum for English and associated classroom texts, the dominant discourse of ‘straight, white female’ heroines as exemplified in the globally popular young adult novel The hunger games and other texts popular with Australian students are critiqued, with an argument made for expanding notions of what it means to ‘attend to’ gender and sexuality through textual choice and critical pedagogy. The authors show how texts that feature LGBTQ characters and storylines continue to be marginalized and constructed as taboo and demonstrate how curricular choices can and do impact academic outcomes for marginalized students. Issues of gender and sexuality are framed as a cross-curriculum imperative, with recommendations made for the explicit inclusion of materials exploring gender and sexuality in the official curriculum of all key learning areas.

How innovation and R&D happen in the upstream oil & gas industry : insights from a global survey

Few would disagree that the upstream oil & gas industry has become more technology-intensive over the years. But how does innovation happen in the industry? Specifically, what ideas and inputs flow from which parts of the sector׳s value network, and where do these inputs go? And how do firms and organizations from different countries contribute differently to this process? This paper puts forward the results of a survey designed to shed light on these questions. Carried out in collaboration with the Society of Petroleum Engineers (SPE), the survey was sent to 469 executives and senior managers who played a significant role with regard to R&D and/or technology deployment in their respective business units. A total of 199 responses were received from a broad range of organizations and countries around the world. Several interesting themes and trends emerge from the results, including: (1) service companies tend to file considerably more patents per innovation than other types of organization; (2) over 63% of the deployed innovations reported in the survey originated in service companies; (3) neither universities nor government-led research organizations were considered to be valuable sources of new information and knowledge in the industry׳s R&D initiatives, and; (4) despite the increasing degree of globalization in the marketplace, the USA still plays an extremely dominant role in the industry׳s overall R&D and technology deployment activities. By providing a detailed and objective snapshot of how innovation happens in the upstream oil & gas sector, this paper provides a valuable foundation for future investigations and discussions aimed at improving how R&D and technology deployment are managed within the industry. The methodology did result in a coverage bias within the survey, however, and the limitations arising from this are explored.

Gain's in knowledge, attitude and skills of counselors across three trainings programs

The Global Fund to Fight AIDS, Tuberculosis and Malaria (GFATM) sponsored by the G20 nations has helped fund the development of training programs for HIV/AIDS counselors in India. To date no study has examined the effectiveness of these training programs. This study, therefore, aimed to examine the impact of a 12 training program in improving the knowledge of new HIV/AIDS counselors in West Bengal and compare benefits of three training programs. Pre and post measures were taken from 87 counsellors attending three training programs organized by the GFATM-7 team of the Department of Applied Psychology, University of Calcutta. Overall pre and post training scores of three training programs together show significant improvements in knowledge. The findings from this study provide confidence that the 12 day training program can be effectively implemented among West Bengal HIV/AIDS counsellors.

Language change in socially structured populations

Language contact is a significant external social factor that impacts on the change in natural languages over time. In some circumstances this corresponds to language competition, in which individuals in a population choose one language over another based on their social interactions. We investigated the dynamics of language change in two initially separate populations of agents that were then mixed with levels of influence determined by the social classes of the two populations, with 16 different combinations tested. As expected, the study found that how the communities interact with each other impacts on the communal language developed. However, it was also found that the acquisition of new words was substantial even with limited interaction between populations and low levels of influence, and that comprehension could be well established across language groups even when production of words from the other language group was low.

Interpreting discovered patterns in terms of ontology concepts

Semantic Web offers many possibilities for future Web technologies. Therefore, it is a need to search for ways that can bring the huge amount of unstructured documents from current Web to Semantic Web automatically. One big challenge in searching for such ways is how to understand patterns by both humans and machine. To address this issue, we present an innovative model which interprets patterns to high level concepts. These concepts can explain the patterns' meanings in a human understandable way while improving the information filtering performance. The model is evaluated by comparing it against one state-of-the-art benchmark model using standard Reuters dataset. The results show that the proposed model is successful. The significance of this model is three fold. It gives a way to interpret text mining output, provides a technique to find concepts relevant to the whole set of patterns which is an essential feature to understand the topic, and to some extent overcomes information mismatch and overload problems of existing models. This model will be very useful for knowledge based applications.

Methotrexate-conjugated PEGylated dendrimers show differential patterns of deposition and activity in tumour-burdened lymph nodes after intravenous and subcutaneous administration in rats

The current study sought to explore whether the subcutaneous administration of lymph-targeted dendrimers, conjugated with a model chemotherapeutic (methotrexate, MTX), was able to enhance anticancer activity against lymph node metastases. The lymphatic pharmacokinetics and antitumour activity of PEGylated polylysine dendrimers conjugated to MTX [D-MTX(OH)] via a tumour-labile hexapeptide linker was examined in rats and compared to a similar system where MTX was α-carboxyl O-tert-butylated [D-MTX(OtBu)]. The latter has previously been shown to exhibit longer plasma circulation times. D-MTX(OtBu) was well absorbed from the subcutaneous injection site via the lymph, and 3 to 4%/g of the dose was retained by sentinel lymph nodes. In contrast, D-MTX(OH) showed limited absorption from the subcutaneous injection site, but absorption was almost exclusively via the lymph. The retention of D-MTX(OH) by sentinel lymph nodes was also significantly elevated (approximately 30% dose/g). MTX alone was not absorbed into the lymph. All dendrimers displayed lower lymph node targeting after intravenous administration. Despite significant differences in the lymph node retention of D-MTX(OH) and D-MTX(OtBu) after subcutaneous and intravenous administration, the growth of lymph node metastases was similarly inhibited. In contrast, the administration of MTX alone did not significantly reduce lymph node tumour growth. Subcutaneous administration of drug-conjugated dendrimers therefore provides an opportunity to improve drug deposition in downstream tumour-burdened lymph nodes. In this case, however, increased lymph node biodistribution did not correlate well with antitumour activity, possibly suggesting constrained drug release at the site of action.

Improved Security Analysis of Fugue-256 (Poster)

We present some improved analytical results as part of the ongoing work on the analysis of Fugue-256 hash function, a second round candidate in the NIST’s SHA3 competition. First we improve Aumasson and Phans’ integral distinguisher on the 5.5 rounds of the final transformation of Fugue-256 to 16.5 rounds. Next we improve the designers’ meet-in-the-middle preimage attack on Fugue-256 from 2480 time and memory to 2416. Finally, we comment on possible methods to obtain free-start distinguishers and free-start collisions for Fugue-256.

Evaluative decision-making for high-quality professional development: Cultivating an evaluative stance

Unprecedented policy attention to early childhood education internationally has highlighted the crucial need for a skilled early years workforce. Consequently, professional development of early years educators has become a global policy imperative. At the same time, many maintain that professional development research has reached an impasse. In this paper, we offer a new approach to addressing this impasse. In contrast to calls for a redesign of comparative studies of professional development programs, or for the refinement of researcher-constructed professional development evaluation frameworks, we argue the need to cultivate what we refer to as an ‘evaluative stance’ amongst all involved in making decisions about professional development in the early years – from senior bureaucrats with responsibilities for funding professional development programs to individual educators with choices about which professional development opportunities to take up. Drawing on three bodies of literature -- evaluation capacity building, personal epistemology, and co-production -- that, for the most part, have been overlooked with respect to early years professional learning this paper proposes a conceptual framework to explain why cultivating an evaluative stance in professional development decision-making has rich possibilities for systemic, sustainable, and transformative change in early years education.