Computational epigenetic profiling of CpG islets in MTHFR

Computational epigenetics is a new area of research focused on exploring how DNA methylation patterns affect transcription factor binding that affect gene expression patterns. The aim of this study was to produce a new protocol for the detection of DNA methylation patterns using computational analysis which can be further confirmed by bisulfite PCR with serial pyrosequencing. The upstream regulatory element and pre-initiation complex relative to CpG islets within the methylenetetrahydrofolate reductase gene were determined via computational analysis and online databases. The 1,104 bp long CpG island located near to or at the alternative promoter site of methylenetetrahydrofolate reductase gene was identified. The CpG plot indicated that CpG islets A and B, within the island, contained 62 and 75 % GC content CpG ratios of 0.70 and 0.80–0.95, respectively. Further exploration of the CpG islets A and B indicates that the transcription start sites were GGC which were absent from the TATA boxes. In addition, although six PROSITE motifs were identified in CpG B, no motifs were detected in CpG A. A number of cis-regulatory elements were found in different regions within the CpGs A and B. Transcription factors were predicted to bind to CpGs A and B with varying affinities depending on the DNA methylation status. In addition, transcription factor binding may influence the expression patterns of the methylenetetrahydrofolate reductase gene by recruiting chromatin condensation inducing factors. These results have significant implications for the understanding of the architecture of transcription factor binding at CpG islets as well as DNA methylation patterns that affect chromatin structure.

Security Analysis of Randomize-Hash-then-Sign Digital Signatures

At CRYPTO 2006, Halevi and Krawczyk proposed two randomized hash function modes and analyzed the security of digital signature algorithms based on these constructions. They showed that the security of signature schemes based on the two randomized hash function modes relies on properties similar to the second preimage resistance rather than on the collision resistance property of the hash functions. One of the randomized hash function modes was named the RMX hash function mode and was recommended for practical purposes. The National Institute of Standards and Technology (NIST), USA standardized a variant of the RMX hash function mode and published this standard in the Special Publication (SP) 800-106. In this article, we first discuss a generic online birthday existential forgery attack of Dang and Perlner on the RMX-hash-then-sign schemes. We show that a variant of this attack can be applied to forge the other randomize-hash-then-sign schemes. We point out practical limitations of the generic forgery attack on the RMX-hash-then-sign schemes. We then show that these limitations can be overcome for the RMX-hash-then-sign schemes if it is easy to find fixed points for the underlying compression functions, such as for the Davies-Meyer construction used in the popular hash functions such as MD5 designed by Rivest and the SHA family of hash functions designed by the National Security Agency (NSA), USA and published by NIST in the Federal Information Processing Standards (FIPS). We show an online birthday forgery attack on this class of signatures by using a variant of Dean’s method of finding fixed point expandable messages for hash functions based on the Davies-Meyer construction. This forgery attack is also applicable to signature schemes based on the variant of RMX standardized by NIST in SP 800-106. We discuss some important applications of our attacks and discuss their applicability on signature schemes based on hash functions with ‘built-in’ randomization. Finally, we compare our attacks on randomize-hash-then-sign schemes with the generic forgery attacks on the standard hash-based message authentication code (HMAC).

On Randomizing Hash Functions to Strengthen the Security of Digital Signatures

Halevi and Krawczyk proposed a message randomization algorithm called RMX as a front-end tool to the hash-then-sign digital signature schemes such as DSS and RSA in order to free their reliance on the collision resistance property of the hash functions. They have shown that to forge a RMX-hash-then-sign signature scheme, one has to solve a cryptanalytical task which is related to finding second preimages for the hash function. In this article, we will show how to use Dean’s method of finding expandable messages for finding a second preimage in the Merkle-Damgård hash function to existentially forge a signature scheme based on a t-bit RMX-hash function which uses the Davies-Meyer compression functions (e.g., MD4, MD5, SHA family) in 2 t/2 chosen messages plus 2 t/2 + 1 off-line operations of the compression function and similar amount of memory. This forgery attack also works on the signature schemes that use Davies-Meyer schemes and a variant of RMX published by NIST in its Draft Special Publication (SP) 800-106. We discuss some important applications of our attack.

Sustainability of public health interventions to reduce the risk of dioxin exposure at severe dioxin hot spots in Vietnam

Severe dioxin contamination at Bien Hoa and Da Nang airbases, Vietnam is of international concern. Public Health risk reduction programs were implemented in Bien Hoa in 2007-2009 and in Da Nang in 2009-2011. In 2009 and 2011 we reported the encouraging results of these interventions in improving the knowledge, attitude and practices (KAP) of local residents in reducing the dioxin exposure risk through foods. In 2013 we revisited these dioxin hot spots, aimed to evaluate whether the results of the intervention were maintained and to identify factors affecting the sustainability of the programs. To assess this, 16 in-depth interviews, six focus group discussions, and pre and post intervention KAP surveys were undertaken. 800 respondents from six intervention wards and 200 respondents from Buu Long Ward (the control site) were randomly selected to participate in the surveys. The results showed that as of 2013, the programs were rated as "moderately sustained" with a score of 3.3 out of 5.0 (cut off points 2.5 to <3.5) for Bien Hoa, and "well sustained" with a score of 3.8 out of 5.0 (cut off points 3.5 to <4.5) for Da Nang. Most formal intervention program activities had ceased and dioxin risk communication activities were no longer integrated into local routine health education programs. However, the main outcomes were maintained and were better than that in the control ward. Migration, lack of official guidance from City People's Committees and local authorities as well as the politically sensitive nature of dioxin issues were the main challenges for the sustainability of the programs.

Fabrication of Nb2O5 nanosheets for high-rate lithium ion storage applications

Nb2O5 nanosheets are successfully synthesized through a facile hydrothermal reaction and followed heating treatment in air. The structural characterization reveals that the thickness of these sheets is around 50 nm and the length of sheets is 500~800 nm. Such a unique two dimensional structure enables the nanosheet electrode with superior performance during the charge-discharge process, such as high specific capacity (~184 mAh.g-1) and rate capability. Even at a current density of 1 A.g-1, the nanosheet electrode still exhibits a specific capacity of ~90 mAh.g-1. These results suggest the Nb2O5 nanosheet is a promising candidate for high-rate lithium ion storage applications.

Protecting Australia's children: A cross-jurisdictional review of domestic violence protection order legislation

Increasingly, domestic violence is being treated as a child protection issue, and children affected by domestic violence are recognised as experiencing a form of child abuse. Domestic violence protection order legislation – as a key legal response to domestic violence – may offer an important legal option for the protection of children affected by domestic violence. In this article, we consider the research that establishes domestic violence as a form of child abuse, and review the provisions of State and Territory domestic violence protection order legislation to assess whether they demonstrate an adequate focus on the protection of children.

Bikeshare's impact on active travel: Evidence from the United States, Great Britain, and Australia

Over 800 cities globally now offer bikeshare programs. One of their purported benefits is increased physical activity. Implicit in this claim is that bikeshare replaces sedentary modes of transport, particularly car use. This paper estimates the median changes in physical activity levels as a result of bikeshare in the cities of Melbourne, Brisbane, Washington, D.C., London, and Minneapolis/St. Paul. This study is the first known multi-city evaluation of the active travel impacts of bikeshare programs. To perform the analysis, data on mode substitution (i.e. the modes that bikeshare replaces) were used to determine the extent of shift from sedentary to active transport modes (e.g. when a car trip is replaced by bikeshare). Potentially offsetting these gains, reductions in physical activity when walking trips are replaced by bikeshare was also estimated. Finally a Markov Chain Monte Carlo analysis was conducted to estimate confidence bounds on estimated impacts on active travel given uncertainties in data sources. The results indicate that on average 60% of bikeshare trips replace sedentary modes of transport (from 42% in Minneapolis/St. Paul to 67% in Brisbane). When bikeshare replaces a walking trip, there is a reduction in active travel time because walking a given distance takes longer than cycling. Considering the active travel balance sheet for the cities included in this analysis, bikeshare activity in 2012 has an overall positive impact on active travel time. This impact ranges from an additional 1.4 million minutes of active travel for the Minneapolis/St. Paul bikeshare program, to just over 74 million minutes of active travel for the London program The analytical approach adopted to estimate bikeshare’s impact on active travel may act as the basis for future bikeshare evaluations or feasibility studies.

Quantitative characterization of kaolinite dispersibility in styrene–butadiene rubber composites by fractal dimension

A fractal method was introduced to quantitatively characterize the dispersibility of modified kaolinite (MK) and precipitated silica (PS) in styrene–butadiene rubber (SBR) matrix based on the lower magnification transmission electron microscopic images. The fractal dimension (FD) is greater, and the dispersion is worse. The fractal results showed that the dispersibility of MK in the latex blending sample is better than that in the mill blending samples. With the increase of kaolinite content, the FD increases from 1.713 to 1.800, and the dispersibility of kaolinite gradually decreases. There is a negative correlation between the dispersibility and loading content. With the decrease of MK and increase of PS, the FD significantly decreases from 1.735 to 1.496 and the dipersibility of kaolinite remarkably increases. The hybridization can improve the dispersibility of fillers in polymer matrix. The FD can be used to quantitatively characterize the aggregation and dispersion of kaolinite sheets in rubber matrix.

A vibrational spectroscopic study of the anhydrous phosphate mineral sidorenkite Na3Mn(PO4)(CO3)

Sidorenkite is a very rare low-temperature hydrothermal mineral, formed very late in the crystallization of hyperagpaitic pegmatites in a differentiated alkalic massif (Mt. Alluaiv, Kola Peninsula, Russia). Sidorenkite Na3Mn(PO4)(CO3) is a phosphate–carbonate of sodium and manganese. Such a formula with two oxyanions lends itself to vibrational spectroscopy. The sharp Raman band at 959 cm−1 and 1012 cm−1 are assigned to the PO43− stretching modes, whilst the Raman bands at 1044 cm−1 and 1074 cm−1 are attributed to the CO32− stretching modes. It is noted that no Raman bands at around 800 cm−1 for sidorenkite were observed. The infrared spectrum of sidorenkite shows a quite intense band at 868 cm−1 with other resolved component bands at 850 and 862 cm−1. These bands are ascribed to the CO32− out-of-plane bend (ν2) bending mode. The series of Raman bands at 622, 635, 645 and 704 cm−1 are assigned to the ν4 phosphate bending modes. The observation of multiple bands supports the concept of a reduction in symmetry of the carbonate anion from D3h or even C2v.

Modified MLVA for genotyping Queensland invasive Streptococcus pneumoniae

Background Globally, over 800 000 children under five die each year from infectious diseases caused by Streptococcus pneumoniae. To understand genetic relatedness between isolates, study transmission routes, assess the impact of human interventions e.g. vaccines, and determine infection sources, genotyping methods are required. The ‘gold standard’ genotyping method, Multi-Locus Sequence Typing (MLST), is useful for long-term and global studies. Another genotyping method, Multi-Locus Variable Number of Tandem Repeat Analysis (MLVA), has emerged as a more discriminatory, inexpensive and faster technique; however there is no universally accepted method and it is currently suitable for short-term and localised epidemiology studies. Currently Australia has no national MLST database, nor has it adopted any MLVA method for short-term or localised studies. This study aims to improve S. pneumoniae genotyping methods by modifying the existing MLVA techniques to be more discriminatory, faster, cheaper and technically less demanding than previously published MLVA methods and MLST. Methods Four different MLVA protocols, including a modified method, were applied to 317 isolates of serotyped invasive S. pneumoniae isolated from sterile body sites of Queensland children under 15 years from 2007–2012. MLST was applied to 202 isolates for comparison. Results The modified MLVA4 is significantly more discriminatory than the ‘gold standard’ MLST method. MLVA4 has similar discrimination compared to other MLVA techniques in this study). The failure to amplify particular loci in previous MLVA methods were minimised in MLVA4. Failure to amplify BOX-13 and Spneu19 were found to be serotype specific. Conclusion We have modified a highly discriminatory MLVA technique for genotyping Queensland invasive S. pneumoniae. MLVA4 has the ability to enhance our understanding of the pneumococcal epidemiology and the changing genetics of the pneumococcus in localised and short-term studies.

What do most Americans think of cost-effectiveness research in health care?

My impression is that explicit data on the cost-effectiveness of different health care services are not valued highly by US policy makers. An example is a recent decision to approve ipilimumab for the treatment of metastatic melanoma. The extra health benefit over standard treatment is 2.1 months in previously untreated patients and the cost is $120,000 for 4 doses. This is poor value for money. Had $120,000 been allocated to an intensive lifestyle modification programme for diabetes risk (Diabet Med. 2004 Nov;21(11):1229-36) then 67 years of life or 800 months could have been returned. A massive increase in health benefits for the same costs.

A phase II trial of brivanib in recurrent or persistent endometrial cancer: An NRG oncology/gynecologic oncology group study

PURPOSE Brivanib, an oral, multi-targeted tyrosine kinase inhibitor with activity against vascular endothelial growth factor (VEGF) and fibroblast growth factor receptor (FGFR) was investigated as a single agent in a phase II trial to assess the activity and tolerability in recurrent or persistent endometrial cancer (EMC). PATIENTS AND METHODS Eligible patients had persistent or recurrent EMC after receiving one to two prior cytotoxic regimens, measurable disease, and performance status of ≤2. Treatment consisted of brivanib 800 mg orally every day until disease progression or prohibitive toxicity. Primary endpoints were progression-free survival (PFS) at six months and objective tumor response. Expression of multiple angiogenic proteins and FGFR2 mutation status was assessed. RESULTS Forty-five patients were enrolled. Forty-three patients were eligible and evaluable. Median age was 64 years. Twenty-four patients (55.8%) received prior radiation. Median number of cycles was two (range 1-24). No GI perforations but one rectal fistula were seen. Nine patients had grade 3 hypertension, with one experiencing grade 4 confusion. Eight patients (18.6%; 90% CI 9.6%-31.7%) had responses (one CR and seven PRs), and 13 patients (30.2%; 90% CI 18.9%-43.9%) were PFS at six months. Median PFS and overall survival (OS) were 3.3 and 10.7 months, respectively. When modeled jointly, VEGF and angiopoietin-2 expression may diametrically predict PFS. Estrogen receptor-α (ER) expression was positively correlated with OS. CONCLUSION Brivanib is reasonably well tolerated and worthy of further investigation based on PFS at six months in recurrent or persistent EMC.

Instant coffee with high chlorogenic acid levels protects humans against oxidative damage of macromolecules

Scope: Coffee is among the most frequently consumed beverages. Its consumption is inversely associated to the incidence of diseases related to reactive oxygen species; the phenomenon may be due to its antioxidant properties. Our primary objective was to investigate the impact of consumption of a coffee containing high levels of chlorogenic acids on the oxidation of proteins, DNA and membrane lipids; additionally, other redox biomarkers were monitored in an intervention trial. Methods and results: The treatment group (n=36) consumed instant coffee co-extracted from green and roasted beans, whereas the control consumed water (800 mL/P/day, 5 days). A global statistical analysis of four main biomarkers selected as primary outcomes showed that the overall changes are significant. 8-Isoprostaglandin F2α in urine declined by 15.3%, 3-nitrotyrosine was decreased by 16.1%, DNA migration due to oxidized purines and pyrimidines was (not significantly) reduced in lymphocytes by 12.5 and 14.1%. Other markers such as the total antioxidant capacity were moderately increased; e.g. LDL and malondialdehyde were shifted towards a non-significant reduction. Conclusion: The oxidation of DNA, lipids and proteins associated with the incidence of various diseases and the protection against their oxidative damage may be indicative for beneficial health effects of coffee.

Investigating in-domain data requirements for PLDA training

This paper analyzes the limitations upon the amount of in- domain (NIST SREs) data required for training a probabilistic linear discriminant analysis (PLDA) speaker verification system based on out-domain (Switchboard) total variability subspaces. By limiting the number of speakers, the number of sessions per speaker and the length of active speech per session available in the target domain for PLDA training, we investigated the relative effect of these three parameters on PLDA speaker verification performance in the NIST 2008 and NIST 2010 speaker recognition evaluation datasets. Experimental results indicate that while these parameters depend highly on each other, to beat out-domain PLDA training, more than 10 seconds of active speech should be available for at least 4 sessions/speaker for a minimum of 800 speakers. If further data is available, considerable improvement can be made over solely out-domain PLDA training.

The Cougar Point tuff: Implications for thermochemical zonation and longevity of high-temperature, large-volume silicic magmas of the Miocene Yellowstone hotspot

The 12.7-10.5 Ma Cougar Point Tuff in southern Idaho, USA, consists of 10 large-volume (>10²-10³ km³ each), high-temperature (800-1000 °C), rhyolitic ash-flow tuffs erupted from the Bruneau-Jarbidge volcanic center of the Yellowstone hotspot. These tuffs provide evidence for compositional and thermal zonation in pre-eruptive rhyolite magma, and suggest the presence of a long-lived reservoir that was tapped by numerous large explosive eruptions. Pyroxene compositions exhibit discrete compositional modes with respect to Fe and Mg that define a linear spectrum punctuated by conspicuous gaps. Airfall glass compositions also cluster into modes, and the presence of multiple modes indicates tapping of different magma volumes during early phases of eruption. Equilibrium assemblages of pigeonite and augite are used to reconstruct compositional and thermal gradients in the pre-eruptive reservoir. The recurrence of identical compositional modes and of mineral pairs equilibrated at high temperatures in successive eruptive units is consistent with the persistence of their respective liquids in the magma reservoir. Recurrence intervals of identical modes range from 0.3 to 0.9 Myr and suggest possible magma residence times of similar duration. Eruption ages, magma temperatures, Nd isotopes, and pyroxene and glass compositions are consistent with a long-lived, dynamically evolving magma reservoir that was chemically and thermally zoned and composed of multiple discrete magma volumes.