Structural fingerprints of transcription factor binding site regions

Fourier transforms are a powerful tool in the prediction of DNA sequence properties, such as the presence/absence of codons. We have previously compiled a database of the structural properties of all 32,896 unique DNA octamers. In this work we apply Fourier techniques to the analysis of the structural properties of human chromosomes 21 and 22 and also to three sets of transcription factor binding sites within these chromosomes. We find that, for a given structural property, the structural property power spectra of chromosomes 21 and 22 are strikingly similar. We find common peaks in their power spectra for both Sp1 and p53 transcription factor binding sites. We use the power spectra as a structural fingerprint and perform similarity searching in order to find transcription factor binding site regions. This approach provides a new strategy for searching the genome data for information. Although it is difficult to understand the relationship between specific functional properties and the set of structural parameters in our database, our structural fingerprints nevertheless provide a useful tool for searching for function information in sequence data. The power spectrum fingerprints provide a simple, fast method for comparing a set of functional sequences, in this case transcription factor binding site regions, with the sequences of whole chromosomes. On its own, the power spectrum fingerprint does not find all transcription factor binding sites in a chromosome, but the results presented here show that in combination with other approaches, this technique will improve the chances of identifying functional sequences hidden in genomic data

Dynamics of digital diffusion and disadoption:A longitudinal analysis of indigenous and other Australians

The digital divide between Indigenous and other Australians describes the unequal access to information and communications technology (ICT) between these groups. Historically, researchers have focused on acquiring new technology, but we argue that it is important to understand all the dynamics of digital usage, including the loss of access to ICT within a household. For long-lived technology such as internet access, it is particularly important to consider that retention of access to the technology. This paper conducts a longitudinal analysis of changes in internet usage for Indigenous and non-Indigenous Australian households using the Australian Census Longitudinal Dataset, 2006–2016. While earlier work analyses the digital divide in terms of ‘diffusion’ or adoption of ICT, this paper shows that the failure to retain internet access is also important in driving the digital divide. The dynamics of the digital divide have important and ongoing implications for addressing broader socioeconomic disadvantages experienced by Indigenous Australians. The COVID-19 pandemic underscores the urgency of policy addressing the digital divide, given the renewed momentum for remote learning and telecommuting

Reforming the public health system in England

The abolition of Public Health England (PHE) during the COVID-19 pandemic has raised concerns about the future of the public health system in the UK, particularly in England. The two new bodies established in haste to replace PHE prompt reflection on the executive agency's fate and the need to identify any lessons to ensure that a public health system is put in place that is fit for purpose. The UK COVID-19 Inquiry provides an opportunity to make recommendations, but it will need to act quickly to avoid recommendations being ignored. Two areas of concern are highlighted in this Viewpoint: the respective remits of the new bodies and their governance arrangements. Both issues demand urgent attention if the new structures are to succeed and avoid a similar fate to that which befell PHE. But underlying these concerns is a much larger challenge arising from the UK's broken political system. The political system in the UK suffers from several systemic weaknesses, including departmentalism, poor implementation, an inability or unwillingness of those in power to listen to the truth, and chronic short-termism at the expense of long-term planning. Overhauling the UK's dysfunctional political system is a prerequisite for successfully improving the public health system

Biodiversity Education Initiative for Middle School Students

This report, prepared for the Smithsonian Institution\u27s Monitoring and Assessment of Biodiversity Program, details the research done to determine the current world state of biodiversity education and the best possible methods and format for a biodiversity education program targeted at middle school students. Within the report is an explanation of the purpose, need, goals, methods, execution, results, and recommendations of this project

Chandra Observation of an X-ray Flare at Saturn: Evidence for Direct Solar Control on Saturn's Disk X-ray Emissions

Saturn was observed by Chandra ACIS-S on 20 and 26-27 January 2004 for one full Saturn rotation (10.7 hr) at each epoch. We report here the first observation of an X-ray flare from Saturn's non-auroral (low-latitude) disk, which is seen in direct response to an M6-class flare emanating from a sunspot that was clearly visible from both Saturn and Earth. Saturn's disk X-ray emissions are found to be variable on time scales of hours to weeks to months, and correlated with solar F10.7 cm flux. Unlike Jupiter, X-rays from Saturn's polar (auroral) region have characteristics similar to those from its disk. This report, combined with earlier studies, establishes that disk X-ray emissions of the giant planets Saturn and Jupiter are directly regulated by processes happening on the Sun. We suggest that these emissions could be monitored to study X-ray flaring from solar active regions when they are on the far side and not visible to Near-Earth space weather satellites.Comment: Total 12 pages including 4 figure

Haplotype analysis of common variants in the BRCA1 gene and risk of sporadic breast cancer

INTRODUCTION: Truncation mutations in the BRCA1 gene cause a substantial increase in risk of breast cancer. However, these mutations are rare in the general population and account for little of the overall incidence of sporadic breast cancer. METHOD: We used whole-gene resequencing data to select haplotype tagging single nucleotide polymorphisms, and examined the association between common haplotypes of BRCA1 and breast cancer in a nested case-control study in the Nurses' Health Study (1323 cases and 1910 controls). RESULTS: One haplotype was associated with a slight increase in risk (odds ratio 1.18, 95% confidence interval 1.02–1.37). A significant interaction (P = 0.05) was seen between this haplotype, positive family history of breast cancer, and breast cancer risk. Although not statistically significant, similar interactions were observed with age at diagnosis and with menopausal status at diagnosis; risk tended to be higher among younger, pre-menopausal women. CONCLUSIONS: We have described a haplotype in the BRCA1 gene that was associated with an approximately 20% increase in risk of sporadic breast cancer in the general population. However, the functional variant(s) responsible for the association are unclear

Why do some women still prefer traditional birth attendants and home delivery?: a qualitative study on delivery care services in West Java Province, Indonesia

<p>Abstract</p> <p>Background</p> <p>Trained birth attendants at delivery are important for preventing both maternal and newborn deaths. West Java is one of the provinces on Java Island, Indonesia, where many women still deliver at home and without the assistance of trained birth attendants. This study aims to explore the perspectives of community members and health workers about the use of delivery care services in six villages of West Java Province.</p> <p>Methods</p> <p>A qualitative study using focus group discussions (FGDs) and in-depth interviews was conducted in six villages of three districts in West Java Province from March to July 2009. Twenty FGDs and 165 in-depth interviews were conducted involving a total of 295 participants representing mothers, fathers, health care providers, traditional birth attendants and community leaders. The FGD and in-depth interview guidelines included reasons for using a trained or a traditional birth attendant and reasons for having a home or an institutional delivery.</p> <p>Results</p> <p>The use of traditional birth attendants and home delivery were preferable for some community members despite the availability of the village midwife in the village. Physical distance and financial limitations were two major constraints that prevented community members from accessing and using trained attendants and institutional deliveries. A number of respondents reported that trained delivery attendants or an institutional delivery were only aimed at women who experienced obstetric complications. The limited availability of health care providers was reported by residents in remote areas. In these settings the village midwife, who was sometimes the only health care provider, frequently travelled out of the village. The community perceived the role of both village midwives and traditional birth attendants as essential for providing maternal and health care services.</p> <p>Conclusions</p> <p>A comprehensive strategy to increase the availability, accessibility, and affordability of delivery care services should be considered in these West Java areas. Health education strategies are required to increase community awareness about the importance of health services along with the existing financing mechanisms for the poor communities. Public health strategies involving traditional birth attendants will be beneficial particularly in remote areas where their services are highly utilized.</p

Public health by organizational fix?

In August 2020 the UK government announced without warning the abolition of Public Health England (PHE), the principal UK agency for the promotion and protection of public health. We undertook a research programme seeking to understand the factors surrounding this decision. While the underlying issues are complex two competing interpretations have emerged: an 'official' explanation, which highlights the failure of PHE to scale up its testing capacity in the early weeks of the COVID-19 pandemic as the fundamental reason for closing it down and a 'sceptical' interpretation, which ascribes the decision to blame-avoidance behaviour on the part of leading government figures. This paper reviews crucial claims in these two competing explanations exploring the arguments for and against each proposition. It concludes that neither is adequate and that the inability adequately to address the problem of testing (which triggered the decision to close PHE) lies deeper in the absence of the norms of responsible government in UK politics and the state. However our findings do provide some guidance to the two new organizations established to replace PHE to maximize their impact on public health. We hope that this information will contribute to the independent national COVID inquiry

Lake and catchment-scale determinants of aquatic vegetation across almost 1,000 lakes and the contrasts between lake types

Aim The factors controlling macrophyte (aquatic plant) composition are complex, recent research having shown that the well-studied effects of lake environmental factors (the so-called “environmental filter”) can be constrained by hydrological and landscape factors. We investigated the factors determining macrophyte composition in lakes over water body and catchment- scales and the transferability of this pattern across lake types. Location Almost 1000 lakes distributed across Britain. Taxon Lake macrophytes Methods Lakes were partitioned into five types based on subdivision of alkalinity and elevation gradients. Data from botanical surveys were used to compare the spatial turnover and nestedness components of beta diversity between lake types. The relative importance of lake environment (based on local physicochemical data), hydrology (e.g. lake and stream density), landscape (e.g. fragmentation indices, land cover) and spatial autocorrelation in explaining variation in macrophyte composition were derived from variance partitioning. Results Species composition showed strong spatial structuring, suggestive of overland dispersal, enhanced by spatially-correlated abiotic factors such as alkalinity and elevation. Catchment-scale factors (e.g. land use, connectivity) promoted the establishment of different communities (more or less diverse, or differing in composition) but were of secondary importance. Turnover in composition between upland lakes was lower than in other lake types, reflecting a more specialist flora and increased potential for propagule exchange due to spatial aggregation and higher hydrological connectivity. Main conclusions Vegetation composition in lakes is more spatially-structured than previously appreciated, consistent with the importance of dispersal limitation, but this does not apply evenly to all lakes, being most acute in lowland high alkalinity lakes. Thus, spatially-structured abiotic factors, such as alkalinity, influence macrophyte composition most (suggestive of niche filtering) in high alkalinity lakes where human impacts tend to be greatest, although nestedness was also lowest in such lakes. By contrast, hydrological connectivity has a proportionally stronger structuring role in upland lakes