Development of the Web

A seminar for BNU students who have participated in the FutureLearn Web Science MOOC

Accretion, Primordial Black Holes and Standard Cosmology

Primordial Black Holes evaporate due to Hawking radiation. We find that the evaporation time of primordial black holes increase when accretion of radiation is included.Thus depending on accretion efficiency more and more number of primordial black holes are existing today, which strengthens the idea that the primordial black holes are the proper candidate for dark matter.Comment: 11 pages, 3 figure

Viability of primordial black holes as short period gamma-ray bursts

It has been proposed that the short period gamma-ray bursts, which occur at a rate of $\sim 10 {\rm yr^{-1}}$, may be evaporating primordial black holes (PBHs). Calculations of the present PBH evaporation rate have traditionally assumed that the PBH mass function varies as $M_{{\rm BH}}^{-5/2}$. This mass function only arises if the density perturbations from which the PBHs form have a scale invariant power spectrum. It is now known that for a scale invariant power spectrum, normalised to COBE on large scales, the PBH density is completely negligible, so that this mass function is cosmologically irrelevant. For non-scale-invariant power spectra, if all PBHs which form at given epoch have a fixed mass then the PBH mass function is sharply peaked around that mass, whilst if the PBH mass depends on the size of the density perturbation from which it forms, as is expected when critical phenomena are taken into account, then the PBH mass function will be far broader than $M_{{\rm BH}}^{-5/2}$. In this paper we calculate the present day PBH evaporation rate, using constraints from the diffuse gamma-ray background, for both of these mass functions. If the PBH mass function has significant finite width, as recent numerical simulations suggest, then it is not possible to produce a present day PBH evaporation rate comparable with the observed short period gamma-ray burst rate. This could also have implications for other attempts to detect evaporating PBHs.Comment: 5 pages, 2 figures, version to appear in Phys. Rev. D with additional reference

The Shifting Origins of International Law

Both state-centrism and Euro-centrism are under challenge in international law today and this double challenge, this work argues, is being fruitfully mirrored back into the study of the history of international law. It examines, in the first section, the effects of the rise of positivism as a method of norm-identification and the role of methodological nationalism over the study of the history of international law in the modern foundational period of international law. This is extended by an examination of how this bequeathed a double exclusionary bias regarding time and space to the study of the history of international law as well as a reiterative focus on a series of canonical events and authors to the exclusion of others such as those related to the Islamic history of international law. In the second section, the analysis turns to address why this state of historiographical affairs is changing, specifically highlighting intra-disciplinary developments within the field of the history of international law and the effects that the “international turn in the writing of history” is having on the writing of a new history of international law for a global age. The conclusion reflects on some of the tasks ahead by providing a series of historiographical signposts for the history of international law as a field of new research

Meaningful cognitive decline is uncommon in virally suppressed HIV, but sustained impairment, subtle decline and abnormal cognitive aging are not

Background: High antiretroviral therapy (ART) coverage and viral suppression among people with HIV (PWH) in Australia provide a unique context to study individual cognitive trajectories, cognitive aging and factors associated with longitudinal cognitive function during chronic and stable HIV disease. Methods: Participants from the Predictors of Adherence to Antiretroviral Therapy study (n = 457, recruited between September 2013 and November 2015, median age = 52 years, and all with HIV RNA 0.5). Meaningful cognitive change was statistically defined (decline or improvement versus stability, i.e., 90% CI, that is p < 0.05, 2-tailed) using a novel evidence-based change score: the linear mixed-effect regression (LMER)-based GZS change score. A separate LMER model with a top-down variable selection approach identified the independent effects of age and other demographic, HIV disease characteristics, socioeconomic and health-related factors on the demographically corrected GZS. The combined definitions of change and cross-sectional impairment enabled the identification of cognitive trajectories. Findings: At Month-12 and Month-24, 6% and 7% showed meaningful cognitive decline and 4% and 3% improved respectively. Only 1% showed sustained decline. Incident impairment due to subtle cognitive decline (i.e., below the threshold of meaningful cognitive decline) was 31% and 25% at Month-12 and Month-24, while 14% showed sustained impairment (i.e., cognitively impaired at all study visits). Older age (≥50 years) and time interaction was associated with lower demographically corrected GZS (β = −0.31, p < 0.001). Having a regular relationship, excellent English proficiency, and perceived stigma (avoidance) were associated with higher GZS (all p < 0.05). Relying on government subsidy, severe depression, and lower belief in ART necessity and higher concerns were associated with lower GZS (all p < 0.05). No HIV disease characteristics had a significant effect. Interpretations: Meaningful cognitive decline was not different from normal expectation in chronic stable HIV disease. Despite this, subtle cognitive decline, sustained cognitive impairment, and greater than normative-age cognitive aging were evident. Funding: Funding for the PAART study was provided in part by unrestricted educational grants from Gilead Sciences (www.gilead.com) (Grant Number: IN-AU-264- 0131), the Balnaves Foundation (www.balnavesfoundation.com), the Victorian Department of Health and Human Services (Australia) (www.dhs.vic.gov.au/home), Western Australia Health (www.health.wa.gov.au), the ACT Ministry of Health (Australia) (www.health.act.gov.au), and in-kind support from the Queensland Department of Health (Australia) (www.health.qld.gov.au), and NHMRC Partnership grant APP1058474 (PI: Carr, Andrew)

GeneTIER: prioritization of candidate disease genes using tissue-specific gene expression profiles.

Motivation In attempts to determine the genetic causes of human disease, researchers are often faced with a large number of candidate genes. Linkage studies can point to a genomic region containing hundreds of genes, while the high-throughput sequencing approach will often identify a great number of non-synonymous genetic variants. Since systematic experimental verification of each such candidate gene is not feasible, a method is needed to decide which genes are worth investigating further. Computational gene prioritization presents itself as a solution to this problem, systematically analyzing and sorting each gene from the most to least likely to be the disease-causing gene, in a fraction of the time it would take a researcher to perform such queries manually. Results Here we present GeneTIER (Gene TIssue Expression Ranker), a new web-based application for candidate gene prioritization. GeneTIER replaces knowledge-based inference traditionally used in candidate disease gene prioritization applications with experimental data from tissue-specific gene expression datasets and thus largely overcomes the bias towards the better characterized genes/diseases that commonly afflict other methods. We show that our approach is capable of accurate candidate gene prioritization and illustrate its strengths and weaknesses using case study examples. Availability and Implementation Freely available on the web at http://dna.leeds.ac.uk/GeneTIER/ Contact: [email protected]

The effects of attachment style on coping with visible skin conditions and responsiveness to a compassion based self-help intervention

No abstract available

A Chromosome 7 Pericentric Inversion Defined at Single-Nucleotide Resolution Using Diagnostic Whole Genome Sequencing in a Patient with Hand-Foot-Genital Syndrome.

Next generation sequencing methodologies are facilitating the rapid characterisation of novel structural variants at nucleotide resolution. These approaches are particularly applicable to variants initially identified using alternative molecular methods. We report a child born with bilateral postaxial syndactyly of the feet and bilateral fifth finger clinodactyly. This was presumed to be an autosomal recessive syndrome, due to the family history of consanguinity. Karyotype analysis revealed a homozygous pericentric inversion of chromosome 7 (46,XX,inv(7)(p15q21)x2) which was confirmed to be heterozygous in both unaffected parents. Since the resolution of the karyotype was insufficient to identify any putatively causative gene, we undertook medium-coverage whole genome sequencing using paired-end reads, in order to elucidate the molecular breakpoints. In a two-step analysis, we first narrowed down the region by identifying discordant read-pairs, and then determined the precise molecular breakpoint by analysing the mapping locations of "soft-clipped" breakpoint-spanning reads. PCR and Sanger sequencing confirmed the identified breakpoints, both of which were located in intergenic regions. Significantly, the 7p15 breakpoint was located 523 kb upstream of HOXA13, the locus for hand-foot-genital syndrome. By inference from studies of HOXA locus control in the mouse, we suggest that the inversion has delocalised a HOXA13 enhancer to produce the phenotype observed in our patient. This study demonstrates how modern genetic diagnostic approach can characterise structural variants at nucleotide resolution and provide potential insights into functional regulation