The favoured cluster structures of model glass formers

We examine the favoured cluster structures for two new potentials, which both behave as monatomic model glass-formers in bulk. We find that the oscillations in the interatomic potential lead to global minima that are non-compact arrangements of linked 13-atom icosahedra. We find that the structural properties of the clusters correlate with the glass-forming propensities of the potentials, and with the fragilities of the corresponding supercooled liquids.Comment: 9 pages, 7 figures; new section added and error in potential parameters correcte

PIPc study: development of indicators of potentially inappropriate prescribing in children (PIPc) in primary care using a modified Delphi technique

OBJECTIVE: There is limited evidence regarding the quality of prescribing for children in primary care. Several prescribing criteria (indicators) have been developed to assess the appropriateness of prescribing in older and middle-aged adults but few are relevant to children. The objective of this study was to develop a set of prescribing indicators that can be applied to prescribing or dispensing data sets to determine the prevalence of potentially inappropriate prescribing in children (PIPc) in primary care settings. DESIGN: Two-round modified Delphi consensus method. SETTING: Irish and UK general practice. PARTICIPANTS: A project steering group consisting of academic and clinical general practitioners (GPs) and pharmacists was formed to develop a list of indicators from literature review and clinical expertise. 15 experts consisting of GPs, pharmacists and paediatricians from the Republic of Ireland and the UK formed the Delphi panel. RESULTS: 47 indicators were reviewed by the project steering group and 16 were presented to the Delphi panel. In the first round of this exercise, consensus was achieved on nine of these indicators. Of the remaining seven indicators, two were removed following review of expert panel comments and discussion of the project steering group. The second round of the Delphi process focused on the remaining five indicators, which were amended based on first round feedback. Three indicators were accepted following the second round of the Delphi process and the remaining two indicators were removed. The final list consisted of 12 indicators categorised by respiratory system (n=6), gastrointestinal system (n=2), neurological system (n=2) and dermatological system (n=2). CONCLUSIONS: The PIPc indicators are a set of prescribing criteria developed for use in children in primary care in the absence of clinical information. The utility of these criteria will be tested in further studies using prescribing databases

Eligibility rates and representativeness of the General Medical Services scheme population in Ireland 2017-2021: A methodological report [version 1; peer review: 2 approved]

Background: In Ireland, the means tested General Medical Services (GMS) scheme provides access to a range of healthcare services at no or low cost to approximately one third of the population. Individuals eligible for the GMS scheme are often a focus of research, as a population that account for a large proportion of healthcare services use. The aim of this study is to describe the eligibility rates and representativeness of the GMS scheme population over time, with respect to age group, sex, and geographical area in Ireland. Methods: Population data was obtained from the Central Statistics Office (CSO), using 2016 Census figures and projected population figures for 2017-2021. GMS eligibility figures for 2016-2021 were obtained from the HSE Primary Care Reimbursement Service (PCRS). GMS eligibility rates and relative rates of eligibility were calculated for 2016-2021 by age group and sex. Additionally, 2016 eligibility rates were calculated by geographical area. Results: The crude eligibility rate decreased from 36.4% in 2016 to 31.2% in 2020, with a slight increase to 31.6% in 2021. In the 75+ years age group, 78.2% of the total population were eligible for the GMS scheme in 2021. The age group with the lowest rate of eligible individuals was the 25-34 age group, with 19.5% eligible in 2021. The eligibility rate was higher among females compared to males throughout the study period. The highest eligibility rate was seen in Donegal, with a crude rate of 52.8%. Dublin had the lowest rate, with a crude rate of 29.3%. Conclusions: GMS eligibility varies greatly depending on age, sex, and geographical area, and decreased between 2016 and 2021. This study uses the most up-to-date data available to provide age group, sex and area-based figures for GMS eligibility which may inform planning and conduct of research focusing on GMS-eligible individuals

Local air pollution and asthma among over-50s in Ireland. ESRI Research Bulletin 202008 June 2020.

Researchers today published a study showing that over-50s in Ireland living in areas with higher levels of air pollution are more likely to have asthma. The study, published in the International Journal of Epidemiology, was carried out by a team from ESRI, TCD, RCSI, TU Dublin and IT Carlow

Comparing species tree estimation with large anchored phylogenomic and small Sanger-sequenced molecular datasets: an empirical study on Malagasy pseudoxyrhophiine snakes

Background Using molecular data generated by high throughput next generation sequencing (NGS) platforms to infer phylogeny is becoming common as costs go down and the ability to capture loci from across the genome goes up. While there is a general consensus that greater numbers of independent loci should result in more robust phylogenetic estimates, few studies have compared phylogenies resulting from smaller datasets for commonly used genetic markers with the large datasets captured using NGS. Here, we determine how a 5-locus Sanger dataset compares with a 377-locus anchored genomics dataset for understanding the evolutionary history of the pseudoxyrhophiine snake radiation centered in Madagascar. The Pseudoxyrhophiinae comprise ~86 % of Madagascar’s serpent diversity, yet they are poorly known with respect to ecology, behavior, and systematics. Using the 377-locus NGS dataset and the summary statistics species-tree methods STAR and MP-EST, we estimated a well-supported species tree that provides new insights concerning intergeneric relationships for the pseudoxyrhophiines. We also compared how these and other methods performed with respect to estimating tree topology using datasets with varying numbers of loci. Methods Using Sanger sequencing and an anchored phylogenomics approach, we sequenced datasets comprised of 5 and 377 loci, respectively, for 23 pseudoxyrhophiine taxa. For each dataset, we estimated phylogenies using both gene-tree (concatenation) and species-tree (STAR, MP-EST) approaches. We determined the similarity of resulting tree topologies from the different datasets using Robinson-Foulds distances. In addition, we examined how subsets of these data performed compared to the complete Sanger and anchored datasets for phylogenetic accuracy using the same tree inference methodologies, as well as the program *BEAST to determine if a full coalescent model for species tree estimation could generate robust results with fewer loci compared to the summary statistics species tree approaches. We also examined the individual gene trees in comparison to the 377-locus species tree using the program MetaTree. Results Using the full anchored dataset under a variety of methods gave us the same, well-supported phylogeny for pseudoxyrhophiines. The African pseudoxyrhophiine Duberria is the sister taxon to the Malagasy pseudoxyrhophiines genera, providing evidence for a monophyletic radiation in Madagascar. In addition, within Madagascar, the two major clades inferred correspond largely to the aglyphous and opisthoglyphous genera, suggesting that feeding specializations associated with tooth venom delivery may have played a major role in the early diversification of this radiation. The comparison of tree topologies from the concatenated and species-tree methods using different datasets indicated the 5-locus dataset cannot beused to infer a correct phylogeny for the pseudoxyrhophiines under any method tested here and that summary statistics methods require 50 or more loci to consistently recover the species-tree inferred using the complete anchored dataset. However, as few as 15 loci may infer the correct topology when using the full coalescent species tree method *BEAST. MetaTree analyses of each gene tree from the Sanger and anchored datasets found that none of the individual gene trees matched the 377-locus species tree, and that no gene trees were identical with respect to topology. Conclusions Our results suggest that ≥50 loci may be necessary to confidently infer phylogenies when using summaryspecies-tree methods, but that the coalescent-based method *BEAST consistently recovers the same topology using only 15 loci. These results reinforce that datasets with small numbers of markers may result in misleading topologies, and further, that the method of inference used to generate a phylogeny also has a major influence on the number of loci necessary to infer robust species trees. Electronic supplementary material The online version of this article (doi:10.1186/s12862-015-0503-1) contains supplementary material, which is available to authorized users

DASSL “Data Access Sharing Storage & Linkage” Proof-of-Concept: Health and Related Data Linkage in Ireland.

Objective The DASSL Model, conceived by the Health Research Board, aims to overcome challenges to linking data in Ireland including lack of unique patient identifiers, inconsistent application of legislation and siloed data. The objective of the Proof-of-Concept is to develop and test a demonstrator technical infrastructure to support this model. Approach A stakeholder committee of representatives from government, health services, data controllers, patients/public and researchers was established. National and international data sharing and linkage landscapes were reviewed via interviews, scientific papers and grey literature. Five case studies were developed to demonstrate different linkages, data and research purposes, with synthetic data mimicking real health/social datasets generated using data dictionaries, data controller input, national statistics and Synthpop, Synthetic Data Vault and General Adversarial Networks. The technical infrastructure remains under development with linkage software being evaluated. Stakeholders will test this infrastructure and a final report will outline considerations for a national solution. Results Synthetic versions of administrative data, patient registries, electronic patient records, longitudinal cohorts, imaging and genomics are being generated. Matching variables and content data will be split and securely shared respectively with the Trusted Third Party (TTP) and Health Data Hub (HDH) on a project-by-project basis and at regular intervals. The selected linkage software will be used to match both unique identifiers and personally-identifiable data using probabilistic and deterministic techniques between datasets and with a population spine. The encrypted linkage key will be shared with the HDH, where the data view for each case study will be created by the Research Support Unit using the content data. A locked down virtual Safe Haven will support researcher access with disclosure control check on any outputs. Conclusion A DASSL infrastructure could support sharing, linking and analysis of health and social data in Ireland. However, high quality data including matching variables need to be collected to produce beneficial findings. A national rollout requires a governance and legislative model, improvements in data collection, further public engagement and significant resourcing

A Global Jet/Circulation Model for Young Stars

Powerful, highly collimated jets, surrounded by bipolar molecular outflows, are commonly observed near Young Stellar Objects (YSOs). In the usual theoretical picture of star formation, a jet is ejected from a magnetized accretion disk, with a molecular outflow being driven either by the jet or by a wider wind coming from the disk. Here, we propose an alternative global model for the flows surrounding YSOs. In addition to a central accretion-ejection engine driving the jet, the molecular outflow is powered by the infalling matter and follows a circulation pattern around the central object without necessarily being entrained by a jet. It is shown that the model produces a heated pressure-driven outflow with magneto-centrifugal acceleration and collimation. We report solutions for the three different parts of this self-similar model, i.e. the jet, the infalling envelope and the circulating matter that eventually forms the molecular outflow. This new picture of the accretion/outflow phase provides a possible explanation for several observed properties of YSO outflows. The most relevant ones are the presence of high mass molecular outflows around massive protostars, and a realistic fraction (typically 0.1) of the accretion flow that goes into the jet.Comment: accepted for publication in Astronomy and Astrophysic

Status of the VERITAS Observatory

VERITAS, an Imaging Atmospheric Cherenkov Telescope (IACT) system for gammma-ray astronomy in the GeV-TeV range, has recently completed its first season of observations with a full array of four telescopes. A number of astrophysical gamma-ray sources have been detected, both galactic and extragalactic, including sources previously unknown at TeV energies. We describe the status of the array and some highlight results, and assess the technical performance, sensitivity and shower reconstruction capabilities.Comment: Submitted to Proceedings of "4th Heidelberg International Symposium on High Energy Gamma-Ray Astronomy 2008

A national facility for biological cryo-electron microscopy

Three-dimensional electron microscopy is an enormously powerful tool for structural biologists. It is now able to provide an understanding of the molecular machinery of cells, disease processes and the actions of pathogenic organisms from atomic detail through to the cellular context. However, cutting-edge research in this field requires very substantial resources for equipment, infrastructure and expertise. Here, a brief overview is provided of the plans for a UK national three-dimensional electron-microscopy facility for integrated structural biology to enable internationally leading research on the machinery of life. State-of-the-art equipment operated with expert support will be provided, optimized for both atomic-level single-particle analysis of purified macromolecules and complexes and for tomography of cell sections. The access to and organization of the facility will be modelled on the highly successful macromolecular crystallography (MX) synchrotron beamlines, and will be embedded at the Diamond Light Source, facilitating the development of user-friendly workflows providing near-real-time experimental feedback

Podocyte specific knock out of selenoproteins does not enhance nephropathy in streptozotocin diabetic C57BL/6 mice

<p>Abstract</p> <p>Background</p> <p>Selenoproteins contain selenocysteine (Sec), commonly considered the 21^stgenetically encoded amino acid. Many selenoproteins, such as the glutathione peroxidases and thioredoxin reductases, protect cells against oxidative stress by functioning as antioxidants and/or through their roles in the maintenance of intracellular redox balance. Since oxidative stress has been implicated in the pathogenesis of diabetic nephropathy, we hypothesized that selenoproteins protect against this complication of diabetes.</p> <p>Methods</p> <p>C57BL/6 mice that have a podocyte-specific inability to incorporate Sec into proteins (denoted in this paper as PodoTrsp^-/-) and control mice were made diabetic by intraperitoneal injection of streptozotocin, or were injected with vehicle. Blood glucose, body weight, microalbuminuria, glomerular mesangial matrix expansion, and immunohistochemical markers of oxidative stress were assessed.</p> <p>Results</p> <p>After 3 and 6 months of diabetes, control and PodoTrsp^-/-mice had similar levels of blood glucose. There were no differences in urinary albumin/creatinine ratios. Periodic acid-Schiff staining to examine mesangial matrix expansion also demonstrated no difference between control and PodoTrsp^-/-mice after 6 months of diabetes, and there were no differences in immunohistochemical stainings for nitrotyrosine or NAD(P)H dehydrogenase, quinone 1.</p> <p>Conclusion</p> <p>Loss of podocyte selenoproteins in streptozotocin diabetic C57BL/6 mice does not lead to increased oxidative stress as assessed by nitrotyrosine and NAD(P)H dehydrogenase, quinone 1 immunostaining, nor does it lead to worsening nephropathy.</p