An Anglo-Saxon execution cemetery at Walkington Wold, Yorkshire

This paper presents a re-evaluation of a cemetery excavated over 30 years ago at Walkington Wold in east Yorkshire. The cemetery is characterized by careless burial on diverse alignments, and by the fact that most of the skeletons did not have associated crania. The cemetery has been variously described as being the result of an early post-Roman massacre, as providing evidence for a ‘Celtic’ head cult or as an Anglo-Saxon execution cemetery. In order to resolve the matter, radiocarbon dates were acquired and a re-examination of the skeletal remains was undertaken. It was confirmed that the cemetery was an Anglo-Saxon execution cemetery, the only known example from northern England, and the site is set into its wider context in the paper

Development and Implementation of an Academic-Community Partnership to Enhance Care among Homeless Persons

An academic-community partnership between a Health Care for the Homeless (HCH) clinic and a school of pharmacy was created in 2005 to provide medication education and identify medication related problems. The urban community based HCH clinic in the Richmond, VA area provides primary health care to the homeless, uninsured and underinsured. The center also offers eye care, dental care, mental health and psychiatric care, substance abuse services, case management, laundry and shower facilities, and mail services at no charge to those in need. Pharmacist services are provided in the mental health and medical clinics. A satisfaction survey showed that the providers and staff (n = 13) in the clinic were very satisfied with the integration of pharmacist services. The quality and safety of medication use has improved as a result of the academic-community collaborative. Education and research initiatives have also resulted from the collaborative. This manuscript describes the implementation, outcomes and benefits of the partnership for both the HCH clinic and the school of pharmacy. Type: Clinical Experienc

Pulsar-wind nebulae and magnetar outflows: observations at radio, X-ray, and gamma-ray wavelengths

We review observations of several classes of neutron-star-powered outflows: pulsar-wind nebulae (PWNe) inside shell supernova remnants (SNRs), PWNe interacting directly with interstellar medium (ISM), and magnetar-powered outflows. We describe radio, X-ray, and gamma-ray observations of PWNe, focusing first on integrated spectral-energy distributions (SEDs) and global spectral properties. High-resolution X-ray imaging of PWNe shows a bewildering array of morphologies, with jets, trails, and other structures. Several of the 23 so far identified magnetars show evidence for continuous or sporadic emission of material, sometimes associated with giant flares, and a few possible "magnetar-wind nebulae" have been recently identified.Comment: 61 pages, 44 figures (reduced in quality for size reasons). Published in Space Science Reviews, "Jets and Winds in Pulsar Wind Nebulae, Gamma-ray Bursts and Blazars: Physics of Extreme Energy Release

Identification of Putative Cytoskeletal Protein Homologues in the Protozoan Host \u3cem\u3eHartmannella vermiformis\u3c/em\u3e as Substrates for Induced Tyrosine Phosphatase Activity Upon Attachment to the Legionnaires\u27 Disease Bacterium, \u3cem\u3eLegionella pneumophila\u3c/em\u3e

The Legionnaires\u27 disease bacterium, Legionella pneumophila, is a facultative intracellular pathogen that invades and replicates within two evolutionarily distant hosts, free living protozoa and mammalian cells. Invasion and intracellular replication within protozoa are thought to be major factors in the transmission of Legionnaires\u27 disease. We have recently reported the identification of a galactose/N-acetyl-d-galactosamine (Gal/GalNAc) lectin in the protozoan host Hartmannella vermiformis as a receptor for attachment and invasion by L. pneumophila (Venkataraman, C., B.J. Haack, S. Bondada, and Y.A. Kwaik. 1997. J. Exp. Med. 186:537–547). In this report, we extended our studies to the effects of bacterial attachment and invasion on the cytoskeletal proteins of H. vermiformis. We first identified the presence of many protozoan cytoskeletal proteins that were putative homologues to their mammalian counterparts, including actin, pp125FAK, paxillin, and vinculin, all of which were basally tyrosine phosphorylated in resting H. vermiformis. In addition to L. pneumophila–induced tyrosine dephosphorylation of the lectin, bacterial attachment and invasion was associated with tyrosine dephosphorylation of paxillin, pp125FAK, and vinculin, whereas actin was minimally affected. Inhibition of bacterial attachment to H. vermiformis by Gal or GalNAc monomers blocked bacteria-induced tyrosine dephosphorylation of detergent-insoluble proteins. In contrast, inhibition of bacterial invasion but not attachment failed to block bacteria-induced tyrosine dephosphorylation of H. vermiformis proteins. This was further supported by the observation that 10 mutants of L. pneumophila that were defective in invasion of H. vermiformis were capable of inducing tyrosine dephosphorylation of H. vermiformis proteins. Entry of L. pneumophila into H. vermiformis was predominantly mediated by noncoated receptor-mediated endocytosis (93%) but coiling phagocytosis was infrequently observed (7%). We conclude that attachment but not invasion by L. pneumophila into H. vermiformis was sufficient and essential to induce protein tyrosine dephosphorylation in H. vermiformis. These manipulations of host cell processes were associated with, or followed by, entry of the bacteria by a noncoated receptor-mediated endocytosis. A model for attachment and entry of L. pneumophila into H. vermiformis is proposed

Seed dormancy and germination in Dodonaea viscosa (Sapindaceae) from south-western Saudi Arabia

Dodonaea viscosa (Sapindaceae) is widespread in the mountainous highlands of the southwestern part of the Kingdom of Saudi Arabia, where it is a medicinally important species for the people of Saudi Arabia. Seeds of this species were collected from Mount Atharb in the Al-Baha region, at an altitude of 2100 m. The aims of this study were to determine if the seeds of D. viscosa have physical dormancy (i.e. a water-impermeable seed coat) and, if so, what treatments would break dormancy, and what conditions promote germination after dormancy has been broken. The dormancy-breaking treatments included: soaking of seeds in concentrated sulfuric acid (H2SO4) for 10 minutes, immersion in boiling water for 10 minutes and exposure to 50 °C for 1 minute. After seeds had been pre-treated with H2SO4, to break dormancy, they were incubated at constant temperatures from 5 to 35°C, under 12-h photoperiods or in continuous darkness, and germination recorded. Salinity tolerance was investigated by incubating acid-scarified seeds in 0, 100, 200 and 300 mM NaCl in the light at 25°C. Untreated seeds had low final germination (30%). Seeds that had been acid-scarified, immersed in boiling water or exposed to 50 °C all achieved 91% subsequently when incubated at 25°C. Thus, seeds of this species in Saudi Arabia have physical dormancy, which can be broken by all three treatments designed to increase the permeability of the testa. After pre-treatment, there was a broad optimum constant temperature for germination that ranged between 5-25°C but germination was inhibited by higher temperatures (30 and 35°C). Light had little effect on this germination response. Scarified seeds were also sensitive to salinity, with the highest germination in distilled water and complete inhibition in 400 mM NaCl. Seeds that failed to germinate in saline treatments were mostly able to germinate on transfer to distilled water, suggesting osmotic inhibition

An Integrated TCGA Pan-Cancer Clinical Data Resource to Drive High-Quality Survival Outcome Analytics

For a decade, The Cancer Genome Atlas (TCGA) program collected clinicopathologic annotation data along with multi-platform molecular profiles of more than 11,000 human tumors across 33 different cancer types. TCGA clinical data contain key features representing the democratized nature of the data collection process. To ensure proper use of this large clinical dataset associated with genomic features, we developed a standardized dataset named the TCGA Pan-Cancer Clinical Data Resource (TCGA-CDR), which includes four major clinical outcome endpoints. In addition to detailing major challenges and statistical limitations encountered during the effort of integrating the acquired clinical data, we present a summary that includes endpoint usage recommendations for each cancer type. These TCGA-CDR findings appear to be consistent with cancer genomics studies independent of the TCGA effort and provide opportunities for investigating cancer biology using clinical correlates at an unprecedented scale. Analysis of clinicopathologic annotations for over 11,000 cancer patients in the TCGA program leads to the generation of TCGA Clinical Data Resource, which provides recommendations of clinical outcome endpoint usage for 33 cancer types

Capturing wheat phenotypes at the genome level

Recent technological advances in next-generation sequencing (NGS) technologies have dramatically reduced the cost of DNA sequencing, allowing species with large and complex genomes to be sequenced. Although bread wheat (Triticum aestivum L.) is one of the world’s most important food crops, efficient exploitation of molecular marker-assisted breeding approaches has lagged behind that achieved in other crop species, due to its large polyploid genome. However, an international public–private effort spanning 9 years reported over 65% draft genome of bread wheat in 2014, and finally, after more than a decade culminated in the release of a gold-standard, fully annotated reference wheat-genome assembly in 2018. Shortly thereafter, in 2020, the genome of assemblies of additional 15 global wheat accessions was released. As a result, wheat has now entered into the pan-genomic era, where basic resources can be efficiently exploited. Wheat genotyping with a few hundred markers has been replaced by genotyping arrays, capable of characterizing hundreds of wheat lines, using thousands of markers, providing fast, relatively inexpensive, and reliable data for exploitation in wheat breeding. These advances have opened up new opportunities for marker-assisted selection (MAS) and genomic selection (GS) in wheat. Herein, we review the advances and perspectives in wheat genetics and genomics, with a focus on key traits, including grain yield, yield-related traits, end-use quality, and resistance to biotic and abiotic stresses. We also focus on reported candidate genes cloned and linked to traits of interest. Furthermore, we report on the improvement in the aforementioned quantitative traits, through the use of (i) clustered regularly interspaced short-palindromic repeats/CRISPR-associated protein 9 (CRISPR/Cas9)-mediated gene-editing and (ii) positional cloning methods, and of genomic selection. Finally, we examine the utilization of genomics for the next-generation wheat breeding, providing a practical example of using in silico bioinformatics tools that are based on the wheat reference-genome sequence

Physically Similar Systems - A History of the Concept

PreprintThe concept of similar systems arose in physics, and appears to have originated with Newton in the seventeenth century. This chapter provides a critical history of the concept of physically similar systems, the twentieth century concept into which it developed. The concept was used in the nineteenth century in various fields of engineering (Froude, Bertrand, Reech), theoretical physics (van der Waals, Onnes, Lorentz, Maxwell, Boltzmann) and theoretical and experimental hydrodynamics (Stokes, Helmholtz, Reynolds, Prandtl, Rayleigh). In 1914, it was articulated in terms of ideas developed in the eighteenth century and used in nineteenth century mathematics and mechanics: equations, functions and dimensional analysis. The terminology physically similar systems was proposed for this new characterization of similar systems by the physicist Edgar Buckingham. Related work by Vaschy, Bertrand, and Riabouchinsky had appeared by then. The concept is very powerful in studying physical phenomena both theoretically and experimentally. As it is not currently part of the core curricula of STEM disciplines or philosophy of science, it is not as well known as it ought to be

Comprehensive analysis of epigenetic clocks reveals associations between disproportionate biological ageing and hippocampal volume

The concept of age acceleration, the difference between biological age and chronological age, is of growing interest, particularly with respect to age-related disorders, such as Alzheimer’s Disease (AD). Whilst studies have reported associations with AD risk and related phenotypes, there remains a lack of consensus on these associations. Here we aimed to comprehensively investigate the relationship between five recognised measures of age acceleration, based on DNA methylation patterns (DNAm age), and cross-sectional and longitudinal cognition and AD-related neuroimaging phenotypes (volumetric MRI and Amyloid-β PET) in the Australian Imaging, Biomarkers and Lifestyle (AIBL) and the Alzheimer’s Disease Neuroimaging Initiative (ADNI). Significant associations were observed between age acceleration using the Hannum epigenetic clock and cross-sectional hippocampal volume in AIBL and replicated in ADNI. In AIBL, several other findings were observed cross-sectionally, including a significant association between hippocampal volume and the Hannum and Phenoage epigenetic clocks. Further, significant associations were also observed between hippocampal volume and the Zhang and Phenoage epigenetic clocks within Amyloid-β positive individuals. However, these were not validated within the ADNI cohort. No associations between age acceleration and other Alzheimer’s disease-related phenotypes, including measures of cognition or brain Amyloid-β burden, were observed, and there was no association with longitudinal change in any phenotype. This study presents a link between age acceleration, as determined using DNA methylation, and hippocampal volume that was statistically significant across two highly characterised cohorts. The results presented in this study contribute to a growing literature that supports the role of epigenetic modifications in ageing and AD-related phenotypes