Characterizing the diversity and commensal origins of penA mosaicism in the genus Neisseria

Mosaic penA alleles formed through horizontal gene transfer (HGT) have been instrumental to the rising incidence of ceftriaxone-resistant gonococcal infections. Although interspecies HGT of regions of the penA gene between Neisseria gonorrhoeae and commensal Neisseria species has been described, knowledge concerning which species are the most common contributors to mosaic penA alleles is limited, with most studies examining only a small number of alleles. Here, we investigated the origins of recombinant penA alleles through in silico analyses that incorporated 1700 penA alleles from 35 513 Neisseria isolates, comprising 15 different Neisseria species. We identified Neisseria subflava and Neisseria cinerea as the most common source of recombinant sequences in N. gonorrhoeae penA. This contrasted with Neisseria meningitidis penA, for which the primary source of recombinant DNA was other meningococci, followed by Neisseria lactamica. Additionally, we described the distribution of polymorphisms implicated in antimicrobial resistance in penA, and found that these are present across the genus. These results provide insight into resistance-related changes in the penA gene across human-associated Neisseria species, illustrating the importance of genomic surveillance of not only the pathogenic Neisseria, but also of the oral niche-associated commensals from which these pathogens are sourcing key genetic variation

Fossilized anuran soft tissues reveal a new taphonomic model for the Eocene Geiseltal Konservat-Lagerstätte, Germany

The Eocene Geiseltal Konservat-Lagerstätte (Germany) is famous for reports of three dimensionally preserved soft tissues with sub-cellular detail. The proposed mode of preservation, direct replication in silica, is not known in other fossils and has not been verified using modern approaches. Here, we investigated the taphonomy of the Geiseltal anurans using diverse microbeam imaging and chemical analytical techniques. Our analyses confirm the preservation of soft tissues in all body regions but fail to yield evidence for silicified soft tissues. Instead, the anuran soft tissues are preserved as two layers that differ in microstructure and composition. Layer 1 comprises sulfur-rich carbonaceous microbodies interpreted as melanosomes. Layer 2 comprises the mid-dermal Eberth-Katschenko layer, preserved in calcium phosphate. In addition, patches of original aragonite crystals define the former position of the endolymphatic sac. The primary modes of soft tissue preservation are therefore sulfurization of melanosomes and phosphatization of more labile soft tissues, i.e., skin. This is consistent with the taphonomy of vertebrates in many other Konservat-Lagerstätten. These findings emphasize an emerging model for pervasive preservation of vertebrate soft tissues via melanosome films, particularly in stagnation-type deposits, with phosphatization of more labile tissues where tissue biochemistry is favorable

Winter distribution of willow flycatcher subspecies

The article presents a study which examines the migratory connectivity in the Willow Flycatcher subspecies throughout the winter range using mitochondrial DNA sequences as well as the morphological characteristics of 68 museum specimens obtained in the winter range in Costa Rica. It notes that the findings reveal that the overlapping and distinct regions of the winter range were occupied by the four subspecies. The specific breeding of these species is connected to the winter grounds

High performance single photon sources from photolithographically defined pillar microcavities

We demonstrate that single photons can be generated from single InAs/GaAs quantum dots in photolithographically defined pillar microcavities. Pillars with a 1.9 µm diameter cavity show a four fold enhancement in the radiative decay rate due to the Purcell effect and a photon collection efficiency into a lens of up to 10%. Measurements of the second order correlation function reveal a greater than fifty fold reduction in the multi-photon emission rate compared to a laser of the same intensity

Vein Hosted Copper Deposits of the Allihies Mining Area, Southwest Ireland – A New Structural and Chronological Evaluation

This paper presents new data for historical vein-hosted copper sulfide deposits in the Late Paleozoic Munster and South Munster basins of SW Ireland. Detailed mapping, 3D modelling, fluid inclusion microthermometry and geochronology from the Allihies area of the Beara Peninsula have led to a new interpretation of the timing and development of ore mineralization. Macro- and microstructural studies reveal that the ore-bearing, mainly east–west-striking quartz veins are directly related to early extensional, basinal normal faults. Molybdenite Re–Os dating of the main-stage Cu lode yields ages from 367.3 ± 5.5 to 366.4 ± 1.9 Ma. This early vein system experienced subsequent late Carboniferous Variscan deformation, including cleavage development, sinistral SW–NE strike-slip faulting, cataclastic deformation and recrystallization. The new timing of Cu mineralization in SW Ireland has major implications for its relationship to the base metal deposits of the Irish Midlands

Diagnostic accuracy of the magnetocardiograph for patients with suspected acute coronary syndrome

Background We aimed to estimate the diagnostic accuracy of the VitalScan magnetocardiograph (MCG) for suspected acute coronary syndrome (ACS). Methods We undertook a prospective cohort study evaluating the diagnostic accuracy of the MCG in adults with suspected ACS. The reference standard of ACS was determined by an independent adjudication committee based on 30-day investigations and events. The cohort was split into a training sample, to derive the MCG algorithm and an algorithm combining MCG with a modified Manchester Acute Coronary Syndrome (MACS) clinical probability score, and a validation sample, to estimate diagnostic accuracy. Results We recruited 756 participants and analysed data from 680 (293 training, 387 validation), of whom 96 (14%) had ACS. In the training sample, the respective area under the receiver operating characteristic (AUROC) curves were the following: MCG 0.66 (95% CI 0.58 to 0.74), MACS 0.64 (95% CI 0.54 to 0.73) and MCG+MACS 0.70 (95% CI 0.63 to 0.77). MCG specificity was 0.16 (95% CI 0.12 to 0.21) at the threshold achieving acceptable sensitivity for rule-out (>0.98). In the validation sample (n=387), the respective AUROCs were the following: MCG 0.56 (95% CI 0.48 to 0.64), MACS 0.69 (95% CI 0.61 to 0.77) and MCG+MACS 0.64 (95% CI 0.56 to 0.72). MCG sensitivity was 0.89 (95% CI 0.77 to 0.95) and specificity 0.15 (95% CI 0.12 to 0.20) at the rule-out threshold. MCG+MACS sensitivity was 0.85 (95% CI 0.73 to 0.92) and specificity 0.30 (95% CI 0.25 to 0.35). Conclusion The VitalScan MCG is currently unable to accurately rule out ACS and is not yet ready for use in clinical practice. Further developmental research is required

Species prioritization for monitoring and management in regional multiple species conservation plans.

Successful conservation plans are not solely achieved by acquiring optimally designed reserves. Ongoing monitoring and management of the biodiversity in those reserves is an equally important, but often neglected or poorly executed, part of the conservation process. In this paper we address one of the first and most important steps in designing a monitoring program - deciding what to monitor. We present a strategy for prioritizing species for monitoring and management in multispecies conservation plans. We use existing assessments of threatened status, and the degree and spatial and temporal extent of known threats to link the prioritization of species to the overarching goals and objectives of the conservation plan. We consider both broad and localized spatial scales to capture the regional conservation context and the practicalities of local management and monitoring constraints. Spatial scales that are commensurate with available data are selected. We demonstrate the utility of this strategy through application to a set of 85 plants and animals in an established multispecies conservation plan in San Diego County, California, USA. We use the prioritization to identify the most prominent risk factors and the habitats associated with the most threats to species. The protocol highlighted priorities that had not previously been identified and were not necessarily intuitive without systematic application of the criteria; many high-priority species have received no monitoring attention to date, and lower-priority species have. We recommend that in the absence of clear focal species, monitoring threats in highly impacted habitats may be a way to circumvent the need to monitor all the targeted species

Hepatocellular Carcinoma with Immature T-Cell (T-lymphoblastic) Proliferation

Indolent T-lymphoblastic proliferation has been rarely reported in the upper aerodigestive tract. The lymphoid cells associated with this condition have the morphological and phenotypical features of immature thymocytes. However, their pathogenesis and biology are unknown. We present an unusual type of tumor infiltrating lymphocytes in a case with hepatocellular carcinoma, presumed to be a T-lymphoblastic proliferation. A 58-yr-old female patient presented with indigestion and a palpable epigastric mass. The abdominal computed tomography revealed a mass in the S6 region of the liver. A hepatic segmentectomy was performed. Microscopic examination showed dense isolated nests of monomorphic lymphoid cells within the tumor. Immunohistochemically, the lymphoid cells were positive for CD3, terminal deoxymucleotide transferase (TdT) and CD1a. In addition, they showed dual expression of CD4 and CD8. The polymerase chain reaction used to examine the T-cell antigen receptor gamma gene rearrangement showed polyclonal T-cell proliferation. This is the second case of hepatocellular carcinoma combined with indolent T-lymphoblastic proliferation identified by an unusual tumor infiltrating lymphocytes