Halcyornis toliapicus (aves: Lower Eocene, England) indicates advanced neuromorphology in Mesozoic Neornithes

Our recent X-ray micro computer-tomographic (μCT) investigations of Prophaethon shrubsolei and Odontopteryx toliapica from the Lower Eocene London Clay Formation of England revealed the avian brain to have been essentially modern in form by 55 Ma, but that an important vision-related synapomorphy of living birds, the eminentia sagittalis of the telencephalon, was poorly developed. This evidence suggested that the feature probably appeared close to the end of the Mesozoic. Here we use μCT analysis to describe the endocranium of Halcyornis toliapicus, also from the London Clay Formation. The affinities of Halcyornis have been hotly debated, with the taxon referred to the Charadriiformes (Laridae), Coraciiformes (Alcedinidae, and its own family Halcyornithidae) and most recently that Halcyornithidae may be a possible senior synonym of Pseudasturidae (Pan-Psittaciformes). Unlike Prophaethon and Odontopteryx, the eminentia sagittalis of Halcyornis is strongly developed and comparable to that of living species. Like those London Clay taxa, the eminentia sagittalis occupies a rostral position on the telencephalon. The senses of Halcyornis appear to have been well developed. The length of the cochlear duct of the inner ear indicates a hearing sensitivity within the upper range of living species, and enlarged olfactory lobes suggest a reasonable reliance on sense of smell. The optic nerves were especially well developed which, together with the strong development of the eminentia sagittalis, indicates a high degree of visual specialization in Halcyornis. The advanced development of the eminentia sagittalis further supports a Mesozoic age for the appearance of this structure and associated neural architectural complexity found in extant Aves. The eminentia sagittalis of living Psittaciformes is situated caudally on the telencephalon, making a Pan-Psittaciformes relationship unlikely for Halcyorni

Climate-driven expansion of blanket bogs in Britain during the Holocene

Blanket bog occupies approximately 6 % of the area of the UK today. The Holocene expansion of this hyperoceanic biome has previously been explained as a consequence of Neolithic forest clearance. However, the present distribution of blanket bog in Great Britain can be predicted accurately with a simple model (PeatStash) based on summer temperature and moisture index thresholds, and the same model correctly predicts the highly disjunct distribution of blanket bog worldwide. This finding suggests that climate, rather than land-use history, controls blanket-bog distribution in the UK and everywhere else. We set out to test this hypothesis for blanket bogs in the UK using bioclimate envelope modelling compared with a database of peat initiation age estimates. We used both pollen-based reconstructions and climate model simulations of climate changes between the mid-Holocene (6000 yr BP, 6 ka) and modern climate to drive PeatStash and predict areas of blanket bog. We compiled data on the timing of blanket-bog initiation, based on 228 age determinations at sites where peat directly overlies mineral soil. The model predicts large areas of northern Britain would have had blanket bog by 6000 yr BP, and the area suitable for peat growth extended to the south after this time. A similar pattern is shown by the basal peat ages and new blanket bog appeared over a larger area during the late Holocene, the greatest expansion being in Ireland, Wales and southwest England, as the model predicts. The expansion was driven by a summer cooling of about 2 °C, shown by both pollen-based reconstructions and climate models. The data show early Holocene (pre-Neolithic) blanket-bog initiation at over half of the sites in the core areas of Scotland, and northern England. The temporal patterns and concurrence of the bioclimate model predictions and initiation data suggest that climate change provides a parsimonious explanation for the early Holocene distribution and later expansion of blanket bogs in the UK, and it is not necessary to invoke anthropogenic activity as a driver of this major landscape change

Chromophoric Dissolved Organic Matter and Dissolved Organic Carbon in Lakes Across an Elevational Gradient From the Mountains to the Sea

Dissolved organic matter (DOM) in lakes across elevation gradients is a complex function of topography, climate, vegetation coverage, land use, and lake properties. To examine sources and processing of DOM from sea level to mountain lakes (3–1,574 m), we measured dissolved organic carbon (DOC) concentrations and chromophoric dissolved organic matter (CDOM) optical properties, lake characteristics, and water quality parameters in 62 freshwater lakes in the Pacific Northwest, USA. Higher elevation lakes had lower DOC concentrations and absorbance. These lakes had higher forest cover and minimal wetlands in their watershed, in addition to low nutrients, water temperatures, and chlorophyll a in the lake itself. Two humic-like and one protein-like fluorescent component were identified from excitation-emission matrix spectroscopy. The index of recent autochthonous contribution (BIX), fluorescence index (FIX), and SR optical indices showed that most lakes were dominated by terrestrially derived material. The humification index (HIX) and specific ultra-violet absorbance (SUVA254) were consistent with more aromatic humic CDOM at lower elevations. The lower fluorescence of humic-like components at higher elevation was attributed to lower inputs from vegetation. The relative contribution of the protein-like component increased at higher elevation. This may be due to reduced allochthonous terrestrial inputs relative to in situ production of autochthonous material or increased photochemical/biological degradation of allochthonous material. Differences in optical characteristics associated with the amount and source of CDOM were observed across the elevational gradient. These differences were driven by characteristics at both within-lake and watershed scales

MRI and gravimetric studies of hydrology in drip irrigated heaps and its effect on the propagation of bioleaching microorganisms

Heap bioleaching performance is dependent on the contacting of the leach solution with the ore bed, hence on the system hydrodynamics. In this study two experimental setups were used to examine hydrodynamics associated with irrigation from a single drip emitter, one of the most common methods of heap irrigation. A specialist magnetic resonance imaging (MRI) method which is insensitive to the metal content of the ore was used to examine the liquid flow into an ore bed in the immediate vicinity of an irrigation point. The distribution of liquid in, microbial colonisation of and mineral recovery from a bioleach of a large scale 132 kg “ore slice” were subsequently monitored using sample ports positioned along the breadth and height of the reactor. In both systems the lateral movement of the liquid increased with bed depth, though preferential flow was evident. The majority of the liquid flow was in the region directly below the irrigation point and almost no liquid exchange occurred in the areas of lowest liquid content at the upper corners of the bed in which fluid exchange was driven by capillary action. The MRI studies revealed that the liquid distribution was unchanging following an initial settling of the ore bed and that, at steady state, the majority (~60%) of the liquid flowed directly into established large channels. The limited lateral movement of the liquid had a significant impact on the local leaching efficiencies and microbial colonisation of the ore with cell concentrations in the regions of lowest liquid content lying below the detection limit. Hence poor lateral liquid distribution with drip irrigation, and the associated impact on colonisation was identified as a significant disadvantage of this irrigation approach. Further, the need to optimise fluid exchange throughout the ore bed was identified as key for optimisation of leaching performance

Prospective genomic surveillance of methicillin-resistant Staphylococcus aureus (MRSA) associated with bloodstream infection, England, 1 October 2012 to 30 September 2013.

BackgroundMandatory reporting of methicillin-resistant Staphylococcus aureus (MRSA) bloodstream infections (BSI) has occurred in England for over 15years. Epidemiological information is recorded, but routine collection of isolates for characterisation has not been routinely undertaken. Ongoing developments in whole-genome sequencing (WGS) have demonstrated its value in outbreak investigations and for determining the spread of antimicrobial resistance and bacterial population structure. Benefits of adding genomics to routine epidemiological MRSA surveillance are unknown.AimTo determine feasibility and potential utility of adding genomics to epidemiological surveillance of MRSA.MethodsWe conducted an epidemiological and genomic survey of MRSA BSI in England over a 1-year period (1 October 2012--30 September 2013).ResultsDuring the study period, 903 cases of MRSA BSI were reported; 425 isolates were available for sequencing of which, 276 (65%) were clonal complex (CC) 22. Addition of 64 MRSA genomes from published outbreak investigations showed that the study genomes could provide context for outbreak isolates and supported cluster identification. Comparison to other MRSA genome collections demonstrated variation in clonal diversity achieved through different sampling strategies and identified potentially high-risk clones e.g. USA300 and local expansion of CC5 MRSA in South West England.ConclusionsWe demonstrate the potential utility of combined epidemiological and genomic MRSA BSI surveillance to determine the national population structure of MRSA, contextualise previous MRSA outbreaks, and detect potentially high-risk lineages. These findings support the integration of epidemiological and genomic surveillance for MRSA BSI as a step towards a comprehensive surveillance programme in England.This work was supported by grants from the UK Clinical Research Collaboration Translational Infection Research Initiative, and the Medical Research Council (Grant Number G1000803) with contributions to the Grant from the Biotechnology and Biological Sciences Research Council, the National Institute for Health Research on behalf of the Department of Health, and the Chief Scientist Office of the Scottish Government Health Directorate (to Prof. Peacock); and the Wellcome Trust (to Prof. Parkhill [Grant 098051], Prof. Peacock). MST is a Wellcome Trust Clinical PhD Fellow at the University of Cambridge. MET is a Clinician Scientist Fellow, supported by the Academy of Medical Sciences and the Health Foundation, and by the National Institute for Health Research Cambridge Biomedical Research Centre. FC is supported by the Wellcome Trust (201344/Z/16/Z)

Fluorinated benzalkylsilane molecular rectifiers

We report on the synthesis and electrical properties of nine new alkylated silane self-assembled monolayers (SAMs) – (EtO)3Si(CH2)nN = CHPhX where n = 3 or 11 and X = 4-CF[subscript 3], 3,5-CF[subscript 3], 3-F-4-CF[subscript 3], 4-F, or 2,3,4,5,6-F, and explore their rectification behavior in relation to their molecular structure. The electrical properties of the films were examined in a metal/insulator/metal configuration, with a highly-doped silicon bottom contact and a eutectic gallium-indium liquid metal (EGaIn) top contact. The junctions exhibit high yields (>90%), a remarkable resistance to bias stress, and current rectification ratios (R) between 20 and 200 depending on the structure, degree of order, and internal dipole of each molecule. We found that the rectification ratio correlates positively with the strength of the molecular dipole moment and it is reduced with increasing molecular length.National Science Foundation (U.S.) (Award ECCS 1254757)Wake Forest University (Pilot Research Grant

Early Clinical and Subclinical Visual Evoked Potential and Humphrey's Visual Field Defects in Cryptococcal Meningitis.

Cryptococcal induced visual loss is a devastating complication in survivors of cryptococcal meningitis (CM). Early detection is paramount in prevention and treatment. Subclinical optic nerve dysfunction in CM has not hitherto been investigated by electrophysiological means. We undertook a prospective study on 90 HIV sero-positive patients with culture confirmed CM. Seventy-four patients underwent visual evoked potential (VEP) testing and 47 patients underwent Humphrey's visual field (HVF) testing. Decreased best corrected visual acuity (BCVA) was detected in 46.5% of patients. VEP was abnormal in 51/74 (68.9%) right eyes and 50/74 (67.6%) left eyes. VEP P100 latency was the main abnormality with mean latency values of 118.9 (±16.5) ms and 119.8 (±15.7) ms for the right and left eyes respectively, mildly prolonged when compared to our laboratory references of 104 (±10) ms (p<0.001). Subclinical VEP abnormality was detected in 56.5% of normal eyes and constituted mostly latency abnormality. VEP amplitude was also significantly reduced in this cohort but minimally so in the visually unimpaired. HVF was abnormal in 36/47 (76.6%) right eyes and 32/45 (71.1%) left eyes. The predominant field defect was peripheral constriction with an enlarged blind spot suggesting the greater impact by raised intracranial pressure over that of optic neuritis. Whether this was due to papilloedema or a compartment syndrome is open to further investigation. Subclinical HVF abnormalities were minimal and therefore a poor screening test for early optic nerve dysfunction. However, early optic nerve dysfunction can be detected by testing of VEP P100 latency, which may precede the onset of visual loss in CM

Impact of the Macrophyte Nymphaea odorata (Lily Pads) on Dissolved Organic Matter (DOM) in a Lake

(Files are available for download below.) Macrophytes are a potential source of dissolved organic matter (DOM) in lakes. To probe the contribution of Nymphaea odorata (lily pads), dissolved organic carbon concentrations (DOC) and optical properties of chromophoric DOM were measured in a lake in the Pacific Northwest, United States over a year. Lily pads are prevalent around the shoreline during summer, dying back in fall. Indices of recent autochthonous contribution (BIX), fluorescence (FIX) and SR showed the lake was dominated by terrestrially-derived material. DOC concentrations were not correlated with rainfall, but were positively correlated with absorption coefficients. Values were highest in the summer dry season and decreased in the winter wet season, suggesting a source in the lake being diluted by precipitation rather than a dominant source from watershed runoff. Humic-like and protein-like fluorescent components were identified from excitation-emission matrix spectroscopy in lake waters and lily pad leachates. The protein-like component was highest during the summer, indicative of an in situ autochthonous source. Lily pad leachates had BIX, FIX, and SR values characteristic of terrestrial material and lake samples. However, leachates had lower humification index (HIX), specific ultraviolet absorbance (SUVA), flu/abs ratios and spectral slope (S) values. Higher absorption coefficients and DOC concentrations in the lake in summer were correlated with lower HIX, SUVA, flu/abs and S values, consistent with material leaching from lily pads. Seasonal trends in optical indices, absorption coefficients and DOC concentrations are consistent with lily pads being a significant DOM source in the lake, particularly in the summer dry season with low watershed runoff. This is for the supporting data for the paper in Limnology and Oceanography, specifically the absorbance and fluorescence spectra of the Lake Louise water samples (taken weekly over the course of a year). These files include large spreadsheets with raw and corrected absorbance and fluorescence intensity data as a function of wavelength, as well as the raw and corrected absorbance and fluorescence 3D excitation-emission matrix spectra (EEMs). These files are in .opj format, which is readable with commercially available Origin graphing software. Data includes tables with optical parameters and indices for absorbance and fluorescence for the weekly lake water samples, and spreadsheets with raw and corrected absorbance and fluorescence intensity data as a function of wavelength, as well as raw and corrected absorbance and fluorescence 3D excitation-emission matrix spectra (EEMs)

Supporting Information for Chromophoric Dissolved Organic Matter (CDOM) Across an Elevational Gradient from Sea Level to Mountain Lakes in the Pacific Northwest

This dataset is in support of Juetten et al., which has been submitted to the Journal of Geophysical Research Biogeosciences for consideration for publication. Chromophoric dissolved organic matter (CDOM) in lakes across elevation gradients is a complex function of topography, climate, vegetation coverage, land use, and lake properties. To examine sources and processing of CDOM from sea level to mountain lakes (3 to 1574 m), we measured CDOM optical properties, lake characteristics, and water quality parameters in 62 freshwater lakes in the Pacific Northwest, USA. Higher elevation lakes had lower dissolved organic carbon (DOC) and absorbance. These lakes had higher forest cover, minimal wetlands or crops, low nutrients, cooler water temperatures, and low chlorophyll a. Two humic-like and one protein-like fluorescent component were identified from excitation-emission matrix spectroscopy (EEMs). The index of recent autochthonous contribution (BIX), fluorescence index (FIX) and SR optical indices indicated that most lakes were dominated by terrestrially-derived material. The humification index (HIX) and specific ultra-violet absorbance (SUVA) were consistent with more aromatic humic CDOM at lower elevations. Fluorescence of humic-like components was lower at higher elevation, indicating reduced amounts of CDOM, attributed to lower inputs from vegetation. The relative contribution of the protein-like component increased at higher elevation, because allochthonous terrestrial inputs are reduced relative to in situ production of autochthonous material or higher photochemical and biological degradation of allochthonous material. Differences in optical characteristics associated with CDOM levels and some characteristics associated with CDOM source and quality were observed across the elevational gradient. These differences were driven by characteristics at both within-lake and watershed scales, suggesting a more complete understanding of CDOM patterns can be gained by examining factors at multiple spatial scales. The dataset available below is supplementary information to the paper in a Word file format. This includes: a figure corresponding to the RDA Figure 6 in the manuscript giving the lake names; a table giving sampling dates, elevations, locations and watershed characteristics for the lakes; a table comparing water quality parameters for deep vs, surface water samples from Lake Padden in 2011; and a table giving the measured water quality parameters for the lakes from summer 2018

Differential regulation of Krüppel-like factor family transcription factor expression in neonatal rat cardiac myocytes: effects of endothelin-1, oxidative stress and cytokines

Krüppel-like transcription factors (Klfs) modulate fundamental cell processes. Cardiac myocytes are terminally-differentiated, but hypertrophy in response to stimuli such as endothelin-1. H2O2 or cytokines promote myocyte apoptosis. Microarray studies of neonatal rat myocytes identified several Klfs as endothelin-1-responsive genes. We used quantitative PCR for further analysis of Klf expression in neonatal rat myocytes. In response to endothelin-1, Klf2 mRNA expression was rapidly increased ( approximately 9-fold; 15-30 min) with later increases in expression of Klf4 and Klf6 ( approximately 5-fold; 30-60 min). All were regulated as immediate early genes (cycloheximide did not inhibit the increases in expression). Klf5 expression was increased at 1-2 h ( approximately 13-fold) as a second phase response (cycloheximide inhibited the increase). These increases were transient and attenuated by U0126. H2O2 increased expression of Klf2, Klf4 and Klf6, but interleukin-1beta or tumor necrosis factor alpha downregulated Klf2 expression with no effect on Klf4 or Klf6. Of the Klfs which repress transcription, endothelin-1 rapidly downregulated expression of Klf3, Klf11 and Klf15. The dynamic regulation of expression of multiple Klf family members in cardiac myocytes suggests that, as a family, they are actively involved in regulating phenotypic responses (hypertrophy and apoptosis) to extracellular stimuli