Satellite imaging reveals increased proportion of population exposed to floods.

Flooding affects more people than any other environmental hazard and hinders sustainable development1,2. Investing in flood adaptation strategies may reduce the loss of life and livelihood caused by floods3. Where and how floods occur and who is exposed are changing as a result of rapid urbanization4, flood mitigation infrastructure5 and increasing settlements in floodplains6. Previous estimates of the global flood-exposed population have been limited by a lack of observational data, relying instead on models, which have high uncertainty3,7-11. Here we use daily satellite imagery at 250-metre resolution to estimate flood extent and population exposure for 913 large flood events from 2000 to 2018. We determine a total inundation area of 2.23 million square kilometres, with 255-290 million people directly affected by floods. We estimate that the total population in locations with satellite-observed inundation grew by 58-86 million from 2000 to 2015. This represents an increase of 20 to 24 per cent in the proportion of the global population exposed to floods, ten times higher than previous estimates7. Climate change projections for 2030 indicate that the proportion of the population exposed to floods will increase further. The high spatial and temporal resolution of the satellite observations will improve our understanding of where floods are changing and how best to adapt. The global flood database generated from these observations will help to improve vulnerability assessments, the accuracy of global and local flood models, the efficacy of adaptation interventions and our understanding of the interactions between landcover change, climate and floods.

Milk of ruminants in ceramic baby bottles from prehistoric child graves.

The study of childhood diet, including breastfeeding and weaning, has important implications for our understanding of infant mortality and fertility in past societies1. Stable isotope analyses of nitrogen from bone collagen and dentine samples of infants have provided information on the timing of weaning2; however, little is known about which foods were consumed by infants in prehistory. The earliest known clay vessels that were possibly used for feeding infants appear in Neolithic Europe, and become more common throughout the Bronze and Iron Ages. However, these vessels-which include a spout through which liquid could be poured-have also been suggested to be feeding vessels for the sick or infirm3,4. Here we report evidence for the foods that were contained in such vessels, based on analyses of the lipid 'fingerprints' and the compound-specific δ13C and Δ13C values of the major fatty acids of residues from three small, spouted vessels that were found in Bronze and Iron Age graves of infants in Bavaria. The results suggest that the vessels were used to feed infants with milk products derived from ruminants. This evidence of the foodstuffs that were used to either feed or wean prehistoric infants confirms the importance of milk from domesticated animals for these early communities, and provides information on the infant-feeding behaviours that were practised by prehistoric human groups.

Tick-borne Encephalitis Identified in Ireland: Diagnosis and Outcome.

Presentation Tick borne encephalitis (TBE) is not endemic in Ireland and diagnostic tests are seldom requested. We describe the first notified case in Ireland. A 50-year-old female returned from Lithuania and presented with fever and new neurologic signs. Diagnosis TBE was diagnosed by detection of TBE virus specific antibodies in serum and cerebrospinal fluid (CSF). Treatment The patient was managed with observation and supportive care consisting of intravenous fluids and analgesia. Discussion The case highlights the importance of awareness of TBE among physicians and travellers to guide appropriate testing and vaccination. TBE is being recognised in non-endemic countries posing an emerging risk to public health.

Blood Pressure, Orthostatic Hypotension and Falls in Patients with Advanced Cancer.

Aim Orthostatic Hypotension (OH) is an indicator of deteriorating autonomic dysfunction. Adherence to BP and OH measurement guidelines in an inpatient specialist palliative care unit (SPCU) was unknown. Compliance of BP and OH measurement in an advanced cancer cohort was audited. Methods A retrospective analysis of four consecutive months of patients admitted with an advanced cancer diagnosis to the inpatient SPCU was conducted. Data was obtained from 168 clinical records, and audited against current institutional clinical standards. Results Falls risk screening including BP and OH measurements were not measured on admission in 19% (n=32) cases as recommended by institutional guidelines. Where falls risks were identified in 94 (69%) patients only 71 (76%) of these had completed risk assessments. OH testing was incomplete or not conducted in 59% (n=42) of risk assessments. This had patient care and safety implications e.g. under-reporting falls risk. In addition, institutional guidelines were inflexible in clinical practice specific to a palliative care cohort of patient. Conclusions Institutional guidelines need regular reviewing. In cases where a healthcare professional determines it is inappropriate to perform an assessment, we recommend a modification to the tools allowing for recording of this decision. OH is an underestimated reality in hospice populations and the impact on hospice services is worthy of further study.

Epidemiological typing of Neisseria gonorrhoeae and detection of markers associated with antimicrobial resistance directly from urine samples using next generation sequencing.

OBJECTIVES: To investigate the potential for next generation sequencing (NGS) to be used directly on clinical specimens that have tested positive for Neisseria gonorrhoeae by nucleic acid amplification testing (NAAT), to generate information on epidemiological genotyping and antimicrobial resistance (AMR) markers. METHODS: DNA was extracted from 13 N. gonorrhoeae NAAT-positive urine specimens, enriched for microbial DNA and sequenced using the Ion Torrent PGM workflow. Sequences that aligned to the human genome were filtered out and the remaining sequences were de novo assembled. The resulting contigs were searched for regions of interest using Ridom SeqSphere. MLST and NG-MAST alleles were assigned according to the schemes at PubMLST.org and NG-MAST.net, respectively. RESULTS: In total, 11 of the 13 samples tested generated a sufficient number of N. gonorrhoeae sequence reads to provide full coverage of the genome at a depth of 6-130×. Complete MLST and NG-MAST sequence types could be generated for each of these samples. The presence of 10 different AMR markers was investigated, and both previously reported and novel mutations were identified in genes associated with reduced susceptibility to several antimicrobials. CONCLUSIONS: We found that sequencing the entire genome of N. gonorrhoeae directly from clinical samples is possible using NGS, and that multiple levels of N. gonorrhoeae typing information can be generated. As NAAT only testing becomes more common, this method could be used to detect both known and novel mutations associated with AMR and to generate genotyping information, supporting AMR and epidemiological surveillance in the absence of culturing.

Polyol production during heterofermentative growth of the plant isolate Lactobacillus florum 2F.

AIMS: This study examined the fermentative growth and polyol production of Lactobacillus florum and other plant-associated lactic acid bacteria (LAB). METHODS AND RESULTS: Sugar consumption and end-product production were measured for Lact. florum 2F in the presence of fructose, glucose and both sugars combined. The genome of Lact. florum was examined for genes required for mannitol and erythritol biosynthesis. The capacity for other plant-associated LAB to synthesize polyols was also assessed. CONCLUSIONS: Lactobacillus florum exhibited higher growth rates and cell yields in the presence of both fructose and glucose. Lactobacillus florum 2F produced lactate, acetate and ethanol as well as erythritol and mannitol. Lactobacillus florum 2F synthesized mannitol during growth on fructose and erythritol during growth on glucose. Gene and protein homology searches identified a mannitol dehydrogenase in the Lact. florum 2F genome but not the genes responsible for erythritol biosynthesis. Lastly, we found that numerous other heterofermentative LAB species synthesize erythritol and/or mannitol. SIGNIFICANCE AND IMPACT OF THE STUDY: Lactobacillus florum is a recently identified, plant-associated, fructophilic LAB species. Our results show that Lact. florum growth rates and heterofermentation end-products differ depending on the sugar substrates present and growth yields can be improved when combinations of sugars are provided. Lactobacillus florum 2F produces erythritol and mannitol, two polyols that are relevant to foods and potentially also in plant environments. The capacity for polyol biosynthesis appears to be common among plant-associated, LAB species.

Azithromycin suppresses P. gingivalis LPS-induced pro-inflammatory cytokine and chemokine production by human gingival fibroblasts in vitro.

OBJECTIVE: Azithromycin is a macrolide antibiotic that appears to have both antibacterial and anti-inflammatory properties. This study aimed to investigate the effect of azithromycin on the production of pro-inflammatory cytokines and chemokines by human gingival fibroblasts (HGF) in vitro. MATERIALS AND METHODS: The effects of azithromycin (0.1 to 10 µg/mL) on the production of interleukin-6 (IL-6), interleukin-8 (IL-8), monocyte chemoattractant protein 1 (MCP-1), and growth-regulated oncogene (GRO) by human gingival fibroblasts cultured in the presence or absence of Porphyromonas gingivalis lipopolysaccharide (LPS) was studied. Cytokine and chemokine protein levels in the culture supernatant were assessed using a Luminex® multiplex immunoassay. RESULTS: P. gingivalis LPS induced cytokine/chemokine (IL-6, IL-8, MCP-1, and GRO) protein production in HGFs, and this effect was suppressed by azithromycin at all concentrations tested. CONCLUSIONS: This study demonstrates that azithromycin suppresses P. gingivalis LPS-induced cytokine/chemokine protein production in HGF, which may explain some of the clinical benefits observed with the adjunctive use of azithromycin in the treatment of periodontitis. CLINICAL RELEVANCE: The current study examines the anti-inflammatory properties of azithromycin which may make it useful as an adjunct treatment to periodontitis. Specifically, we used azithromycin to modulate the production of pro-inflammatory cytokines by gingival fibroblasts known to be important in periodontal inflammation.

Real-time investigation of a Legionella pneumophila outbreak using whole genome sequencing.

Legionella pneumophila is the main pathogen responsible for outbreaks of Legionnaires' disease, which can be related to contaminated water supplies such as cooling towers or water pipes. We combined conventional molecular methods and whole genome sequence (WGS) analysis to investigate an outbreak of L. pneumophila in a large Australian hospital. Typing of these isolates using sequence-based typing and virulence gene profiling, was unable to discriminate between outbreak and non-outbreak isolates. WGS analysis was performed on isolates during the outbreak, as well as on unlinked isolates from the Public Health Microbiology reference collection. The more powerful resolution provided by analysis of whole genome sequences allowed outbreak isolates to be distinguished from isolates that were temporally and spatially unassociated with the outbreak, demonstrating that this technology can be used in real-time to investigate L. pneumophila outbreaks.

Gridless adult cervical spine radiography and its' effect on image quality and radiation dose: A phantom study.

INTRODUCTION: Imaging of the cervical spine in general radiography is most frequently performed using an anti-scatter grid. The purpose of this study was to investigate the effects of a gridless setting on image quality and radiation dose during digital radiography of the anteroposterior (AP) and lateral (LAT) cervical spine. METHODS: A phantom study was performed with a variety of tube voltages (63-75 kV) with and without an anti-scatter grid. The tube current time product (mAs) and dose area product (DAP) were recorded and used to calculate effective dose (ED) and individual organ dose using PCXMC 2.0 software, as well as entrance surface dose (ESD) and objective image quality: signal-to-noise ratio (SNR) and contrast-to-noise ratio (CNR). Subjective visual image quality grading characteristics (VGC) was performed by five qualified radiographers. RESULTS: In a gridless setting, the AP and LAT positions showed significantly lower DAP (1.6 µGym2; 61.3 % and 1.6 µGym2; 51.2%), ESD (27.6 µGy; 57.3% and 77.2 µGy; 47.2%) and ED (4.2 µSv; 61.3% and 2.3 µSv; 48.9%). In a gridless setting in the AP position, there is a slight significant deterioration in image quality. In the lateral projection, on the other hand, the image quality without the use of grid was only significantly reduced in three of six criteria and there was no difference in the objective image quality between the two settings examined. CONCLUSION: The results of this study show that gridless setting significantly decreases radiation dose and image quality, but the quality in the lateral projection is still acceptable for diagnostic purpose. IMPLICATIONS FOR PRACTICE: The protocol without the use of the anti-scatter grid in cervical spine radiography leads to a reduction in the radiation dose in both projections, but the image quality in the AP is significantly reduced for all criteria examined, with a slight deterioration in image quality in the lateral projection.

Descriptive record of the activity of military critical care transfer teams deployed to London in April 2020 to undertake transfer of patients with COVID-19.

In the face of the COVID-19 outbreak, military healthcare teams were deployed to London to assist the London Ambulance Service t transfer ventilated patients between medical facilities. This paper describes the preparation and activity of these military teams, records the lessons identified (LI) and reviews the complications encountered'. The teams each had two members. A consultant or registrar in emergency medicine (EM) and pre-hospitalemergency medicine (PHEM)E or anaesthesia and an emergency nurse or paramedic. Following a period of training, the teams undertook 52 transfers over a 14-day period. LI centred around minimising both interruption to ventilation and risk of aerosolisation of infectious particles and thus the risk of transmission of COVID-19 to the treating clinicians. Three patient-related complications (6% of all transfers) were identified. This was the first occasion on which the Defence Medical Services (DMS) were the main focus of a large-scale clinical military aid to the civil authorities. It demonstrated that DMS personnel have the flexibility to deliver a novel effect and the ability to seamlessly and rapidly integrate with a civilian organisation. It highlighted some clinical lessons that may be useful for future prehospital emergency care taskings where patients may have a transmissible respiratory pathogen. It also showed that clinicians from different backgrounds are able to safely undertake secondary transfer of ventilated patients. This approacmay enhance flexibility in future operational patient care pathways.

Protective mucosal immunity elicited by targeted iliac lymph node immunization with a subunit SIV envelope and core vaccine in macaques.

Prevention of sexually transmitted HIV infection was investigated in macaques by immunization with a recombinant SIV (simian immunodeficiency virus) envelope gp 120 and core p27 vaccine. In two independent series of experiments, we used the novel targeted iliac lymph node (TILN) route of immunization, aiming close to the iliac lymph nodes draining the genitorectal mucosa. Rectal challenge with the SIVmac 32H J5 molecular clone in two series induced total protection in four out of seven macaques immunized by TILN, compared with infection in 13 of 14 unimmunized macaques or immunized by other routes (P = 0.025). The remaining three macaques showed either a decrease in viral load ( > 90%) or transient viremia, indicating that all seven TILN-immunized macaques showed total or partial protection (P = 0.001). Protection was associated with significant increase in the iliac lymph nodes of IgA antibody-secreting cells to p27 (P < 0.02), CD8-suppressor factor (P < 0.01), and the chemokines RANTES and MIP-1 beta (P < 0.01).

Human tumor necrosis factor alpha gene regulation in phorbol ester stimulated T and B cell lines.

The minimal region of the human tumor necrosis factor alpha (TNF-alpha) gene promoter necessary for its transcriptional induction by phorbol esters (PMA) in human T and B lymphocyte cell lines has been localized between -52 and +89 nucleotides (nt) relative to the gene's transcriptional start site. Comparison of these sequences to those required to mediate virus or lipopolysaccharide (LPS) induction of the gene reveal significant differences, and thus, the sequence requirements for PMA induction are distinct from those that mediate induction by virus or LPS. Although three sites in the TNF-alpha promoter (kappa 1, kappa 2, and kappa 3) specifically bind the transcription factor NF-kappa B in lymphoid nuclear extracts, TNF-alpha mRNA induction by PMA does not correlate with NF-kappa B binding activities displayed by different T and B cell lines. Moreover, kappa 1-kappa 3 can each be deleted from the TNF-alpha promoter with little effect on the gene's inducibility by PMA. Therefore, TNF-alpha mRNA induction by PMA, like its induction by virus and LPS, is not primarily mediated by NF-kappa B, but rather is mediated through other sequences and protein factors. Surprisingly, multimers of kappa 1-kappa 3 can confer PMA inducibility on a heterologous promoter in a B (Raji), but not a T (HUT78) cell line. However they are not functional on a truncated TNF-alpha promoter, indicating that promoter context and cell type specificity influence the PMA inducible function of these NF-kappa B binding sites.

The protein tyrosine kinase p56lck regulates cell adhesion mediated by CD4 and major histocompatibility complex class II proteins.

The CD4 protein is expressed on a subset of human T lymphocytes that recognize antigen in the context of major histocompatibility complex (MHC) class II molecules. Using Chinese hamster ovary (CHO) cells expressing human CD4, we have previously demonstrated that the CD4 protein can mediate cell adhesion by direct interaction with MHC class II molecules. In T lymphocytes, CD4 can also function as a signaling molecule, presumably through its intracellular association with p56lck, a member of the src family of protein tyrosine kinases. In the present report, we show that p56lck can affect cell adhesion mediated by CD4 and MHC class II molecules. The expression of wild-type p56lck in CHO-CD4 cells augments the binding of MHC class II+ B cells, whereas the expression of a mutant p56lck protein with elevated tyrosine kinase activity results in decreased binding of MHC class II+ B cells. Using site-specific mutants of p56lck, we demonstrate that the both the enzymatic activity of p56lck and its association with CD4 are required for this effect on CD4/MHC class II adhesion. Further, the binding of MHC class II+ B cells induces CD4 at the cell surface to become organized into structures resembling adhesions-type junctions. Both wild-type and mutant forms of p56lck influence CD4-mediated adhesion by regulating the formation of these structures. The wild-type lck protein enhances CD4/MHC class II adhesion by augmenting the formation of CD4-associated adherens junctions whereas the elevated tyrosine kinase activity of the mutant p56lck decreases CD4-mediated cell adhesion by preventing the formation of these structures.

Downregulation of cell-surface CD4 expression by simian immunodeficiency virus Nef prevents viral super infection.

The nef gene product encoded by the mac239 proviral clone of simian immunodeficiency virus (SIV) markedly enhances viral replication and pathogenesis in vivo. We have used this biologically active nef isolate to examine the phenotype of Nef in retrovirally transduced human T cells in culture. SIV Nef is shown to dramatically inhibit cell-surface expression of the CD4 glycoprotein without significantly affecting the total steady-state level of cellular CD4. This downregulation of the cell-surface CD4 receptor for human immunodeficiency virus type 1 (HIV-1) infection correlated with the acquisition of resistance to superinfection by HIV-1. However, SIV Nef did not affect the level of gene expression directed by the HIV-1 long terminal repeat. It is hypothesized that downregulation of cell-surface CD4 by Nef facilitates the efficient release of infectious progeny virions and, hence, viral spread in vivo.

Analysis of progressive deletions of the transmembrane and cytoplasmic domains of influenza hemagglutinin.

Site-directed oligonucleotide mutagenesis has been used to introduce chain termination codons into the cloned DNA sequences encoding the carboxy-terminal transmembrane (27 amino acids) and cytoplasmic (10 amino acids) domains of influenza virus hemagglutinin (HA). Four mutant genes were constructed which express truncated forms of HA that lack the cytoplasmic domain and terminate at amino acids 9, 14, 17, or 27 of the wild-type hydrophobic domain. Analysis of the biosynthesis and intracellular transport of these mutants shows that the cytoplasmic tail is not needed for the efficient transport of HA to the cell surface; the stop-transfer sequences are located in the hydrophobic domain; 17 hydrophobic amino acids are sufficient to anchor HA stably in the membrane; and mutant proteins with truncated hydrophobic domains show drastic alterations in transport, membrane association, and stability.

Mutations in the cytoplasmic domain of the influenza virus hemagglutinin affect different stages of intracellular transport.

Mutations have been introduced into the cloned DNA sequences coding for influenza virus hemagglutinin (HA), and the resulting mutant genes have been expressed in simian cells by the use of SV40-HA recombinant viral vectors. In this study we analyzed the effect of specific alterations in the cytoplasmic domain of the HA molecule on its rate of biosynthesis and transport, cellular localization, and biological activity. Several of the mutants displayed abnormalities in the pathway of transport from the endoplasmic reticulum to the cell surface. One mutant HA remained within the endoplasmic reticulum; others were delayed in reaching the Golgi apparatus after core glycosylation had been completed in the endoplasmic reticulum, but then progressed at a normal rate from the Golgi apparatus to the cell surface; another was delayed in transport from the Golgi apparatus to the plasma membrane. However, two mutants were indistinguishable from wild-type HA in their rate of movement from the endoplasmic reticulum through the Golgi apparatus to the cell surface. We conclude that changes in the cytoplasmic domain can powerfully influence the rate of intracellular transport and the efficiency with which HA reaches the cell surface. Nevertheless, absolute conservation of this region of the molecule is not required for maturation and efficient expression of a biologically active HA on the surface of infected cells.

Heterologous transmembrane and cytoplasmic domains direct functional chimeric influenza virus hemagglutinins into the endocytic pathway.

Chimeric genes were created by fusing DNA sequences encoding the ectodomain of the influenza virus hemagglutinin (HA) to DNA coding for the transmembrane and cytoplasmic domains of either the G glycoprotein of vesicular stomatitis virus or the gC glycoprotein of Herpes simplex virus 1. CV-1 cells infected with SV40 vectors carrying the recombinant genes expressed large amounts of the chimeric proteins, HAG or HAgC on their surfaces. Although the ectodomains of HAG and HAgC differed in their immunological properties from that of HA, the chimeras displayed the biological functions characteristic of the wild-type protein. Both HAG and HAgC bound erythrocytes as efficiently as HA did and, after brief exposure to an acidic environment, induced the fusion of erythrocyte and CV-1 cell membranes. However, the behavior of HAG and HAgC at the cell surface differed from that of HA in several important respects. HAG and HAgC were observed to collect in coated pits whereas wild-type HA was excluded from those structures. In the presence of chloroquine, which inhibits the exit of receptors from endosomes, HAG and HAgC accumulated in intracellular vesicles. By contrast, chloroquine had no effect on the location of wild-type HA. HAG and HAgC labeled at the cell surface exhibited a temperature-dependent acquisition of resistance to extracellular protease at a rate similar to the rates of internalization observed for many cell surface receptors. HA acquired resistance to protease at a rate at least 20-fold slower. We conclude that HAG and HAgC are efficiently routed into the endocytic pathway and HA is not. However, like HA, HAG was degraded slowly, raising the possibility that HAG recycles to the plasma membrane.

The genome sequence of Drosophila melanogaster.

The fly Drosophila melanogaster is one of the most intensively studied organisms in biology and serves as a model system for the investigation of many developmental and cellular processes common to higher eukaryotes, including humans. We have determined the nucleotide sequence of nearly all of the approximately 120-megabase euchromatic portion of the Drosophila genome using a whole-genome shotgun sequencing strategy supported by extensive clone-based sequence and a high-quality bacterial artificial chromosome physical map. Efforts are under way to close the remaining gaps; however, the sequence is of sufficient accuracy and contiguity to be declared substantially complete and to support an initial analysis of genome structure and preliminary gene annotation and interpretation. The genome encodes approximately 13,600 genes, somewhat fewer than the smaller Caenorhabditis elegans genome, but with comparable functional diversity.

The role of alcohol in deaths presenting to the coroner's service in Cork City and County.

A retrospective study was conducted in order to determine the prevalence and concentration of alcohol in post-mortem blood samples sent for toxicological analysis in Cork City and County in 2003 and 2004. Post mortem reports of these deaths were reviewed for the presence or absence of alcohol at the time of autopsy, blood alcohol concentration (BAC) at time of death, age and sex of the decedents. Of samples sent for blood alcohol analysis (BAA), 38.4% were positive for alcohol. Significant differences were found between the proportions of alcohol positive cases by cause of death. Alcohol positive cases were significantly younger (44.3 +/- 17.8 years) than alcohol negative cases (51.9 +/- 19.4 years) and fifty two percent of drivers were positive for alcohol at the time of death. Awareness of the harmful and potentially fatal effects of alcohol should continue to be raised within the community, so as to prevent future fatalities.