Using open-access taxonomic and spatial information to create a comprehensive database for the study of Mammalian and avian livestock and pet infections

AbstractWhat are all the species of pathogen that affect our livestock? As 6 out of every 10 human pathogens came from animals, with a good number from livestock and pets, it seems likely that the majority that emerge in the future, and which could threaten or devastate human health, will come from animals. Only 10 years ago, the first comprehensive pathogen list was compiled for humans; we still have no equivalent for animals. Here we describe the creation of a novel pathogen database, and present outputs from the database that demonstrate its value.The ENHanCEd Infectious Diseases database (EID2) is open-access and evidence-based, and it describes the pathogens of humans and animals, their host and vector species, and also their global occurrence. The EID2 systematically collates information on pathogens into a single resource using evidence from the NCBI Taxonomy database, the NCBI Nucleotide database, the NCBI MeSH (Medical Subject Headings) library and PubMed. Information about pathogens is assigned using data-mining of meta-data and semi-automated literature searches.Here we focus on 47 mammalian and avian hosts, including humans and animals commonly used in Europe as food or kept as pets. Currently, the EID2 evidence suggests that:•Within these host species, 793 (30.5%) pathogens were bacteria species, 395 (15.2%) fungi, 705 (27.1%) helminths, 372 (14.3%) protozoa and 332 (12.8%) viruses.•The odds of pathogens being emerging compared to not emerging differed by taxonomic division, and increased when pathogens had greater numbers of host species associated with them, and were zoonotic rather than non-zoonotic.•The odds of pathogens being zoonotic compared to non-zoonotic differed by taxonomic division and also increased when associated with greater host numbers.•The pathogens affecting the greatest number of hosts included: Escherichia coli, Giardia intestinalis, Toxoplasma gondii, Anaplasma phagocytophilum, Cryptosporidium parvum, Rabies virus, Staphylococcus aureus, Neospora caninum and Echinococcus granulosus.•The pathogens of humans and domestic animal hosts are characterised by 4223 interactions between pathogen and host species, with the greatest number found in: humans, sheep/goats, cattle, small mammals, pigs, dogs and equids.•The number of pathogen species varied by European country. The odds of a pathogen being found in Europe compared to the rest of the world differed by taxonomic division, and increased if they were emerging compared to not emerging, or had a larger number of host species associated with them

Existing Data Format for Two-Parameter Beta-Gamma Histograms for Radioxenon

There is a need to establish a commonly acceptable format for storing beta-gated coincidence data for stations in the International Monitoring System (IMS) for the Comprehensive Nuclear-Test-Ban Treaty (CTBT). The current aerosol RMS type data format is not applicable for radioxenon in that the current format contains implicit assumptions specific to conventional gamma-ray spectrometry. Some assumptions in the current RMS format are not acceptable for the beta-gated spectra expected from the U.S. Department of Energy PNNL Automated Radioxenon Sampler-Analyzer (ARSA) and other similar systems under use or development from various countries. The RMS data format is not generally applicable for radioxenon measurements in the CTBT for one or more of the following main reasons: 1) The RMS format does not currently support 2-dimensional data. That is, the RMS data format is setup for a simple l-dimensional gamma-ray energy histogram. Current data available from the ARSA system and planned for other radioxenon monitors includes spectral information from gamma-rays and betas/conversion electrons. It is worth noting that the beta/conversion electron energy information will be used to separate the contributions from the different radioxenons. 2) The RMS data format assumes that the conversion between counts and activity can be calculated based (in part) on a simple calibration curve (detector efficiency curve) that depends only on energy of the gamma-ray. In the case of beta-gated gamma-ray spectra and for 2-dimensional spectra, there are generally two detector calibration curves that must be convoluted, the lower energy cutoff for the betas must be considered, and the energy acceptance window must be taken into account to convert counts into activity. . 3) The RMS format has header information that contains aerosol-specific information that allows the activity (Bq) calculated to be converted into a concentration (Bq/SCM). This calculation is performed by dividing the activity calculated (Bq) into number of standard cubic meters of air (SCM) passed through the filters. Most xenon-samplers do not have a 100% collection and transfer efficiency, and these efficiencies should not be assumed constant, so that the total volume flow through the sampler may not be used to convert activity into concentration. There is a pretty straightforward analogy that requires, instead, the total volume of xenon gas measured by the xenon station for the conversion. The following paper describes one possible file format for storing the multi-parameter beta-gamma coincidence spectra generated by the DOE PNNL ARSA sampler. This format proposal was generated as a draft guide to begin discussions

An aerosol challenge model of tuberculosis in Mauritian cynomolgus macaques

Background New interventions for tuberculosis are urgently needed. Non-human primate (NHP) models provide the most relevant pre-clinical models of human disease and play a critical role in vaccine development. Models utilising Asian cynomolgus macaque populations are well established but the restricted genetic diversity of the Mauritian cynomolgus macaques may be of added value. Methods Mauritian cynomolgus macaques were exposed to a range of doses of M. tuberculosis delivered by aerosol, and the outcome was assessed using clinical, imaging and pathology-based measures. Results All macaques developed characteristic clinical signs and disease features of tuberculosis (TB). Disease burden and the ability to control disease were dependent on exposure dose. Mauritian cynomolgus macaques showed less variation in pulmonary disease burden and total gross pathology scores within exposure dose groups than either Indian rhesus macaques or Chinese cynomolgus macaques Conclusions The genetic homogeneity of Mauritian cynomolgus macaques makes them a potentially useful model of human tuberculosis

Electrophysiological modeling in generalized epilepsy using surface EEG and anatomical brain structures

Deep brain structures involve significantly in the pathology of brain diseases such as epilepsy, Alzheimer, and Parkinson. Physiological brain modeling has become an emerging approach to investigate the coupling dynamics of the brain activity ofthese diseases. We propose a method using the surface EEG signals integrated with the anatomical individual brain to build the electrophysiological model of the epileptic patient’s brain. The EEG-driven model is used to investigate the deep brain activities of 23 patients diagnosed with generalized epilepsy from CHB-MIT Scalp EEG Database. Significant changes in the electrical activities in hippocampus, accumbens, amygdala, provide us insights into the dynamics ofactive brain regions during epilepsy. All of these brain regions show the significant energy variation defined by 5 features (Mean, Max, Min, Standard deviation, Power spectral density) with the p-value < 0.05 in both pre-ictal vs ictal and ictal vs post-ictal. Such result shows the potential of using EEG as a tool to capture the deep brain activity of epilepsy and other diseases that alter deep brain structures. The proposed model may be used to enhance the sensitivity of detecting and predicting epilepsy, detect the progression of the brain lesion, and support the decision-making for a brain medical intervention

Superconducting nanowire photon number resolving detector at telecom wavelength

The optical-to-electrical conversion, which is the basis of optical detectors, can be linear or nonlinear. When high sensitivities are needed single-photon detectors (SPDs) are used, which operate in a strongly nonlinear mode, their response being independent of the photon number. Nevertheless, photon-number resolving (PNR) detectors are needed, particularly in quantum optics, where n-photon states are routinely produced. In quantum communication, the PNR functionality is key to many protocols for establishing, swapping and measuring entanglement, and can be used to detect photon-number-splitting attacks. A linear detector with single-photon sensitivity can also be used for measuring a temporal waveform at extremely low light levels, e.g. in long-distance optical communications, fluorescence spectroscopy, optical time-domain reflectometry. We demonstrate here a PNR detector based on parallel superconducting nanowires and capable of counting up to 4 photons at telecommunication wavelengths, with ultralow dark count rate and high counting frequency

Human foot outperforms the hand in mechanical pain discrimination

Tactile discrimination has been extensively studied, but mechanical pain discrimination remains poorly characterised. Here, we measured the capacity for mechanical pain discrimination using a two-alternative forced choice paradigm, with force-calibrated indentation stimuli (Semmes-Weinstein monofilaments) applied to the hand and foot dorsa of healthy human volunteers. In order to characterise the relationship between peripheral nociceptor activity and pain perception, we recorded single-unit activity from myelinated (A) and unmyelinated (C) mechanosensitive nociceptors in the skin using microneurography. At the perceptual level, we found that the foot was better at discriminating noxious forces than the hand, which stands in contrast to that for innocuous force discrimination, where the hand performed better than the foot. This observation of superior mechanical pain discrimination on the foot compared to the hand could not be explained by the responsiveness of individual nociceptors. We found no significant difference in the discrimination performance of either the myelinated or unmyelinated class of nociceptors between skin regions. This suggests the possibility that other factors such as skin biophysics, receptor density or central mechanisms may underlie these regional differences

Equity In Health care financing in low-and middle-income countries: A systematic review of evidence from studies using benefit and financing incidence analyses

© 2016 Asante et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. Introduction: Health financing reforms in low-and middle-income countries (LMICs) over the past decades have focused on achieving equity in financing of health care delivery through universal health coverage. Benefit and financing incidence analyses are two analytical methods for comprehensively evaluating how well health systems perform on these objectives. This systematic review assesses progress towards equity in health care financing in LMICs through the use of BIA and FIA. Methods and Findings: Key electronic databases including Medline, Embase, Scopus, Global Health, CinAHL, EconLit and Business Source Premier were searched. We also searched the grey literature, specifically websites of leading organizations supporting health care in LMICs. Only studies using benefit incidence analysis (BIA) and/or financing incidence analysis (FIA) as explicit methodology were included. A total of 512 records were obtained from the various sources. The full texts of 87 references were assessed against the selection criteria and 24 were judged appropriate for inclusion. Twelve of the 24 studies originated from sub-Saharan Africa, nine from the Asia-Pacific region, two from Latin America and one from the Middle East. The evidence points to a pro-rich distribution of total health care benefits and progressive financing in both sub-Saharan Africa and Asia-Pacific. In the majority of cases, the distribution of benefits at the primary health care level favoured the poor while hospital level services benefit the better-off. A few Asian countries, namely Thailand, Malaysia and Sri Lanka, maintained a pro-poor distribution of health care benefits and progressive financing. Conclusion: Studies evaluated in this systematic review indicate that health care financing in LMICs benefits the rich more than the poor but the burden of financing also falls more on the rich. There is some evidence that primary health care is pro-poor suggesting a greater investment in such services and removal of barriers to care can enhance equity. The results overall suggest that there are impediments to making health care more accessible to the poor and this must be addressed if universal health coverage is to be a reality

PCR Primers for Metazoan Mitochondrial 12S Ribosomal DNA Sequences

Background: Assessment of the biodiversity of communities of small organisms is most readily done using PCR-based analysis of environmental samples consisting of mixtures of individuals. Known as metagenetics, this approach has transformed understanding of microbial communities and is beginning to be applied to metazoans as well. Unlike microbial studies, where analysis of the 16S ribosomal DNA sequence is standard, the best gene for metazoan metagenetics is less clear. In this study we designed a set of PCR primers for the mitochondrial 12S ribosomal DNA sequence based on 64 complete mitochondrial genomes and then tested their efficacy. Methodology/Principal Findings: A total of the 64 complete mitochondrial genome sequences representing all metazoan classes available in GenBank were downloaded using the NCBI Taxonomy Browser. Alignment of sequences was performed for the excised mitochondrial 12S ribosomal DNA sequences, and conserved regions were identified for all 64 mitochondrial genomes. These regions were used to design a primer pair that flanks a more variable region in the gene. Then all of the complete metazoan mitochondrial genomes available in NCBI’s Organelle Genome Resources database were used to determine the percentage of taxa that would likely be amplified using these primers. Results suggest that these primers will amplify target sequences for many metazoans. Conclusions/Significance: Newly designed 12S ribosomal DNA primers have considerable potential for metazoa

Equity in utilization of antiretroviral therapy for HIV-infected people in South Africa: a systematic review

INTRODUCTION: About half a million people in South Africa are deprived of antiretroviral therapy (ART), and there is little systematic knowledge on who they are – e.g. by severity of disease, sex, or socio-economic status (SES). We performed a systematic review to determine the current quantitative evidence-base on equity in utilization of ART among HIV-infected people in South Africa. METHOD: We conducted a literature search based on the Cochrane guidelines. A study was included if it compared for different groups of HIV infected people (by sex, age, severity of disease, area of living, SES, marital status, ethnicity, religion and/or sexual orientation (i.e. equity criteria)) the number initiating/adhering to ART with the number who did not. We considered ART utilization inequitable for a certain criterion (e.g. sex) if between groups (e.g. men versus women) significant differences were reported in ART initiation/adherence. RESULTS: Twelve studies met the inclusion criteria. For sex, 2 out of 10 studies that investigated this criterion found that men are less likely than women to utilize ART, while the other 8 found no differences. For age, 4 out of 8 studies found inequities and reported less utilization for younger people. For area of living, 3 out of 4 studies showed that those living in rural areas or certain provinces have less access and 2 out of 6 studies looking at SES found that people with lower SES have less access. One study which looked at the marital status found that those who are married are less likely to utilize ART. For severity of disease, 5 out of 6 studies used more than one outcome measure for disease stage and reported within their study contradicting results. One of the studies reported inconclusive findings for ethnicity and no study had looked at religion and sexual orientation. CONCLUSION: It seems that men, young people, those living in certain provinces or rural areas, people who are unemployed or with a low educational level, and those being unmarried have less access to ART. As studies stem from different contexts and use different methods conclusions should be taken with caution