Laboratory-based Data Research Articles

α-Pinene-Derived organic coatings on acidic sulfate aerosol impacts secondary organic aerosol formation from isoprene in a box model

Fine particulate matter (PM2.5) is known to have an adverse impact on public health and is an important climate forcer. Secondary organic aerosol (SOA) contributes up to 80% of PM2.5 worldwide and multiphase reactions are an important pathway to form SOA. Aerosol-phase state is thought to influence the reactive uptake of gas-phase precursors to aerosol particles by altering diffusion rates within particles. Current air quality models do not include the impact of diffusion-limiting organic coatings on SOA formation. This work examines how α-pinene-derived organic coatings change the predicted formation of SOA from the acid-catalyzed multiphase reactions of isoprene epoxydiols (IEPOX). A box model, with inputs provided from field measurements taken at the Look Rock (LRK) site in Great Smokey Mountains National Park during the 2013 Southern Oxidant and Aerosol Study (SOAS), was modified to incorporate the latest laboratory-based kinetic data accounting for organic coating influences. Including an organic coating influence reduced the modeled reactive uptake when relative humidity was in the 55–80% range, with predicted IEPOX-derived SOA being reduced by up to 33%. Only sensitivity cases with a large increase in Henry's Law values of an order of magnitude or more or in particle reaction rates resulted in the large statistically significant differences form base model performance. These results suggest an organic coating layer could have an impact on IEPOX-derived SOA formation and warrant consideration in regional and global scale models.

Ecotoxicological characterization of the antiepileptic drug carbamazepine using eight aquatic species: baseline study for future higher tier tests

Ecotoxicological effects of the antiepileptic drug carbamazepine (CBZ) were investigated in one primary producer (Desmodesmus subspicatus) and seven invertebrate species (Daphnia magna, Daphnia pulex, Ceriodaphnia dubia, Gammarus fossarum, Potamopyrgus antipodarum, Lumbriculus variegatus and Chironomus riparius) using OECD and US EPA guidelines for chronic toxicity testing. The present data set was used to conduct a hazard assessment for CBZ including confirmatory data. While most of our results were in accordance with previous studies, published effect data for C. dubia and D. pulex could not be confirmed, even though they have previously been considered to be the most sensitive invertebrate species to CBZ exposure. The non-biting midge, C. riparius, was the most sensitive test organism in the present study. From an EC10 of 406 µg/L and a no observed effect concentration (NOEC) of 400 µg/L, a predicted no effect concentration (PNEC) of 8 µg/L was calculated. With regard to realistic predicted and measured environmental concentrations, the environmental risk can be considered as low for CBZ when the assessment is based on laboratory-based effect data. To conduct a refined and more realistic assessment, this study provides foundational data for two future, higher tier studies: one multiple-stressor experiment and one mesocosm study.

Can surgical site infections be controlled through microbiological surveillance? A three-year laboratory-based surveillance at an orthopaedic unit, retrospective observatory study

ObjectiveThe aims of the study were to analyse the surgical site infections (SSIs) in patients operated at an orthopaedic ward and to describe the drug-resistance of the aetiology of those infections. Also, analyse the possibility of SSI control through microbiological surveillance. Additionally, we have studied the information inferred by aggregating cumulative antibiograms for the SSIs of the studied orthopaedic unit.DesignCross-sectional studies carried out in 2013–2015.Setting and patientsOrthopaedic and Trauma Surgery Unit in Sosnowiec, Poland; 5995 patients, 5239 operations.MethodsRetrospective laboratory-based data collection study of surgical site infections.ResultsSSI incidence rate was 6.6%, in the implantations—hip prosthesis 5.8% and knee prosthesis 5.4%, about 6 times higher compared with European HAI-Net. SSIs were usually caused by Gram-positive bacteria (56%). The prevalence of MDR microorganisms was 22.6%, and mainly concerned the Gram-negative bacilli: 97.6% of Acinetobacter baumannii and 50.0% of Klebsiella pneumoniae were multidrug-resistant. On the basis of what the Formula for Rational Empiric Antimicrobial Therapy analysis has shown, the use of amikacin, imipenem and ciprofloxacin has been recommended as the most efficient in the empirical therapy of SSIs.ConclusionsThe infection control was a significant problem at the studied orthopaedic unit, as evidenced by the SSI incidence rate significantly higher than expected. We suggest implementing the infection control and prevention based on evidence-based medicine, and a unit-based surveillance. A cumulative unit-based antibiogram reflects the drug-susceptibility pattern for the strains from the infections acquired at the unit.

Importance of Experimental Environmental Conditions in Estimating Risks and Associated Uncertainty of Transgenic Fish Prior to Entry into Nature

Salmonids show a high degree of phenotypic plasticity that can differ among genotypes, and this variation is one of the major factors contributing to uncertainty in extrapolating laboratory-based risk assessment data to nature. Many studies have examined the relative growth and survival of transgenic and non-transgenic salmonids, and the results have been highly variable due to genotype × environment interactions. The relative survival of fast- and slow-growing strains can reverse depending on the environment, but it is not clear which specific environmental characteristics are driving these responses. To address this question, two experiments were designed where environmental conditions were varied to investigate the contribution of rearing density, food amount, food type, habitat complexity, and risk of predation on relative growth and survival of fast-growing transgenic and slow-growing wild-type coho salmon. The first experiment altered density (high vs. low) and food amount (high vs. low). Density impacted the relative growth of the genotypes, where transgenic fish grew more than non-transgenic fish in low density streams, regardless of food level. Density also affected survival, with high density causing increased mortality for both genotypes, but the mortality of transgenic relative to non-transgenic fish was lower within the high-density streams, regardless of food level. The second experiment altered habitat complexity (simple vs. complex), food type (artificial vs. natural), amount of food (normal vs. satiation), and risk of predation (present vs. absent). Results from this experiment showed that genotype affected growth and survival, but genotype effects were modulated by one or more environmental factors. The effect of genotype on survival was influenced by all examined environmental factors, such that no predictable trend in relative survival of transgenic versus non-transgenic fry emerged. This was primarily due to variations in survival of non-transgenic fish under different environmental conditions (non-transgenic fry had highest survival in hatchery conditions, and lowest survival in complex conditions with natural food fed at a normal level with or without predators). Transgenic fry survival was only significantly influenced by predator presence. The effects of genotype on mass and length were significantly modulated by food type only. Transgenic fry were able to gain a large size advantage over non-transgenic fish when fed artificial food under all habitat types. These experiments support the observations of dynamic responses in growth and survival depending on the environment, and demonstrate the challenge of applying laboratory-based experiments to risk assessment in nature.

Evaluation of whole-genome sequencing for outbreak detection of Verotoxigenic Escherichia coli O157:H7 from the Canadian perspective

BackgroundRapid and accurate identification of Verotoxigenic Escherichia coli (VTEC) O157:H7 is dependent on well-established, standardized and highly discriminatory typing methods. Currently, conventional subtyping tests for foodborne bacterial pathogen surveillance are rapidly being replaced with whole-genome sequencing (WGS) in public health laboratories. The capacity of WGS to revolutionize global foodborne disease surveillance has positioned this tool to become the new gold standard; however, to ensure evidence standards for public health decision making can still be achieved, the performance of WGS must be thoroughly validated against current gold standard methods prior to implementation. Here we aim to verify the performance of WGS in comparison to pulsed-field gel electrophoresis (PFGE) and multiple-locus variable-number tandem repeat analysis (MLVA) for eight retrospective outbreaks of VTEC O157:H7 from the Canadian perspective. Since real-time implementation and routine use of WGS in public health laboratories is highly reliant on standardized data analysis tools, we also provide a comparative analysis of two popular methodologies for WGS analyses; an in-house developed single nucleotide variant phylogenomics (SNVPhyl) pipeline and the BioNumerics whole genome multilocus sequence typing (wgMLST) tool. To provide a useful and consistent starting point for examining laboratory-based surveillance data for VTEC O157:H7 in Canada, we also aim to describe the number of genetic differences observed among outbreak-associated isolates.ResultsWGS provided enhanced resolution over traditional subtyping methods, and accurately distinguished outbreak-related isolates from non-outbreak related isolates with high epidemiological concordance. WGS also illuminated potential linkages between sporadic cases of illness and contaminated food, and isolates spanning multiple years. The topologies generated by SNVPhyl and wgMLST were highly congruent with strong statistical support. Few genetic differences were observed among outbreak-related isolates (≤5 SNVs/ < 10 wgMLST alleles) unless the outbreak was suspected to be multi-strain.ConclusionsThis study validates the superiority of WGS and indicates the BioNumerics wgMLST schema is suitable for surveillance and cluster detection of VTEC O157:H7. These findings will provide a useful and consistent starting point for examining WGS data for prospective laboratory-based surveillance of VTEC O157:H7, but however, the data will continue to be interpreted according to context and in combination with epidemiological and food safety evidence to inform public-health decision making in Canada.

Seasonal influenza activity based on laboratory surveillance in Malaysia, 2011-2016.

Influenza seasonality in equatorial countries is little understood. Seasonal and alert influenza thresholds were determined for Malaysia, using laboratory-based data obtained from the Malaysia Influenza Surveillance System and a major teaching hospital, from 2011 to 2016. Influenza was present year-round, with no clear annual seasons. Variable periods of higher transmission occurred inconsistently, in November to December, January to March, July to September, or a combination of these. These coincide with seasons in the nearby southeast Asian countries or winter seasons of the northern and southern hemispheres. Changes in the predominant circulating influenza type were only sometimes associated with increased transmission. The data can provide public health interventions such as vaccines.

Incidence of single-drug resistant, multidrug-resistant and extensively drug-resistant Escherichia coli urinary tract infections: An Australian laboratory-based retrospective study.

The aim of this study was to evaluate the incidence of single-drug resistant, multidrug-resistant (MDR), extensively drug-resistant (XDR) and pandrug-resistant (PDR) Escherichia coli urinary tract infections (UTIs) in a sample of Australian Capital Territory (ACT) residents. Laboratory-based retrospective data from all ACT residents whose urine samples were processed from January 2009 to December 2013 at ACT Pathology were utilised. Multivariate logistic regression models were constructed to determine the associations of age, sex, urine sample source and socioeconomic status with risk of resistant infections. A total of 146 915 urine samples from 57 837 ACT residents were identified over 5 years. The mean±standard deviation age of residents at first sample submitted was 48±26years, and 64.4% were female. The 5-year incidence of single-drug resistant E. coli UTI was high for ampicillin, trimethoprim and cefazolin (6.8%, 3.5% and 1.9%, respectively). No PDR E. coli UTI was detected. Five-year incidences of MDR and XDR E. coli UTIs were 1.9% and 0.2%, respectively, which is low in comparison with international rates. Female sex and age ≥38 years were significantly associated with single-drug and multidrug resistance. The risk of single-drug resistance was significantly higher in samples from after-hours general practice (GP) clinics compared with hospitals, office-hours GP clinics, and community and specialist health services (adjusted odds ratio=2.6, 95% confidence interval 2.2-3.1). These findings have significant implications for antimicrobial prescribing given the identified risk factors for the detection of resistance, especially in patients attending after-hours GP clinics.

Can the compressive strength of concrete be estimated from knowledge of the mixture proportions?: New insights from statistical analysis and machine learning methods

The use of statistical and machine learning approaches to predict the compressive strength of concrete based on mixture proportions, on account of its industrial importance, has received significant attention. However, previous studies have been limited to small, laboratory-produced data sets. This study presents the first analysis of a large data set (>10,000 observations) of measured compressive strengths from actual (job-site) mixtures and their corresponding actual mixture proportions. Predictive models are applied to examine relationships between the mixture design variables and strength, and to thereby develop an estimate of the (28-day) strength. These models are also applied to a laboratory-based data set of strength measurements published by Yeh et al. (1998) and the performance of the models across both data sets is compared. Furthermore, to illustrate the value of such models beyond simply strength prediction, they are used to design optimal concrete mixtures that minimize cost and embodied CO2 impact while satisfying imposed target strengths.

I-LAB: Connecting clinical laboratories to infectious diseases surveillance systems

Introduction Improving systems for epidemiological surveillance of infectious diseases in West Africa is a well-recognized priority for global health. Standard surveillance reporting procedures within the region typically involve paper-based notifications sent by clinical laboratories to district and/or provincial centres, which are then aggregated and transferred to Ministries of Health for analysis and production of monthly consolidated reports. The quality and relevance of such reports are often compromised by the fact that many laboratories submit incomplete data, fail to submit reports in a timely manner, or completely neglect to submit reports. Traditional manual data entry is laborious, prone to human error, results in lengthy delays, and is not well-suited for timely, automated early warning systems. Development of innovative mobile eHealth tools is viewed as a key strategy for helping countries meet the requirements of the International Health Regulations (IHR). The District Health Information Software (DHIS2) is an open-source software platform for reporting, analysis and dissemination of data that has now been adopted in more than 60 countries as an integral part of national health information systems. Here, we showcase successes of DHIS2 adoption in the clinical laboratories of Senegal. Using this open-source platform, laboratories across the country have been able to enter data via a mobile phone or computer, which are then captured on a centralized internet server with the capacity to rapidly produce reports. Methods In 2014, Senegal's Ministry of Health (MoH) identified 11 notifiable diseases to be included in pilot implementation of the DHIS2 electronic surveillance system. Training on DHIS2 reporting done by Laboratory Directorate was initiated in 118 of 120 targeted clinical laboratories, operating at all levels of the healthcare system (i.e. in health posts, community centres, district hospitals, and referral centres). Laboratory personnel were trained to use the system autonomously, and two representatives from the Senegalese MoH were designated as coordinators of the DHIS2 system. The MOH continues to provide ongoing support to participating laboratories for both users and supervisors responsible for managing the system. Results As of December 2017, 118 laboratories have been trained in the use of the tool, and 91 (87%) laboratories utilized the software to transmit complete weekly reports. Among those laboratories transmitting complete data, 94 (80%) were doing so without any external prompting or support. The weekly reports comprise information on clinically suspected cases as well as diagnostic methods used for confirmation/elimination. Approximately 35 laboratories have capacity for microbial culture, and 24 of these conduct routines antimicrobial susceptibility testing; culture results and resistance profiles are systematically captured in DHIS2 when available with a dedicated monthly report. Conclusions Thanks to these improved e-health tools, the frequency and reliability of laboratory-based surveillance data has greatly increased and enabled improved reporting on disease trends from the Senegalese Ministry of Health to the World Health Organization (WHO). Ongoing challenges for implementation include ensuring sustained Internet access from all sites, and meeting continued training needs to address frequent turnover of laboratory personnel. Based on this success, the system has been extended to new applications. A comprehensive mapping of laboratory resources in the network, including inventories of equipment, numbers of trained personnel, and diagnostic capacity has been developed and is used today by the MoH to define the national laboratory strategy. This laboratory-based surveillance system will accelerate the reaction time and contribute to the global health security; furthermore, the Senegalese experience could be replicated in other countries to improve overall surveillance capacity.

Cascading speciation among mutualists and antagonists in a tree–beetle–fungi interaction

Cascading speciation is predicted to occur when multiple interacting species diverge in parallel as a result of divergence in one species promoting adaptive differentiation in other species. However, there are few examples where ecological interactions among taxa have been shown to result in speciation that cascades across multiple trophic levels. Here, we test for cascading speciation occurring among the western pine beetle (Dendroctonus brevicomis), its primary host tree (Pinus ponderosa), and the beetle's fungal mutualists (Ceratocystiopsis brevicomi and Entomocorticium sp. B). We assembled genomes for the beetle and a fungal symbiont and then generated reduced representation genomic data (RADseq) from range-wide samples of these three interacting species. Combined with published data for the host tree, we present clear evidence that the tree, the beetle, and the fungal symbionts are all genetically structured into at least two distinct groups that have strongly codiverged with geographical isolation. We then combine our genomic results with diverse population and laboratory-based data to show evidence for reproductive isolation at each level of the cascade and for coevolution of both antagonistic and mutualistic species interactions within this complex network.

Q fever: an under-reported reportable communicable disease.

The objective of this study was to provide real-world clinical laboratory-based data to supplement Centers for Disease Control and Prevention (CDC) reporting of Q fever. We analysed titre results of specimens submitted to a large US clinical laboratory for Coxiella burnetii IgG antibody testing from 2010 through 2016. Presumptive Q fever was defined as acute (phase II IgG titre ⩾1:128, phase I titre <1:1024) or chronic (phase I IgG titre ⩾1:1024), based on the results from a single serum specimen. During 2010-2016, an average of 328 presumptive acute Q fever cases were identified at Quest each year, nearly three times the annual average reported to the CDC (122). During the same period, the number of chronic cases identified annually at Quest Diagnostics (34) was similar to that reported to the CDC (29). These findings suggest that CDC data may underestimate the incidence of acute Q fever.

Experimental and Numerical Investigations on the Mechanical Characteristics of Carbon Fiber Sensors.

Carbon fiber-based materials possess excellent mechanical properties and show linear piezoresistive behavior, which make them good candidate materials for strain measurements. They have the potential to be used as sensors for various applications such as damage detection, stress analysis and monitoring of manufacturing processes and quality. In this paper, carbon fiber sensors are prepared to perform reliable strain measurements. Both experimental and computational studies were carried out on commercially available carbon fibers in order to understand the response of the carbon fiber sensors due to changes in the axial strain. Effects of parameters such as diameter, length, and epoxy-hardener ratio are discussed. The developed numerical model was calibrated using laboratory-based experimental data. The results of the current study show that sensors with shorter lengths have relatively better sensitivity. This is due to the fact short fibers have low initial resistance, which will increase the change of resistance over initial resistance. Carbon fibers with low number of filaments exhibit linear behavior while nonlinear behavior due to transverse resistance is significant in fibers with large number of filaments. This study will allow researchers to predict the behavior of the carbon fiber sensor in real life and it will serve as a basis for designing carbon fiber sensors to be used in different applications.

Hydro-geomorphic controls on the development and distribution of acid sulfate soils in Central Java, Indonesia

Coastal planning policies and regulations in Indonesia have not adequately considered acid sulfate soils (ASS) as a constraint on development. Aquaculture is often undertaken in unsuitable areas, and fish and shrimp culture systems, in particular, fail after a short period of production because of the impacts of ASS on pond water quality and, subsequently, on fish and shrimp health. This study describes a mapping approach based on an understanding of the hydro-geomorphic controls on the formation and the distribution of ASS in Central Java, Indonesia. The underlying approach was to identify associations between ASS development and distribution within estuarine hydro-geomorphological units (HGUs). This study utilized a multi-level methodology involving multi-resolution, remotely-sensed data and GIS analysis, coupled with field and laboratory-based data, to obtain hydro-geomorphic and soil information at different mapping scales. An estuary classification scheme for Central Java identified river, tide and wave-dominated estuaries as the dominant estuary types. HGUs were identified in each estuary type to define the relationships between landform development processes and pyrite concentration in soil layers. Thirty-nine HGUs were classified based on landforms, marine and fluvial hydrology, geomorphic processes, land use, and vegetation types. Field and laboratory assessment of soil properties were undertaken to identify the horizontal distribution of ASS in the HGUS and its vertical character in soil profiles. In contrast to previous studies, the results showed that estuaries located in low-energy environments on the north coast have low (<0.1%) pyrite concentrations in 90% of their HGUs. Decades-old intensive aquaculture and dredging activities, that led to repeated oxidation and leaching, were identified as factors for low pyrite concentrations. On the south coast, the combination of a high river and marine energy environment created scattered landforms with soils that have very high (4–9%) pyrite concentrations. These ASS-bearing HGUs mostly developed in low- energy estuarine environments overlying former high river energy environments. The information generated for each HGU facilitated the development of an ASS mapping model that incorporates knowledge on the relationship between soil and landform formation in Central Java estuaries. Knowing where ASS occur is essential to minimize the risk of environment degradation. Using multi-resolution, remotely sensed data decreases cost and labour, compared to more traditional mapping approaches, especially to identify sampling sites for field surveys. The resulting maps and mapping methods will improve land capability assessment for brackishwater aquaculture and other coastal land use in Indonesia.

The Therapeutic Efficacy of Botulinum Toxin in Treating Scleroderma-Associated Raynaud's Phenomenon: A Randomized, Double-Blind, Placebo-Controlled Clinical Trial.

To assess the therapeutic efficacy of local injections of botulinum toxin type A (Btx-A) in improving blood flow to the hands of patients with Raynaud's phenomenon (RP) secondary to scleroderma. In this randomized, double-blind, placebo-controlled clinical trial, patients with scleroderma-associated RP received Btx-A (50 units in 2.5 ml sterile saline) in one randomly selected hand and sterile saline (2.5 ml) in the opposite hand. Follow-up at 1 and 4 months postinjection included laser Doppler imaging of hands, patient-reported outcomes, and physical examination. We compared outcomes using paired t-tests and population-average generalized models with generalized estimating equations. Of 40 patients enrolled, 25 had limited scleroderma and 15 had diffuse scleroderma. From baseline to 1-month follow-up, there was a greater reduction in average blood flow in Btx-A-treated hands compared to placebo-treated hands. The model estimated that this difference was statistically significant (average difference -30.08 flux units [95% confidence interval -56.19, -3.98], P for interaction = 0.024). This difference was mainly influenced by patients with longstanding RP and diffuse scleroderma. Change in blood flow at 4-month follow-up was not significantly different between groups. Clinical measures (QuickDASH, McCabe Cold Sensitivity Score, pain on a visual analog scale, and Raynaud's Condition Score) improved slightly for Btx-A-treated hands. Our laboratory-based laser Doppler imaging flow data do not support using Btx-A to treat RP in all scleroderma patients. The secondary clinical outcomes suggest some positive effect, but its clinical meaningfulness is questionable. The role of Btx-A in treating RP should be further studied with more homogeneous patient populations and in unique clinical situations such as acute digital ischemia.

Flow through a very porous obstacle in a shallow channel.

A theoretical model, informed by numerical simulations based on the shallow water equations, is developed to predict the flow passing through and around a uniform porous obstacle in a shallow channel, where background friction is important. This problem is relevant to a number of practical situations, including flow through aquatic vegetation, the performance of arrays of turbines in tidal channels and hydrodynamic forces on offshore structures. To demonstrate this relevance, the theoretical model is used to (i) reinterpret core flow velocities in existing laboratory-based data for an array of emergent cylinders in shallow water emulating aquatic vegetation and (ii) reassess the optimum arrangement of tidal turbines to generate power in a tidal channel. Comparison with laboratory-based data indicates a maximum obstacle resistance (or minimum porosity) for which the present theoretical model is valid. When the obstacle resistance is above this threshold the shallow water equations do not provide an adequate representation of the flow, and the theoretical model over-predicts the core flow passing through the obstacle. The second application of the model confirms that natural bed resistance increases the power extraction potential for a partial tidal fence in a shallow channel and alters the optimum arrangement of turbines within the fence.

An important agent in gastroenteritis: Campylobacter

Campylobacter infections are common in both developed and developing countries. The reported incidence of culture confirmed infections shows variability among countries due to culturing procedures. (1). Here we report laboratory-based surveillance data collected between 2013 and 2015 in Yeditepe University Hospital Microbiology Laboratory. Among 2807 feces cultures, Salmonella spp. (n=135), Campylobacter spp. (n=118), Aeromonas spp. (n=6) and Shigella spp. (n=3), isolates were detected. Out of 118 Campylobacter spp. isolates, the distribution was as follows: C. jejuni (n=101), C. upsaliensis (n=8), C. coli (n=6) and other species (n=3). The fecal samples were cultured in Campylobacter-BAP medium (Salubris, Turkey) and incubated under microaerophilic conditions (CampyGen, Oxoid, UK) at 42°C for 48 hours. Suspected colonies were examined by Gram stain and evaluated for oxidase and catalase positivity; and then were first confirmed by Campylobacter latex agglutination test (Dryspot, Oxoid, UK). They were identified by API CAMPY biochemical identification system (BioMerieux, France). Antimicrobial susceptibility of isolates against erythromycin was also tested with API CAMPY system (BioMerieux, France); ciprofloxacin and gentamicin susceptibilies were tested by E-test (bioMerieux, France). The distribution of isolates, demographic information and seasonal epidemiology in patients with Campylobacter positive cultures are shown. It seems there is no definite season for campylobacteriosis. We mostly isolate from the pediatric patients. (Table 1, Figure 1) Beyond detecting difficulties by culture, antibiotic resistance becomes a problem. In the EFSA/ECDC report 2013, the highest frequency of resistance was observed for nalidixic acid (47.8%) and ciprofloxacin (44.4%) followed by ampicillin (35.3%) and tetracycline (30.5%); low resistance levels were observed to erythromycin (3.5%) and gentamicin (0.4%). According to FDA/CDC/UDSA Report 2013 resistance to tetracycline was most common (45.9%), followed by ciprofloxacin (23.5% in C. jejuni and 35.8% in C. coli). Macrolide resistance was observed in 1.7%-2.7% (2). During the study period, our resistance rates were detected as 13% for erythromycin, 11% for ciprofloxacin. It seems a slight increase in erythromycin resistance in our strains comparing to 2009-2012 rates (from 7% to 13%) (3). No resistance was seen in gentamicin. Fecal culture procedures should be applied in our routine laboratories to see the surveillance of Campylobacteriosis and find our national rate in resistance to antibiotics.

Environmental risk assessment of selected organic chemicals based on TOC test and QSAR estimation models

Environmental risks of organic chemicals have been greatly determined by their persistence, bioaccumulation, and toxicity (PBT) and physicochemical properties. Major regulations in different countries and regions identify chemicals according to their bioconcentration factor (BCF) and octanol–water partition coefficient (Kow), which frequently displays a substantial correlation with the sediment sorption coefficient (Koc). Half-life or degradability is crucial for the persistence evaluation of chemicals. Quantitative structure activity relationship (QSAR) estimation models are indispensable for predicting environmental fate and health effects in the absence of field- or laboratory-based data. In this study, 39 chemicals of high concern were chosen for half-life testing based on total organic carbon (TOC) degradation, and two widely accepted and highly used QSAR estimation models (i.e., EPI Suite and PBT Profiler) were adopted for environmental risk evaluation. The experimental results and estimated data, as well as the two model-based results were compared, based on the water solubility, Kow, Koc, BCF and half-life. Environmental risk assessment of the selected compounds was achieved by combining experimental data and estimation models. It was concluded that both EPI Suite and PBT Profiler were fairly accurate in measuring the physicochemical properties and degradation half-lives for water, soil, and sediment. However, the half-lives between the experimental and the estimated results were still not absolutely consistent. This suggests deficiencies of the prediction models in some ways, and the necessity to combine the experimental data and predicted results for the evaluation of environmental fate and risks of pollutants.

Extending two-dimensional histology into the third dimension through conventional micro computed tomography

Histological examination achieves sub-micrometer resolution laterally. In the third dimension, however, resolution is limited to section thickness. In addition, histological sectioning and mounting sections on glass slides introduce tissue-dependent stress and strain. In contrast, state-of-the-art hard X-ray micro computed tomography (μCT) systems provide isotropic sub-micrometer resolution and avoid sectioning artefacts. The drawback of μCT in the absorption contrast mode for visualising physically soft tissue is a low attenuation difference between anatomical features. In this communication, we demonstrate that formalin-fixed paraffin-embedded human cerebellum yields appropriate absorption contrast in laboratory-based μCT data, comparable to conventional histological sections. Purkinje cells, for example, are readily visible. In order to investigate the pros and cons of complementary approaches, two- and three-dimensional data were manually and automatically registered. The joint histogram of histology and the related μCT slice allows for a detailed discussion on how to integrate two-dimensional information from histology into a three-dimensional tomography dataset. This methodology is not only rewarding for the analysis of the human cerebellum, but it also has relevance for investigations of tissue biopsies and post-mortem applications. Our data indicate that laboratory-based μCT as a modality can fill the gap between synchrotron radiation-based μCT and histology for a variety of tissues. As the information from haematoxylin and eosin (H&E) stained sections and μCT data is related, one can colourise local X-ray absorption values according to the H&E stain. Hence, μCT data can correlate and virtually extend two-dimensional (2D) histology data into the third dimension.

Persistent Sex Disparities in Invasive Pneumococcal Diseases in the Conjugate Vaccine Era.

Few studies have characterized the role of sex on the incidence of invasive pneumococcal disease (IPD). We examined sex differences in rates of IPD, and trends after the introduction of pneumococcal conjugate vaccines (PCVs). We used active population and laboratory-based IPD surveillance data from the Centers for Disease Control and Prevention Active Bacterial Core surveillance program (1998-2013) in Tennessee. Population-based rates of IPD by sex, race, age group, and PCV era were calculated. Rates were compared using incidence rate ratios. Throughout the study years, rates of IPD were higher in male than in female subjects, particularly in children <2 years and adults 40-64 years of age, with male subjects having IPD rates 1.5-2 times higher than female subjects. The proportions of comorbid conditions were similar in male and female subjects . Sex rate differences persisted after stratification by race. Although the introductions of 7-valent PCV (PCV7) and 13-valent PCV (PCV13) were associated with declines in IPD rates in both sexes, rates of IPD after PCV13 were still significantly higher in male than in female subjects among children and adults 40-64 and >74 years of age. Rates of IPD were generally higher in male than in female subjects. These sex differences were observed in different race groups and persisted after introduction of both PCVs.

Predicting Mortality in Low-Income Country ICUs: The Rwanda Mortality Probability Model (R-MPM).

IntroductionIntensive Care Unit (ICU) risk prediction models are used to compare outcomes for quality improvement initiatives, benchmarking, and research. While such models provide robust tools in high-income countries, an ICU risk prediction model has not been validated in a low-income country where ICU population characteristics are different from those in high-income countries, and where laboratory-based patient data are often unavailable. We sought to validate the Mortality Probability Admission Model, version III (MPM0-III) in two public ICUs in Rwanda and to develop a new Rwanda Mortality Probability Model (R-MPM) for use in low-income countries.MethodsWe prospectively collected data on all adult patients admitted to Rwanda’s two public ICUs between August 19, 2013 and October 6, 2014. We described demographic and presenting characteristics and outcomes. We assessed the discrimination and calibration of the MPM0-III model. Using stepwise selection, we developed a new logistic model for risk prediction, the R-MPM, and used bootstrapping techniques to test for optimism in the model.ResultsAmong 427 consecutive adults, the median age was 34 (IQR 25–47) years and mortality was 48.7%. Mechanical ventilation was initiated for 85.3%, and 41.9% received vasopressors. The MPM0-III predicted mortality with area under the receiver operating characteristic curve of 0.72 and Hosmer-Lemeshow chi-square statistic p = 0.024. We developed a new model using five variables: age, suspected or confirmed infection within 24 hours of ICU admission, hypotension or shock as a reason for ICU admission, Glasgow Coma Scale score at ICU admission, and heart rate at ICU admission. Using these five variables, the R-MPM predicted outcomes with area under the ROC curve of 0.81 with 95% confidence interval of (0.77, 0.86), and Hosmer-Lemeshow chi-square statistic p = 0.154.ConclusionsThe MPM0-III has modest ability to predict mortality in a population of Rwandan ICU patients. The R-MPM is an alternative risk prediction model with fewer variables and better predictive power. If validated in other critically ill patients in a broad range of settings, the model has the potential to improve the reliability of comparisons used for critical care research and quality improvement initiatives in low-income countries.