Shrinking a large dataset to identify variables associated with increased risk of Plasmodium falciparum infection in Western Kenya

Large datasets are often not amenable to analysis using traditional single-step approaches. Here, our general objective was to apply imputation techniques, principal component analysis (PCA), elastic net and generalized linear models to a large dataset in a systematic approach to extract the most meaningful predictors for a health outcome. We extracted predictors for Plasmodium falciparum infection, from a large covariate dataset while facing limited numbers of observations, using data from the People, Animals, and their Zoonoses (PAZ) project to demonstrate these techniques: data collected from 415 homesteads in western Kenya, contained over 1500 variables that describe the health, environment, and social factors of the humans, livestock, and the homesteads in which they reside. The wide, sparse dataset was simplified to 42 predictors of P. falciparum malaria infection and wealth rankings were produced for all homesteads. The 42 predictors make biological sense and are supported by previous studies. This systematic data-mining approach we used would make many large datasets more manageable and informative for decision-making processes and health policy prioritization

Air Sampling and Analysis Method for Volatile Organic Compounds (VOCs) Related to Field-Scale Mortality Composting Operations

In biosecure composting, animal mortalities are so completely isolated during the degradation process that visual inspection cannot be used to monitor progress or the process status. One novel approach is to monitor the volatile organic compounds (VOCs) released by decaying mortalities and to use them as biomarkers of the process status. A new method was developed to quantitatively analyze potential biomarkers—dimethyl disulfide, dimethyl trisulfide, pyrimidine, acetic acid, propanoic acid, 3-methylbutanoic acid, pentanoic acid, and hexanoic acid—from field-scale biosecure mortality composting units. This method was based on collection of air samples from the inside of biosecure composting units using portable pumps and solid phase microextraction (SPME). Among four SPME fiber coatings, 85 μm CAR/PDMS was shown to extract the greatest amount of target analytes during a 1 h sampling time. The calibration curves had high correlation coefficients, ranging from 96 to 99%. Differences between the theoretical concentrations and those estimated from the calibration curves ranged from 1.47 to 20.96%. Method detection limits of the biomarkers were between 11 pptv and 572 ppbv. The applicability of the prepared calibration curves was tested for air samples drawn from field-scale swine mortality composting test units. Results show that the prepared calibration curves were applicable to the concentration ranges of potential biomaker compounds in a biosecure animal mortality composting unit

Laboratory scale evaluation of volatile organic compound emissions as indication of swine carcass degradation inside biosecure composting units

Biosecure livestock mortality composting systems have been used to dispose of diseased livestock mortalities. In those types of system, visual inspection of carcass degradation is not possible and monitoring VOCs (volatile organic compounds) released by carcasses is a new approach to assess progress of the composting process. In this study, field-scale livestock mortality composting systems were simulated and a laboratory scale composting system with aerobic and anaerobic test units was designed to collect VOC samples from the headspace of decaying plant materials (70 g dry weight) and swine tissues (70 g dry weight) at controlled operating temperatures. Headspace samples were collected with SPME (solid phase microextraction) and analyzed by a GC–MS (gas chromatography–mass spectrometry) system. Among the 43 VOCs identified, dimethyl disulfide, dimethyl trisulfide, and pyrimidine were found to be marker compounds of the mortality composting process. These compounds were only found to be produced by decaying swine tissues but not produced by decaying plant materials. The highest marker VOC emissions were measured during the first three weeks, and VOCs were not detected after the 6th week of the process, which indicates degradation processes were completed and compost materials microbially stabilized (no additional VOC production). Results of respiration tests also showed that compost materials were stabilized. Results of this study can be useful for field-scale composting operations but more studies are needed to show the effects of size and aeration rate of the composting units

Spatial multi-criteria decision analysis to predict suitability for African swine fever endemicity in Africa

Background African swine fever (ASF) is endemic in several countries of Africa and may pose a risk to all pig producing areas on the continent. Official ASF reporting is often rare and there remains limited awareness of the continent-wide distribution of the disease. In the absence of accurate ASF outbreak data and few quantitative studies on the epidemiology of the disease in Africa, we used spatial multi-criteria decision analysis (MCDA) to derive predictions of the continental distribution of suitability for ASF persistence in domestic pig populations as part of sylvatic or domestic transmission cycles. In order to incorporate the uncertainty in the relative importance of different criteria in defining suitability, we modelled decisions within the MCDA framework using a stochastic approach. The predictive performance of suitability estimates was assessed via a partial ROC analysis using ASF outbreak data reported to the OIE since 2005. Results Outputs from the spatial MCDA indicate that large areas of sub-Saharan Africa may be suitable for ASF persistence as part of either domestic or sylvatic transmission cycles. Areas with high suitability for pig to pig transmission (‘domestic cycles’) were estimated to occur throughout sub-Saharan Africa, whilst areas with high suitability for introduction from wildlife reservoirs (‘sylvatic cycles’) were found predominantly in East, Central and Southern Africa. Based on average AUC ratios from the partial ROC analysis, the predictive ability of suitability estimates for domestic cycles alone was considerably higher than suitability estimates for sylvatic cycles alone, or domestic and sylvatic cycles in combination. Conclusions This study provides the first standardised estimates of the distribution of suitability for ASF transmission associated with domestic and sylvatic cycles in Africa. We provide further evidence for the utility of knowledge-driven risk mapping in animal health, particularly in data-sparse environments.</p

Identification and evaluation of VOCs evolved from warm season swine mortality composts

The intensive production of swine in Iowa (28.4 % of the U.S.A production) inevitably results in high amounts of piggery waste including animal carcasses. Composting is an environmentally sound and relatively inexpensive method to dispose swine mortalities especially when the carcasses are diseased. Measurement of VOC emissions is an alternative to test progress and completion of the process. In this study, diseased swine mortalities are composted in summer conditions of Central Iowa. Corn silage, oat straw and corn stalks are used as envelope materials. Once a week, air samples are collected from the center of test units and sampled with 85 µm Carboxen/ polydimethylsiloxane (CAR/PDMS) solid phase microextraction (SPME) fiber. Samples were analyzed using gas chromatography (GC) - mass spectrometry (MS). The objective of the study is to investigate the potential usage of VOCs as indicators of swine mortality degradation. It is found that nitrogen and sulfur containing compounds can be used as indicators of the composting process. Sulfur-containing compounds are detected from all test units. Nitrogen-containing compounds are detected from only corn silage test units. It is concluded that carcass degradation is incomplete in all of the test units. Carcass degradation in corn stalks and oat straw test units is better than corn silage test units. These results are supported with respiration rate results. Respiration rates of the remaining swine carcasses are found to be between 5-7 mg CO2-C g VS-1d-1 and swine carcasses are categorized as moderately unstable composts

Reconstruction of the trachea with a tubed radial forearm free flap

AbstractBackgroundWe present the case of a patient with adenoid cystic carcinoma of the trachea who had 60 mm of the trachea excised and reconstructed with a stented radial forearm free flap. The patient was well in the immediate postoperative period with good function of the neotrachea. Problems developing after the reconstruction included proximal stricture, sputum retention, and recurrent pneumonia.ResultThe patient died of malignant hypercalcemia 16 months after the reconstruction. To our knowledge this is the first reported case of a total tracheal resection and reconstruction with a combination of free tissue transfer and internal stenting.ConclusionWe conclude that tracheal reconstruction has the potential to provide a reliable airway in patients not able to be reconstructed with a primary anastomosis