Terminal restriction fragment length polymorphism is an “old school” reliable technique for swift microbial community screening in anaerobic digestion

The microbial community in anaerobic digestion has been analysed through microbial fingerprinting techniques, such as terminal restriction fragment length polymorphism (TRFLP), for decades. In the last decade, high-throughput 16S rRNA gene amplicon sequencing has replaced these techniques, but the time-consuming and complex nature of high-throughput techniques is a potential bottleneck for full-scale anaerobic digestion application, when monitoring community dynamics. Here, the bacterial and archaeal TRFLP profiles were compared with 16S rRNA gene amplicon profiles (Illumina platform) of 25 full-scale anaerobic digestion plants. The α-diversity analysis revealed a higher richness based on Illumina data, compared with the TRFLP data. This coincided with a clear difference in community organisation, Pareto distribution, and co-occurrence network statistics, i.e., betweenness centrality and normalised degree. The β-diversity analysis showed a similar clustering profile for the Illumina, bacterial TRFLP and archaeal TRFLP data, based on different distance measures and independent of phylogenetic identification, with pH and temperature as the two key operational parameters determining microbial community composition. The combined knowledge of temporal dynamics and projected clustering in the β-diversity profile, based on the TRFLP data, distinctly showed that TRFLP is a reliable technique for swift microbial community dynamics screening in full-scale anaerobic digestion plants

Managing Hyperglycemia in Critically Ill Patients: Where are We Now?

Hyperglycemia is common in critically ill patients and is associated with increased morbidity, mortality, rate of infections and length of hospital stay. For decades, hyperglycemia in critically ill population was considered an adaptive response and interventions were only considered if diabetic ketoacidosis (DKA) or severe hyperosmolar states developed. Furnary et al published studies showing lower sternal wound infection rates in cardiac surgical patients with control of glucose (180-220 mg/dl). This led to the dissemination of the “Portland Protocol,” but it was not widely accepted.1, 2 Management of hyperglycemia changed with the publication of Van Den Berghe study.3 This was a prospective, randomized, controlled study involving adults admitted to a surgical intensive care unit (ICU) who were receiving mechanical ventilation (MV). A total of 1548 patients were enrolled with patients randomly assigned to two groups. One group received intensive insulin therapy (IIT) with goal blood glucose of 80-110 mg/dl. The second group received conventional treatment whereby insulin was given only if the blood glucose level exceeded 215 mg/dl with goal glucose level of 180-200 mg/dl. Pages: 20-23

Septic arthritis of the hip in children: Aga Khan University Hospital experience in Pakistan

Objective: To present clinical, radiological and bacteriological features and short term outcome of septic arthritis of the hip in children.Methods: There were 23 male and 16 female children, including 6 neonates and 10 infants with a mean age of 3.9 years. Diagnosis of septic hip was made on clinical grounds, supplemented by X-rays, leukocyte count and the erythrocyte sedimentation rate (ESR). Thirty nine patients with 40 hips were followed for a mean time period of 76 weeks. All patients had a positive joint aspirate (pus) and underwent surgical decompression along with intravenous antibiotic therapy.Results: Symptoms of pain, fever and restricted range of hip motion were common to all patients. The mean leukocyte count was 14,000 and the mean ESR was 63 mm. Cultures of blood and joint aspirate were positive in 9 and 28 patients respectively. Staphylococus Aureus was the commonest organism (14 patients) identified, and only one patient had Hemophilus influenzae. Seven patients had a mixed osteoarticular infection. Positive clinical response was noted in the mean time period of 8.6 days. In follow-up, four cases developed myositis ossificans and 2 cases showed signs of partial growth plate destruction.Conclusion: Our findings of the absence of H. influenzae and the presence of a number of gut organisms are different from the previous studies. Duration of symptoms was an important prognostic factor and correlated well with the final outcome. Early surgical decompression was found to be the treatment of choice. A combined osteoarticular infection should be kept in mind in cases which show a poor response after the initial joint debridement

A Heterogeneity-Based Temporal Stability Assessment of Pedestrian Crash Injury Severity Using an Aggregated Crash and Hospital Data Set

This study utilized a unique approach to crash data analysis by examining the temporal stability of pedestrian crash injury severity and its contributory factors. Police-reported crash data and EMS-related injury data from Nebraska were obtained from 2014 to 2018, and random parameter ordered probit models for injury severity were estimated for each year to account for unobserved heterogeneity. Four discrete levels of injury severity were considered for model estimation: fatality, disabling injury/suspected serious injury, visible injury/possible injury, and no injury. Data were filtered based on several important variables of interest, such as pedestrian characteristics, crash characteristics, environmental and weather characteristics, road surface characteristics, pedestrian location of crash, pre-crash pedestrian conditions, contributory circumstances of a crash, presence of work zones, and time gap between actual crash-time and police-reported time. A series of likelihood ratio tests were used to determine the temporal stability of factors over the course of two consecutive years and then over all individual time periods. The likelihood ratio tests showed temporal instability among explanatory variables for different time periods as well as for consecutive years. The random-parameters ordered probit models estimated a random distribution for the following indicators: old pedestrian indicator, pedestrian not visible due to dark clothing indicator, marked crosswalk at intersection indicator, time gap of 10-30 minutes between actual crash-time and police-reported time, chest area injury, work zone indicator, and ice on road indicator. This exploratory research suggests significant policy implications to help improve pedestrian safety

Metagenomic sequencing unravels gene fragments with phylogenetic signatures of O2-tolerant NiFe membrane-bound hydrogenases in lacustrine sediment

Many promising hydrogen technologies utilising hydrogenase enzymes have been slowed by the fact that most hydrogenases are extremely sensitive to O2. Within the group 1 membrane-bound NiFe hydrogenase, naturally occurring tolerant enzymes do exist, and O2 tolerance has been largely attributed to changes in iron–sulphur clusters coordinated by different numbers of cysteine residues in the enzyme’s small subunit. Indeed, previous work has provided a robust phylogenetic signature of O2 tolerance [1], which when combined with new sequencing technologies makes bio prospecting in nature a far more viable endeavour. However, making sense of such a vast diversity is still challenging and could be simplified if known species with O2-tolerant enzymes were annotated with information on metabolism and natural environments. Here, we utilised a bioinformatics approach to compare O2-tolerant and sensitive membrane-bound NiFe hydrogenases from 177 bacterial species with fully sequenced genomes for differences in their taxonomy, O2 requirements, and natural environment. Following this, we interrogated a metagenome from lacustrine surface sediment for novel hydrogenases via high-throughput shotgun DNA sequencing using the Illumina™ MiSeq platform. We found 44 new NiFe group 1 membrane-bound hydrogenase sequence fragments, five of which segregated with the tolerant group on the phylogenetic tree of the enzyme’s small subunit, and four with the large subunit, indicating de novo O2-tolerant protein sequences that could help engineer more efficient hydrogenases

The Effects of Inaccurate and Missing Highway-Rail Grade Crossing Inventory Data on Crash Model Estimation and Crash Prediction

ABSTRACT: Most highway-rail grade crossing (HRGC) crash models in the US rely on the Federal Railroad Administration’s (FRA) highway/rail crossing inventory database. Any errors and/or incomplete information in this database affects the estimated crash model parameters and subsequent crash predictions. Using 560 HRGCs in Nebraska, this study illustrates differences in crash predictions obtained from the FRA’s new (2020) Accident Prediction and Severity (APS) model when: 1) using the unaltered, original FRA HRGC inventory dataset as input, and 2) using a field-validated inventory dataset for those 560 HRGCs as input to the new APS model. Results showed that the predictions using the two different input datasets were statistically significantly different. HRGC hazard rankings from the two predictions as well as FRA’s Web Accident Prediction System (WBAPS) were different from each other. Estimation of new zero-inflated negative binomial models using 5-year reported HRGC crashes and the two inventory datasets for the 560 HRGCs enabled model parameter estimate and marginal value comparisons showing differences in estimated coefficients’ expected-magnitudes and average marginal effects. The conclusions were that erroneous and missing data in the unaltered FRA HRGC inventory dataset led to statistically different crash predictions compared to corrected and complete (field validated) HRGC inventory dataset and estimated crash prediction model parameters and their respective marginal values were different for comparative models based on the two different HRGC inventory datasets

Weathering of the Ethiopian volcanic province: a new weathering index to characterize and compare soils

© Walter de Gruyter Berlin/Boston 2015.Soil formation occurs through numerous physical and chemical weathering processes acting to alter the parent rock on the Earths surface. Samples of surface soils were collected over a range of elevations (2000-3600 m) from profiles directly overlying basaltic to more felsic parent rocks, over a region in NW Ethiopia. The soils were investigated to determine their chemical composition and X-ray diffraction was used to identify and quantify individual mineral phases. The data set was analyzed using non-parametric statistics (Spearmans Rank and Mann-Whitney U tests) to compare the soils forming over the two parent rocks. Principal component analysis (PCA) was used to identify the mineral alteration assemblage and formation during pedogenesis. The extent of alteration was quantified using several chemical weathering indices (Chemical Index of Alteration = CIA; Chemical Index of Weathering = CIW), including an index calculated by multivariate analyses of the soil chemical composition data (weathering W index). Further to this we devised and tested a new weathering index (Wmin) using multivariate analysis of the soil mineralogy, to estimate the extent of weathering and physico-chemical proprieties of the parent rock from which the soil formed. The soils present a fair to advanced stage of alteration, with abundant iron (Fe) oxides (up to 40 wt%) and phyllosilicates (up to 57 wt%), including kaolinite-smectite (K-S) mixed-layer phases. The K-S was composed of either 30-50% kaolinite or 94-98% kaolinite layers. Discrete kaolinite was also present. The bimodal K-S mineralogical composition is likely due to two precursor phases: feldspar for the kaolinite-rich K-S and volcanic glass for the smectite-rich K-S. K-S with intermediate composition (50-94% kaolinite) was rare, due to its instability. Statistical analysis showed significant differences between the chemical compositions of the soils developed on the two different parent volcanic compositions. The soils overlying the more felsic parent rocks were less altered than those overlying the flood basalt. When comparing the weathering indices calculated in this study, we conclude that while the CIA and CIW may be more readily determined, the W and Wmin indices can elucidate information on the composition of the original rock from which they formed. The W index is more sensitive to certain variables when compared with the newly derived mineralogical Wmin index; however the Wmin index takes into account mineral phases within the sample, which provides a more detailed interpretation of weathering rates than chemistry alone. In addition the Wmin index correlated with meteorological variables, such as elevation (and consequently temperature and precipitation), known to influence the degree of pedogenesis. The Wmin index can be used to enhance our understanding of the processes that occur during weathering processes to supplement information gained from traditional chemical weathering indices

Motor Vehicle Drivers\u27 Knowledge of Safely Traversing Highway-Rail Grade Crossings

This study investigates motor vehicle drivers’ socioeconomic, personality, and attitudinal factors associated with their knowledge of safely traversing highway-rail grade crossings (HRGCs). A survey of randomly selected Nebraska households solicited responses from licensed drivers (N= 980, response rate = 39 percent). Of the total thirty-one questions on the questionnaire, nine pertained to respondents’ knowledge of safely navigating HRGCs (e.g., what does a crossbuck sign require a driver to do when approaching a rail crossing?). Correct answers to the questions provided a measure of respondents’ knowledge of safely traversing HRGCs and led to their classification in five ordered categories. A random parameter probit model then assessed associations among respondents’ socioeconomic, personality, and attitudinal characteristics and the five ordered categories of their HRGC negotiation knowledge. The estimated model revealed that drivers with lower education levels, unemployed drivers, those 11 that disliked waiting at HRGCs, and those who did not receive information on HRGC safety had lower 12 levels of knowledge of safely negotiating HRGCs. Attentive drivers at HRGCs and those who routinely 13 stopped in response to active train warning devices (even if they had a chance to get across before train 14 arrival) were associated with higher levels of knowledge. Drivers who had negative or indifferent 15 attitudes toward HRGCs or engaged in risky driving behaviors were less knowledgeable about safe 16 HRGC navigation. The research findings are useful for targeted driver education and traffic safety 17 programs, safety professionals, and policymakers engaged in HRGC safety