Challenges during Operation and Shutdown of Waxy Crude Pipelines

Transportation of waxy crude oil faces great challenges due to shear and temperature dependency. At high temperatures, waxy crude exhibits low viscous Newtonian behavior where the resistance to flow due to friction is low, and hence low pumping pressure is required to transport it. At low temperatures, however, the crude exhibits shear thinning non-Newtonian behavior where its apparent viscosity becomes shear-dependent. In such cases, the operated pipeline needs to maintain a high pressure to guarantee a continuous flow. Moreover, due to heat transfer between the internal pipeline and surroundings, oil temperature declines along the pipeline. It follows that the crude viscosity and, hence, frictional resistance increase. If the flow is interrupted for any reason, i.e., emergency or planned shutdown, then the restartability of the pipeline becomes a challenge because of the nonexistence of heating generated from friction. In this chapter, the challenges normally facing transportation of waxy crude oil will be discussed. The chapter will introduce the rheological properties of waxy crude oil and explain and describe how these properties can affect the pressure losses inside the pipeline during its operation and shutdown. The measures that need to be considered when designing a waxy crude pipeline will be discussed

Incidence and predictive biomarkers of Clostridioides difficile infection in hospitalized patients receiving broad-spectrum antibiotics

Trial enrichment using gut microbiota derived biomarkers by high-risk individuals can improve the feasibility of randomized controlled trials for prevention of Clostridioides difficile infection (CDI). Here, we report in a prospective observational cohort study the incidence of CDI and assess potential clinical characteristics and biomarkers to predict CDI in 1,007 patients ≥ 50 years receiving newly initiated antibiotic treatment with penicillins plus a beta- lactamase inhibitor, 3rd/4th generation cephalosporins, carbapenems, fluoroquinolones or clindamycin from 34 European hospitals. The estimated 90-day cumulative incidences of a first CDI episode is 1.9% (95% CI 1.1-3.0). Carbapenem treatment (Hazard Ratio (95% CI): 5.3 (1.7-16.6)), toxigenic C. difficile rectal carriage (10.3 (3.2-33.1)), high intestinal abundance of Enterococcus spp. relative to Ruminococcus spp. (5.4 (2.1-18.7)), and low Shannon alpha diversity index as determined by 16 S rRNA gene profiling (9.7 (3.2-29.7)), but not nor- malized urinary 3-indoxyl sulfate levels, predicts an increased CDI risk

FROM SEQUENCING READS TO MICROBIAL DIVERSITY: BIOINFORMATIC ALGORITHMS FOR PROCESSING AMPLICON SEQUENCING DATA

The development of high-throughput sequencing technologies has revolutionized the field of microbial ecology by offering a cost-efficient method to assess microbial diversity at an unseen depth using 16S RNA amplicon sequencing approaches. Different preprocessing algorithms need to be performed to obtain a collection of highly reliable sequencing reads, ending with a clustering step to group them into Operational Taxonomic Units (OTUs) However, this approach is posing various challenges: the removal of PCR artefacts (called chimera), correction of sequencing errors resulting from the sequencing technologies and clustering those sequences into OTUs. In this work various bioinformatics tools were developed to tackle those challenges. First, an ensemble classifier for chimera detection was developed named CATCh, which obtained a higher performance on different types of sequencing data compared to existing tools. Secondly, two artificial intelligence-based algorithms, NoDe and IPED, able to treat sequencing errors within 454 pyrosequencing and Illumina MiSeq data respectively, were introduced. A benchmarking study was performed comparing NoDe and IPED, showing a more pronounced decrease of the error rate compared to other state-of-the art tools. Thirdly, a new method was developed introducing an adaptive cut-off score in the OTU clustering step, as such making the results of the OTU clustering less sensitive to variations in evolutionary rates between taxonomic lineages and to the region of the 16S rRNA gene targeted for amplification. Implementing such a dynamic cut-off value resulted in closer correspondence between the number of OTUs and the actual diversity of the samples. Finally, a benchmark analysis comparing existing pipelines for 16S rRNA metagenomics data processing was performed, showing that an integration of our in-house developed algorithms achieved the highest accuracy. Conclusively, the newly developed pipeline within this PhD translates amplicon sequencing data into high-quality OTUs tendering robust diversity estimates.status: publishe

IPED: a highly efficient denoising tool for Illumina MiSeq Paired-end 16S rRNA gene amplicon sequencing data

The development of high-throughput sequencing technologies has revolutionized the field of microbial ecology via the sequencing of phylogenetic marker genes (e.g. 16S rRNA gene amplicon sequencing). Denoising, the removal of sequencing errors, is an important step in preprocessing amplicon sequencing data. The increasing popularity of the Illumina MiSeq platform for these applications requires the development of appropriate denoising methods.status: publishe

AGRICULTURE AND BIOLOGY JOURNAL OF NORTH AMERICA Effect of changing crop rotations on machinery management using adecision-aid Model

ABSTRACT To aid decision makers in seasonal planning of machinery in multi-farms a computer model for selecting optimum machinery sizes, machinery scheduling, evaluation of machinery operating plans and estimation of costs of field operations was developed. The developed model employ linear programming and Pert techniques to asses and improve degree of resources utilization . Input data was collected from Rahad irrigation Scheme for the last five years . The model verification was made by comparing actual performance of machinery scheduling program used in Rahad Scheme for two, three and four course rotations in the last five years with outputs generated by the model. Model Application resulted in decreasing demand for tractors and costs of used operations in the Rahad.It resulted in increase in labour demand with increase in cropping intensity and decrease in power usage. Introduction of optimization processes improved power saving and distribution markedly with introduction of summer and winter crops. Sensitivity analysis of the model indicated clear effects of both area cultivated and costs of agricultural operation to changes in input parameters

Optimization Model for Machinery Selection of Multi-Crop Farms in Elsuki Agricultural Scheme

The optimization machinery model was developed to aid decision-makers and farm machinery managers in determining the optimal number of tractors, scheduling the agricultural operation and minimizing machinery total costs. For purpose of model verification, validation and application input data was collected from primary & secondary sources from Elsuki agricultural scheme for two seasons namely 2011-2012 and 2013-2014. Model verification was made by comparing the numbers of tractors of Elsuki agricultural scheme for season 2011-2012 with those estimated by the model. The model succeeded in reducing the number of tractors and operation total cost by 23%. The effect of optimization model on elements of direct cost saving indicated that the highest cost saving is reached with depreciation, repair and maintenance (23%) and the minimum cost saving is attained with fuel cost (22%). Sensitivity analysis in terms of change in model input for each of cultivated area and total costs of operations showing that: Increasing the operation total cost by 10% decreased the total number of tractors after optimization by 23% and total cost of operations was also decreased by 23%. Increasing the cultivated area by 10%, decreased the total number of tractors after optimization by(12%) and total cost of operations was also decreased by 12% (16669206 SDG(1111280 $) to 14636376 SDG(975758$)). For the case of multiple input effect of the area and operation total cost resulted in decrease maximum number of tractors by 12%, and the total cost of operations also decreased by 12%. It is recommended to apply the optimization model as pre-requisite for improving machinery management during implementation of machinery scheduling

Dissecting the role of the gut microbiome and fecal microbiota transplantation in radio- and immunotherapy treatment of colorectal cancer

Abstract: Colorectal cancer (CRC) is one of the most commonly diagnosed cancers and poses a major burden on the human health worldwide. At the moment, treatment of CRC consists of surgery in combination with (neo)adjuvant chemotherapy and/or radiotherapy. More recently, immune checkpoint blockers (ICBs) have also been approved for CRC treatment. In addition, recent studies have shown that radiotherapy and ICBs act synergistically, with radiotherapy stimulating the immune system that is activated by ICBs. However, both treatments are also associated with severe toxicity and efficacy issues, which can lead to temporary or permanent discontinuation of these treatment programs. There's growing evidence pointing to the gut microbiome playing a role in these issues. Some microorganisms seem to contribute to radiotherapy-associated toxicity and hinder ICB efficacy, while others seem to reduce radiotherapy-associated toxicity or enhance ICB efficacy. Consequently, fecal microbiota transplantation (FMT) has been applied to reduce radio- and immunotherapy-related toxicity and enhance their efficacies. Here, we have reviewed the currently available preclinical and clinical data in CRC treatment, with a focus on how the gut microbiome influences radio- and immunotherapy toxicity and efficacy and if these treatments could benefit from FMT

Modeling the Effects of Cypermethrin Toxicity on Ovalbumin-Induced Allergic Pneumonitis Rats: Macrophage Phenotype Differentiation and p38/STAT6 Signaling Are Candidate Targets of Pirfenidone Treatment

Although the classic form of asthma is characterized by chronic pneumonitis with eosinophil infiltration and steroid responsivity, asthma has multifactorial pathogenesis and various clinical phenotypes. Previous studies strongly suggested that chemical exposure could influence the severity and course of asthma and reduce its steroid responsiveness. Cypermethrin (CYP), a common pesticide used in agriculture, was investigated for the possible aggravation of the ovalbumin (OVA)-induced allergic pneumonitis and the possible induction of steroid resistance in rats. Additionally, it was investigated whether pirfenidone (PFD) could substitute dexamethasone, as an alternative treatment option, for the induced steroid resistance. Fifty-six male Wistar albino rats were randomly divided into seven groups: control, PFD alone, allergic pneumonitis, CYP alone, allergic pneumonitis/CYP-exposed, allergic pneumonitis/CYP/dexamethasone (Dex), and allergic pneumonitis/CYP/PFD-treated groups. Allergic pneumonitis was induced by three intraperitoneal OVA injections administered once a week, followed by an intranasal OVA instillation challenge. CYP (25 mg/kg/d), Dex (1 mg/kg/d), and PFD (100 mg/kg/d) were administered orally from day 15 to the end of the experiment. Bronchoalveolar lavage fluid (BALF) was analyzed for cytokine levels. Hematoxylin and eosin (H&E) and periodic acid Schiff (PAS)-stained lung sections were prepared. Immunohistochemical identification of p38 MAPK and lung macrophages was performed. The inflammatory/oxidative status of the lung and PCR-quantification of the STAT6, p38 MAPK, MUC5AC, and IL-13 genes were carried out. The allergic pneumonitis-only group showed eosinophil-mediated inflammation (p p p < 0.05) by PFD, meanwhile not by dexamethasone treatment. Pirfenidone could replace dexamethasone treatment in the current rat model of CYP-induced severe steroid-resistant asthma via inhibiting the M1 macrophage differentiation through modulation of the STAT6/p38 MAPK pathway