Ultrasonic wave propagation in cylindrical vessels and implications for ultrasonic reactor design

Reactors in which processes are enhanced by ultrasound are hampered by the lack of a theoretical framework on their design. Simulation results of ultrasonic wave propagation in a cylindrical geometry are presented in this work, which are then used to develop guidelines for the design of ultrasonic reactors. These guidelines are used to design a new type of reactor with a novel geometry, operating at a frequency of 27kHz, 39kHz and 82kHz. This reactor is characterized using Weissler's reaction dosimetr

Exact analytical solution to ultrasonic interfacial reflection enabling optimal oil film thickness measurement

The ultrasonic reflection from a lubricated interface has been widely analyzed to measure fluid film thickness, with different algorithms being applied to overcome measurement accuracy and resolution issues. Existing algorithms use either the amplitude or the phase angle of the ultrasonic interfacial reflection. In this paper, a new algorithm (named the “exact model – complex”) that simultaneously utilizes both the amplitude and the phase of the complex ultrasonic reflection coefficient is proposed and mathematically derived. General procedures for theoretical analysis in terms of measurement accuracy and uncertainty are proposed and applied to the new algorithm, the beneficial features of which (as compared to other existing algorithms) can be summarized as: 1) a direct calculation, instead of an iterative approximation, 2) guaranteed maximum measurement accuracy, and 3) acceptable measurement uncertainty. None of the existing methods have showed this combination of benefits. Moreover, two groups of raw data from previous experimental studies are utilized to further validate the practical feasibility of the new algorithm. Overall, the proposed “exact model – complex” algorithm fully exploits the potential of ultrasonic reflection for oil film thickness measurement, with an accurate and a convenient calculation suited to practical implementation

Scaling up isoniazid preventive therapy in Zimbabwe: has operational research influenced policy and practice?

Setting: Following the operational research study conducted during the isoniazid preventive therapy (IPT) pilot phase in Zimbabwe, recommendations for improvement were adopted by the national antiretroviral therapy (ART) programme. Objectives: To compare before (January 2013-June 2014) and after the recommendations (July 2014-December 2015), the extent of IPT scale-up and IPT completion rates, and after the recommendations the risk factors for IPT non-completion, in 530 ART clinics. Design: Retrospective cohort study. Results: People living with the human immunodeficiency virus newly initiating IPT increased every quarter (Q), from 585 in Q 1, 2013 to 4246 in Q 4, 2015, with 5648 new IPT initiations in the 18 months before the recommendations compared to 20 513 in the 18 months after the recommendations were made. The number of ART clinics initiating IPT increased from 10 (2%) in Q 1, 2013 to 198 (37%) in Q 4, 2015. Overall IPT completion rates were 89% in the post-recommendation period compared with 81% in the pilot phase (P < 0.001). After adjusting for confounders, being lost to follow-up from clinic review visits 1 year prior to IPT initiation was associated with a higher risk of not completing IPT, while having synchronised IPT and ART resupplies was associated with a lower risk. Conclusions: Implementation of recommendations from the initial operational research study have improved IPT scale-up in Zimbabwe

Characterising school-age health and function in rural Zimbabwe using the SAHARAN toolbox

INTRODUCTION: We developed the School-Age Health, Activity, Resilience, Anthropometry and Neurocognitive (SAHARAN) toolbox to address the shortage of school-age assessment tools that combine growth, physical and cognitive function. Here we present i) development, acceptability and feasibility of the SAHARAN toolbox; ii) characteristics of a pilot cohort; and iii) associations between the domains measured in the cohort. METHODS: Growth was measured with anthropometry, knee-heel length and skinfold thicknesses. Bioimpedance analysis measured lean mass index and phase angle. Cognition was assessed using the mental processing index, derived from the Kaufman Assessment Battery for Children version 2, a fine motor finger-tapping task, and School Achievement Test (SAT). Physical function combined grip strength, broad jump and the 20m shuttle-run test to produce a total physical score. A caregiver questionnaire was performed in parallel. RESULTS: The SAHARAN toolbox was feasible to implement in rural Zimbabwe, and highly acceptable to children and caregivers following some minor modifications. Eighty children with mean (SD) age 7.6 (0.2) years had mean height-for-age (HAZ) and weight-for-age Z-scores (WAZ) of -0.63 (0.81) and -0.55 (0.85), respectively. Lean mass index and total skinfold thicknesses were related to WAZ and BMI Z-score, but not to HAZ. Total physical score was associated with unit rises in HAZ (1.29, 95% CI 0.75, 1.82, p<0.001), and lean mass index (0.50, 95% CI 0.16, 0.83, p = 0.004), but not skinfold thicknesses. The SAT was associated with unit increases in the mental processing index and child socioemotional score. The caregiver questionnaire identified high levels of adversity and food insecurity. CONCLUSIONS: The SAHARAN toolbox provided a feasible and acceptable holistic assessment of child growth and function in mid-childhood. We found clear associations between growth, height-adjusted lean mass and physical function, but not cognitive function. The SAHARAN toolbox could be deployed to characterise school-age growth, development and function elsewhere in sub-Saharan Africa

Dietary patterns and colorectal cancer risk in Zimbabwe: A population based case-control study

BACKGROUND: The rising incidence of colorectal cancer in sub-Saharan Africa may be partly caused by changing dietary patterns. We sought to establish the association between dietary patterns and colorectal cancer in Zimbabwe. METHODS: One hundred colorectal cancer cases and 200 community-based controls were recruited. Data were collected using a food frequency questionnaire, and dietary patterns derived by principal component analysis. Generalised linear and logistic regression models were used to assess the associations between dietary patterns, participant characteristics and colorectal cancer. RESULTS: Three main dietary patterns were identified: traditional African, urbanised and processed food. The traditional African diet appeared protective against colorectal cancer (Odds Ratio (OR) 0.35; 95% Confidence Interval (CI), 0.21 – 0.58), which had no association with the urban (OR 0.68; 95% CI, 0.43–1.08), or processed food (OR 0.91; 0.58–1.41) patterns. The traditional African diet was associated with rural domicile, (OR 1.26; 95% CI, 1.00–1.59), and a low income (OR1.48; 95% CI, 1.06–2.08). The urbanised diet was associated with urban domicile (OR 1.70; 95% CI, 1.38–2.10), secondary (OR 1.30; 95% CI, 1.07–1.59) or tertiary education (OR 1.48; 95% CI, 1.11–1.97), and monthly incomes of $201–500 (OR 1.30; 95$1000/month (OR 1.48; 95% CI, 1.02–2.15). CONCLUSION: A shift away from protective, traditional African dietary patterns may partly explain the rising incidence of colorectal cancer in sub-Saharan Africa.IS

A contiguous de novo genome assembly of sugar beet EL10 (Beta vulgaris L.)

A contiguous assembly of the inbred ‘EL10’ sugar beet (Beta vulgaris ssp. vulgaris) genome was constructed using PacBio long-read sequencing, BioNano optical mapping, Hi-C scaffolding, and Illumina short-read error correction. The EL10.1 assembly was 540 Mb, of which 96.2% was contained in nine chromosome-sized pseudomolecules with lengths from 52 to 65 Mb, and 31 contigs with a median size of 282 kb that remained unassembled. Gene annotation incorporating RNA-seq data and curated sequences via the MAKER annotation pipeline generated 24,255 gene models. Results indicated that the EL10.1 genome assembly is a contiguous genome assembly highly congruent with the published sugar beet reference genome. Gross duplicate gene analyses of EL10.1 revealed little large-scale intra-genome duplication. Reduced gene copy number for well-annotated gene families relative to other core eudicots was observed, especially for transcription factors. Variation in genome size in B. vulgaris was investigated by flow cytometry among 50 individuals producing estimates from 633 to 875 Mb/1C. Read-depth mapping with short-read whole-genome sequences from other sugar beet germplasm suggested that relatively few regions of the sugar beet genome appeared associated with high-copy number variation

Generation of ESTs for Flowering Gene Discovery and SSR Marker Development in Upland Cotton

BACKGROUND: Upland cotton, Gossypium hirsutum L., is one of the world's most important economic crops. In the absence of the entire genomic sequence, a large number of expressed sequence tag (EST) resources of upland cotton have been generated and used in several studies. However, information about the flower development of this species is rare. METHODOLOGY/PRINCIPAL FINDINGS: To clarify the molecular mechanism of flower development in upland cotton, 22,915 high-quality ESTs were generated and assembled into 14,373 unique sequences consisting of 4,563 contigs and 9,810 singletons from a normalized and full-length cDNA library constructed from pooled RNA isolated from shoot apexes, squares, and flowers. Comparative analysis indicated that 5,352 unique sequences had no high-degree matches to the cotton public database. Functional annotation showed that several upland cotton homologs with flowering-related genes were identified in our library. The majority of these genes were specifically expressed in flowering-related tissues. Three GhSEP (G. hirsutum L. SEPALLATA) genes determining floral organ development were cloned, and quantitative real-time PCR (qRT-PCR) revealed that these genes were expressed preferentially in squares or flowers. Furthermore, 670 new putative microsatellites with flanking sequences sufficient for primer design were identified from the 645 unigenes. Twenty-five EST-simple sequence repeats were randomly selected for validation and transferability testing in 17 Gossypium species. Of these, 23 were identified as true-to-type simple sequence repeat loci and were highly transferable among Gossypium species. CONCLUSIONS/SIGNIFICANCE: A high-quality, normalized, full-length cDNA library with a total of 14,373 unique ESTs was generated to provide sequence information for gene discovery and marker development related to upland cotton flower development. These EST resources form a valuable foundation for gene expression profiling analysis, functional analysis of newly discovered genes, genetic linkage, and quantitative trait loci analysis

SHINE Transcription Factors Act Redundantly to Pattern the Archetypal Surface of Arabidopsis Flower Organs

Floral organs display tremendous variation in their exterior that is essential for organogenesis and the interaction with the environment. This diversity in surface characteristics is largely dependent on the composition and structure of their coating cuticular layer. To date, mechanisms of flower organ initiation and identity have been studied extensively, while little is known regarding the regulation of flower organs surface formation, cuticle composition, and its developmental significance. Using a synthetic microRNA approach to simultaneously silence the three SHINE (SHN) clade members, we revealed that these transcription factors act redundantly to shape the surface and morphology of Arabidopsis flowers. It appears that SHNs regulate floral organs' epidermal cell elongation and decoration with nanoridges, particularly in petals. Reduced activity of SHN transcription factors results in floral organs' fusion and earlier abscission that is accompanied by a decrease in cutin load and modified cell wall properties. SHN transcription factors possess target genes within four cutin- and suberin-associated protein families including, CYP86A cytochrome P450s, fatty acyl-CoA reductases, GSDL-motif lipases, and BODYGUARD1-like proteins. The results suggest that alongside controlling cuticular lipids metabolism, SHNs act to modify the epidermis cell wall through altering pectin metabolism and structural proteins. We also provide evidence that surface formation in petals and other floral organs during their growth and elongation or in abscission and dehiscence through SHNs is partially mediated by gibberellin and the DELLA signaling cascade. This study therefore demonstrates the need for a defined composition and structure of the cuticle and cell wall in order to form the archetypal features of floral organs surfaces and control their cell-to-cell separation processes. Furthermore, it will promote future investigation into the relation between the regulation of organ surface patterning and the broader control of flower development and biological functions

Health Outcomes, Pathogenesis and Epidemiology of Severe Acute Malnutrition (HOPE-SAM): rationale and methods of a longitudinal observational study

INTRODUCTION: Mortality among children hospitalised for complicated severe acute malnutrition (SAM) remains high despite the implementation of WHO guidelines, particularly in settings of high HIV prevalence. Children continue to be at high risk of morbidity, mortality and relapse after discharge from hospital although long-term outcomes are not well documented. Better understanding the pathogenesis of SAM and the factors associated with poor outcomes may inform new therapeutic interventions. METHODS AND ANALYSIS: The Health Outcomes, Pathogenesis and Epidemiology of Severe Acute Malnutrition (HOPE-SAM) study is a longitudinal observational cohort that aims to evaluate the short- and long-term clinical outcomes of HIV-positive and HIV-negative children with complicated SAM, and to identify the risk factors at admission and discharge from hospital that independently predict poor outcomes. Children aged 0-59mo hospitalised for SAM are being enrolled at three tertiary hospitals in Harare, Zimbabwe, and Lusaka, Zambia. Longitudinal mortality, morbidity and nutritional data are being collected at admission, discharge and for 48 weeks post-discharge. Nested laboratory substudies are exploring the role of enteropathy, gut microbiota, metabolomics and cellular immune function in the pathogenesis of SAM using stool, urine and blood collected from participants and from well-nourished controls