A closer look at high-energy X-ray-induced bubble formation during soft tissue imaging.

Improving the scalability of tissue imaging throughput with bright, coherent X-rays requires identifying and mitigating artifacts resulting from the interactions between X-rays and matter. At synchrotron sources, long-term imaging of soft tissues in solution can result in gas bubble formation or cavitation, which dramatically compromises image quality and integrity of the samples. By combining in-line phase-contrast imaging with gas chromatography in real time, we were able to track the onset and evolution of high-energy X-ray-induced gas bubbles in ethanol-embedded soft tissue samples for tens of minutes (two to three times the typical scan times). We demonstrate quantitatively that vacuum degassing of the sample during preparation can significantly delay bubble formation, offering up to a twofold improvement in dose tolerance, depending on the tissue type. However, once nucleated, bubble growth is faster in degassed than undegassed samples, indicating their distinct metastable states at bubble onset. Gas chromatography analysis shows increased solvent vaporization concurrent with bubble formation, yet the quantities of dissolved gasses remain unchanged. By coupling features extracted from the radiographs with computational analysis of bubble characteristics, we uncover dose-controlled kinetics and nucleation site-specific growth. These hallmark signatures provide quantitative constraints on the driving mechanisms of bubble formation and growth. Overall, the observations highlight bubble formation as a critical yet often overlooked hurdle in upscaling X-ray imaging for biological tissues and soft materials and we offer an empirical foundation for their understanding and imaging protocol optimization. More importantly, our approaches establish a top-down scheme to decipher the complex, multiscale radiation-matter interactions in these applications.

Reconstructing microvascular network skeletons from 3D images: What is the ground truth?

Structural changes to microvascular networks are increasingly highlighted as markers of pathogenesis in a wide range of disease, e.g. Alzheimer's disease, vascular dementia and tumour growth. This has motivated the development of dedicated 3D imaging techniques, alongside the creation of computational modelling frameworks capable of using 3D reconstructed networks to simulate functional behaviours such as blood flow or transport processes. Extraction of 3D networks from imaging data broadly consists of two image processing steps: segmentation followed by skeletonisation. Much research effort has been devoted to segmentation field, and there are standard and widely-applied methodologies for creating and assessing gold standards or ground truths produced by manual annotation or automated algorithms. The Skeletonisation field, however, lacks widely applied, simple to compute metrics for the validation or optimisation of the numerous algorithms that exist to extract skeletons from binary images. This is particularly problematic as 3D imaging datasets increase in size and visual inspection becomes an insufficient validation approach. In this work, we first demonstrate the extent of the problem by applying 4 widely-used skeletonisation algorithms to 3 different imaging datasets. In doing so we show significant variability between reconstructed skeletons of the same segmented imaging dataset. Moreover, we show that such a structural variability propagates to simulated metrics such as blood flow. To mitigate this variability we introduce a new, fast and easy to compute super metric that compares the volume, connectivity, medialness, bifurcation point identification and homology of the reconstructed skeletons to the original segmented data. We then show that such a metric can be used to select the best performing skeletonisation algorithm for a given dataset, as well as to optimise its parameters. Finally, we demonstrate that the super metric can also be used to quickly identify how a particular skeletonisation algorithm could be improved, becoming a powerful tool in understanding the complex implication of small structural changes in a network.

Distribution of helminth eggs in environmental and stool samples of farming households along Akaki River in Addis Ababa, Ethiopia.

BACKGROUND: Helminth infections are a public health issue in countries with poor sanitation facilities. However, there little information on the epidemiological association between helminths in wastewater and soil samples and rates of helminth infection among farming households along the Akaki River in Addis Ababa, Ethiopia. METHODS: A cross-sectional study was conducted between November 2021 and February 2022. A stratified random sampling technique was used to select farming households. The sample size for each district was determined by a proportionate allocation to the number of households. From wastewater-irrigated farms, 70 wastewater samples, 28 soil samples, and 86 farmers' stool samples were collected and analyzed for helminths. A questionnaire was used to gather ethnographic data, about farming households, whereas wastewater and soil sample analysis was used to generate quantitative data on helminth loads. The data were systematically analysed by developing themes, and bias evaluated using triangulation validation methodologies. Potential pathways to helminth infection were evaluated by measuring. Total number of helminth eggs in wastewater, soil samples and farmer's stools was investigated using Poisson regression. RESULTS: In this study, 82.9% of wastewater samples, 57.1% of soil samples, and 18.6% of farmers' stool samples contained helminth eggs. The most prevalent helminth was Ascaris lumbricoides in all samples (wastewater 67%, soil 25%, and stool 10.5%), followed by hookworm (wastewater 10%, soil 21.4%, and stool 6.9%) and Trichuris trichiura eggs (wastewater 5.7%, soil 10.7%, and stool 1.2%). There was a positive association between the total number of helminth eggs in wastewater and soil samples with counts in farmers' stool. The Poisson regression coefficients for wastewater and soil were, 1.63 (95% CI = 1.34-1.92) and 1.70 (95% CI = 1.39-2.01), (p < 0.05). CONCLUSIONS: This research has shown a clear association between the total helminth eggs in wastewater and soil samples and farmer stools along the Akaki River. Therefore, an integrated approach is essential to address the issue in this area and prevent the spread of further helminth infections.

Prevalence and risk factors of childhood diarrhea among wastewater irrigating urban farming households in Addis Ababa.

INTRODUCTION: Childhood diarrhea is one of the major contributors to the morbidity of under-five children in Ethiopia. Although researchers determine the risk factors varyingly, the exposure route to the pathogens is usually complicated. This study aims to investigate the prevalence and risk factors of diarrhea among children under the age of five among wastewater irrigation farming households in Addis Ababa, Ethiopia. METHODS: Cross-sectional study was conducted among 402 farming households from November 2021 to February 2022. Data was collected using a face-to-face interviewer-administered questionnaire. Stata version 14 software was used to analyze data. Factors associated with the prevalence of diarrhea was identified using binary logistic regression. Multivariable analysis was carried out to determine an adjusted odds ratio at a confidence level of 95% and level of significance at 0.05. RESULTS: The overall prevalence of under-five children diarrheal cases was 22.3%. The odds of diarrhea are associated with a multitude of variables. Major wastewater-related determinants associated with diarrhea are body washing with irrigation water [AOR: 37.7, 95%CI (3.1, 358)], contaminated cloth with irrigation water [AOR:10.8,95%CI(0.6, 205)], use of protective clothing during farm work [28.9,95%CI (3.9, 215)], use of farm work cloths at home [AOR: 31.7, 95%CI (4.4, 226)], and bringing unwashed farm tools to home [94 (5.7, 1575)]. CONCLUSION: The high prevalence of under-five children diarrheal disease among wastewater irrigation households was strongly associated with factors related to occupational exposure. Thus, to decrease childhood diarrheal among urban agriculture farmers, appropriate precautions need to be taken.

Fecal Contamination in the Wastewater Irrigation System and its Health Threat to Wastewater-Based Farming Households in Addis Ababa, Ethiopia.

Due to rapidly growing demand, the production of vegetables is increasing along the Akaki Rivers. The objective of this study was to examine the degree of fecal contamination and levels of fecal contamination and dissemination throughout the wastewater irrigation system. Irrigation water, irrigated soil, and leafy vegetables were collected twice during 2 vegetable growing seasons, at the maturity period of the growing season, from 19 sampling points along the 2 Akaki Rivers. Composite samples were taken from all sampling points and E.coli was enumerated. The mean E.coli load in wastewater and non-wastewater sources were 1.16±5.53 CFU/100 ml and 2.232±1.292 CFU/100 ml respectively. All counts of E. coli in the wastewater exceeded the WHO's standards indicating that the irrigation water quality was unacceptable. In the wastewater-irrigated and non-wastewater-irrigated soil, the mean E.coli were 3.62 ±1.582 CFU/g and 1.322±87.1 CFU/g respectively. Meanwhile, the mean E.coli counts on the lettuce and Swiss chard were 78 ± 2 CFU/g and 44 ±3CFU/g respectively. The E.coli count on the leafy vegetables was found to be associated with the E.coli in the wastewater and soil. The production of leafy vegetables using wastewater with unacceptably high levels of E.coli and high occupational exposure introduces high levels of risk to the farming communities and to the consumers. Leafy, low-growing raw edible vegetables need careful treatment during food production and harvesting procedures or activities.

Micro to macro scale analysis of the intact human renal arterial tree with Synchrotron Tomography.

Background: The kidney vasculature is exquisitely structured to orchestrate renal function. Structural profiling of the vasculature in intact rodent kidneys, has provided insights into renal haemodynamics and oxygenation, but has never been extended to the human kidney beyond a few vascular generations. We hypothesised that synchrotron-based imaging of a human kidney would enable assessment of vasculature across the whole organ. Methods: An intact kidney from a 63-year-old male was scanned using hierarchical phase-contrast tomography (HiP-CT), followed by semi-automated vessel segmentation and quantitative analysis. These data were compared to published micro-CT data of whole rat kidney. Results: The intact human kidney vascular network was imaged with HiP-CT at 25 µm voxels, representing a 20-fold increase in resolution compared to clinical CT scanners. Our comparative quantitative analysis revealed the number of vessel generations, vascular asymmetry and a structural organisation optimised for minimal resistance to flow, are conserved between species, whereas the normalised radii are not. We further demonstrate regional heterogeneity in vessel geometry between renal cortex, medulla, and hilum, showing how the distance between vessels provides a structural basis for renal oxygenation and hypoxia. Conclusions: Through the application of HiP-CT, we have provided the first quantification of the human renal arterial network, with a resolution comparable to that of light microscopy yet at a scale several orders of magnitude larger than that of a renal punch biopsy. Our findings bridge anatomical scales, profiling blood vessels across the intact human kidney, with implications for renal physiology, biophysical modelling, and tissue engineering.

Trace Element Levels in Nails of Residents of Addis Ababa Are Shaped by Social Factors and Geography.

The Akaki catchment in Ethiopia is home to Addis Ababa and about five million people. Its watercourses receive a variety of wastes released by the residents and industries. River water is being used for irrigation, livestock watering, and other domestic purposes. This study tested the hypothesis that the river pollution would be reflected in higher levels of trace elements in the nails of residents living in Akaki-Kality Sub-City in the downstream, as compared to those living in Gullele Sub-City in the upstream of the Akaki catchment. Samples were taken and subsequently analysed for metals using inductively coupled plasma optical emission spectrometry (ICP-OES). The mean concentrations of Fe, Zn, Cu, Mn, Ni, Cr, Pb, and As in nails from Akaki-Kality were 488 ± 49, 106 ± 10, 5.2 ± 0.3, 13 ± 1.5, 11 ± 8, 2.2 ± 0.3, 0.09 ± 0.01, and 0.16 ± 0.01 µg/g, respectively. Likewise, the concentrations of Fe, Zn, Cu, Mn, Ni, Cr, Pb, and As in nails from Gullele were 1035 ± 135, 251 ± 10, 6.6 ± 0.4, 31 ± 3.7, 7.4 ± 1.7, 2.0 ± 0.3, 0.63 ± 0.01, and 0.25 ± 0.01 µg/g, respectively. Co and Cd were not detected. Contrary to the initial hypothesis, higher metal levels were found in nails of residents living in the upstream rather than the downstream area of the catchment. In particular, the concentrations of Fe (p = 0.000), Zn (p = 0.01), and Mn (p = 0.000) were significantly elevated in nails from Gullele and also high in comparison with internationally reported values. Besides, geography and social factors, especially education level, correlated to trace metals in nails. Most of the elements were significantly lower in the nails of individuals with a university degree compared to those who were illiterate or only completed primary school.

Physicochemical characterization and heavy metals analysis from industrial discharges in Upper Awash River Basin, Ethiopia.

The recent expansion of industries in Addis Ababa is causing additional environmental pollution through wastewater discharges; this is becoming a critical concern. Addis Ababa is located in the upper Awash River basin, and is the main source of industrial pollutants to the river. In this study, physicochemical parameters, nutrients and heavy metal content of wastewaters released from 16 factories, 6 tanneries, 6 beverages and 4 diverse factories, and the Akaki-Kality central wastewater treatment plant in Addis Ababa, were sampled to assess the level of pollutants. Heavy metals were determined using inductively coupled plasma optical emission spectroscopy (ICP-OES). Analysis of nutrients were conducted using Palintest Photometer. Physicochemical characteristics were measured either in situ using a portable micro meter or in the laboratory. Among the measured physicochemical properties, critical issues were observed with electrical conductivity, total dissolved solids and total hardness. Effluents from all of the tanneries, and a number of other factories, were found at levels higher than the maximum limits of various guideline standards. In addition, samples from two of the tanneries (T1 and T5), two beverage factories (B3 and B6) and the central wastewater treatment plant showed elevated concentrations of PO4 3-, which violated the limit (10 mg/l) set by Environmental Protection Agency of Ethiopia (ETHEPA). The two tanneries (T1 and T5) also contained higher SO4 2- than the guideline limit of 1000 mg/l. On the other hand, only one factory, one brewery (B3), exhibited NO3 - above the standard limit of 20 mg/l. Whereas NH3, NH4 +, Cl-, S2- and NO2 - were within the limits in all of the samples. Severe pollution was found in wastewaters from tanneries, where half of them (T1, T5 and T6) contained Cr beyond the maximum limit of 2000 µg/l. Furthermore, a third of the tanneries (T1 and T5) and a beverage factory (B5) contained Fe, Mn, Zn and Cu, higher than the ETHEPA limits of 10000, 5000, 5000 and 2000 µg/l, respectively. Waste disposal from factories without proper treatment can cause great harm to the local people and the environment. Hence, the results of this study call for regulatory bodies to pay close attention to factories, particularly tanneries, in Addis Ababa in implementing adequate treatments of their wastewater discharges.

Urinary 8-OHdG level is not affected by geography and trace elements in nail of residents of Addis Ababa: It is shaped by interactions between different social factors.

The objective of this study was to evaluate the association between exposure to heavy metals and oxidative DNA damage among residents living in the potentially more polluted downstream (Akaki-Kality) area of Addis Ababa, in comparison to the upstream area (Gullele). For this, 8-hydroxy-2'-deoxyguanosine (8-OHdG) was used as a biomarker for oxidative DNA damage and heavy metals (Fe, Zn, Mn, Cu, Ni, Cr, Pb, As) as indicators of exposure. The concentrations of heavy metals in nails were determined using inductively coupled plasma optical emission spectroscopy (ICP-OES), and 8-OHdG in urine using Enzyme-Linked with Immunosorbent Assay (ELISA), from 95 residents of the two areas, upstream and downstream. The urinary 8-OHdG concentration was not significantly different (p = 0.05) between the two Sub-Cities, with mean of 18.50 ± 4.37 ng/mg Creatinine in Akaki-Kality and 17.30 ± 5.83 ng/mg Creatinine in Gullele. Also, there were no statistically significant (p = 0.05) difference among the different demographic groups according to gender, age, educational status, body mass index or habit of alcohol consumption. However, the interactions of sex with age, sex with alcohol consumption and alcohol consumption with education were found to affect the urinary 8-OHdG levels of residents of the two Sub-Cities. The mean concentrations (µg/g) of the elements were 488 and 1035 for Fe, 106 and 251 for Zn, 13.0 and 31.2 for Mn, 5.23 and 6.63 for Cu, 11.2 and 7.39 for Ni, 2.23 and 2.02 for Cr, 0.09 and 0.63 for Pb; and 0.16 and 0.25 for As, in nail samples from Akaki-Kality and Gullele, respectively. The determined concentrations of the heavy metals in nails were not significantly associated (p = 0.05) with the corresponding urinary levels of 8-OHdG. Hence, the observed 8-OHdG might have been caused by environmental exposure to toxic substances other than the analyzed heavy metals.

The fatal trajectory of pulmonary COVID-19 is driven by lobular ischemia and fibrotic remodelling.

BACKGROUND: COVID-19 is characterized by a heterogeneous clinical presentation, ranging from mild symptoms to severe courses of disease. 9-20% of hospitalized patients with severe lung disease die from COVID-19 and a substantial number of survivors develop long-COVID. Our objective was to provide comprehensive insights into the pathophysiology of severe COVID-19 and to identify liquid biomarkers for disease severity and therapy response. METHODS: We studied a total of 85 lungs (n = 31 COVID autopsy samples; n = 7 influenza A autopsy samples; n = 18 interstitial lung disease explants; n = 24 healthy controls) using the highest resolution Synchrotron radiation-based hierarchical phase-contrast tomography, scanning electron microscopy of microvascular corrosion casts, immunohistochemistry, matrix-assisted laser desorption ionization mass spectrometry imaging, and analysis of mRNA expression and biological pathways. Plasma samples from all disease groups were used for liquid biomarker determination using ELISA. The anatomic/molecular data were analyzed as a function of patients' hospitalization time. FINDINGS: The observed patchy/mosaic appearance of COVID-19 in conventional lung imaging resulted from microvascular occlusion and secondary lobular ischemia. The length of hospitalization was associated with increased intussusceptive angiogenesis. This was associated with enhanced angiogenic, and fibrotic gene expression demonstrated by molecular profiling and metabolomic analysis. Increased plasma fibrosis markers correlated with their pulmonary tissue transcript levels and predicted disease severity. Plasma analysis confirmed distinct fibrosis biomarkers (TSP2, GDF15, IGFBP7, Pro-C3) that predicted the fatal trajectory in COVID-19. INTERPRETATION: Pulmonary severe COVID-19 is a consequence of secondary lobular microischemia and fibrotic remodelling, resulting in a distinctive form of fibrotic interstitial lung disease that contributes to long-COVID. FUNDING: This project was made possible by a number of funders. The full list can be found within the Declaration of interests / Acknowledgements section at the end of the manuscript.

Absence of significant association of trace elements in nails with urinary KIM-1 biomarker among residents of Addis Ababa in Upper Awash Basin, Ethiopia: a cross-sectional study.

The Akaki River in the Upper Awash Basin, which flows through Addis Ababa, the capital city of Ethiopia, has been highly polluted by sewage from factories and residential areas. A population-based cross-sectional study was used to assess the association between trace elements and kidney injury from residents living in polluted areas downstream (Akaki-Kality) versus upstream (Gullele) in Sub-Cities of Addis Ababa. A total of 95 individuals (53 from Akaki-Kality and 42 from Gullele) were included in the study. Kidney injury molecule 1 (KIM-1), lead, arsenic, cadmium, cobalt, lead, manganese, zinc, iron, copper, chromium and nickel were evaluated in residents' urine and nail samples. A large proportion (74%) of the sample population contained KIM-1, including 81% residents in Akaki-Kality and 64% residents in Gullele. KIM-1 was, however, not significantly different (p = 0.05) between the two Sub-Cities, with median of 0.224 ng/mL in Akaki-Kality and 0.152 ng/mL in Gullele. Most of the analyzed elements, except Pb, As, Cd and Co, were found in all of the nail samples, with median (µg/g) in the range of 442‒714 Fe, 97.0‒246 Zn, 11.6‒24.1 Mn, 4.49‒5.85 Cu, 1.46‒1.66 Cr and 1.22‒1.41 Ni. The high incidence of KIM-1 indicates a potential for long term renal tubular damage among residents of the Sub-Cities. The concentrations of the elements in nails were, however, not significantly associated (p = 0.05) with the corresponding levels of KIM-1 in urine. Hence, the observed KIM-1 might be related to exposure to toxic substances or factors other than those included in this study.

A multiscale X-ray phase-contrast tomography dataset of a whole human left lung.

Technological advancements in X-ray imaging using bright and coherent synchrotron sources now allows the decoupling of sample size and resolution while maintaining high sensitivity to the microstructures of soft, partially dehydrated tissues. The continuous developments in multiscale X-ray imaging resulted in hierarchical phase-contrast tomography, a comprehensive approach to address the challenge of organ-scale (up to tens of centimeters) soft tissue imaging with resolution and sensitivity down to the cellular level. Using this technique, we imaged ex vivo an entire human left lung at an isotropic voxel size of 25.08 µm along with local zooms down to 6.05-6.5 µm and 2.45-2.5 µm in voxel size. The high tissue contrast offered by the fourth-generation synchrotron source at the European Synchrotron Radiation Facility reveals the complex multiscale anatomical constitution of the human lung from the macroscopic (centimeter) down to the microscopic (micrometer) scale. The dataset provides comprehensive organ-scale 3D information of the secondary pulmonary lobules and delineates the microstructure of lung nodules with unprecedented detail.

Spatiotemporal dynamics and heterogeneity of renal lymphatics in mammalian development and cystic kidney disease.

Heterogeneity of lymphatic vessels during embryogenesis is critical for organ-specific lymphatic function. Little is known about lymphatics in the developing kidney, despite their established roles in pathology of the mature organ. We performed three-dimensional imaging to characterize lymphatic vessel formation in the mammalian embryonic kidney at single-cell resolution. In mouse, we visually and quantitatively assessed the development of kidney lymphatic vessels, remodeling from a ring-like anastomosis under the nascent renal pelvis; a site of VEGF-C expression, to form a patent vascular plexus. We identified a heterogenous population of lymphatic endothelial cell clusters in mouse and human embryonic kidneys. Exogenous VEGF-C expanded the lymphatic population in explanted mouse embryonic kidneys. Finally, we characterized complex kidney lymphatic abnormalities in a genetic mouse model of polycystic kidney disease. Our study provides novel insights into the development of kidney lymphatic vasculature; a system which likely has fundamental roles in renal development, physiology and disease.

Interprofessional capability: A developing framework for interprofessional education.

This article reports on the development of an Interprofessional Capability Framework that articulates the learning outcomes that students need to achieve and continue to develop in order to become capable interprofessional workers. Although there tends to be general agreement around the subject matter to be included under the rubric of interprofessional learning, little information is available regarding the learning outcomes students need to achieve in order to become effective interprofessional workers. The Interprofessional Capability Framework defines capabilities that underpin interprofessional working and are relevant to all health and social care professions. The categories of the Framework were generated utilising grounded theory strategies in the analysis of the Quality Assurance Agency benchmark statements that inform the undergraduate curricula of all health and social care courses in the United Kingdom. This resulted in the conceptualisation of four key domains in which capabilities and learning levels have been articulated: Knowledge in Practice, Ethical Practice, Interprofessional Working and Reflection (learning).