Advances in High-Throughput Analysis: Automated Radiochemical Separations and Nanopillar based Separations and Field Enhanced Spectroscopy

Often the need to analyze a large number of samples coincide with critical time consternates. At such times, the implementation of high-throughput technologies is paramount. In this work we explore some viable pathways for high-throughput analysis and develop advancements in novel forms of detection of materials that are vital in the environmental, biological as well as national security arenas. Through the use of new protocols with high sensitivity and specificity as well as simplified chemical processing and sample preparation we aim to allow for improved throughput, fieldable detection, and rapid data acquisition of extensive sample sets. The methods developed in this work focus on unique platforms of the collection and analysis and combine them with automation and portability. Foremost, analytes of interest must be selectively isolated and concentrated by chemical and/or mechanical processes. Secondly, spectroscopic and physical properties are exploited and enhanced by employing viable detection platforms. Finally, automation and field portability are implemented through a combination of optimized robotics, minimized chemical preparation and/or unique lab on a chip type platforms. Presented are two sub areas of research. One focuses on the automation of a time consuming solid phase extraction process that is coupled to inductively coupled plasma mass spectrometry increasing sample throughput by orders of magnitude. The second focused on the fabrication and use of silicon nanopillars as a platform for separations and enhanced optical analysis. Each section of work focuses on the development of a practical, accessible, and deployable methods of analysis

Impact of climate change on hospital admissions: a case study of the Royal Berkshire Hospital in the UK

Abstract: Global warming is projected to have major implications on global health. It is however not yet clear how this will translate to impacts on the healthcare system. By linking changes in temperature with changes in required bed days at a hospital level, through the use of a simple bed model, we quantify the projected impacts UK hospitals will need to adapt to. We show that there is already a local peak of bed days required in the main summer months due to hot temperatures. The results further show that there will be a significant increase during the main summer in both the mean and maximum number of beds needed, but a non‐significant decrease during the peak winter months. These changes lead to a more constant need of care of the year and shift the seasonal cycle of lowest hospital needs

BlobCUT: A contrastive learning method to support small blob detection in medical imaging

Medical imaging-based biomarkers derived from small objects (e.g., cell nuclei) play a crucial role in medical applications. However, detecting and segmenting small objects (a.k.a. blobs) remains a challenging task. In this research, we propose a novel 3D small blob detector called BlobCUT. BlobCUT is an unpaired image-to-image (I2I) translation model that falls under the Contrastive Unpaired Translation paradigm. It employs a blob synthesis module to generate synthetic 3D blobs with corresponding masks. This is incorporated into the iterative model training as the ground truth. The I2I translation process is designed with two constraints: (1) a convexity consistency constraint that relies on Hessian analysis to preserve the geometric properties and (2) an intensity distribution consistency constraint based on Kullback-Leibler divergence to preserve the intensity distribution of blobs. BlobCUT learns the inherent noise distribution from the target noisy blob images and performs image translation from the noisy domain to the clean domain, effectively functioning as a denoising process to support blob identification. To validate the performance of BlobCUT, we evaluate it on a 3D simulated dataset of blobs and a 3D MRI dataset of mouse kidneys. We conduct a comparative analysis involving six state-of-the-art methods. Our findings reveal that BlobCUT exhibits superior performance and training efficiency, utilizing only 56.6% of the training time required by the state-of-the-art BlobDetGAN. This underscores the effectiveness of BlobCUT in accurately segmenting small blobs while achieving notable gains in training efficiency

An Empirical Characterization of Extended Cool Gas Around Galaxies Using MgII Absorption Features

We report results from a survey of MgII absorbers in the spectra of background QSOs that are within close angular distances to a foreground galaxy at z<0.5, using the Magellan Echellette Spectrograph. We have established a spectroscopic sample of 94 galaxies at a median redshift of = 0.24 in fields around 70 distant background QSOs (z_QSO>0.6), 71 of which are in an 'isolated' environment with no known companions and located at rho <~ 120 h^-1 kpc from the line of sight of a background QSO. The rest-frame absolute B-band magnitudes span a range from M_B-5log h=-16.4 to M_B-5log h=-21.4 and rest-frame B_AB-R_AB colors range from B_AB-R_AB~0 to B_AB-R_AB~1.5. Of these 'isolated' galaxies, we find that 47 have corresponding MgII absorbers in the spectra of background QSOs and rest-frame absorption equivalent width W_r(2796)=0.1-2.34 A, and 24 do not give rise to MgII absorption to sensitive upper limits. Our analysis shows that (1) Wr(2796) declines with increasing distance from 'isolated' galaxies but shows no clear trend in 'group' environments; (2) more luminous galaxies possess more extended MgII absorbing halos with the gaseous radius scaled by B-band luminosity according to R_gas=75x(L_B/L_B*)^(0.35+/-0.03) h^{-1} kpc; (3) there is little dependence between the observed absorber strength and galaxy intrinsic colors; and (4) within R_gas, we find a mean covering fraction of ~70% for absorbers of Wr(2796)>=0.3 A and ~80% for absorbers of Wr(2796)>=0.1 A. The lack of correlation between Wr(2796) and galaxy colors suggests a lack of physical connection between the origin of extended MgII halos and recent star formation history of the galaxies. Finally, we discuss the total gas mass in galactic halos as traced by MgII absorbers. We also compare our results with previous studies.Comment: 20 pages, 13 figures; to appear in the Astrophysical Journal 2010 May 10 issue; a version with higher resolution figures can be found at http://lambda.uchicago.edu/public/tmp/mage_apj.pd

Premature differentiation of nephron progenitor cell and dysregulation of gene pathways critical to kidney development in a model of preterm birth

Preterm birth is a leading cause of neonatal morbidity. Survivors have a greater risk for kidney dysfunction and hypertension. Little is known about the molecular changes that occur in the kidney of individuals born preterm. Here, we demonstrate that mice delivered two days prior to full term gestation undergo premature cessation of nephrogenesis, resulting in a lower glomerular density. Kidneys from preterm and term groups exhibited differences in gene expression profiles at 20- and 27-days post-conception, including significant differences in the expression of fat-soluble vitamin-related genes. Kidneys of the preterm mice exhibited decreased proportions of endothelial cells and a lower expression of genes promoting angiogenesis compared to the term group. Kidneys from the preterm mice also had altered nephron progenitor subpopulations, early Six2 depletion, and altered Jag1 expression in the nephrogenic zone, consistent with premature differentiation of nephron progenitor cells. In conclusion, preterm birth alone was sufficient to shorten the duration of nephrogenesis and cause premature differentiation of nephron progenitor cells. These candidate genes and pathways may provide targets to improve kidney health in preterm infants

‘Plasticosis’: Characterising macro- and microplastic-associated fibrosis in seabird tissues

As biota are increasingly exposed to plastic pollution, there is a need to closely examine the sub-lethal 'hidden' impacts of plastic ingestion. This emerging field of study has been limited to model species in controlled laboratory settings, with little data available for wild, free-living organisms. Highly impacted by plastic ingestion, Flesh-footed Shearwaters (Ardenna carneipes) are thus an apt species to examine these impacts in an environmentally relevant manner. A Masson's Trichrome stain was used to document any evidence of plastic-induced fibrosis, using collagen as a marker for scar tissue formation in the proventriculus (stomach) of 30 Flesh-footed Shearwater fledglings from Lord Howe Island, Australia. Plastic presence was highly associated with widespread scar tissue formation and extensive changes to, and even loss of, tissue structure within the mucosa and submucosa. Additionally, despite naturally occurring indigestible items, such as pumice, also being found in the gastrointestinal tract, this did not cause similar scarring. This highlights the unique pathological properties of plastics and raises concerns for other species impacted by plastic ingestion. Further, the extent and severity of fibrosis documented in this study gives support for a novel, plastic-induced fibrotic disease, which we define as 'Plasticosis,'.Copyright © 2023 The Authors. Published by Elsevier B.V. This is an open access article under the CC BY license (http://creativecommons.org/licenses/by/4.0/). The attached file is the published version of the article.NHM Repositor

Microstructural and Rheological Transitions in Bacterial Biofilms

Abstract Biofilms are aggregated bacterial communities structured within an extracellular matrix (ECM). ECM controls biofilm architecture and confers mechanical resistance against shear forces. From a physical perspective, biofilms can be described as colloidal gels, where bacterial cells are analogous to colloidal particles distributed in the polymeric ECM. However, the influence of the ECM in altering the cellular packing fraction (ϕ) and the resulting viscoelastic behavior of biofilm remains unexplored. Using biofilms of Pantoea sp. (WT) and its mutant (ΔUDP), the correlation between biofilm structure and its viscoelastic response is investigated. Experiments show that the reduction of exopolysaccharide production in ΔUDP biofilms corresponds with a seven‐fold increase in ϕ, resulting in a colloidal glass‐like structure. Consequently, the rheological signatures become altered, with the WT behaving like a weak gel, whilst the ΔUDP displayed a glass‐like rheological signature. By co‐culturing the two strains, biofilm ϕ is modulated which allows us to explore the structural changes and capture a change in viscoelastic response from a weak to a strong gel, and to a colloidal glass‐like state. The results reveal the role of exopolysaccharide in mediating a structural transition in biofilms and demonstrate a correlation between biofilm structure and viscoelastic response