Structure and electron affinity of the 4H-SiC (0001) surfaces: a methodological approach for polar systems.

The ability to accurately and consistently determine the surface electronic properties of polar materials is of great importance for device applications. Polar surface modelling is fundamentally limited by the spontaneous polarisation of these materials in a periodic boundary condition scheme. Surface data are sensitive to supercell parameters, including slab and vacuum thicknesses, as well as the non-equivalence of surface adsorbates on opposite surfaces. Using 4H-SiC as a specific case, this study explores calculation of electron affinities (EAs) of (0001̄) and (0001) surfaces varying chemical termination as a function of computational parameters. We report the impact in terms of band-gap, electric fields across the vacuum and slab for single and double cell slab models, where the latter is constructed with inversional symmetry to eliminate the electric field in the vacuum regions. We find that single cells are sensitive to both slab and vacuum thickness. The band-gap narrows with slab thickness, ultimately vanishing and inducing charge transfer between opposite surfaces. This has a consequence for predicted EAs. Adsorbate species are found to play a crucial role in the rate of narrowing. Back to back cells with inversional symmetry have larger electric fields present across the slab than the single slab cases, resulting in a greater band-gap narrowing effect, but the vacuum thickness dependence is completely removed. We discuss the relative merits of the two approaches.

Exploration of Principal Component Analysis: Deriving Principal Component Analysis Visually Using Spectra.

Spectroscopy rapidly captures a large amount of data that is not directly interpretable. Principal component analysis is widely used to simplify complex spectral datasets into comprehensible information by identifying recurring patterns in the data with minimal loss of information. The linear algebra underpinning principal component analysis is not well understood by many applied analytical scientists and spectroscopists who use principal component analysis. The meaning of features identified through principal component analysis is often unclear. This manuscript traces the journey of the spectra themselves through the operations behind principal component analysis, with each step illustrated by simulated spectra. Principal component analysis relies solely on the information within the spectra, consequently the mathematical model is dependent on the nature of the data itself. The direct links between model and spectra allow concrete spectroscopic explanation of principal component analysis , such as the scores representing "concentration" or "weights". The principal components (loadings) are by definition hidden, repeated and uncorrelated spectral shapes that linearly combine to generate the observed spectra. They can be visualized as subtraction spectra between extreme differences within the dataset. Each PC is shown to be a successive refinement of the estimated spectra, improving the fit between PC reconstructed data and the original data. Understanding the data-led development of a principal component analysis model shows how to interpret application specific chemical meaning of the principal component analysis loadings and how to analyze scores. A critical benefit of principal component analysis is its simplicity and the succinctness of its description of a dataset, making it powerful and flexible.

Safety of thoracic radiotherapy in patients with prior immune-related adverse events from immune checkpoint inhibitors.

BACKGROUND: Immune checkpoint inhibitors (ICIs) and thoracic radiotherapy are increasingly used to treat advanced cancers. Despite data indicating exaggerated radiation toxicities in patients with autoimmune disease, the safety of thoracic radiotherapy in patients with prior ICI-associated immune-related adverse events (irAEs) is undefined. PATIENTS AND METHODS: Patients treated from 2014 to 2020 with ICIs were queried for receipt of corticosteroids and radiotherapy. Patients who received thoracic radiation after symptomatic irAEs were assessed for ≥grade 2 radiation pneumonitis (RP). Characteristics predictive of RP were assessed using logistic regression and response relationships were modeled. RESULTS: Among 496 assessed patients, 41 with irAE history subsequently treated with thoracic radiotherapy were analyzed. Most irAEs were grade 2 (n = 21) and 3 (n = 19). Median time from irAE onset to radiotherapy was 8.1 months. Most patients received stereotactic body radiation therapy (n = 20) or hypofractionated radiotherapy (n = 18). In total, 25 patients (61%) developed ≥grade 2 RP at a median of 4 months from radiotherapy and 11 months from onset of irAEs. Three months from RP onset, 16 of 24 (67%) assessable patients had persistent symptoms. Among patients with prior ICI pneumonitis (n = 6), five patients (83%) developed ≥grade 2 RP (grade 2, n = 3; grade ≥3, n = 2). The mean lung radiation dose (MLD) predicted for RP (odds ratio: 1.60, P = 0.00002). The relationship between MLD and RP was strong (area under the receiver-operating characteristic curve: 0.85) and showed an exaggerated dose-response. Among patients with an MLD >5 Gy (n = 26), 21 patients (81%) developed ≥grade 2 RP. CONCLUSION: This is the first study assessing the toxicity of radiotherapy among patients with prior irAEs from ICIs. Patients with prior irAEs were found to be at very high risk for clinically significant and persistent RP from thoracic radiotherapy. Careful consideration should be given to the possibility of an increased risk of RP, and close monitoring is recommended in these patients.

Silicon and germanium terminated (0 0 1)-(2 [Formula: see text] 1) diamond surface.

Control over the chemical termination of diamond surfaces has shown great promise in the realization of field-emission applications, the selection of charge states of near-surface colour-centres such as NV, and the realisation of surface-conductive channels for electronic device applications. Experimental investigations of ultra-thin Si and Ge layers yield surface states both within the band-gap and resonant with the underlying diamond valence band. In this report, we report the results of density-functional simulations of a range of coverages of Si and Ge on diamond (0 0 1) surfaces. We have found that surface coverage with crystallogen:carbon ratios of 67% and 75% are more stable than both higher and lower coverages on the (0 0 1)-diamond surface, and that they can explain the observation of an occupied band around 1.7 eV below the valence band top. We also report geometries, adsorption energies and electron affinities of these surface structures, and show that the resonant state is made up from conventional spd-covalent [Formula: see text]-bonding orbitals between the surface adsorbates.

Raman spectroscopy as a predictive tool for monitoring osteoporosis therapy in a rat model of postmenopausal osteoporosis.

Pharmacological therapy of osteoporosis reduces bone loss and risk of fracture in patients. Modulation of bone mineral density cannot explain all effects. Other aspects of bone quality affecting fragility and ways to monitor them need to be better understood. Keratinous tissue acts as surrogate marker for bone protein deterioration caused by oestrogen deficiency in rats. Ovariectomised rats were treated with alendronate (ALN), parathyroid hormone (PTH) or estrogen (E2). MicroCT assessed macro structural changes. Raman spectroscopy assessed biochemical changes. Micro CT confirmed that all treatments prevented ovariectomy-induced macro structural bone loss in rats. PTH induced macro structural changes unrelated to ovariectomy. Raman analysis revealed ALN and PTH partially protect against molecular level changes to bone collagen (80% protection) and mineral (50% protection) phases. E2 failed to prevent biochemical change. The treatments induced alterations unassociated with the ovariectomy; increased beta sheet with E2, globular alpha helices with PTH and fibrous alpha helices with both ALN and PTH. ALN is closest to maintaining physiological status of the animals, while PTH (comparable protective effect) induces side effects. E2 is unable to prevent molecular level changes associated with ovariectomy. Raman spectroscopy can act as predictive tool for monitoring pharmacological therapy of osteoporosis in rodents. Keratinous tissue is a useful surrogate marker for the protein related impact of these therapies.The results demonstrate utility of surrogates where a clear systemic causation connects the surrogate to the target tissue. It demonstrates the need to assess broader biomolecular impact of interventions to examine side effects.

A Preliminary Evaluation of the Ability of Keratotic Tissue to Act as a Prognostic Indicator of Hip Fracture Risk.

Studies have shown that Raman spectroscopic analysis of fingernail clippings can help differentiate between post-menopausal women who have and who have not suffered a fracture. However, all studies to date have been retrospective in nature, comparing the proteins in nails sourced from women, post-fracture. The objective of this study was to investigate the potential of a prospective test for hip fracture based on spectroscopic analysis of nail tissue. Archived toenail samples from post-menopausal women aged 50 to 63 years in the Nurses' Health Study were obtained and analysed by Raman spectroscopy. Nails were matched case-controls sourced from 161 women; 82 who underwent a hip fracture up to 20 years after nail collection and 81 age-matched controls. A number of clinical risk factors (CRFs) from the Fracture Risk Assessment (FRAX) tool had been assessed at toenail collection. Using 80% of the spectra, models were developed for increasing time periods between nail collection and fracture. Scores were calculated from these models for the other 20% of the sample and the ability of the score to predict hip fracture was tested in model with and without the CRFs by comparing the odds ratios (ORs) per 1 SD increase in standardised predictive values. The Raman score successfully distinguished between hip fracture cases and controls. With only the score as a predictor, a statistically significant OR of 2.2 (95% confidence interval [CI]: 1.5-3.1) was found for hip fracture for up to 20 years after collection. The OR increased to 3.8 (2.6-5.4) when the CRFs were added to the model. For fractures limited to 13 years after collection, the OR was 6.3 (3.0-13.1) for the score alone. The test based on Raman spectroscopy has potential for identifying individuals who may suffer hip fractures several years in advance. Higher powered studies are required to evaluate the predictive capability of this test.

Raman spectroscopy predicts the link between claw keratin and bone collagen structure in a rodent model of oestrogen deficiency.

Osteoporosis is a common disease characterised by reduced bone mass and an increased risk of fragility fractures. Low bone mineral density is known to significantly increase the risk of osteoporotic fractures, however, the majority of non-traumatic fractures occur in individuals with a bone mineral density too high to be classified as osteoporotic. Therefore, there is an urgent need to investigate aspects of bone health, other than bone mass, that can predict the risk of fracture. Here, we successfully predicted association between bone collagen and nail keratin in relation to bone loss due to oestrogen deficiency using Raman spectroscopy. Raman signal signature successfully discriminated between ovariectomised rats and their sham controls with a high degree of accuracy for the bone (sensitivity 89%, specificity 91%) and claw tissue (sensitivity 89%, specificity 82%). When tested in an independent set of claw samples the classifier gave 92% sensitivity and 85% specificity. Comparison of the spectral changes occurring in the bone tissue with the changes occurring in the keratin showed a number of common features that could be attributed to common changes in the structure of bone collagen and claw keratin. This study established that systemic oestrogen deficiency mediates parallel structural changes in both the claw (primarily keratin) and bone proteins (primarily collagen). This strengthens the hypothesis that nail keratin can act as a surrogate marker of bone protein status where systemic processes induce changes.

The "chicken-and-egg" development of political opinionsThe roles of genes, social status, ideology, and information.

Twin studies have revealed political ideology to be partially heritable. Neurological research has shown that ideological differences are reflected in brain structure and response, suggesting a direct genotype-phenotype link. Social and informational environments, however, also demonstrably affect brain structure and response. This leads to a "chicken-and-egg" question: do genes produce brains with ideological predispositions, causing the preferential absorption of consonant information and thereby forming an ideology, or do social and informational environments do most of the heavy lifting, with genetic evidence the spurious artifact of outdated methodology? Or are both inextricably intertwined contributors? This article investigates the relative contributions of genetic and environmental factors to ideological development using a role-play experiment investigating the development of opinions on a novel political issue. The results support the view that the process is bidirectional, suggesting that, like most traits, political ideology is produced by the complex interplay of genetic and (social/informational) environmental influences.

Low zinc and selenium concentrations in sepsis are associated with oxidative damage and inflammation.

BACKGROUND: Oxidative stress with dysregulated inflammation are hallmarks of sepsis. Zinc and selenium have important antioxidant functions, such that they could be important in patients with sepsis. We used an in vitro approach to assess the effect of zinc and selenium on oxidative stress, mitochondrial function, and inflammatory responses in conditions mimicking sepsis and related the findings to plasma concentrations and biomarkers in patients with and without sepsis. METHODS: Human endothelial cells were exposed to a range of zinc and selenium concentrations in conditions mimicking sepsis. Zinc, selenium, and a series of biomarkers of oxidative stress and inflammation were measured in plasma from critically ill patients with and without sepsis. RESULTS: Culturing cells with different concentrations of zinc caused altered zinc transporter protein expression and cellular zinc content, and selenium affected glutathione peroxidase 3 activity. Although zinc or selenium at physiological concentrations had no effect on interleukin-6 release in vitro, higher concentrations of the trace elements were associated with improved mitochondrial function. Plasma zinc and selenium concentrations were low in patients [zinc: median (range) 4.6 (2.1-6.5) µM in control patients without sepsis and 3.1 (1.5-5.4) µM in patients with sepsis, P=0.002; and selenium: 0.78 (0.19-1.32) µM in control patients and 0.42 (0.22-0.91) µM in sepsis patients, P=0.0009]. Plasma concentrations of interleukin-6, other biomarkers of inflammation, and markers of oxidative damage to proteins and lipids were elevated, particularly in patients with sepsis, and were inversely related to plasma zinc and selenium concentrations. CONCLUSIONS: Zinc and selenium concentrations were reduced in critically ill patients, with increased oxidative stress and inflammatory biomarkers, particularly in patients with sepsis. Oxidative stress as a result of suboptimal selenium and zinc concentrations might contribute to damage of key proteins. CLINICAL TRIAL REGISTRATION: ClinicalTrials.gov: registration number NCT01328509.

Water on Au sputtered films.

Transient changes in the contact angle, Δθ ∼ 10°, of water on gold (Au) reveal reversible wetting of near hydrophobic Au films. The recovery time is temperature dependent. Surface flatness is investigated using AFM and profilometery.

Recyclable chemosensor for oxalate based on bimetallic complexes of a dinucleating bis(iminopyridine) ligand.

Herein we describe bimetallic di-nickel and di-copper complexes [Ni2(L)Br4] (1) and [Cu2(L)Br4(NCMe)2] (2) (L = (1E,1'E)-N,N'-(1,4-phenylenebis(methylene))bis(1-(6-(2,4,6-triisopropylphenyl)pyridin-2-yl)methanimine)) that bind oxalate intramolecularly to form [Ni2(L)Br2(C2O4)(NCMe)] (3) and [Cu2(L)Br2(C2O4)] (4). For the di-nickel complex 1, oxalate incorporation is accompanied by a significant colour change, from red-pink (1) to deep green (3). Mass spectrometric experiments demonstrate that the compound 1 is selective for oxalate versus related mono- and di-carboxylates tested. Oxalate can be released by the addition of slight excess of calcium bromide that forms insoluble calcium oxalate and restores the original Ni2(L)Br4 species. The product of the oxalate release was crystallized as [Ni2(L)Br4]·CaBr2(THF)4 species.

The role of the insulin­like growth factor (IGF) axis in osteogenic and odontogenic differentiation.

The insulin-like growth factor (IGF) axis is a multicomponent molecular network which has important biological functions in the development and maintenance of differentiated tissue function(s). One of the most important functions of the IGF axis is the control of skeletal tissue metabolism by the finely tuned regulation of the process of osteogenesis. To achieve this, the IGF axis controls the activity of several cell types­osteoprogenitor cells, osteoblasts, osteocytes and osteoclasts to achieve the co-ordinated development of appropriate hard tissue structure and associated matrix deposition. In addition, there is an increasing awareness that the IGF axis also plays a role in the process of odontogenesis (tooth formation). In this review, we highlight some of the key findings in both of these areas. A further understanding of the role of the IGF axis in hard tissue biology may contribute to tissue regeneration strategies in cases of skeletal tissue trauma.

IGFBP-5 enhances epithelial cell adhesion and protects epithelial cells from TGFß1-induced mesenchymal invasion.

TGFß1 is a major fibrotic factor and its actions involve induction of epithelial cell death, together with the stimulation and transdifferentiation of fibroblasts into collagen- and fibronectin-secreting myofibroblasts. These actions of TGFß1 are also consistent with a pro-metastatic role, by aiding epithelial cell escape through mesenchymal tissues. Recently IGFBP-5 has been described as a pro-fibrotic (pro-metastatic?) agent and the aim of this study was to compare and contrast the actions of IGFBP-5 with TGFß1. We used NMuMG cells and cloned stable epithelial and mesenchymal lines from the parent cells. TGFß1 induced apoptosis and/or EMT in the epithelial cells, whereas it enhanced mesenchymal cell survival and migration. IGFBP-5, in contrast, enhanced both cell-cell and cell-ECM adhesion and also improved wound closure in epithelial cells whereas, in mesenchymal cells, IGFBP-5 decreased adhesion and migration. Furthermore, IGFBP-5 was able to antagonise the actions of TGFß1. In a co-culture model simulating epithelial-mesenchymal boundaries, IGFBP-5 was able to antagonise the disruptive transgressions induced by TGFß1. Overall, these findings suggest that IGFBP-5 is important in maintaining epithelial-mesenchymal boundaries and thus may limit metastasis and fibrosis by inducing an orderly repair mechanism, very distinct from the fibrotic disruption induced by TGFß1. A role for IGFBP-5 in the inhibition of metastasis is supported by immunohistochemical studies of breast cancer microarrays, where we show that elevated IGFBP-5 expression is associated with increased disease-free survival.

Raman spectroscopy for the detection of AGEs/ALEs.

Raman spectroscopy is a noninvasive, nondestructive tool for capturing multiplexed biochemical information across diverse molecular species including proteins, lipids, DNA, and mineralizations. Based on light scattering from molecules, cells, and tissues, it is possible to detect molecular fingerprints and discriminate between subtly different members of each biochemical class. Raman spectroscopy is ideal for detecting perturbations from the expected molecular structure such as those occurring during senescence and the modification of long-lived proteins by metabolic intermediates as we age. Here, we describe the sample preparation, data acquisition, signal processing, data analysis and interpretation involved in using Raman spectroscopy for detecting age-related protein modifications in complex biological tissues.

Sclera as a surrogate marker for determining AGE-modifications in Bruch's membrane using a Raman spectroscopy-based index of aging.

PURPOSE: Raman spectroscopy is an effective probe of advanced glycation end products (AGEs) in Bruch's membrane. However, because it is the outermost layer of the retina, this extracellular matrix is difficult to analyze in vivo with current technology. The sclera shares many compositional characteristics with Bruch's membrane, but it is much easier to access for in vivo Raman analysis. This study investigated whether sclera could act as a surrogate tissue for Raman-based investigation of pathogenic AGEs in Bruch's membrane. METHODS: Human sclera and Bruch's membrane were dissected from postmortem eyes (n = 67) across a wide age range (33-92 years) and were probed by Raman spectroscopy. The biochemical composition, AGEs, and their age-related trends were determined from data reduction of the Raman spectra and compared for the two tissues. RESULTS: Raman microscopy demonstrated that Bruch's membrane and sclera are composed of a similar range of biomolecules but with distinct relative quantities, such as in the heme/collagen and the elastin/collagen ratios. Both tissues accumulated AGEs, and these correlated with chronological age (R(2) = 0.824 and R(2) = 0.717 for sclera and Bruch's membrane, respectively). The sclera accumulated AGE adducts at a lower rate than Bruch's membrane, and the models of overall age-related changes exhibited a lower rate (one-fourth that of Bruch's membrane) but a significant increase with age (P < 0.05). CONCLUSIONS: The results suggest that the sclera is a viable surrogate marker for estimating AGE accumulation in Bruch's membrane and for reliably predicting chronological age. These findings also suggest that sclera could be a useful target tissue for future patient-based, Raman spectroscopy studies.

Red meat from animals offered a grass diet increases plasma and platelet n-3 PUFA in healthy consumers.

Red meat from grass-fed animals, compared with concentrate-fed animals, contains increased concentrations of long-chain (LC) n-3 PUFA. However, the effects of red meat consumption from grass-fed animals on consumer blood concentrations of LC n-3 PUFA are unknown. The aim of the present study was to compare the effects on plasma and platelet LC n-3 PUFA status of consuming red meat produced from either grass-fed animals or concentrate-fed animals. A randomised, double-blinded, dietary intervention study was carried out for 4 weeks on healthy subjects who replaced their habitual red meat intake with three portions per week of red meat (beef and lamb) from animals offered a finishing diet of either grass or concentrate (n 20 consumers). Plasma and platelet fatty acid composition, dietary intake, blood pressure, and serum lipids and lipoproteins were analysed at baseline and post-intervention. Dietary intakes of total n-3 PUFA, as well as plasma and platelet concentrations of LC n-3 PUFA, were significantly higher in those subjects who consumed red meat from grass-fed animals compared with those who consumed red meat from concentrate-fed animals (P < 0·05). No significant differences in concentrations of serum cholesterol, TAG or blood pressure were observed between groups. Consuming red meat from grass-fed animals compared with concentrate-fed animals as part of the habitual diet can significantly increase consumer plasma and platelet LC n-3 PUFA status. As a result, red meat from grass-fed animals may contribute to dietary intakes of LC n-3 PUFA in populations where red meat is habitually consumed.

Multiplex analysis of age-related protein and lipid modifications in human Bruch's membrane.

Aging of the human retina is characterized by progressive pathology, which can lead to vision loss. This progression is believed to involve reactive metabolic intermediates reacting with constituents of Bruch's membrane, significantly altering its physiochemical nature and function. We aimed to replace a myriad of techniques following these changes with one, Raman spectroscopy. We used multiplexed Raman spectroscopy to analyze the age-related changes in 7 proteins, 3 lipids, and 8 advanced glycation/lipoxidation endproducts (AGEs/ALEs) in 63 postmortem human donors. We provided an important database for Raman spectra from a broad range of AGEs and ALEs, each with a characteristic fingerprint. Many of these adducts were shown for the first time in human Bruch's membrane and are significantly associated with aging. The study also introduced the previously unreported up-regulation of heme during aging of Bruch's membrane, which is associated with AGE/ALE formation. Selection of donors ranged from ages 32 to 92 yr. We demonstrated that Raman spectroscopy can identify and quantify age-related changes in a single nondestructive measurement, with potential to measure age-related changes in vivo. We present the first directly recorded evidence of the key role of heme in AGE/ALE formation.

Identifying the spatial distribution of vitamin E, pulmonary surfactant and membrane lipids in cells and tissue by confocal Raman microscopy.

Every organ compromises of several different cell types. When studying the effects of a chosen compound within this organ or tissue uptake, localisation, metabolism, and the effect itself can be expected to differ between cells. Using the example of Vitamin E in pulmonary tissue we introduce confocal Raman Microscopy as a superior method to localise lipid-soluble compounds within tissues and cells. We describe the analyses of vitamin E, its oxidation products, and metabolites as well as pulmonary surfactant phospholipids in fixed lung tissue sections. Examples of main structural membrane lipids (PC, cholesterol) and an example of a lipid-signalling molecule (ceramide) are also included. Confocal Raman microscopy is a non-destructive optical method of analysing chemical and physical composition of solids, liquids, gases, gels, and solutions. The method is rich in information allowing discrimination of chemically similar molecules (including geometric isomers) and sensitive monitoring of subtle physical interactions. Additionally, Raman spectroscopy is relatively insensitive to water allowing the analysis of aqueous solutions and suspensions typical in biochemistry. In contrast, Raman spectroscopy is sensitive to non-polar molecules making it ideal for lipidomics research.

Role of insulin-like growth factor binding proteins in mammary gland development.

Insulin-like growth factors (IGFs) play an important role in mammary gland development and their effects are, in turn, influenced by a family of 6 IGF-binding proteins (IGFBPs). The IGFBPs are expressed in time- and tissue-specific fashion during the periods of rapid growth and involution of the mammary gland. The precise roles of these proteins in vivo have, however, been difficult to determine. This review examines the indirect evidence (evolution, chromosomal location and roles in lower life-forms) the evidence from in vitro studies and the attempts to examine their roles in vivo, using IGFBP-deficient and over-expression models. Evidence exists for a role of the IGFBPs in inhibition of the survival effects of IGFs as well as in IGF-enhancing effects from in vitro studies. The location of the IGFBPs, often associated with the extracellular matrix, suggests roles as a reservoir of IGFs or as a potential barrier, restricting access of IGFs to distinct cellular compartments. We also discuss the relative importance of IGF-dependent versus IGF-independent effects. IGF-independent effects include nuclear localization, activation of proteases and interaction with a variety of extracellular matrix and cell surface proteins. Finally, we examine the increasing evidence for the IGFBPs to be considered as part of a larger family of extracellular matrix proteins involved in morphogenesis and tissue re-modeling.