An investigation of the clinical impact and therapeutic relevance of a DNA damage immune response (DDIR) signature in patients with advanced gastroesophageal adenocarcinoma.

BACKGROUND: An improved understanding of which gastroesophageal adenocarcinoma (GOA) patients respond to both chemotherapy and immune checkpoint inhibitors (ICI) is needed. We investigated the predictive role and underlying biology of a 44-gene DNA damage immune response (DDIR) signature in patients with advanced GOA. MATERIALS AND METHODS: Transcriptional profiling was carried out on pretreatment tissue from 252 GOA patients treated with platinum-based chemotherapy (three dose levels) within the randomized phase III GO2 trial. Cross-validation was carried out in two independent GOA cohorts with transcriptional profiling, immune cell immunohistochemistry and epidermal growth factor receptor (EGFR) fluorescent in situ hybridization (FISH) (n = 430). RESULTS: In the GO2 trial, DDIR-positive tumours had a greater radiological response (51.7% versus 28.5%, P = 0.022) and improved overall survival in a dose-dependent manner (P = 0.028). DDIR positivity was associated with a pretreatment inflamed tumour microenvironment (TME) and increased expression of biomarkers associated with ICI response such as CD274 (programmed death-ligand 1, PD-L1) and a microsatellite instability RNA signature. Consensus pathway analysis identified EGFR as a potential key determinant of the DDIR signature. EGFR amplification was associated with DDIR negativity and an immune cold TME. CONCLUSIONS: Our results indicate the importance of the GOA TME in chemotherapy response, its relationship to DNA damage repair and EGFR as a targetable driver of an immune cold TME. Chemotherapy-sensitive inflamed GOAs could benefit from ICI delivered in combination with standard chemotherapy. Combining EGFR inhibitors and ICIs warrants further investigation in patients with EGFR-amplified tumours.

Sulfinamide Formation from the Reaction of Bacillithiol and Nitroxyl.

Bacillithiol (BSH) replaces glutathione (GSH) as the most prominent low-molecular-weight thiol in many low G + C gram-positive bacteria. BSH plays roles in metal binding, protein/enzyme regulation, detoxification, redox buffering, and bacterial virulence. Given the small amounts of BSH isolated from natural sources and relatively lengthy chemical syntheses, the reactions of BSH with pertinent reactive oxygen, nitrogen, and sulfur species remain largely unexplored. We prepared BSH and exposed it to nitroxyl (HNO), a reactive nitrogen species that influences bacterial sulfur metabolism. The profile of this reaction was distinct from HNO oxidation of GSH, which yielded mixtures of disulfide and sulfinamide. The reaction of BSH and HNO (generated from Angeli's salt) gives only sulfinamide products, including a newly proposed cyclic sulfinamide. Treatment of a glucosamine-cysteine conjugate, which lacks the malic acid group, with HNO forms disulfide, implicating the malic acid group in sulfinamide formation. This finding supports a mechanism involving the formation of an N-hydroxysulfenamide intermediate that dehydrates to a sulfenium ion that can be trapped by water or internally trapped by an amide nitrogen to give the cyclic sulfinamide. The biological relevance of BSH reactivity toward HNO is provided through in vivo experiments demonstrating that Bacillus subtilis exposed to HNO shows a growth phenotype, and a strain unable to produce BSH shows hypersensitivity toward HNO in minimal medium cultures. Thiol analysis of HNO-exposed cultures shows an overall decrease in reduced BSH levels, which is not accompanied by increased levels of BSSB, supporting a model involving the formation of an oxidized sulfinamide derivative, identified in vivo by high-pressure liquid chromatography/mass spectrometry. Collectively, these findings reveal the unique chemistry and biology of HNO with BSH in bacteria that produce this biothiol.

The application of epiphenotyping approaches to DNA methylation array studies of the human placenta.

BACKGROUND: Genome-wide DNA methylation (DNAme) profiling of the placenta with Illumina Infinium Methylation bead arrays is often used to explore the connections between in utero exposures, placental pathology, and fetal development. However, many technical and biological factors can lead to signals of DNAme variation between samples and between cohorts, and understanding and accounting for these factors is essential to ensure meaningful and replicable data analysis. Recently, "epiphenotyping" approaches have been developed whereby DNAme data can be used to impute information about phenotypic variables such as gestational age, sex, cell composition, and ancestry. These epiphenotypes offer avenues to compare phenotypic data across cohorts, and to understand how phenotypic variables relate to DNAme variability. However, the relationships between placental epiphenotyping variables and other technical and biological variables, and their application to downstream epigenome analyses, have not been well studied. RESULTS: Using DNAme data from 204 placentas across three cohorts, we applied the PlaNET R package to estimate epiphenotypes gestational age, ancestry, and cell composition in these samples. PlaNET ancestry estimates were highly correlated with independent polymorphic ancestry-informative markers, and epigenetic gestational age, on average, was estimated within 4 days of reported gestational age, underscoring the accuracy of these tools. Cell composition estimates varied both within and between cohorts, as well as over very long placental processing times. Interestingly, the ratio of cytotrophoblast to syncytiotrophoblast proportion decreased with increasing gestational age, and differed slightly by both maternal ethnicity (lower in white vs. non-white) and genetic ancestry (lower in higher probability European ancestry). The cohort of origin and cytotrophoblast proportion were the largest drivers of DNAme variation in this dataset, based on their associations with the first principal component. CONCLUSIONS: This work confirms that cohort, array (technical) batch, cell type proportion, self-reported ethnicity, genetic ancestry, and biological sex are important variables to consider in any analyses of Illumina DNAme data. We further demonstrate the specific utility of epiphenotyping tools developed for use with placental DNAme data, and show that these variables (i) provide an independent check of clinically obtained data and (ii) provide a robust approach to compare variables across different datasets. Finally, we present a general framework for the processing and analysis of placental DNAme data, integrating the epiphenotype variables discussed here.

Coherent Control of Trapped-Ion Qubits with Localized Electric Fields.

We present a new method for coherent control of trapped ion qubits in separate interaction regions of a multizone trap by simultaneously applying an electric field and a spin-dependent gradient. Both the phase and amplitude of the effective single-qubit rotation depend on the electric field, which can be localized to each zone. We demonstrate this interaction on a single ion using both laser-based and magnetic-field gradients in a surface-electrode ion trap, and measure the localization of the electric field.

Cumulative effects of pre-pandemic vulnerabilities and pandemic-related hardship on psychological distress among pregnant individuals.

OBJECTIVE: Our primary objective was to determine whether pre-existing vulnerabilities and resilience factors combined with objective hardship resulted in cumulative (i.e., additive) effects on psychological distress in pregnant individuals during the COVID-19 pandemic. A secondary objective was to determine whether any of the effects of pandemic-related hardship were compounded (i.e., multiplicative) by pre-existing vulnerabilities. METHOD: Data are from a prospective pregnancy cohort study, the Pregnancy During the COVID-19 Pandemic study (PdP). This cross-sectional report is based upon the initial survey collected at recruitment between April 5, 2020 and April 30, 2021. Logistic regressions were used to evaluate our objectives. RESULTS: Pandemic-related hardship substantially increased the odds of scoring above the clinical cut-off on measures of anxiety and depression symptoms. Pre-existing vulnerabilities had cumulative (i.e., additive) effects on the odds of scoring above the clinical cut-off on measures of anxiety and depression symptoms. There was no evidence of compounding (i.e., multiplicative) effects. Social support had a protective effect on anxiety and depression symptoms, but government financial aid did not. CONCLUSION: Pre-pandemic vulnerability and pandemic-related hardship had cumulative effects on psychological distress during the COVID-19 pandemic. Adequate and equitable responses to pandemics and disasters may require more intensive supports for those with multiple vulnerabilities.

The Impact of SARS-COV-2 on two Colorectal Cancer screening centres.

BowelScreen paused activity in March 2020 to prioritise the response to the COVID-19 pandemic. The aim of this study was to examine the impact of this delay. Cases affected by the pause and subsequently completed were compared to the same period in 2019. Endoscopy and histology data were obtained from the BowelScreen database and patient records. One-hundred and seven colonoscopies were performed during the study period. This compared with 224 colonoscopies during the same period in 2019. Median lead time to colonoscopy in 2020 was 74 days compared to 34 days in 2019. Adenoma detection rate was 59% for both periods. Advanced adenoma and cancer detection rates were similar in both periods. While there was a marked reduction in activity and significant delays for BowelScreen patients during the first wave of the COVID-19 pandemic, this does not appear to have impacted on clinical outcomes for patients who attended for screening colonoscopy.

Can retrospectively fusing SPECT to CT images reduce radiation doses in myocardial perfusion imaging?

INTRODUCTION: To establish if the CT dataset acquired during the stress element of myocardial perfusion imaging can be fused to the subsequent rest scan to reduce radiation doses from these procedures. METHODS: 86 rest scans were processed and evaluated using a self-designed project specific tool. Recording processing time, the time between the two data sets selected for fusion and assessing radiographic reports to ensure produced images were of diagnostic quality. RESULTS: 70% of fused scans were acquired 6-7 days apart; the mean (SD) processing time was calculated as 2.03 (0.36) minutes. The Pearson's correlation between these two variables was determined to be 0.22, showing a slight positive correlation although not statistically significant. 100% of the images produced were of diagnostic quality. CONCLUSION: Rest scans can be fused to a previously acquired CT, careful consideration should be given when positioning the patient and to the time interval between acquiring the two data sets, departmental guidelines can assist with this. Staff training may also be beneficial to ensure staff can assess if data sets are fusible prior to completing a scan. IMPLICATIONS FOR PRACTICE: This data provides evidence that retrospective fusion can reduce patient radiation doses in myocardial perfusion imaging without compromising diagnostic outcomes. Dose optimisation is an essential part of the ionising radiation (medical exposure) regulations therefore retrospective fusion should be considered in practice to ensure departmental compliance, although it is noteworthy this study is solely based in a single centred one camera department.

High throughput analysis of MHC class I and class II diversity of Zambian indigenous cattle populations.

The classical MHC class I and class II molecules play key roles in determining the antigenic-specificity of CD8+ and CD4+ T-cell responses-as such characterisation of the repertoire of MHCI and MHCII allelic diversity is fundamental to our ability to understand, and potentially, exploit how genetic diversity influences the outcome of immune responses. Cattle remain one of the most economically livestock species, with particular importance to many small-holder farmers in low-and-middle income countries (LMICs). However, our knowledge of MHC (BoLA) diversity in the indigenous breeds that form the mainstay of cattle populations in many LMICs remains very limited. In this study we develop a MiSeq-based platform to enable the rapid analysis of BoLA-DQA and BoLA-DQB, and combine this with similar platforms to analyse BoLA-I and BoLA-DRB repertoires, to study a large cohort of cattle (~800 animals) representing the 3 major indigenous breeds (Angoni, Barotse, Tonga) in Zambia. The data presented confirms the capacity of this high-throughput and high-resolution approach to provide a full characterisation of the MHCI-MHCII genotypes of cattle for which little previous MHC sequence data has been obtained. The cattle in Zambia were found to express a diverse range of MHCI, MHCII and extended MHCI-MHCII haplotypes. The combined MHCI-MHCII genotyping now possible opens new opportunities to rapidly expand our knowledge of MHC diversity in cattle that could find applications in a related translational disciplines such as vaccine development.

Discovery of endogenous nitroxyl as a new redox player in Arabidopsis thaliana.

Nitroxyl (HNO) is the one-electron reduced and protonated congener of nitric oxide (•NO), owning a distinct chemical profile. Based on real-time detection, we demonstrate that HNO is endogenously formed in Arabidopsis. Senescence and hypoxia induce shifts in the redox balance, triggering HNO decay or formation mediated by non-enzymatic •NO/HNO interconversion with cellular reductants. The stimuli-dependent HNO generation supports or competes with •NO signalling, depending on the local redox environment.

Surface waves and crustal structure on Mars.

We detected surface waves from two meteorite impacts on Mars. By measuring group velocity dispersion along the impact-lander path, we obtained a direct constraint on crustal structure away from the InSight lander. The crust north of the equatorial dichotomy had a shear wave velocity of approximately 3.2 kilometers per second in the 5- to 30-kilometer depth range, with little depth variation. This implies a higher crustal density than inferred beneath the lander, suggesting either compositional differences or reduced porosity in the volcanic areas traversed by the surface waves. The lower velocities and the crustal layering observed beneath the landing site down to a 10-kilometer depth are not a global feature. Structural variations revealed by surface waves hold implications for models of the formation and thickness of the martian crust.

Prevalence and Molecular Identification of Schistosoma haematobium among Children in Lusaka and Siavonga Districts, Zambia.

Schistosomiasis remains a public health concern in Zambia. Urinary schistosomiasis caused by Schistosoma haematobium is the most widely distributed infection. The aim of the current study was to determine the prevalence and risk factors of urinary schistosomiasis and identify the strain of S. haematobium among children in the Siavonga and Lusaka districts in Zambia. Urine samples were collected from 421 primary school children and S. haematobium eggs were examined under light microscopy. A semi-structured questionnaire was used to obtain information on the socio-demographic characteristics and the potential risk factors for urinary schistosomiasis. DNA of the parasite eggs was extracted from urine samples and the internal transcribed spacer gene was amplified, sequenced and phylogenetically analysed. The overall prevalence of S. haematobium was 9.7% (41/421) (95% CI: 7.16-13.08), male participants made up 6.2% (26/232) (95% CI: 4.15-9.03), having a higher burden of disease than female participants who made up 3.5% (15/421) (95% CI: 2.01-5.94). The age group of 11-15 years had the highest overall prevalence of 8.3% (35/421) (5.94-11.48). Participants that did not go fishing were 0.008 times less likely to be positive for schistosomiasis while participants whose urine was blood-tinged or cloudy on physical examination and those that lived close to water bodies were 9.98 and 11.66 times more likely to test positive for schistosomiasis, respectively. A phylogenetic tree analysis indicated that S. haematobium isolates were closely related to pure S. haematobium from Zimbabwe and hybrids of S. haematobium × S. bovis from Benin, Senegal and Malawi. The current study shows that urinary schistosomiasis is endemic in the study areas and is associated with water contact, and S. haematobium isolated is closely related to hybrids of S. bovis × S. haematobium strain, indicating the zoonotic potential of this parasite.

Characterization of colonization kinetics and virulence potential of Salmonella Enteritidis in chickens by photonic detection.

The light emitting module lux operon (luxCDABE) of Photorhabdus luminescens can be integrated into a "dark" bacterium for expression under a suitable promoter. The technique has been used to monitor kinetics of infection, e.g., by studying gene expression in Salmonella using mouse models in vivo and ex vivo. Here, we applied the bioluminescence imaging (BLI) technique to track Salmonella Enteritidis (SEn) strains carrying the lux operon expressed under a constitutive promoter sequence (sigma 70) in chicken after oral challenge. Detectable photon signals were localized in the crop, small intestine, cecum, and yolk sac in orally gavaged birds. The level of colonization was determined by quantification of signal intensity and SEn prevalence in the cecum and yolk sac. Furthermore, an isogenic SEn mutant strain tagged with the lux operon allowed for us to assess virulence determinants regarding their role in colonization of the cecum and yolk sac. Interestingly, mutations of SPI-1(Salmonella Pathogenicity Island 1) and fur (ferric uptake regulator) showed significantly decreased colonization in yolk sac that was correlated with the BLI data. A similar trend was detected in a ΔtonB strain by analyzing enrichment culture data. The inherently low quantum yield, light scattering, and absorption by tissues did not facilitate detection of signals from live birds. However, the detection limit of lux operon has the potential to be improved by resonance energy transfer to a secondary molecule. As a proof-of-concept, we were able to show that sensitization of a fluorescent-bound molecule known as the lumazine protein (LumP) improved the limit of detection to a certain extent.

Para-Substituted O-Benzyl Sulfohydroxamic Acid Derivatives as Redox-Triggered Nitroxyl (HNO) Sources.

Nitroxyl shows a unique biological profile compared to the gasotransmitters nitric oxide and hydrogen sulfide. Nitroxyl reacts with thiols as an electrophile, and this redox chemistry mediates much of its biological chemistry. This reactivity necessitates the use of donors to study nitroxyl's chemistry and biology. The preparation and evaluation of a small library of new redox-triggered nitroxyl sources is described. The condensation of sulfonyl chlorides and properly substituted O-benzyl hydroxylamines produced O-benzyl-substituted sulfohydroxamic acid derivatives with a 27-79% yield and with good purity. These compounds were designed to produce nitroxyl through a 1, 6 elimination upon oxidation or reduction via a Piloty's acid derivative. Gas chromatographic headspace analysis of nitrous oxide, the dimerization and dehydration product of nitroxyl, provides evidence for nitroxyl formation. The reduction of derivatives containing nitro and azide groups generated nitrous oxide with a 25-92% yield, providing evidence of nitroxyl formation. The oxidation of a boronate-containing derivative produced nitrous oxide with a 23% yield. These results support the proposed mechanism of nitroxyl formation upon reduction/oxidation via a 1, 6 elimination and Piloty's acid. These compounds hold promise as tools for understanding nitroxyl's role in redox biology.

Oxford Nanopore Sequencing Reveals an Exotic Broad bean mottle virus Genome within Australian Grains Post-Entry Quarantine.

A Broad bean mottle virus (BBMV) isolate (S52) obtained from an infected Vicia faba leaf sample from Syria was sequenced using Oxford Nanopore long-read sequencing at the Australian border. The genome had 95.6%, 98.2%, and 93.4% nucleotide sequence identity to BBMV strains RNA1 (Bawden), RNA2 (Mo), and RNA3 (Bawden).

High Affinity Iron Acquisition Systems Facilitate but Are Not Essential for Colonization of Chickens by Salmonella Enteritidis.

The roles of TonB mediated Fe3+ (ferric iron) uptake via enterobactin (involving biosynthesis genes entABCDEF) and Fe2+ (ferrous iron) uptake through the FeoABC transporter are poorly defined in the context of chicken-Salmonella interactions. Both uptake systems are believed to be the major contributors of iron supply in the Salmonella life cycle. Current evidence suggests that these iron uptake systems play a major role in pathogenesis in mammals and as such, they represent promising antibacterial targets with therapeutic potential. We investigated the role of these iron uptake mechanisms regarding the ability of Salmonella Enteritidis (SEn) strains to colonize in a chicken infection model. Further we constructed a bioluminescent reporter to sense iron limitation during gastrointestinal colonization of Salmonella in chicken via ex vivo imaging. Our data indicated that there is some redundancy between the ferric and ferrous iron uptake mechanisms regarding iron acquisition during SEn pathogenesis in chicken. We believe that this redundancy of iron acquisition in the host reservoir may be the consequence of adaptation to unique avian environments, and thus warrants further investigation. To our knowledge, this the first report providing direct evidence that both enterobactin synthesis and FeoABC mediated iron uptake contribute to the virulence of SEn in chickens.

Autochthonous Leishmania infantum in Dogs, Zambia, 2021.

Leishmaniases are neglected tropical diseases of humans and animals. We detected Leishmania infantum in 3 mixed-breed dogs in Zambia that had no travel history outside the country. Our findings suggest presence of and probable emergence of leishmaniasis in Zambia, indicating the need for physicians and veterinarians to consider the disease during diagnosis.

Connecting the food and agriculture sector to nutrition interventions for improved health outcomes.

To achieve the Sustainable Development Goal of zero hunger, multi-sectoral strategies to improve nutrition are necessary. Building towards this goal, the food and agriculture sector must be considered when designing nutritional interventions. Nevertheless, most frameworks designed to guide nutritional interventions do not adequately capture opportunities for integrating nutrition interventions within the food and agriculture sector. This paper aims to highlight how deeply connected the food and agriculture sector is to underlying causes of malnutrition and identify opportunities to better integrate the food and agriculture sector and nutrition in low and middle income countries. In particular, this paper: (1) expands on the UNICEF conceptual framework for undernutrition to integrate the food and agriculture sector and nutrition outcomes, (2) identifies how nutritional outcomes and agriculture are linked in six important ways by defining evidence-based food and agriculture system components within these pathways: as a source of food, as a source of income, through food prices, women's empowerment, women's utilization of time, and women's health and nutritional status, and (3) shows that the food and agriculture sector facilitates interventions through production, processing and consumption, as well as through farmer practices and behavior. Current frameworks used to guide nutrition interventions are designed from a health sector paradigm, leaving agricultural aspects not sufficiently leveraged. This paper concludes by proposing intervention opportunities to rectify the missed opportunities generated by this approach. Program design should consider the ways that the food and agriculture sector is linked to other critical sectors to comprehensively address malnutrition. This framework is designed to help the user to begin to identify intervention sites that may be considered when planning and implementing multi-sectoral nutrition programs. Supplementary Information: The online version contains supplementary material available at 10.1007/s12571-022-01262-3.

Articular spacers in two-stage revision arthroplasty for prosthetic joint infection of the hip and the knee.

Use of articular antibiotic-eluting cement spacers during two-stage revision arthroplasty for prosthetic joint infection (PJI) is a long-established and proven adjunctive technique during first-stage surgery. Articular spacers come in many forms, either static or dynamic. The authors present an instructional review of current evidence regarding their use. A total of 45 studies (for spacer use in PJI involving either hip or knee) were analysed for data regarding eradication rate, functional outcomes, mechanical complications and the impact on second-stage surgery. A large number of case series and retrospective cohort studies were retrieved, with only a small number of prospective studies (2). High levels of infection eradication were commonly reported (>80%). Outcome scores were commonly reported as indicating good-to-excellent function and pain levels. Second-stage procedures were often not required when dynamic spacers were used. Static spacers were associated with more mechanical complications in both the hip and the knee. In the hip, dynamic spacers were more commonly associated with instability compared to static spacers. Consideration should be given to the use of dual-mobility or constrained definitive acetabular components in these cases at second-stage surgery. The use of antibiotic-eluting polymethylmethacrylate articular spacers in two-stage revision for PJI of hip and knee arthroplasty achieves a high rate of infection eradication. Dynamic spacers may confer a variety of benefits compared to static spacers, with a similar rate of infection eradication.

Oxidative degradation of triblock-copolymer surfactant and its effects on self-assembly.

We investigate the degradation behaviour of a triblock-copolymer surfactant made from polyethylene oxide (PEO) and polypropylene oxide (PPO) (PEO-PPO-PEO), highlighting how the aggregation behaviour of this polymer in water alters with ageing. Samples aged at room temperature were compared to samples degraded using accelerated ageing at elevated temperatures. We find that large mass losses occurred to the polymer surfactant which resulted in a change in the aggregation behaviour, with larger, rod-like or planar aggregates forming at longer degradation times. We look at how this change in aggregation behaviour changes the formulation stability of these polymers, specifically, the interaction of the polymer surfactant with poly(N-isopropylacrylamide) microgels. It is known that these species associate and form gels at elevated temperatures. This paper highlights how commonly used polymeric surfactants can degrade over time, resulting in dramatic changes to aggregation behaviour and therefore, formulation properties.

Outpatient ureteric stent removal following kidney transplantation.

During a kidney transplant, a plastic tube (stent) is placed in the ureter, connecting the new kidney to the bladder, in order to keep the new join open during the initial phase of transplantation. The stent is then removed after a few weeks via a camera procedure (cystoscopy), as it is no longer needed. The present study compared performing this in the operating theatre or in clinic for transplanted patients using a new single-use type of camera with an integrated grasper system. The results have shown that it is safe and cost-effective to do this in clinic, despite patients being susceptible to infection after transplantation.