Prevalence of mutations in common tumour types in Northern England and comparable utility of national and international Trial Finders.

PURPOSE: Tumour genomic profiling is of increasing importance in early phase trials to match patients to targeted therapeutics. Mutations vary by demographic group; however, regional differences are not characterised. This was investigated by comparing mutation prevalence for common cancers presenting to Newcastle Experimental Cancer Medicine Centre (ECMC) to The Cancer Genome Atlas (TCGA) and utility of trial matching modalities. METHODS: Detailed clinicogenomic data were obtained for patients presenting September 2017-December 2020. Prevalence of mutations in lung, colorectal, breast and prostate cancer was compared to TCGA GDC Data Portal. Experimental Cancer (EC) Trial Finder utility in matching trials was compared to a Molecular Tumour Board (MTB) and commercial sequencing reports. RESULTS: Of 311 patients with advanced cancer, this consisted of lung (n = 131, 42.1%), colorectal (n = 44, 14.1%), breast (n = 36, 11.6%) and prostate (n = 18, 5.6%). More than one mutation was identified in the majority (n = 260, 84%). Significant prevalence differences compared to TCGA were identified, including a high prevalence of EGFR in lung (P = 0.001); RB1 in breast (P = 0.0002); and multiple mutations in prostate cancer. EC Trial Finder demonstrated significantly different utility than sequencing reports in identifying trials (P = 0.007). CONCLUSIONS: Regional differences in mutations may exist with advanced stage accounting for prevalence of specific mutations. A national Trial Finder shows utility in finding targeted trials whilst commercial sequencing reports may over-report 'actionable' mutations. Understanding local prevalence and trial availability could increase enrolment onto matched early phase trials.

Excess mortality in Glasgow: further evidence of 'political effects' on population health.

OBJECTIVES: The aim of the study was to update previous analyses of 'excess mortality' in Glasgow (Scotland) relative to the similar postindustrial cities of Liverpool and Manchester (England). The excess is defined as mortality after adjustment for socio-economic deprivation; thus, we sought to compare changes over time in both the deprivation profiles of the cities and the levels of deprivation-adjusted mortality in Glasgow relative to the other cities. This is important not only because the original analyses are now increasingly out of date but also because since publication, important (prepandemic) changes to mortality trends have been observed across all parts of the United Kingdom. STUDY DESIGN AND METHODS: Replicating as far as possible the methods of the original study, we developed a three-city deprivation index based on the creation of spatial units in Glasgow that were of similar size to those in Liverpool and Manchester (average population sizes of approximately 1600, 1500 and 1700 respectively) and an area-based measure of 'employment deprivation'. Mortality and matching population data by age, sex and small area were obtained from national agencies for two periods: 2003-2007 (the period covered by the original study) and 2014-2018. The rates of employment deprivation for each city's small areas were calculated for both periods. Indirectly standardised mortality ratios (SMRs) were calculated for Glasgow relative to Liverpool and Manchester, standardised by age and three-city deprivation decile. For context, city-level trends in age-standardised mortality rates by year, sex and city were also calculated. RESULTS: There was evidence of a stalling of improvement in mortality rates in all three cities from the early 2010s. After adjustment for area deprivation, all-cause mortality in Glasgow in 2014-2018 was c.12% higher than in Liverpool and Manchester for all ages (SMR 112.4, 95% CI 111.1-113.6) and c.17% higher for deaths under 65 years (SMR 117.1, 95% CI 114.5-119.7). The excess was higher for males (17% compared with 9% for deaths at all ages; 25% compared with 5% for 0-64 years) and for particular causes of death such as suicide and drug-related and alcohol-related causes. The results were broadly similar to those previously described for 2003-2007, although the excess for premature mortality was notably lower. In part, this was explained by changes in levels of employment deprivation, which had decreased to a greater degree in the English cities: this was particularly true of Manchester (a reduction of -43%, compared with -38% in Liverpool and -31% in Glasgow) where the overall population size had also increased to a much greater extent than in the other cities. CONCLUSIONS: High levels of excess mortality persist in Glasgow. With the political causes recently established - the excess is a 'political effect', not a 'Glasgow effect' - political solutions are required. Thus, previously published recommendations aimed at addressing poverty, inequality and vulnerability in the city are still highly relevant. However, given the evidence of more recent, UK-wide, political effects on mortality - widening mortality inequalities resulting from UK Government 'austerity' measures - additional policies at UK Government level to protect, and restore, the income of the poorest in society are also urgently needed.

Development of Multiwell-Plate Methods Using Pure Cultures of Methanogens To Identify New Inhibitors for Suppressing Ruminant Methane Emissions.

Hydrogenotrophic methanogens typically require strictly anaerobic culturing conditions in glass tubes with overpressures of H2 and CO2 that are both time-consuming and costly. To increase the throughput for screening chemical compound libraries, 96-well microtiter plate methods for the growth of a marine (environmental) methanogen Methanococcus maripaludis strain S2 and the rumen methanogen Methanobrevibacter species AbM4 were developed. A number of key parameters (inoculum size, reducing agents for medium preparation, assay duration, inhibitor solvents, and culture volume) were optimized to achieve robust and reproducible growth in a high-throughput microtiter plate format. The method was validated using published methanogen inhibitors and statistically assessed for sensitivity and reproducibility. The Sigma-Aldrich LOPAC library containing 1,280 pharmacologically active compounds and an in-house natural product library (120 compounds) were screened against M. maripaludis as a proof of utility. This screen identified a number of bioactive compounds, and MIC values were confirmed for some of them against M. maripaludis and M. AbM4. The developed method provides a significant increase in throughput for screening compound libraries and can now be used to screen larger compound libraries to discover novel methanogen-specific inhibitors for the mitigation of ruminant methane emissions.IMPORTANCE Methane emissions from ruminants are a significant contributor to global greenhouse gas emissions, and new technologies are required to control emissions in the agriculture technology (agritech) sector. The discovery of small-molecule inhibitors of methanogens using high-throughput phenotypic (growth) screening against compound libraries (synthetic and natural products) is an attractive avenue. However, phenotypic inhibitor screening is currently hindered by our inability to grow methanogens in a high-throughput format. We have developed, optimized, and validated a high-throughput 96-well microtiter plate assay for growing environmental and rumen methanogens. Using this platform, we identified several new inhibitors of methanogen growth, demonstrating the utility of this approach to fast track the development of methanogen-specific inhibitors for controlling ruminant methane emissions.

A Toll-like receptor-1 variant and its characteristic cellular phenotype is associated with severe malaria in Papua New Guinean children.

Genetic factors are likely to contribute to low severe malaria case fatality rates in Melanesian populations, but association studies can be underpowered and may not provide plausible mechanistic explanations if significant associations are detected. In preparation for a genome-wide association study, 29 candidate single-nucleotide polymorphisms (SNPs) with minor allele frequencies >5% were examined in a case-control study of 504 Papua New Guinean children with severe malaria. In parallel, an immunological substudy was performed on convalescent peripheral blood mononuclear cells (PBMCs) from cases and controls. Following stimulation with a Toll-like receptor (TLR) 1/2 agonist, effector cytokines and chemokines were assayed. The only significant genetic association observed involved a nonsynonymous SNP (TLR1rs4833095) in the TLR1 gene. A recessive (TT) genotype was associated with reduced odds of severe malaria of 0.52 (95% confidence interval (0.29-0.90), P=0.006). Concentrations of pro-inflammatory cytokines interleukin-1ß and tumour necrosis factor α were significantly higher in severe malaria cases compared with healthy controls, but lower in children with the protective recessive (TT) genotype. A genetic variant in TLR1 may contribute to the low severe malaria case fatality rates in this region through a reduced pro-inflammatory cellular phenotype.

Vulnerability to food insecurity in urban slums: experiences from Nairobi, Kenya.

Food and nutrition security is critical for economic development due to the role of nutrition in healthy growth and human capital development. Slum residents, already grossly affected by chronic poverty, are highly vulnerable to different forms of shocks, including those arising from political instability. This study describes the food security situation among slum residents in Nairobi, with specific focus on vulnerability associated with the 2007/2008 postelection crisis in Kenya. The study from which the data is drawn was nested within the Nairobi Urban Health and Demographic Surveillance System (NUHDSS), which follows about 70,000 individuals from close to 30,000 households in two slums in Nairobi, Kenya. The study triangulates data from qualitative and quantitative sources. It uses qualitative data from 10 focus group discussions with community members and 12 key-informant interviews with community opinion leaders conducted in November 2010, and quantitative data involving about 3,000 households randomly sampled from the NUHDSS database in three rounds of data collection between March 2011 and January 2012. Food security was defined using the Household Food Insecurity Access Scale (HFIAS) criteria. The study found high prevalence of food insecurity; 85% of the households were food insecure, with 50% being severely food insecure. Factors associated with food security include level of income, source of livelihood, household size, dependence ratio; illness, perceived insecurity and slum of residence. The qualitative narratives highlighted household vulnerability to food insecurity as commonplace but critical during times of crisis. Respondents indicated that residents in the slums generally eat for bare survival, with little concern for quality. The narratives described heightened vulnerability during the 2007/2008 postelection violence in Kenya in the perception of slum residents. Prices of staple foods like maize flour doubled and simultaneously household purchasing power was eroded due to worsened unemployment situation. The use of negative coping strategies to address food insecurity such as reducing the number of meals, reducing food variety and quality, scavenging, and eating street foods was prevalent. In conclusion, this study describes the deeply intertwined nature of chronic poverty and acute crisis, and the subsequent high levels of food insecurity in urban slum settings. Households are extremely vulnerable to food insecurity; the situation worsening during periods of crisis in the perception of slum residents, engendering frequent use of negative coping strategies. Effective response to addressing vulnerability to household food insecurity among the urban poor should focus on both the underlying vulnerabilities of households due to chronic poverty and added impacts of acute crises.

Malignant spinal cord compression: NICE guidance, improvements and challenges.

BACKGROUND AND AIM: Malignant spinal cord compression (mSCC) is one of the most serious complications of cancer. Recent NICE guidance has aimed to improve patient pathways and outcomes for patients with mSCC. We have examined the current presentations, management and outcomes for patients with mSCC in West London following the implementation of the NICE guidance. MATERIALS AND METHODS: The electronic records and clinical notes were reviewed for all patients assessed for confirmed or potential mSCC at Charing Cross Hospital in 2012. Details on the number of referrals, the proportion with confirmed mSCC, the cancer diagnosis, treatment and outcome were analysed. RESULTS: 191 patients were reviewed with 127 (66%) cases of confirmed mSCC. The commonest tumour types were prostate cancer (26 cases), lung cancer (26), breast cancer (21) and kidney cancer (15). 21% of the patients had no previous cancer diagnosis; mSCC was their presenting diagnostic event. Radiotherapy was the predominant management, 24% of the patients had first line surgical treatment. At presentation 62% of patients were either chair or bed bound. Treatment brought important mobility benefits to all patients groups with 20% of the initially chair or bed bound patients leaving the hospital with independent mobility. CONCLUSION: Enhanced patients pathways with ease of access, rapid assessment and prompt treatment can improve outcomes. Despite these pathways many patients still present with gross motor impairment and over 20% have no previous diagnosis of cancer. Ongoing work to maintain awareness for patients and primary care of the diagnosis and emergency pathways is essential to optimize outcomes.

Prospective evaluation of systolic arterial pressure control with a phenylephrine infusion regimen during spinal anaesthesia for caesarean section.

BACKGROUND: Hypotension and nausea occur frequently during spinal anaesthesia for caesarean section. The aim of this evaluation was to assess systolic arterial pressure control with our routine prophylactic intravenous phenylephrine infusion regimen. We audited a local standard for an incidence of hypotension of ≤ 25% during the first 15 min of anaesthesia. METHODS: One hundred healthy women undergoing elective caesarean section were assessed. Following intravenous preload with 10 mL/kg Hartmann's solution, 0.5% hyperbaric bupivacaine 2.8 mL combined with diamorphine 400 µg was given intrathecally in the sitting position. Intravenous phenylephrine was then started at 67 µg/min (the maximum rate). Systolic arterial pressure was recorded every 2 min. The infusion was titrated, according to local guidelines, to maintain systolic arterial pressure close to baseline. RESULTS: The median dose of phenylephrine given by infusion was 1000 [interquartile range 670-1000]µg, with 51 patients not requiring any change to the infusion rate. Eleven patients (11%, 95% CI 6-19) developed hypotension, defined as a systolic arterial pressure <80% of baseline. A further four patients were given a bolus of phenylephrine for suspected hypotension. The incidence of hypotension or suspected hypotension was therefore 15% (95% CI 9-24). Thirteen patients (13%, 95% CI 7-21) developed nausea. No patient vomited. CONCLUSIONS: Our routine phenylephrine infusion regimen was effective at minimizing hypotension and nausea during relatively high-dose spinal anaesthesia. This was achieved with a low intervention rate, in conjunction with a 2-min rather than a 1-min non-invasive blood pressure cycle time and a relatively low volume of intravenous fluid.

Distinct distribution of killer-cell immunoglobulin-like receptor genes in the Mugil and Ilaita areas of Papua New Guinea.

The frequency of the killer-cell immunoglobulin-like receptor (KIR) genes and transmembrane alleles of KIR2DL4 were studied in coastal (Mugil community) and inland (Ilaita community) communities in Papua New Guinea. Linkage disequilibria between KIR genes and between alleles of KIR2DL4 and the KIR genes were similar to those found in other populations suggesting conservation of the usual gene order in Papua New Guinean haplotypes. Significant differences in the frequency of KIR genes were found between the two populations despite being separated by only 300 km. Examples of individuals who lacked the KIR2DL4 gene and others whose KIR2DL4 allele appeared to have 11 adenines in the polyadenine tract in exon 6 were identified. A relatively low frequency of the KIR A haplotype was found in both populations and particularly in the inland community. The KIR gene frequencies were consistent with the inland Ilaita community being closely related to Australian Aborigines and southern Indians, whereas the KIR gene frequencies of the coastal Mugil community appeared to have been influenced either by recent or ancient admixture from populations with a higher frequency of the KIR A haplotype.

Robert Koch redux: malaria immunology in Papua New Guinea.

Over a century ago, the malaria expedition of the brilliant microbiologist Robert Koch to the Dutch East Indies (Indonesia) and German New Guinea (now Papua New Guinea, or PNG), resulted in profound observations that are still central to our current understanding of the epidemiology and acquisition of immunity to the malaria parasite Plasmodium. The tradition of malaria research in PNG pioneered by Koch continues to this day, with a number of recent studies still continuing to elucidate his original concepts and hypotheses. These include age and exposure-related acquisition of immunity, species-specific and cross-species immunity, correlates of protective immunity and determining the prospects for anti-malaria vaccines.

Regulating immunity to malaria.

The optimal outcome of a malaria infection is that parasitized cells are killed and degraded without inducing significant pathology. Since much of the pathology of malaria infection can be immune-mediated, this implies that immune responses have to be carefully regulated. The mechanisms by which anti-malarial immune responses are believed to be regulated were discussed at the recent Malaria Immunology Workshop (Bloomberg School of Public Health, Johns Hopkins University, Baltimore, Maryland, USA; February 2005). Potential regulatory mechanisms include regulatory T cells, which have been shown to significantly modify cellular immune responses to various protozoan infections, including leishmania and malaria; neutralising antibodies to pro-inflammatory malarial toxins such as glycosylphosphatidylinositol and haemozoin; and self-regulating networks of effector molecules. Innate and adaptive immune responses are further moderated by the broader immunological environment, which is influenced by both the genetic background of the host and by co-infection with other pathogens. A detailed understanding of the interplay between these different immunoregulatory processes may facilitate the rationale design of vaccines and novel therapeutics.

Successful defibrillation in water: a preliminary study.

Mild hypothermia (32-34 deg C) treatment alleviates vital organ damage after cardiac arrest. A new cooling device, the Thermosuit operates by applying of a thin layer of water directly to the body surface. Hypothermic patients may experience sequential fibrillation. Therefore, we examined whether defibrillation could be administered safely and effectively in water. A 35 kg swine was anesthetized and placed inside the Thermosuit system. This consists of a water containing surround and pumping system. Conventional AED disposable defibrillation electrodes were applied to the animal's chest. Fibrillation was created by applying a 50-volt signal to a pacing wire introduced into the heart. Following a 30-second period of fibrillation, defibrillation was attempted using Medtronic AED 1000 defibrillator. Defibrillation voltage and current were measured. There were three test cases: dry in the system, wet in the functioning system, and damp. Cooling water in the system was contaminated with saline to simulate potential conditions in clinical application. In each fibrillation-defibrillation sequence, the heart was restarted successfully; this required less than 220 joules. Only a small difference was measured in the overall defibrillation voltage and current as applied to the electrodes for the different cases. Thus, underwater defibrillation is safe and can be performed effectively.

Stimulation of innate immune responses by malarial glycosylphosphatidylinositol via pattern recognition receptors.

The glycosylphosphatidylinositol (GPI) anchor of Plasmodium falciparum is thought to function as a critical toxin that contributes to severe malarial pathogenesis by eliciting the production of proinflammatory responses by the innate immune system of mammalian hosts. Analysis of the fine structure of P. falciparum GPI suggests a requirement for the presence of both core glycan and lipid moieties in the recognition and signalling of parasite glycolipids by host immune cells. It has been demonstrated that GPI anchors of various parasitic protozoa can mediate cellular immune responses via members of the Toll-like family of pattern recognition receptors (TLRs). Recent studies indicate that GPI anchors of P. falciparum and other protozoa are preferentially recognized by TLR-2, involving the MyD88-dependent activation of specific signalling pathways that mediate the production of proinflammatory cytokines and nitric oxide from host macrophages in vitro. However, the contribution of malaria GPI toxin to severe disease syndromes and the role of specific TLRs or other pattern recognition receptors in innate immunity in vivo is only just beginning to be characterized. A better understanding of the molecular mechanisms underlying severe malarial pathogenesis may yet lead to substantial new insights with important implications for the development of novel therapeutics for malaria treatment.

Immediate post-dosing paralysis following severe soman and VX toxicosis in guinea pigs.

There have been numerous studies of the central nervous system (CNS) involvement in organophosphate (OP) poisoning showing status epilepticus and/or 'electrographic seizures'. Brain damage has been demonstrated as 'neuronal necrosis' primarily in the cortex, thalamus and hippocampus. To the authors' knowledge there have been no reports of partial/total paralysis following close upon OP exposure although delayed paralysis has been reported. This report summarizes the immediate, OP induced paralytic events recorded in guinea pigs during development of the Canadian reactive skin decontaminant lotion (RSDL). As part of the development work, supra-lethal cutaneous doses of OP were applied to large numbers of guinea pigs followed by decontamination with the RSDL or predecessor lotions and solvents. Soman (pinacolyl methylphosphonofluoridate; GD) challenges were applied to 1277 animals and S-(2-diisopropyl-aminoethyl) methylphosphorothiolate (VX) challenges to 108. The classic sequence of clinical signs--ptyalism, tremors, fasciculations, convulsions, apnea and flaccid paralysis before death--was seen in the 658 animals that died and in many of the survivors. Eighty-four of 688 survivors of GD and 4 of 39 survivors of VX showed random paralysis of various distal regions following recovery from an insult which produced convulsions and/or flaccid paralysis. Because the experiments were designed to assess the decontamination procedures, there were no apparent relationships between the amounts of OP applied and the sequellae recorded. The observations of paralysis were also incidental to the prime focus of the experiments. Because of this, only ten animals paralysed following GD exposure were examined for histological effects. The pathologist diagnosed 'encephalomalacia' and 'focal necrotic lesions' in the cerebral cortex and 'focal necrotic lesions' in one spinal cord. Of the 84 guinea pigs paralysed after GD challenge, one was not decontaminated and the decontaminants used on the remainder were sufficiently varied that there appeared to be no relationship between the type of decontaminant and the resulting paralysis.

Drugs and syringe drivers: a survey of adult specialist palliative care practice in the United Kingdom and Eire.

Subcutaneous delivery of drugs using a syringe driver is common practice within specialist palliative care units. There is, however, little documented information regarding clinical practice. A survey performed in 1992 reported that at least 28 drugs were used in combination with others in a single syringe driver. The aim of the present study was to reassess practice in this field and to enquire more specifically about newer drugs. Postal questionnaires were sent to all adult specialist palliative care in-patient units in the UK and Eire (n = 208). One hundred and sixty-five units (79%) responded. The most common syringe driver in use was the Graseby 26 (61% of responding units). Most units delivered the contents of the syringe over 24 h, and water was usually used as the diluent in 90% of cases. The maximum number of drugs that respondents were prepared to mix in a single syringe was usually three (51%) or four (35%). In the UK, all units used diamorphine in doses from 2.5 mg/24 h upwards. All respondents also used haloperidol, in doses from 0.5 to 60 mg/24 h. A total of 28 different drugs were used in syringe drivers. The most common combinations were diamorphine and midazolam (37%), diamorphine and levomepromazine (35%), diamorphine and haloperidol (33%), and diamorphine and cyclizine (31%). In conclusion, there is much in common with regard to the way in which drugs are delivered in syringe drivers. However, a wide variety of drugs and drug combinations are still in use.

In vivo uptake of radiolabeled antibody to proliferating smooth muscle cells in a swine model of coronary stent restenosis.

UNLABELLED: Z2D3 is a monoclonal chimeric antibody fragment that is directed against a protein expressed on the surface of proliferating smooth muscle cells. The purpose of this study was to investigate the uptake of 111In-labeled Z2D3 F(ab')2 in a swine model of coronary neointimal proliferation after overexpansion coronary stenting. METHODS: Twenty-two domestic swine underwent overexpansion coronary stenting of 2 vessels. Fifteen swine survived 2-4 wk, at which time they received an injection of 111In Z2D3 F(ab')2 and underwent planar imaging. After the swine were killed, the hearts were excised and imaged on the detector. The cross-sectional area of each stented vessel was measured with digital morphometry. RESULTS: Pathology could be correlated with imaging for 24 vessels. The cross-sectional area of stenosis comprising neointimal proliferation ranged from 8% to 95%, with a mean +/- SD of 41% +/- 21%. The maximal stenosis ranged from 13% to 95%, with a mean of 51% +/- 20%. Seventeen of 24 vessels (71%) showed focal uptake on in vivo imaging, and 7 of 24 (29%) did not. Twenty of 24 (83%) showed uptake on ex vivo imaging. Of 11 stented vessels with maximal vessel stenosis less than 50%, 7 (64%) showed uptake both in vivo and ex vivo, and of 13 stented vessels with maximal vessel stenosis greater than 50%, 10 (77%) showed uptake both in vivo and ex vivo. CONCLUSION: Uptake of a radiolabeled antibody directed against a component of proliferating neointimal tissue can be visualized in the coronary arteries on in vivo imaging using a scintillation gamma camera.

Pathogenesis of malaria.

As the mortality rate of 20-30% for severe falciparum malaria under even the best clinical conditions testifies, access to antimalarial drugs is not sufficient to prevent an appreciable mortality from this disease. Understanding the cause of death at a cellular level is essential if additional rational treatments are to be developed. Here, Ian Clark and Louis Schofield discuss recent work presented at the Molecular Approaches to Malaria conference, Lorne, Australia, 2-5 February 2000, that updates the cytokine-based concept of malarial disease.

Myocardial uptake of a (99m)Tc-nitroheterocycle in a swine model of occlusion and reperfusion.

UNLABELLED: The purpose of this study was to evaluate the window for scan positivity of the radiolabeled nitroheterocycle (99m)Tc-BRU-59-21 in the peri-ischemic period using a swine model of occlusion and reperfusion. METHODS: A balloon catheter was placed in the left anterior descending coronary artery in each of 19 domestic swine. Blood flow and hemodynamic measurements were made at baseline, during occlusion, and at 15 and 180 min after reperfusion. A dose of approximately 925 MBq (99m)Tc-BRU-59-21 was injected before a brief (6 min) period of coronary occlusion at the following times: 15 min (n = 2), 5 min (n = 2), and 2.2 min (n = 5). In 5 experiments the dose was injected 15 min after reperfusion. Animals underwent SPECT imaging 3 h later. Animals were then killed, and hearts were removed, sliced, stained with triphenyl tetrazolium chloride, and imaged on the detector. RESULTS: The risk region became ischemic during occlusion on the basis of severe reduction in blood flow and lactate production, but necrosis occurred in only 3 experiments. Focal tracer uptake was seen in the risk region in animals injected 5 and 2.2 min before occlusion but not in animals injected 15 min before occlusion and 15 min after reperfusion. CONCLUSION: The window for scan positivity for (99m)Tc-BRU-59-21 injected in the peri-ischemic period is short using this model of balloon occlusion and reperfusion in swine.