Global isoform-specific transcript alterations and deregulated networks in clear cell renal cell carcinoma.

Extensive genome-wide analyses of deregulated gene expression have now been performed for many types of cancer. However, most studies have focused on deregulation at the gene-level, which may overlook the alterations of specific transcripts for a given gene. Clear cell renal cell carcinoma (ccRCC) is one of the best-characterized and most pervasive renal cancers, and ccRCCs are well-documented to have aberrant RNA processing. In the present study, we examine the extent of aberrant isoform-specific RNA expression by reporting a comprehensive transcript-level analysis, using the new kallisto-sleuth-RATs pipeline, investigating coding and non-coding differential transcript expression in ccRCC. We analyzed 50 ccRCC tumors and their matched normal samples from The Cancer Genome Altas datasets. We identified 7,339 differentially expressed transcripts and 94 genes exhibiting differential transcript isoform usage in ccRCC. Additionally, transcript-level coexpression network analyses identified vasculature development and the tricarboxylic acid cycle as the most significantly deregulated networks correlating with ccRCC progression. These analyses uncovered several uncharacterized transcripts, including lncRNAs FGD5-AS1 and AL035661.1, as potential regulators of the tricarboxylic acid cycle associated with ccRCC progression. As ccRCC still presents treatment challenges, our results provide a new resource of potential therapeutics targets and highlight the importance of exploring alternative methodologies in transcriptome-wide studies

A Microfluidic Platform for Precision Small-volume Sample Processing and Its Use to Size Separate Biological Particles with an Acoustic Microdevice.

A major advantage of microfluidic devices is the ability to manipulate small sample volumes, thus reducing reagent waste and preserving precious sample. However, to achieve robust sample manipulation it is necessary to address device integration with the macroscale environment. To realize repeatable, sensitive particle separation with microfluidic devices, this protocol presents a complete automated and integrated microfluidic platform that enables precise processing of 0.15-1.5 ml samples using microfluidic devices. Important aspects of this system include modular device layout and robust fixtures resulting in reliable and flexible world to chip connections, and fully-automated fluid handling which accomplishes closed-loop sample collection, system cleaning and priming steps to ensure repeatable operation. Different microfluidic devices can be used interchangeably with this architecture. Here we incorporate an acoustofluidic device, detail its characterization, performance optimization, and demonstrate its use for size-separation of biological samples. By using real-time feedback during separation experiments, sample collection is optimized to conserve and concentrate sample. Although requiring the integration of multiple pieces of equipment, advantages of this architecture include the ability to process unknown samples with no additional system optimization, ease of device replacement, and precise, robust sample processing

Malaria intervention scale-up in Africa : effectiveness predictions for health programme planning tools, based on dynamic transmission modelling

Scale-up of malaria prevention and treatment needs to continue to further important gains made in the past decade, but national strategies and budget allocations are not always evidence-based. Statistical models were developed summarizing dynamically simulated relations between increases in coverage and intervention impact, to inform a malaria module in the Spectrum health programme planning tool.; The dynamic Plasmodium falciparum transmission model OpenMalaria was used to simulate health effects of scale-up of insecticide-treated net (ITN) usage, indoor residual spraying (IRS), management of uncomplicated malaria cases (CM) and seasonal malaria chemoprophylaxis (SMC) over a 10-year horizon, over a range of settings with stable endemic malaria. Generalized linear regression models (GLMs) were used to summarize determinants of impact across a range of sub-Sahara African settings.; Selected (best) GLMs explained 94-97 % of variation in simulated post-intervention parasite infection prevalence, 86-97 % of variation in case incidence (three age groups, three 3-year horizons), and 74-95 % of variation in malaria mortality. For any given effective population coverage, CM and ITNs were predicted to avert most prevalent infections, cases and deaths, with lower impacts for IRS, and impacts of SMC limited to young children reached. Proportional impacts were larger at lower endemicity, and (except for SMC) largest in low-endemic settings with little seasonality. Incremental health impacts for a given coverage increase started to diminish noticeably at above ~40 % coverage, while in high-endemic settings, CM and ITNs acted in synergy by lowering endemicity. Vector control and CM, by reducing endemicity and acquired immunity, entail a partial rebound in malaria mortality among people above 5 years of age from around 5-7 years following scale-up. SMC does not reduce endemicity, but slightly shifts malaria to older ages by reducing immunity in child cohorts reached.; Health improvements following malaria intervention scale-up vary with endemicity, seasonality, age and time. Statistical models can emulate epidemiological dynamics and inform strategic planning and target setting for malaria control

Detection limits of organic compounds achievable with intense, short-pulse lasers

Many organic molecules have strong absorption bands which can be accessed by ultraviolet short pulse lasers to produce efficient ionization. This resonant multiphoton ionization scheme has already been exploited as an ionization source in time-of-flight mass spectrometers used for environmental trace analysis. In the present work we quantify the ultimate potential of this technique by measuring absolute ion yields produced from the interaction of 267 nm femtosecond laser pulses with the organic molecules indole and toluene, and gases Xe, N2 and O2. Using multiphoton ionization cross sections extracted from these results, we show that the laser pulse parameters required for real-time detection of aromatic molecules at concentrations of one part per trillion in air and a limit of detection of a few attomoles are achievable with presently available commercial laser systems. The potential applications for the analysis of human breath, blood and tissue samples are discussed

The Home Literacy Environment as a Predictor of the Early Literacy Development of Children at Family-Risk of Dyslexia

The home literacy environment (HLE) predicts language and reading development in typically developing children; relatively little is known about its association with literacy development in children at family-risk of dyslexia. We assessed the HLE at age 4 years, precursor literacy skills at age 5, and literacy outcomes at age 6, in a sample of children at family-risk of dyslexia (n = 116) and children with no known risk (n = 72). Developmental relationships between the HLE and literacy were comparable between the groups; an additional effect of storybook exposure on phoneme awareness was observed in the family-risk group only. The effects of socioeconomic status on literacy were partially mediated by variations in the HLE; in turn, effects of the HLE on literacy were mediated by precursor skills (oral language, phoneme awareness, and emergent decoding) in both groups. Findings are discussed in terms of possible gene–environment correlation mechanisms underpinning atypical literacy development

Bioaccessibility performance data for fifty-seven elements in guidance material BGS 102

BGS 102, a guidance material for bioaccessible arsenic (As) and lead (Pb), was produced during validation of the in vitro Unified Bioaccessibility Method (UBM). This paper reports a compilation of reproducible bioaccessible guidance values for fifty-five additional elements in BGS 102, providing guidance for analysts to broaden the scope of UBM analyses for a wider range of elements based on data collected over an average of 60 separate analytical batches per element. Data are presented in categories for both gastric (STOM) and gastrointestinal (STOM + INT) extraction phases, where reproducibility, measured as relative standard deviation (RSD) was; ≤ 10% RSD for 27 elements (Mg, Al, Si, P, Ca, Cr, Mn, Co, Ni, As, Rb, Sr, Y, Ba, La, Ce, Pr, Nd, Sm, Eu, Tb, Gd, Dy, Ho, Er, Tm, Yb); between 10 and 20% RSD for 10 elements (Li, K, V, Fe, Cu, Zn, Cd, Lu, Pb, U); and ≥ 20% RSD for 19 elements in the gastric phase (Be, B, S, Ti, Ga, Se, Zr, Nb, Mo, Ag, Sn, Sb, Cs, Hf, Ta, W, Tl, Bi, Th). Two elements (Mg, Rb) met the ≤ 10% RSD criteria in the UBM gastrointestinal extraction phase due to the alkaline conditions of this phase precipitating out the majority of determinands. Certain elements, including Na, K, Zn and Se, were found to be a significant component of the extraction fluids with proportionally higher concentrations compared to the guidance material. Bioaccessible fractions (%BAF) were also calculated, but were found to be a less reproducible format for confirming the accuracy of measurements. The low concentration of some elements of interest in BGS 102, such as antimony (Sb), justifies the preparation of an alternative certified reference material (CRM). This paper presents an opportunity to broaden the scope of the UBM method to address food security issues (e.g. Fe and Zn micronutrient deficiencies) and contributions to dietary intake from extraneous dust or soil through evidence of the analytical possibilities and current limitations requiring further investigation

Medical Transport of Children with Complex Chronic Conditions

One of the most notable trends in child health has been the increase in the number of children with special health care needs, including those with complex chronic conditions. Care of these children accounts for a growing fraction of health care resources. We examine recent developments in health care, especially with regard to medical transport and prehospital care, that have emerged to adapt to this remarkable demographic trend. One such development is the focus on care coordination, including the dissemination of the patient-centered medical home concept. In the prehospital setting, the need for greater coordination has catalyzed the development of the emergency information form. Training programs for prehospital providers now incorporate specific modules for children with complex conditions. Another notable trend is the shift to a family-centered model of care. We explore efforts toward regionalization of care, including the development of specialized pediatric transport teams, and conclude with recommendations for a research agenda

Associations between multimorbidity and neuropathology in dementia: Consideration of functional cognitive disorders, psychiatric illness and dementia mimics

\ua9 The Author(s), 2024. Published by Cambridge University Press on behalf of Royal College of Psychiatrists.Background Multimorbidity, the presence of two or more health conditions, has been identified as a possible risk factor for clinical dementia. It is unclear whether this is due to worsening brain health and underlying neuropathology, or other factors. In some cases, conditions may reflect the same disease process as dementia (e.g. Parkinson\u27s disease, vascular disease), in others, conditions may reflect a prodromal stage of dementia (e.g. depression, anxiety and psychosis). Aims To assess whether multimorbidity in later life was associated with more severe dementia-related neuropathology at autopsy. Method We examined ante-mortem and autopsy data from 767 brain tissue donors from the UK, identifying physical multimorbidity in later life and specific brain-related conditions. We assessed associations between these purported risk factors and dementia-related neuropathological changes at autopsy (Alzheimer\u27s-disease related neuropathology, Lewy body pathology, cerebrovascular disease and limbic-predominant age-related TDP-43 encephalopathy) with logistic models. Results Physical multimorbidity was not associated with greater dementia-related neuropathological changes. In the presence of physical multimorbidity, clinical dementia was less likely to be associated with Alzheimer\u27s disease pathology. Conversely, conditions which may be clinical or prodromal manifestations of dementia-related neuropathology (Parkinson\u27s disease, cerebrovascular disease, depression and other psychiatric conditions) were associated with dementia and neuropathological changes. Conclusions Physical multimorbidity alone is not associated with greater dementia-related neuropathological change; inappropriate inclusion of brain-related conditions in multimorbidity measures and misdiagnosis of neurodegenerative dementia may better explain increased rates of clinical dementia in multimorbidit

Neurodegenerative brain changes are associated with area deprivation in the United Kingdom: findings from the Brains for Dementia Research study

Socioeconomic disadvantage is associated with greater risk of dementia. This has been theorised to reflect inequalities in cognitive reserve, healthcare access, lifestyle, and other health factors which may contribute to the clinical manifestation of dementia. We aimed to assess whether area deprivation in the United Kingdom was associated with greater risk or severity of the specific neurodegenerative diseases which lead to dementia in a multi-centre cohort with autopsy assessment. Participants underwent clinical assessment prior to brain tissue donation post-mortem. Each then underwent detailed, standardised neuropathological assessment. National area deprivation statistics were derived for each participant’s neighbourhood, for use as a predictor in binary and ordinal logistic models assessing the respective presence and severity of staging of key neuropathological changes, adjusting for theorised confounders. Individuals from among the 20% most deprived neighbourhoods in the United Kingdom had significantly higher neurofibrillary tangle and neuritic plaque staging, and increased risk of cerebral amyloid angiopathy. These findings were not explained by a greater risk of diabetes or hypertension, APOE genotype, alcohol misuse or tobacco smoking, sex, or age differences. A sensitivity analysis conditioning on baseline cognitive impairment did not meaningfully change the observed association. Socioeconomic disadvantage may contribute to dementia incidence through a greater severity of specific neuropathological changes (neurofibrillary tangles, neuritic plaques, and cerebral amyloid angiopathy), independent of other indirect influences. Mechanisms through which deprivation is associated with these require further exploration

Beyond locutionary denotations: exploring trust between practitioners and policy

This study reports the findings of a research on the trust relationship between practitioners in the Skills for Life (SfL) area and the policy that informs their practice. The exploration of this relationship was premised on an extended notion of trust relationship which draws from the Speech Act theory of Austin (1962; Searle 1969; Kissine 2008), leading to the claim that the existence of different layers of imports in textual analysis makes it possible for a trust relationship to exist between the human/physical and the non human/non physical. The study found that the majority of practitioners in the SfL field trust policy to deliver its inherent policy only to a limited extent. Amongst others, the study identified the impact of the perlocutionary import of policy text on practitioners as a viable reason for this limited level of trust. Such perlocutionary imports, it also found, have adverse impact on practitioners who are considered to have drawn from previous experience to mediate the import of contemporary policies