Mapping genetic effects on cell type-specific chromatin accessibility and annotating complex immune trait variants using single nucleus ATAC-seq in peripheral blood.

Gene regulation is highly cell type-specific and understanding the function of non-coding genetic variants associated with complex traits requires molecular phenotyping at cell type resolution. In this study we performed single nucleus ATAC-seq (snATAC-seq) and genotyping in peripheral blood mononuclear cells from 13 individuals. Clustering chromatin accessibility profiles of 96,002 total nuclei identified 17 immune cell types and sub-types. We mapped chromatin accessibility QTLs (caQTLs) in each immune cell type and sub-type using individuals of European ancestry which identified 6,901 caQTLs at FDR < .10 and 4,220 caQTLs at FDR < .05, including those obscured from assays of bulk tissue such as with divergent effects on different cell types. For 3,941 caQTLs we further annotated putative target genes of variant activity using single cell co-accessibility, and caQTL variants were significantly correlated with the accessibility level of linked gene promoters. We fine-mapped loci associated with 16 complex immune traits and identified immune cell caQTLs at 622 candidate causal variants, including those with cell type-specific effects. At the 6q15 locus associated with type 1 diabetes, in line with previous reports, variant rs72928038 was a naïve CD4+ T cell caQTL linked to BACH2 and we validated the allelic effects of this variant on regulatory activity in Jurkat T cells. These results highlight the utility of snATAC-seq for mapping genetic effects on accessible chromatin in specific cell types.

Mapping malaria vectors and insecticide resistance in a high-endemic district of Haryana, India: implications for vector control strategies.

BACKGROUND: Achieving effective control and elimination of malaria in endemic regions necessitates a comprehensive understanding of local mosquito species responsible for malaria transmission and their susceptibility to insecticides. METHODS: The study was conducted in the highly malaria prone Ujina Primary Health Center of Nuh (Mewat) district of Haryana state of India. Monthly entomological surveys were carried out for adult mosquito collections via indoor resting collections, light trap collections, and pyrethrum spray collections. Larvae were also collected from different breeding sites prevalent in the region. Insecticide resistance bioassay, vector incrimination, blood meal analysis was done with the collected vector mosquitoes. RESULTS: A total of 34,974 adult Anopheles mosquitoes were caught during the survey period, out of which Anopheles subpictus was predominant (54.7%). Among vectors, Anopheles stephensi was predominant (15.5%) followed by Anopheles culicifacies (10.1%). The Human Blood Index (HBI) in the case of An. culicifacies and An. stephensi was 6.66 and 9.09, respectively. Vector incrimination results revealed Plasmodium vivax positivity rate of 1.6% for An. culicifacies. Both the vector species were found resistant to DDT, malathion and deltamethrin. CONCLUSION: The emergence of insecticide resistance in both vector species, compromises the effectiveness of commonly used public health insecticides. Consequently, the implementation of robust insecticide resistance management strategies becomes imperative. To effectively tackle the malaria transmission, a significant shift in vector control strategies is warranted, with careful consideration and adaptation to address specific challenges encountered in malaria elimination efforts.

In Silico Analysis of the Phylogenetic and Physiological Characteristics of Sphingobium indicum B90A: A Hexachlorocyclohexane-Degrading Bacterium.

The study focuses on the in silico genomic characterization of Sphingobium indicum B90A, revealing a wealth of genes involved in stress response, carbon monoxide oxidation, ß-carotene biosynthesis, heavy metal resistance, and aromatic compound degradation, suggesting its potential as a bioremediation agent. Furthermore, genomic adaptations among nine Sphingomonad strains were explored, highlighting shared core genes via pangenome analysis, including those related to the shikimate pathway and heavy metal resistance. The majority of genes associated with aromatic compound degradation, heavy metal resistance, and stress response were found within genomic islands across all strains. Sphingobium indicum UT26S exhibited the highest number of genomic islands, while Sphingopyxis alaskensis RB2256 had the maximum fraction of its genome covered by genomic islands. The distribution of lin genes varied among the strains, indicating diverse genetic responses to environmental pressures. Additionally, in silico evidence of horizontal gene transfer (HGT) between plasmids pSRL3 and pISP3 of the Sphingobium and Sphingomonas genera, respectively, has been provided. The manuscript offers novel insights into strain B90A, highlighting its role in horizontal gene transfer and refining evolutionary relationships among Sphingomonad strains. The discovery of stress response genes and the czcABCD operon emphasizes the potential of Sphingomonads in consortia development, supported by genomic island analysis.

Distinct orchid mycorrhizal fungal communities among co-occurring Vanilla species in Costa Rica: root substrate and population-based segregation.

Despite being the second largest family of flowering plants, orchids represent community structure variation in plant-microbial associations, contributes to niche partitioning in metacommunity assemblages. Yet, mycorrhizal communities and interactions remain unknown for orchids that are highly specialized or even obligated in their associations with their mycorrhizal partners. In this study, we sought to compare orchid mycorrhizal fungal (OMF) communities of three co-occurring hemiepiphytic Vanilla species (V. hartii, V. pompona, and V. trigonocarpa) in tropical forests of Costa Rica by addressing the identity of their OMF communities across species, root types, and populations, using high-throughput sequencing. Sequencing the nuclear ribosomal internal transcribed spacer (nrITS) yielded 299 fungal Operational Taxonomic Units (OTUs) from 193 root samples. We showed distinct segregation in the putative OMF (pOMF) communities of the three coexisting Vanilla hosts. We also found that mycorrhizal communities associated with the rare V. hartii varied among populations. Furthermore, we identified Tulasnellaceae and Ceratobasidiaceae as dominant pOMF families in terrestrial roots of the three Vanilla species. In contrast, the epiphytic roots were mainly dominated by OTUs belonging to the Atractiellales and Serendipitaceae. Furthermore, the pOMF communities differed significantly across populations of the widespread V. trigonocarpa and showed patterns of distance decay in similarity. This is the first report of different pOMF communities detected in roots of wild co-occurring Vanilla species using high-throughput sequencing, which provides evidence that three coexisting Vanilla species and their root types exhibited pOMF niche partitioning, and that the rare and widespread Vanilla hosts displayed diverse mycorrhizal preferences.

Protective effect of olopatadine hydrochloride against LPS-induced acute lung injury: via targeting NF-κB signaling pathway.

BACKGROUND: Morbidity and mortality rates associated with acute lung injury/acute respiratory distress syndrome (ALI/ARDS) are high (30-40%). Nuclear factor-kappa B (NF-κB) is a transcription factor, associated with transcription of numerous cytokines leading to cytokine storm, and thereby, plays a major role in ALI/ARDS and in advanced COVID-19 syndrome. METHODS: Considering the role of NF-κB in ALI, cost-effective in silico approaches were utilized in the study to identify potential NF-κB inhibitor based on the docking and pharmacokinetic results. The identified compound was then pharmacologically validated in lipopolysaccharide (LPS) rodent model of acute lung injury. LPS induces ALI by altering alveolar membrane permeability, recruiting activated neutrophils and macrophages to the lungs, and compromising the alveolar membrane integrity and ultimately impairs the gaseous exchange. Furthermore, LPS exposure is associated with exaggerated production of various proinflammatory cytokines in lungs. RESULTS: Based on in silico studies Olopatadine Hydrochloride (Olo), an FDA-approved drug was found as a potential NF-κB inhibitor which has been reported for the first time, and considered further for the pharmacological validation. Intraperitoneal LPS administration resulted in ALI/ARDS by fulfilling 3 out of the 4 criteria described by ATS committee (2011) published workshop report. However, treatment with Olo attenuated LPS-induced elevation of proinflammatory markers (IL-6 and NF-κB), oxidative stress, neutrophil infiltration, edema, and damage in lungs. Histopathological studies also revealed that Olo treatment significantly ameliorated LPS-induced lung injury, thus conferring improvement in survival. Especially, the effects produced by Olo medium dose (1 mg/kg) were comparable to dexamethasone standard. CONCLUSION: In nutshell, inhibition of NF-κB pathway by Olo resulted in protection and reduced mortality in LPS- induced ALI and thus has potential to be used clinically to arrest disease progression in ALI/ARDS, since the drug is already in the market. However, the findings warrant further extensive studies, and also future studies can be planned to elucidate its role in COVID-19-associated ARDS or cytokine storm.

POU2AF3-rearranged sarcomas: A novel tumor defined by fusions of EWSR1 or FUS to a gene formerly designated COLCA2.

Gene fusions involving EWSR1 or FUS as the 5' partner have been reported in a diverse array of sarcomas. Here, we characterize the histopathology and genomics of six tumors harboring a gene fusion between EWSR1 or FUS and POU2AF3, an understudied, putative colorectal cancer predisposition gene. Striking morphologic features reminiscent of synovial sarcoma were observed including a biphasic appearance with variable fusiform to epithelioid cytomorphology and staghorn-type vasculature. RNA sequencing demonstrated variable breakpoints in EWSR1/FUS along with similar breakpoints in POU2AF3 that encompassed a 3' portion of this gene. For cases in which additional information was available, the behavior of these neoplasms was aggressive with local spread and/or distant metastases. Although further studies are needed to confirm the functional significance of our findings, POU2AF3 fusions to EWSR1 or FUS may define a novel type of POU2AF3-rearranged sarcomas with aggressive, malignant behavior.

Extremophiles in Space Exploration.

In the era of deep space exploration, extremophile research represents a key area of research w.r.t space survival. This review thus delves into the intriguing realm of 'Space and Astro Microbiology', providing insights into microbial survival, resilience, and behavioral adaptations in space-like environments. This discussion encompasses the modified behavior of extremophilic microorganisms, influencing virulence, stress resistance, and gene expression. It then shifts to recent studies on the International Space Station and simulated microgravity, revealing microbial responses that impact drug susceptibility, antibiotic resistance, and its commercial implications. The review then transitions into Astro microbiology, exploring the possibilities of interplanetary transit, lithopanspermia, and terraforming. Debates on life's origin and recent Martian meteorite discoveries are noted. We also discuss Proactive Inoculation Protocols for selecting adaptable microorganisms as terraforming pioneers. The discussion concludes with a note on microbes' role as bioengineers in bioregenerative life support systems, in recycling organic waste for sustainable space travel; and in promoting optimal plant growth to prepare Martian and lunar basalt. This piece emphasizes the transformative impact of microbes on the future of space exploration.

An Exploratory-Descriptive Analysis of Training Programs for Leadership in Health Research and Services in India.

BACKGROUND: There are several leadership training programs for health researchers in India. However, there is a need to develop context-tailored leadership and mentoring approaches. OBJECTIVE: The objective of the study is to critically analyze the available leadership training programs in India for health researchers and service providers, for the leadership domains incorporated and overall training approaches. MATERIALS AND METHODS: We used an exploratory-descriptive design to identify and review leadership training programs for health researchers and service providers/managers that had been offered by Indian institutions between 2013 and 2018. Our analytic approach was based on "transformational leadership" and "leader-member exchange" theories of leadership, curricula of popular leadership training programs worldwide, and the International Clinical Epidemiology Network model for leadership in health research in India based on a nationwide primary study. RESULTS: We identified and reviewed 20 leadership training programs. These were heterogeneous in aim, scope (broad-based/thematic), course content, design, target participants and class profile, mode of delivery and training method, duration, frequency, and fund arrangements. The programs infrequently included topics on soft skills, mentoring, risk mitigation, collaboration for research, funding dynamics, institutional transformation, self-view and peer perception, and personal well-being. The programs insufficiently addressed contextual challenges of career exploration and risk mitigation, project management, strategic planning, and decision-making, ethics and integrity, negotiations, networking and collaboration, understanding funding dynamics, and mentoring. Only three programs linked to the training to the participants' ecosystem. CONCLUSIONS: There is a need to develop customized course contents and training strategies that address the requirements of the local context vis-à-vis globally connected research ecosystems.

An overview on the types, applications and health implications of fat replacers.

Driven by the demand of consumers for low-fat foods, the field of fat replacers has made a tremendous breakthrough over the past decade. A fat replacer is a substance that replaces whole or part of the fat in food while asserting the same physiological properties. Based on the source, fat replacers can be carbohydrate, protein or lipid-based. They serve two major purposes in food viz. reducing the calorie content and amount of fat used in the preparation of food products as well as impart fat-like properties. Fat replacers exhibit its functionalities by providing texture, acting as stabilizers, emulsifiers, gelling and thickening agents. It is crucial to select the proper kind of fat replacer because fat functionality varies considerably depending on the meal type and the formulation. Evidence suggests that reducing fat intake can help in controlling body weight and the risk of diseases like type-2 diabetes, hypertension and cardiovascular disease. Consumers should not be misled into believing that fat and calorie-reduced foods may be consumed indefinitely. Fat replacers are most beneficial when they aid in calorie control and promote the consumption of meals that provide essential nutrients. This review aims to provide a deep insight into the fact that fat replacers can be utilized in various food commodities in order to meet the dietary guidelines for reducing fat intake with a healthy lifestyle and prudent dietary approach.

Congeneric temperate orchids recruit similar-yet differentially abundant-endophytic bacterial communities that are uncoupled from soil, but linked to host phenology and population size.

PREMISE: Besides the beneficial plant-fungus symbiosis in mycorrhizal plants, bacteria also enhance plant fitness via tripartite interactions. While bacterial associations are presumably just as important for the obligate mycorrhizal family Orchidaceae, little is known about orchid associating bacteria (OAB). METHODS: We examined the OAB communities of two, congeneric, terrestrial orchids, Platanthera cooperi and Platanthera praeclara, which represent widely disparate North American ecosystems. We tested whether they recruit distinct OAB communities, and whether variability in OAB communities can be linked to phenology, population size, or habitat soil. Genomic DNAs from roots of seedling, vegetative, and reproductive plants and from soil were subjected to Illumina sequencing of V4 and V5 regions of the 16S rRNA gene. RESULTS: We obtained 809 OAB Zero-radius Operational Taxonomic Units (ZOTUs). Despite an overlap of 209 ZOTUs that accounted for >75% relative abundances of their respective OAB communities, the overall community structures of the two orchids were distinct. Within each orchid, distinctions were detected in the OAB communities of large and small populations and the three phenological stages. The OAB ZOTUs were either absent or present with low abundances in soil associated with both orchids. CONCLUSIONS: The two orchids exhibited preferential recruitment of known growth-promoting OAB communities from soil. Their OAB communities also showed considerable overlap despite the large environmental and geographical separation of the two host taxa. Our results lend further support to the emerging evidence that not only the fungi, but root-associated bacteria also have functional importance for orchid ecology.

Co-occurring epiphytic orchids have specialized mycorrhizal fungal niches that are also linked to ontogeny.

Mycorrhizal symbiosis has been related to the coexistence and community assembly of coexisting orchids in few studies despite their obligate dependence on mycorrhizal partners to establish and survive. In hyper-diverse environments like tropical rain forests, coexistence of epiphytic orchids may be facilitated through mycorrhizal fungal specialization (i.e., sets of unique and dominant mycorrhizal fungi associated with a particular host species). However, information on the role of orchid mycorrhizal fungi (OMF) in niche differentiation and coexistence of epiphytic orchids is still scarce. In this study, we sought to identify the variation in fungal preferences of four co-occurring epiphytic orchids in a tropical rainforest in Costa Rica by addressing the identity and composition of their endophytic fungal and OMF communities across species and life stages. We show that the endophytic fungal communities are formed mainly of previously recognized OMF taxa, and that the four coexisting orchid species have both a set of shared mycorrhizal fungi and a group of fungi unique to an orchid species. We also found that adult plants keep the OMF of the juvenile stage while adding new mycobionts over time. This study provides evidence for the utilization of specific OMF that may be involved in niche segregation, and for an aggregation mechanism where adult orchids keep initial fungal mycobionts of the juvenile stage while adding others.

Cheap portable electroformed giant unilamellar vesicles preparation kit.

The membrane of a cell separates the internal and external media of the cell and contributes to a variety of important processes, including gradient maintenance and signal transduction. Synthetic lipid-made vesicles are commonly utilized as cell membrane model systems. These could be liposomes or giant unilamellar vesicles (GUVs) in most cases. Liposomes are typically less than 0.5 microns in size, limiting their use for most microscopy experiments. GUVs are a form of liposomes that ranges in size from 5 to 200 microns and are ideal for examining complex phase behaviors of biomembranes using the classical optical setting. This study details the step-by-step development of a portable, light and low-cost kit for generating GUVs by electroformation. Our kit contains an in-built electronic circuitry, and the GUV generation setup, consisting of 3 ITO-coated glasses with heating electrode connections. Approximately 600 µl of GUVs can be produced in one experiment, while the amount could be increased by changing the dimensions of the GUV generation setup. Finally, the originality of the study comes from the fact that many users from different fields unfamiliar with electronics can use our home-built cost-effective approach instead of their expensive commercial counterparts.

A mechanistic overview of spinal cord injury, oxidative DNA damage repair and neuroprotective therapies.

Despite substantial development in medical treatment strategies scientists are struggling to find a cure against spinal cord injury (SCI) which causes long term disability and paralysis. The prime rationale behind it is the enlargement of primary lesion due to an initial trauma to the spinal cord which spreads to the neighbouring spinal tissues It begins from the time of traumatic event happened and extends to hours and even days. It further causes series of biological and functional alterations such as inflammation, excitotoxicity and ischemia, and promotes secondary lesion to the cord which worsens the life of individuals affected by SCI. Oxidative DNA damage is a stern consequence of oxidative stress linked with secondary injury causes oxidative base alterations and strand breaks, which provokes cell death in neurons. It is implausible to stop primary damage however it is credible to halt the secondary lesion and improve the quality of the patient's life to some extent. Therefore it is crucial to understand the hidden perspectives of cell and molecular biology affecting the pathophysiology of SCI. Thus the focus of the review is to connect the missing links and shed light on the oxidative DNA damages and the functional repair mechanisms, as a consequence of the injury in neurons. The review will also probe the significance of neuroprotective strategies in the present scenario. HIGHLIGHTSSpinal cord injury, a pernicious condition, causes excitotoxicity and ischemia, ultimately leading to cell death.Oxidative DNA damage is a consequence of oxidative stress linked with secondary injury, provoking cell death in neurons.Base excision repair (BER) is one of the major repair pathways that plays a crucial role in repairing oxidative DNA damages.Neuroprotective therapies curbing SCI and boosting BER include the usage of pharmacological drugs and other approaches.

Bi4TaO8Cl as a New Class of Layered Perovskite Oxyhalide Materials for Piezopotential Driven Efficient Seawater Splitting.

Piezocatalytic water splitting is an emerging approach to generate "green hydrogen" that can address several drawbacks of photocatalytic and electrocatalytic approaches. However, existing piezocatalysts are few and with minimal structural flexibility for engineering properties. Moreover, the scope of utilizing unprocessed water is yet unknown and may widely differ from competing techniques due to the constantly varying nature of surface potential. Herein, we present Bi4TaO8Cl as a representative of a class of layered perovskite oxyhalide piezocatalysts with high hydrogen production efficiency and exciting tailorable features including the layer number, multiple cation-anion combination options, etc. In the absence of any cocatalyst and scavenger, an ultrahigh production rate is achievable (1.5 mmol g-1 h-1), along with simultaneous generation of value-added H2O2. The production rate using seawater is somewhat less yet appreciably superior to photocatalytic H2 production by most oxides as well as piezocatalysts and has been illustrated using a double-layer model for further development.

Nutritional management and interventions in complications of pregnancy: A systematic review.

Background: Pregnancy, also known as the "gestation period" which lasts for 37-40 weeks, has been marked as the period of "physiological stress" in a woman's life. A wide range of symptoms, from nausea to ectopic pregnancy, are usually aligned with risk factors like abortion, miscarriage, stillbirth, etc. An estimated total of 15% of total pregnant women face serious complications requiring urgent attention for safe pregnancy survival. Over the past decades, several changes in the environment and nutrition habits have increased the possibility of unfavourable changes during the gestation phase. The diagnostic factors, management and nutritional interventions are targeted and more emphasis has been laid on modifying or managing the nutritional factors in this physiologically stressed phase. Aims: This review focuses on dietary modifications and nutritional interventions for the treatment of complications of pregnancy. Nutritional management has been identified to be one of the primary necessities in addition to drug therapy. It is important to set a healthy diet pattern throughout the gestation phase or even before by incorporating key nutrients into the maternal diet. Methods: The published literature from various databases including PubMed, Google Scholar and ScienceDirect were used to establish the fact of management and treatment of complications of pregnancy. Results: The recommendations of dietary supplements have underlined the concept behind the eradication of maternal deficiencies and improving metabolic profiles. Conclusion: Therefore, the present review summarises the dietary recommendations to combat pregnancy-related complications which are necessary in order to prevent and manage the same.

Malaria vector sibling species distribution in different endemic districts of Punjab, India.

BACKGROUND & OBJECTIVES: Malaria transmission in Punjab, India is mainly seasonal with variation in its endemicity that may be due to varying vector behaviour in different areas of the state, primarily attributed to the existence of sibling species complexes among the vector species. So far there is no report regarding the existence of malaria vectors sibling species in the state of Punjab, therefore, the present study was planned to investigate the status of sibling species of two main vectors of malaria viz. Anopheles culcifacies and Anopheles fluviatilis in different districts of Punjab. METHODS: Mosquito collections were made through hand catch in the morning hours. Malaria vector species An. culicifacies and An. fluviatilis were morphologically identified and man hour density was calculated. Both the vector species were subjected to molecular assays for sibling species identification through amplification of D3 domain of 28S ribosomal DNA by allele-specific PCR. RESULTS: Four sibling species of An. culicifacies, were identified viz. A, B, C and E. Species A was identified from Bhatinda district, species B, C and E from. S.A.S. Nagar and species C from Hoshiarpur. Two sibling species S and T of An. fluviatilis were identified from districts S.A.S. Nagar and Rupnagar. INTERPRETATION & CONCLUSION: Presence of four sibling species of An. culicifacies and two sibling species of An. fluviatilis in Punjab necessitates planning of longitudinal studies to ascertain their role in disease transmission so that appropriate interventions may be applied to achieve malaria elimination.

Nutritional advantages of barnyard millet and opportunities for its processing as value-added foods.

Barnyard millet (Echinochloa species) has received appreciable attention for its susceptibility to biotic and abiotic stresses, multiple harvests in a year and rich in micronutrients, fibers and phytochemicals. It is believed that the consumption of barnyard millet can possess various health benefits against diabetes, cardiovascular diseases, obesity, skin problems, cancer and celiac disease. The flour of barnyard millet is gluten-free and can be incorporated into the diet of celiac and diabetic patients. Considering the nutritional value of millet, various millet-based food products like bread, snack, baby foods, millet wine, porridge, fast foods and millet nutrition powder can be prepared. Future research and developments on barnyard millet and its products may help cope with various diseases known to humans. This paper discusses barnyard millet's nutritional and health benefits as whole grain and its value-added products. The paper also provides insights into the processing of barnyard millet and its effect on the functional properties and, future uses of barnyard millet in the field food industry as ready-to-cook and ready-to-eat products as well as in industrial uses, acting as a potential future crop contributing to food and nutritional security.

Centrosome amplification: a quantifiable cancer cell trait with prognostic value in solid malignancies.

Numerical and/or structural centrosome amplification (CA) is a hallmark of cancers that is often associated with the aberrant tumor karyotypes and poor clinical outcomes. Mechanistically, CA compromises mitotic fidelity and leads to chromosome instability (CIN), which underlies tumor initiation and progression. Recent technological advances in microscopy and image analysis platforms have enabled better-than-ever detection and quantification of centrosomal aberrancies in cancer. Numerous studies have thenceforth correlated the presence and the degree of CA with indicators of poor prognosis such as higher tumor grade and ability to recur and metastasize. We have pioneered a novel semi-automated pipeline that integrates immunofluorescence confocal microscopy with digital image analysis to yield a quantitative centrosome amplification score (CAS), which is a summation of the severity and frequency of structural and numerical centrosome aberrations in tumor samples. Recent studies in breast cancer show that CA increases across the disease progression continuum, while normal breast tissue exhibited the lowest CA, followed by cancer-adjacent apparently normal, ductal carcinoma in situ and invasive tumors, which showed the highest CA. This finding strengthens the notion that CA could be evolutionarily favored and can promote tumor progression and metastasis. In this review, we discuss the prevalence, extent, and severity of CA in various solid cancer types, the utility of quantifying amplified centrosomes as an independent prognostic marker. We also highlight the clinical feasibility of a CA-based risk score for predicting recurrence, metastasis, and overall prognosis in patients with solid cancers.

Selection of eligible participants for screening for lung cancer using primary care data.

Lung cancer screening is effective if offered to people at increased risk of the disease. Currently, direct contact with potential participants is required for evaluating risk. A way to reduce the number of ineligible people contacted might be to apply risk-prediction models directly to digital primary care data, but model performance in this setting is unknown. METHOD: The Clinical Practice Research Datalink, a computerised, longitudinal primary care database, was used to evaluate the Liverpool Lung Project V.2 (LLPv2) and Prostate Lung Colorectal and Ovarian (modified 2012) (PLCOm2012) models. Lung cancer occurrence over 5-6 years was measured in ever-smokers aged 50-80 years and compared with 5-year (LLPv2) and 6-year (PLCOm2012) predicted risk. RESULTS: Over 5 and 6 years, 7123 and 7876 lung cancers occurred, respectively, from a cohort of 842 109 ever-smokers. After recalibration, LLPV2 produced a c-statistic of 0.700 (0.694-0.710), but mean predicted risk was over-estimated (predicted: 4.61%, actual: 0.9%). PLCOm2012 showed similar performance (c-statistic: 0.679 (0.673-0.685), predicted risk: 3.76%. Applying risk-thresholds of 1% (LLPv2) and 0.15% (PLCOm2012), would avoid contacting 42.7% and 27.4% of ever-smokers who did not develop lung cancer for screening eligibility assessment, at the cost of missing 15.6% and 11.4% of lung cancers. CONCLUSION: Risk-prediction models showed only moderate discrimination when applied to routinely collected primary care data, which may be explained by quality and completeness of data. However, they may substantially reduce the number of people for initial evaluation of screening eligibility, at the cost of missing some lung cancers. Further work is needed to establish whether newer models have improved performance in primary care data.

Reliability of detection of ultrasound and MRI features of hand osteoarthritis: a systematic review and meta-analysis.

OBJECTIVES: To systematically review the literature on inter- and intra-rater reliability of scoring US and MRI changes in hand OA. METHODS: MEDLINE, EMBASE, CINHAL, Web of Science and AMED were searched from inception to January 2020. Kappa (κ), weighted kappa (κw) and intra-class correlation coefficients for dichotomous, semi-quantitative and summated scores, respectively, and their 95% CI were pooled using a random-effects model. Heterogeneity between studies was assessed and reliability estimates were interpreted using the Landis-Koch classification. RESULTS: Fifty studies met the inclusion criteria (29 US, 17 MRI, 4 involving both modalities). The pooled κ (95% CI) for inter-rater reliability was substantial for US-detected osteophytes [0.66 (0.54, 0.79)], grey-scale synovitis [0.64 (0.32, 0.97)] and power Doppler [0.76, (0.47, 1.05)], whereas intra-rater reliability was almost perfect for osteophytes [0.82 (0.80, 0.84)], central bone erosions (CBEs) [0.83 (0.78, 0.89)] and effusion [0.83 (0.74, 0.91)], and substantial for grey-scale synovitis [0.64 (0.49, 0.79)] and power Doppler [0.70 (0.59, 0.80)]. Inter-rater reliability for dichotomous assessment was substantial for MRI-detected CBEs [0.75 (0.67, 0.83)] and synovitis [0.69 (0.51, 0.87)], slight for osteophytes [0.14 (0.04, 0.25)], and almost perfect for sum score of osteophytes, CBEs, joint space narrowing (JSN), and bone marrow lesions (BMLs) (0.81-0.89). Intra-rater reliability was almost perfect for sum score of MRI synovitis [0.92 (0.87, 0.96)], BMLs [0.88 (0.78, 0.98)], osteophytes [0.86 (0.74, 0.98)], CBEs [0.83 (0.66, 1.00)] and JSN [0.91 (0.87, 0.91)]. CONCLUSION: US and MRI are reliable in detecting hand OA features. US may be preferred due to low cost and increasing availability.