Integrated intracellular organization and its variations in human iPS cells.

Understanding how a subset of expressed genes dictates cellular phenotype is a considerable challenge owing to the large numbers of molecules involved, their combinatorics and the plethora of cellular behaviours that they determine1,2. Here we reduced this complexity by focusing on cellular organization-a key readout and driver of cell behaviour3,4-at the level of major cellular structures that represent distinct organelles and functional machines, and generated the WTC-11 hiPSC Single-Cell Image Dataset v1, which contains more than 200,000 live cells in 3D, spanning 25 key cellular structures. The scale and quality of this dataset permitted the creation of a generalizable analysis framework to convert raw image data of cells and their structures into dimensionally reduced, quantitative measurements that can be interpreted by humans, and to facilitate data exploration. This framework embraces the vast cell-to-cell variability that is observed within a normal population, facilitates the integration of cell-by-cell structural data and allows quantitative analyses of distinct, separable aspects of organization within and across different cell populations. We found that the integrated intracellular organization of interphase cells was robust to the wide range of variation in cell shape in the population; that the average locations of some structures became polarized in cells at the edges of colonies while maintaining the 'wiring' of their interactions with other structures; and that, by contrast, changes in the location of structures during early mitotic reorganization were accompanied by changes in their wiring.

Innate immune dysfunction and neuroinflammation in autism spectrum disorder (ASD).

Autism spectrum disorder (ASD) is a highly heterogeneous neurodevelopmental disorder characterized by communication and social behavior deficits. The presence of restricted and repetitive behaviors often accompanies these deficits, and these characteristics can range from mild to severe. The past several decades have seen a significant rise in the prevalence of ASD. The etiology of ASD remains unknown; however, genetic and environmental risk factors play a role. Multiple hypotheses converge to suggest that neuroinflammation, or at least the interaction between immune and neural systems, may be involved in the etiology of some ASD cases or groups. Repeated evidence of innate immune dysfunction has been seen in ASD, often associated with worsening behaviors. This evidence includes data from circulating myeloid cells and brain resident macrophages/microglia in both human and animal models. This comprehensive review presents recent findings of innate immune dysfunction in ASD, including aberrant innate cellular function, evidence of neuroinflammation, and microglia activation.

The top 100 most cited articles on artificial intelligence in radiology: a bibliometric analysis.

AIM: To identify the most influential publications relating to artificial intelligence (AI) in radiology in order to identify current trends in the literature and to highlight areas requiring further research. MATERIALS AND METHODS: A retrospective bibliometric analysis was performed of the top 100 most cited articles on this topic. Data pertaining to year of publication, publishing journal, journal impact factor, authorship, article title, institution, country, type of article, article subject, and keywords were collected. RESULTS: The number of citations per article for the top 100 list ranged from 254 to 3,576 (median 353). The number of citations per year, per article ranged from 10.4 to 894 (median 65.6). The majority of articles (n=62) were published within the last 10 years. The USA was the most common country of origin (n=44). The journal with the greatest number of articles was IEEE Transactions On Medical Imaging (n=38). University Medical Center Utrecht contributed the greatest number of articles (n=6). There were 92 original research articles, 52 of which were clinical studies. The most common clinical subjects were neuroimaging (n=25) and oncology (n=16). The most common keyword used was "deep learning" (n=34). CONCLUSION: This study provides an in-depth analysis of the top 100 most-cited papers on the use of AI in radiology. It also provides researchers with detailed insight into the current influential papers in this field, the characteristics of those studies, as well as potential future trends in this fast-developing area of radiology.

Towards a farmer-feasible soil health assessment that is globally applicable.

Globally, agriculture has had a significant and often detrimental impact on soil. The continued capacity of soil to function as a living ecosystem that sustains microbes, plants, and animals (including humans), its metaphorical health, is of vital importance across geographic scales. Healthy soil underpins food production and ecosystem resilience against a changing climate. This paper focuses on assessing soil health, an area of increasing interest for farming communities, researchers, industry and policy-makers. Without accessible and reliable soil assessment, any management and interventions to improve soil health are likely to be sub-optimal. Here we explore available soil health assessments (SHAs) that may be feasible for farmers of varying income levels and suitable for broad geographic application. Whilst there is a range of existing approaches to SHA, we find that no one framework currently meets these broad aims. Firstly, reliance on expensive and logistically complex laboratory methods reduces viability and accessibility for many farmers. Secondly, lack of defined indicator baselines and associated thresholds or gradients for soil health prevents the assessment of soil measurements against achieving optima for a given set of local soil-climate conditions. Since soils vary greatly, these baselines and thresholds must be defined considering the local biogeographic context; it is inappropriate to simply transfer calibrated information between contexts. These shortcomings demand progress towards a feasible, globally applicable and context-relevant SHA framework. The most feasible SHAs we identified were developed locally in conjunction with farmers, who have been repeatedly found to assess the health of their soils accurately, often using relatively simple, observable indications. To progress, we propose assessment of which indicators add information to a SHA in local contexts, with a focus on sufficiency, to reduce data burden. Provision of a standardised protocol for measurement and sampling that considers the reliability and accuracy of different methods would also be extremely valuable. For greatest impact, future work should be taken forward through a cross-industry collaborative approach involving researchers, businesses, policy makers, and, above all, farmers, who are both experts and users.

Clinical characteristics, attendance outcomes and deaths of homeless persons in the emergency department: implications for primary health care and community prevention programmes.

OBJECTIVES: Persons experiencing homelessness (PEH) are known to be often excluded from primary health care and community prevention programmes leading to high use of hospital emergency departments (EDs). This study aimed to identify demographic features, clinical characteristics and attendance outcomes of PEH presenting to ED. STUDY DESIGN: Analysis of routinely collected data set. METHODS: Clinical presentations and drug prescription data of PEH who presented a major ED in the West Midlands region of England from 2014 to 2019 were extracted and analysed using descriptive and inferential statistics. RESULTS: During the study period, 3271 of 596,198 presentations were made by PEH; 74% PEH attendees were male. Drug- and alcohol-related conditions, as well as pain and injury constituted the most frequent reasons for presentation, contributing to over half of all presentations. A significantly higher proportion of males (n = 481, 20.3%) presented with drug and alcohol problems than females (n = 93, 11.2%) (P ≤ 0.001). However, pain was the primary reason for presentation for twice as many female patients (n = 189, 22.8%) compared with males (n = 305, 12.9%) (P < 0.001). Nearly one in five left the ED before being assessed and a total of 39 patients (1.2%) died in the ED and 785 (24.0%) required in-patient admissions to the same hospital. CONCLUSIONS: Drug, alcohol and pain including the need of opioid analgesics constituted the majority of presentations made by PEH in ED. The observed rate of death of PEH in ED is 12 times higher than the general population. A very high proportion of PEH also leave the ED before being treated. Future research should focus on strengthening community interventions, particularly to improve access to those at risk of dual diagnoses of substance misuse and mental health problems. Interventions involving multisector collaborations are needed to improve seamless discharge from ED and minimise repeat attendance. Gender differences in the nature of presentations and ED outcomes needs to be investigated further.

Proteomic comparison of osteoarthritic and reference human menisci using data-independent acquisition mass spectrometry.

OBJECTIVE: Recent research in knee osteoarthritis (OA) highlights the role of the meniscus in OA pathology. Our aim was to compare the proteomes of medial and lateral menisci from end-stage medial compartment knee OA patients, with reference menisci from knee-healthy deceased donors, using mass spectrometry. DESIGN: Tissue plugs of Ø3 mm were obtained from the posterior horns of the lateral and medial menisci from one knee of 10 knee-healthy deceased donors and 10 patients undergoing knee replacement. Proteins were extracted and prepared for mass spectrometric analysis. Statistical analysis was conducted on abundance data that was log2-transformed, using a linear mixed effects model and evaluated using pathway analysis. RESULTS: We identified a total of 835 proteins in all samples, of which 331 were included in the statistical analysis. The largest differences could be seen between the medial menisci from OA patients and references, with most proteins showing higher intensities in the medial menisci from OA patients. Several matrix proteins, e.g., matrix metalloproteinase 3 (MMP3) (4.3 times higher values [95%CI 1.8, 10.6]), TIMP1 (3.5 [1.4, 8.5]), asporin (4.1 [1.7, 10.0]) and versican (4.4 [1.8, 10.9]), all showed higher abundance in medial menisci from OA patients compared to medial reference menisci. OA medial menisci also showed increased activation of several pathways involved in inflammation. CONCLUSION: An increase in protein abundance for proteins such as MMP and TIMP1 in the medial menisci from OA patients suggests simultaneous activation of both catabolic and anabolic processes that warrants further attention.

Diagnostic Limitations in Congenital Zika Virus Infection.

This is the first documented case of an infant with congenital Zika virus infection (ZVI) born in Ireland. A term infant was delivered with an antenatal diagnosis of severe microcephaly. First trimester bloods confirmed maternal ZVI and although the infant did not have Zika virus RNA or Zika-specific IgM in her blood or urine, she had multiple clinical features of congenital ZVI and Zika virus RNA was present in the placenta.

Ultra-high field magnetic resonance imaging parameter mapping in the posterior horn of ex vivo human menisci.

OBJECTIVE: To investigate the relationship between meniscus magnetic resonance (MR) relaxation parameters and meniscus degradation through quantitative imaging of ex vivo posterior horns of menisci from subjects with and without knee osteoarthritis (OA). DESIGN: We sampled medial and lateral menisci from ten medial compartment knee OA patients (mean age 63 years) undergoing total knee replacement and from ten deceased donors (references, mean age 51 years). MR relaxation parameters T2*, T2 and T1 of the posterior horn were measured at a 9.4 T scanner. Comparisons were made between OA patients and references (with adjustment for age) as well as between medial and lateral menisci from the same knees. RESULTS: Mean values (standard deviation) of mean T2* were 13 (3.8), 6.9 (2.3), 7.2 (1.9) and 7.2 (1.7) ms for the medial and lateral patient menisci and the medial and lateral reference menisci, respectively. Corresponding values were 17 (3.7), 9.0 (2.2), 12 (4) and 9.0 (1.3) ms for T2 and 1810 (150), 1630 (30), 1580 (90) and 1560 (50) ms for T1. All three relaxation times were significantly longer in medial OA menisci compared to the other groups. Among medial reference menisci, relaxation times (mainly T1) tended to increase with age. CONCLUSIONS: MR relaxation times T2*, T2 and T1 in the posterior horn are longer in the medial menisci of patients with end-stage medial compartment knee OA compared to the corresponding lateral menisci and to reference menisci. The meniscus seems to undergo intrasubstance alterations related to both OA and ageing.

A Life-Saving Palsy: Hereditary Neuropathy with Liability to Pressure Palsies (HNPP) Presenting As Hand Weakness during Cardiopulmonary Resuscitation (CPR) Training

Aim To describe a case of acute and transient hand weakness that developed during cardiopulmonary resuscitation (CPR) training. Hereditary neuropathy with liability to pressure palsies (HNPP) should be considered in patients with recurrent, painless motor or sensory neuropathies at sites of peripheral nerve compression. Methods Nerve conduction studies confirmed neuropraxia of the distal ulnar nerve with a mild background demyelinating peripheral neuropathy. Results A positive family history emerged and HNPP was confirmed by genetic testing. HNPP is most reliably diagnosed by molecular testing for peripheral myelin protein 22 (PMP22) gene deletion or point mutation on chromosome 17p11.2. Conclusion CPR, a procedure carried out by medical professionals on a daily basis, is a high-energy manual task and provides multiple opportunities for nerve compression. This case demonstrates the importance of having a high index of clinical suspicion of this disorder in patients. Recognising a diagnosis of HNPP may prevent unnecessary surgical decompression.

The flagellum in bacterial pathogens: For motility and a whole lot more.

The bacterial flagellum is an amazingly complex molecular machine with a diversity of roles in pathogenesis including reaching the optimal host site, colonization or invasion, maintenance at the infection site, and post-infection dispersal. Multi-megadalton flagellar motors self-assemble across the cell wall to form a reversible rotary motor that spins a helical propeller - the flagellum itself - to drive the motility of diverse bacterial pathogens. The flagellar motor responds to the chemoreceptor system to redirect swimming toward beneficial environments, thus enabling flagellated pathogens to seek out their site of infection. At their target site, additional roles of surface swimming and mechanosensing are mediated by flagella to trigger pathogenesis. Yet while these motility-related functions have long been recognized as virulence factors in bacteria, many bacteria have capitalized upon flagellar structure and function by adapting it to roles in other stages of the infection process. Once at their target site, the flagellum can assist adherence to surfaces, differentiation into biofilms, secretion of effector molecules, further penetration through tissue structures, or in activating phagocytosis to gain entry into eukaryotic cells. Next, upon onset of infection, flagellar expression must be adapted to deal with the host's immune system defenses, either by reduced or altered expression or by flagellar structural modification. Finally, after a successful growth phase on or inside a host, dispersal to new infection sites is often flagellar motility-mediated. Examining examples of all these processes from different bacterial pathogens, it quickly becomes clear that the flagellum is involved in bacterial pathogenesis for motility and a whole lot more.

Colletotrichum higginsianum extracellular LysM proteins play dual roles in appressorial function and suppression of chitin-triggered plant immunity.

The genome of the hemibiotrophic anthracnose fungus, Colletotrichum higginsianum, encodes a large repertoire of candidate-secreted effectors containing LysM domains, but the role of such proteins in the pathogenicity of any Colletotrichum species is unknown. Here, we characterized the function of two effectors, ChELP1 and ChELP2, which are transcriptionally activated during the initial intracellular biotrophic phase of infection. Using immunocytochemistry, we found that ChELP2 is concentrated on the surface of bulbous biotrophic hyphae at the interface with living host cells but is absent from filamentous necrotrophic hyphae. We show that recombinant ChELP1 and ChELP2 bind chitin and chitin oligomers in vitro with high affinity and specificity and that both proteins suppress the chitin-triggered activation of two immune-related plant mitogen-activated protein kinases in the host Arabidopsis. Using RNAi-mediated gene silencing, we found that ChELP1 and ChELP2 are essential for fungal virulence and appressorium-mediated penetration of both Arabidopsis epidermal cells and cellophane membranes in vitro. The findings suggest a dual role for these LysM proteins as effectors for suppressing chitin-triggered immunity and as proteins required for appressorium function.

Emergency department syndromic surveillance providing early warning of seasonal respiratory activity in England.

Seasonal respiratory infections place an increased burden on health services annually. We used a sentinel emergency department syndromic surveillance system to understand the factors driving respiratory attendances at emergency departments (EDs) in England. Trends in different respiratory indicators were observed to peak at different points during winter, with further variation observed in the distribution of attendances by age. Multiple linear regression analysis revealed acute respiratory infection and bronchitis/bronchiolitis ED attendances in patients aged 1-4 years were particularly sensitive indicators for increasing respiratory syncytial virus activity. Using near real-time surveillance of respiratory ED attendances may provide early warning of increased winter pressures in EDs, particularly driven by seasonal pathogens. This surveillance may provide additional intelligence about different categories of attendance, highlighting pressures in particular age groups, thereby aiding planning and preparation to respond to acute changes in EDs, and thus the health service in general.

Actinomyces Species Isolated from Breast Infections.

Actinomycosis is a chronic infection caused by Actinomyces species characterized by abscess formation, tissue fibrosis, and draining sinuses. The spectrum of infections caused by Actinomyces species ranges from classical invasive actinomycosis to a less invasive form of superficial skin and soft tissue infection. We present a review detailing all Actinomyces species isolated from breast infections in NHS Lothian between 2005 and 2013, Actinomyces species isolated from breast infections referred to the United Kingdom Anaerobe Reference Unit between 1988 and 2014, and cases describing Actinomyces breast infections published in the medical literature since 1994. Actinomyces species are fastidious organisms which can be difficult to identify and are likely to be underascertained as a cause of breast infections. Due to improved diagnostic methods, they are increasingly associated with chronic, recurrent breast infections and may play a more significant role in these infections than has previously been appreciated.

Peptidoglycan transformations during Bacillus subtilis sporulation.

While vegetative Bacillus subtilis cells and mature spores are both surrounded by a thick layer of peptidoglycan (PG, a polymer of glycan strands cross-linked by peptide bridges), it has remained unclear whether PG surrounds prespores during engulfment. To clarify this issue, we generated a slender ΔponA mutant that enabled high-resolution electron cryotomographic imaging. Three-dimensional reconstructions of whole cells in near-native states revealed a thin PG-like layer extending from the lateral cell wall around the prespore throughout engulfment. Cryotomography of purified sacculi and fluorescent labelling of PG in live cells confirmed that PG surrounds the prespore. The presence of PG throughout engulfment suggests new roles for PG in sporulation, including a new model for how PG synthesis might drive engulfment, and obviates the need to synthesize a PG layer de novo during cortex formation. In addition, it reveals that B. subtilis can synthesize thin, Gram-negative-like PG layers as well as its thick, archetypal Gram-positive cell wall. The continuous transformations from thick to thin and back to thick during sporulation suggest that both forms of PG have the same basic architecture (circumferential). Endopeptidase activity may be the main switch that governs whether a thin or a thick PG layer is assembled.

Co-ordinate synthesis and protein localization in a bacterial organelle by the action of a penicillin-binding-protein.

Organelles with specialized form and function occur in diverse bacteria. Within the Alphaproteobacteria, several species extrude thin cellular appendages known as stalks, which function in nutrient uptake, buoyancy and reproduction. Consistent with their specialization, stalks maintain a unique molecular composition compared with the cell body, but how this is achieved remains to be fully elucidated. Here we dissect the mechanism of localization of StpX, a stalk-specific protein in Caulobacter crescentus. Using a forward genetics approach, we identify a penicillin-binding-protein, PbpC, which is required for the localization of StpX in the stalk. We show that PbpC acts at the stalked cell pole to anchor StpX to rigid components of the outer membrane of the elongating stalk, concurrent with stalk synthesis. Stalk-localized StpX in turn functions in cellular responses to copper and zinc, suggesting that the stalk may contribute to metal homeostasis in Caulobacter. Together, these results identify a novel role for a penicillin-binding-protein in compartmentalizing a bacterial organelle it itself helps create, raising the possibility that cell wall-synthetic enzymes may broadly serve not only to synthesize the diverse shapes of bacteria, but also to functionalize them at the molecular level.

Using an Emergency Department Syndromic Surveillance System to investigate the impact of extreme cold weather events.

This report describes the development of novel syndromic cold weather public health surveillance indicators for use in monitoring the impact of extreme cold weather on attendances at EDs, using data from the 2010-11 and 2011-12 winters. A number of new surveillance indicators were created specifically for the identification and monitoring of cold weather related ED attendances, using the diagnosis codes provided for each attendance in the Emergency Department Syndromic Surveillance System (EDSSS), the first national syndromic surveillance system of its kind in the UK. Using daily weather data for the local area, a time series analysis to test the sensitivity of each indicator to cold weather was undertaken. Diagnosis codes relating to a health outcome with a potential direct link to cold weather were identified and assigned to a number of 'cold weather surveillance indicators'. The time series analyses indicated strong correlations between low temperatures and cold indicators in nearly every case. The strongest fit with temperature was cold related fractures in females, and that of snowfall was cold related fractures in both sexes. Though currently limited to a small number of sentinel EDs, the EDSSS has the ability to give near real-time detail on the magnitude of the impact of weather events. EDSSS cold weather surveillance fits well with the aims of the Cold Weather Plan for England, providing information on those particularly vulnerable to cold related health outcomes severe enough to require emergency care. This timely information aids those responding to and managing the effects on human health, both within the EDs themselves and in the community as a whole.

The impact of thunderstorm asthma on emergency department attendances across London during July 2013.

BACKGROUND: This study illustrates the potential of using emergency department attendance data, routinely accessed as part of a national syndromic surveillance system, to monitor the impact of thunderstorm asthma. METHODS: The Emergency Department Syndromic Surveillance System (EDSSS) routinely monitors anonymised attendance data on a daily basis across a sentinel network of 35 emergency departments. Attendance data for asthma, wheeze and difficulty breathing are analysed on a daily basis. RESULTS: A statistically significant spike in asthma attendances in two EDSSS emergency departments in London was detected on 23 July 2013, coinciding with a series of large violent thunderstorms across southern England. There was also an increase in the reported severity of these attendances. CONCLUSIONS: This preliminary report illustrates the potential of the EDSSS to monitor the impact of thunderstorms on emergency department asthma attendances. Further work will focus on how this system can be used to quantify the impact on emergency departments, thus potentially improving resource planning and also adding to the thunderstorm asthma evidence-base.

Innate Immune Dysfunction and Neuroinflammation in Autism Spectrum Disorder (ASD).

Autism spectrum disorder (ASD) is a highly heterogeneous neurodevelopmental disorder characterized by communication and social behavior deficits. The presence of restricted and repetitive behaviors often accompanies these deficits, and these characteristics can range from mild to severe. The past several decades have seen a significant rise in the prevalence of ASD. The etiology of ASD remains unknown; however, genetic and environmental risk factors play a role. Multiple hypotheses converge to suggest that neuroinflammation, or at least the interaction between immune and neural systems, may be involved in the etiology of some ASD cases or groups. Repeated evidence of innate immune dysfunction has been seen in ASD, often associated with worsening behaviors. This evidence includes data from circulating myeloid cells and brain resident macrophages/microglia in both human and animal models. This comprehensive review presents recent findings of innate immune dysfunction in ASD, including aberrant innate cellular function, evidence of neuroinflammation, and microglia activation. Appeared originally in Brain Behav Immun 2023; 108:245-254.

Evaluation of presentation, treatment and outcome in dogs with granulomatous steatitis associated with hypercalcaemia: six cases (2019-2023).

OBJECTIVES: To report the presentation, treatment and outcome of dogs with granulomatous steatitis associated with total and ionised hypercalcaemia. METHODS: Six dogs diagnosed with ionised and/or total hypercalcaemia and histologically diagnosed granulomatous steatitis were evaluated to determine the clinical signs, clinical findings, response to treatment and outcome. These cases were seen at different primary care and referral veterinary hospitals in the United Kingdom between 2019 and 2023. RESULTS: No alternative aetiology to explain the total and/or ionised hypercalcaemia or steatitis was identified. The most common presenting signs were lethargy, anorexia or hyporexia, vomiting and polyuria/polydipsia. Other clinical signs included weight loss, discomfort and panting. Five out of the six dogs responded to prednisolone. Four dogs were alive at the time of writing, one dog was lost to follow-up and one dog died 2 weeks post-diagnosis. CLINICAL SIGNIFICANCE: It is well-established that granulomatous disease can cause hypercalcaemia. In this case series we found granulomatous steatitis associated with total and/or ionised hypercalcaemia. Dogs diagnosed with granulomatous steatitis should have ionised calcium measured, which may prompt further diagnostics and treatment options. Dogs with hypercalcaemia should be evaluated for evidence of steatitis where more common differentials have been excluded.