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Funder: Open Targets, Funder: European Molecular Biology Laboratory (EMBL) (4843), Background Single-cell RNA-sequencing is revolutionising the study of cellular and tissue-wide heterogeneity in a large number of biological scenarios, from highly tissue-specific studies of disease to human-wide cell atlases. A central task in single-cell RNA-sequencing analysis design is the calculation of cell type-specific genes in order to study the differential impact of different replicates (e.g. tumour vs. non-tumour environment) on the regulation of those genes and their associated networks. The crucial task is the efficient and reliable calculation of such cell type-specific ‘marker’ genes. These optimise the ability of the experiment to isolate highly-specific cell phenotypes of interest to the analyser. However, while methods exist that can calculate marker genes from single-cell RNA-sequencing, no such method places emphasise on specific cell phenotypes for downstream study in e.g. differential gene expression or other experimental protocols (spatial transcriptomics protocols for example). Here we present , a general computational framework for extracting key marker genes from single-cell RNA-sequencing data which reliably characterise highly-specific and niche populations of cells in numerous different biological data-sets. Results extracts robust and biologically well-motivated marker genes, which characterise a given single-cell RNA-sequencing data-set better than existing computational approaches for general marker gene calculation. We demonstrate the utility of through its substantial performance improvement over several existing methods in the field. Furthermore, we evaluate the markers on spatial transcriptomics data, demonstrating they identify highly localised compartments of the mouse cortex. Conclusion is a new methodology for calculating robust markers genes from large single-cell RNA-sequencing data-sets, and has implications for e.g. effective gene identification for probe design in downstream analyses spatial transcriptomics experiments. has been fully-integrated with the framework and provides a valuable bioinformatics tool for cell type characterisation and validation in every-growing data-sets spanning over 50 different cell types across hundreds of thousands of cells.

Background Single-cell RNA sequencing (scRNA-Seq) experiments are gaining ground to study the molecular processes that drive normal development as well as the onset of different pathologies. Finding an effective and efficient low-dimensional representation of the data is one of the most important steps in the downstream analysis of scRNA-Seq data, as it could provide a better identification of known or putatively novel cell-types. Another step that still poses a challenge is the integration of different scRNA-Seq datasets. Though standard computational pipelines to gain knowledge from scRNA-Seq data exist, a further improvement could be achieved by means of machine learning approaches. Results Autoencoders (AEs) have been effectively used to capture the non-linearities among gene interactions of scRNA-Seq data, so that the deployment of AE-based tools might represent the way forward in this context. We introduce here scAEspy, a unifying tool that embodies: (1) four of the most advanced AEs, (2) two novel AEs that we developed on purpose, (3) different loss functions. We show that scAEspy can be coupled with various batch-effect removal tools to integrate data by different scRNA-Seq platforms, in order to better identify the cell-types. We benchmarked scAEspy against the most used batch-effect removal tools, showing that our AE-based strategies outperform the existing solutions. Conclusions scAEspy is a user-friendly tool that enables using the most recent and promising AEs to analyse scRNA-Seq data by only setting up two user-defined parameters. Thanks to its modularity, scAEspy can be easily extended to accommodate new AEs to further improve the downstream analysis of scRNA-Seq data. Considering the relevant results we achieved, scAEspy can be considered as a starting point to build a more comprehensive toolkit designed to integrate multi single-cell omics.

The ontogeny of the human haematopoietic system during fetal development has previously been characterized mainly through careful microscopic observations1. Here we reconstruct a phylogenetic tree of blood development using whole-genome sequencing of 511 single-cell-derived haematopoietic colonies from healthy human fetuses at 8 and 18 weeks after conception, coupled with deep targeted sequencing of tissues of known embryonic origin. We found that, in healthy fetuses, individual haematopoietic progenitors acquire tens of somatic mutations by 18 weeks after conception. We used these mutations as barcodes and timed the divergence of embryonic and extra-embryonic tissues during development, and estimated the number of blood antecedents at different stages of embryonic development. Our data support a hypoblast origin of the extra-embryonic mesoderm and primitive blood in humans. Whole-genome sequencing of haematopoietic colonies from human fetuses reveals the somatic mutations acquired by individual progenitors, which are used as barcodes to construct a phylogenetic tree of blood development.

BACKGROUND/OBJECTIVES To compare the Australian Dietary Guideline Index (DGI-2013) and the Pyramid-based Mediterranean Diet Score (pyrMDS) as measures of diet quality in an ethnically diverse group of older men. SUBJECTS/METHODS Seven hundred and ninety-four older men aged ≥75 participated in wave 3 (2012-2013) of the Concord Health and Ageing in Men Project. Dietary intake was assessed using a validated diet history questionnaire. Ethnicity was based on self-reported country of birth and categorised as Australian-born (418 men), Italian or Greek migrants (188), and other migrants (188). Incident cardiovascular outcomes until March 2018 were measured using the composite of major adverse cardiovascular events (MACE), which comprises all-cause mortality, acute myocardial infarction, congestive cardiac failure, coronary revascularisation and/or ischaemic stroke. Ability to predict incident cardiovascular outcomes and all-cause mortality were compared between standardised DGI-2013 pyrMDS scores by comparison of hazard ratios, discrimination (Harrell's C-statistic) and calibration (calibration plots). RESULTS Italian and Greek migrant men had significantly lower DGI-2013 scores (91.7 vs. 93.9; p = 0.01) but significantly higher pyrMDS scores (8.8 vs. 8.2; p

The ontogeny of the human haematopoietic system during fetal development has previously been characterized mainly through careful microscopic observations1. Here we reconstruct a phylogenetic tree of blood development using whole-genome sequencing of 511 single-cell-derived haematopoietic colonies from healthy human fetuses at 8 and 18 weeks after conception, coupled with deep targeted sequencing of tissues of known embryonic origin. We found that, in healthy fetuses, individual haematopoietic progenitors acquire tens of somatic mutations by 18 weeks after conception. We used these mutations as barcodes and timed the divergence of embryonic and extra-embryonic tissues during development, and estimated the number of blood antecedents at different stages of embryonic development. Our data support a hypoblast origin of the extra-embryonic mesoderm and primitive blood in humans.

Background People with intellectual disability (ID) have multiple and complex health needs, more frequent healthcare episodes, and experience poorer health outcomes. Research conducted two decades ago showed that medical professionals were lacking in the knowledge and skills required to address the complex needs of this patient group. The aim of the current study was to determine whether Australian undergraduate medical schools that offer ID health education content had changed the amount and nature of such teaching over this period. Methods Identical or equivalent questionnaire items were compared across eight Australian medical schools that participated in curricula audits conducted in 1995 (referred to as T1) and 2013/14 (T2). The audits were of the nature of the ID content, methods used to teach it, and who taught it. Results There was no significant difference in the number of hours of compulsory ID content offered to medical students at T2 (total = 158.3 h; median = 2.8 h per ID unit) compared with T1 (total = 171 h; median = 2.5 h). At T2 compared with T1, units with ID content taught in the area of general practice had increased (2 units; 3.6% to 7 units; 16.3%), while decreases were seen in paediatrics (22 units; 40.0% to 10 units; 23.3%) and psychiatry (10 units; 18.2% to 4 units; 9.3%). The number of schools using problem- and/or enquiry-based learning rose to six at T2 from one at T1. Inclusive teaching practices (people with ID develop or deliver content) in compulsory/elective units had increased at T2 (10 units; 23.3%) compared with T1 (6 units; 10.9%), but direct clinical contact with people with ID had decreased (29 units; 52.7% to 11 units; 25.6%). Conclusions Overall, little progress has been made to address the gaps in ID education for medical students identified from an audit conducted in 1995. Renewal of ID content in medical curricula is indicated as a key element in efforts to improve workforce capacity in this area and reduce barriers to care, with the aim of reversing the poor health outcomes currently seen for this group.

Background Conflicting evidence exists regarding the association of socioeconomic status (SES) with mortality among older people and little is known about the mechanisms underlying this association. We investigated the association of SES with mortality among older Australian men. We also investigated potential mediating effects of health-related behaviours in SES-mortality associations. Methods We used data from a prospective population-based cohort (the Concord Health and Aging in Men Project), in Sydney, Australia. The main outcomes were all-cause and cause-specific mortality. Educational attainment, occupational position, source of income, housing tenure, and a cumulative SES score were assessed at baseline. Longitudinally assessed alcohol consumption, smoking, physical activity, and body mass index were investigated as potential mediators. Associations were quantified using Cox regression. Results We evaluated 1527 men (mean age: 77.4 ± 5.5 years). During a mean follow-up time of 9.0 years, 783 deaths occurred. For deaths from all causes, the adjusted hazard ratio (HR) for the lowest tertile of cumulative SES score versus the highest tertile was 1.44 (95% CI 1.21 to 1.70); the corresponding sub-HRs were 1.35 (0.96 to 1.89) for cardiovascular disease (CVD) mortality; 1.58 (1.15 to 2.18) for cancer mortality, and 1.86 (1.36 to 2.56) for non-CVD, non-cancer mortality. SES-mortality associations were attenuated by 11–25% after adjustment for mediating health-related behaviours. Conclusion Low SES is associated with increased mortality in older Australian men and health-related behaviours accounted for less than one-fourth of these associations. Further research is needed to fully understand the mechanisms underlying SES inequalities in mortality among older people.

Neurodevelopmental disorders, including autism spectrum disorder, have complex polygenic etiologies. Single-gene mutations in patients can help define genetic factors and molecular mechanisms underlying neurodevelopmental disorders. Here we describe individuals with monogenic heterozygous microdeletions in ANKS1B, a predicted risk gene for autism and neuropsychiatric diseases. Affected individuals present with a spectrum of neurodevelopmental phenotypes, including autism, attention-deficit hyperactivity disorder, and speech and motor deficits. Neurons generated from patient-derived induced pluripotent stem cells demonstrate loss of the ANKS1B-encoded protein AIDA-1, a brain-specific protein highly enriched at neuronal synapses. A transgenic mouse model of Anks1b haploinsufficiency recapitulates a range of patient phenotypes, including social deficits, hyperactivity, and sensorimotor dysfunction. Identification of the AIDA-1 interactome using quantitative proteomics reveals protein networks involved in synaptic function and the etiology of neurodevelopmental disorders. Our findings formalize a link between the synaptic protein AIDA-1 and a rare, previously undefined genetic disease we term ANKS1B haploinsufficiency syndrome., Understanding of the genetic factors and molecular mechanisms underlying neurodevelopmental disorders remains incomplete. In this study, authors show that microdeletions in the gene ANKS1B lead to loss of the neuronal synapse-enriched protein AIDA-1 and to a novel neurodevelopmental syndrome

Human lungs enable efficient gas exchange and form an interface with the environment, which depends on mucosal immunity for protection against infectious agents. Tightly controlled interactions between structural and immune cells are required to maintain lung homeostasis. Here, we use single-cell transcriptomics to chart the cellular landscape of upper and lower airways and lung parenchyma in healthy lungs, and lower airways in asthmatic lungs. We report location-dependent airway epithelial cell states and a novel subset of tissue-resident memory T cells. In the lower airways of patients with asthma, mucous cell hyperplasia is shown to stem from a novel mucous ciliated cell state, as well as goblet cell hyperplasia. We report the presence of pathogenic effector type 2 helper T cells (TH2) in asthmatic lungs and find evidence for type 2 cytokines in maintaining the altered epithelial cell states. Unbiased analysis of cell-cell interactions identifies a shift from airway structural cell communication in healthy lungs to a TH2-dominated interactome in asthmatic lungs.

Unexplained fatigue is commonly reported in the general population, with varying severity. Myalgic encephalomyelitis/chronic fatigue syndrome (ME/CFS) sits at the extreme of the fatigue continuum, yet more individuals experience unexplained prolonged fatigue (1–6-month duration) or chronic fatigue (> 6 months) that, although debilitating, does not fulfil ME/CFS criteria. This review examines the empirical literature comparing symptoms for those with prolonged fatigue, chronic fatigue and ME/CFS. Substantial overlap of self-reported psychological, physical and functional impairments exists between chronic fatigue and ME/CFS. The conversion rate from prolonged or chronic fatigue to ME/CFS is not understood. Current research has failed to uncover factors accounting for differences in fatigue trajectories, nor incorporate comprehensive, longitudinal assessments extending beyond self-reported symptoms. Distinguishing factors between prolonged fatigue, chronic fatigue and ME/CFS remain poorly understood, highlighting a need for longitudinal studies integrating biopsychosocial approaches to inform early management and targeted rehabilitation strategies.

Background Individuals with intellectual disability experience higher rates of physical and mental health conditions compared with the general population, yet have inequitable access to health care services. Improving the workplace capacity of medical professionals to meet the needs of this population is one way to reduce barriers to care and improve health outcomes. Using diverse pedagogy appropriate to learning outcomes to teach medical students about intellectual disability is a necessary step in improving future workplace capacity. However, there is a lack of research into how, and by whom, medical students are taught about intellectual disability. The aim of this study was to investigate this through an audit of Australian medical school curricula. Methods The Deans of Australian universities that provide accredited medical degrees (n = 20) were invited by email to participate in a two-phase audit of intellectual disability content in the curricula. Phase 1 (n = 14 schools) involved the Dean’s delegate completing a telephone interview or questionnaire regarding medical course structure. If intellectual disability content was identified, a unit coordinator was invited to complete a survey regarding how this content was taught and by whom (Phase 2; n = 12 schools). Results There was considerable variability across Australian medical schools regarding methods used to teach content about intellectual disability. Didactic teaching methods were most frequently used (62% of units included some form of lecture), but workshops and tutorials were reasonably well represented (34% of units contained one or both). Thirty-six percent of units included two or more teaching methods. Almost all schools (83%) used some problem- and/or enquiry-based learning. Educator backgrounds included medicine, nursing, and allied health. A majority of schools (n = 9, 75%) involved people with intellectual disability designing and teaching content, but the extent to which this occurred was inconsistent. Conclusions Renewing curricula around intellectual disability across all medical schools by introducing varied teaching methods and the inclusion of people with intellectual disability would assist students to develop knowledge, skills, attitudes, and confidence in intellectual disability health. Such renewal offers the potential to reduce barriers to service this population regularly face, thereby improving their health outcomes.

Background Acute outbreaks of Actinobacillus pleuropneumoniae (APP) require rapid, effective, parenteral antimicrobial treatment. The efficacy and safety of a single, short-acting, high dose of marbofloxacin (Forcyl® swine 160 mg/mL) compared with 1 or 2 doses of 7.5 mg/kg enrofloxacin in APP outbreaks in European farms was studied. Methods A controlled, randomised block, blinded, multicentre, field study was conducted on four farms with acute respiratory disease associated with APP. Animals with clinical signs of respiratory disease were allocated similarly to intramuscular treatments of either a single dose 8 mg/kg marbofloxacin on day 0 or, 7.5 mg/kg enrofloxacin (Baytril 1nject®) on day 0 and again on day 2, if clinical signs had not improved. Results The results were similar for intention to treat (242 pigs) and per protocol populations (239 pigs). On day 0, all pigs had pyrexia (means, 40.6 °C), moderate to severe clinical signs (depression, cough, dyspnoea). Following treatment, animals improved rapidly and on day 7, clinical signs were absent or mild in all pigs and mean temperatures for each treatment were 0.05). The primary efficacy criterion, animals cured, for marbofloxacin and enrofloxacin was 81.8 and 81.4% on day 7, and 84.2 and 82.2% on day 21, respectively. Results for cure, respiratory disease removals and mortalities, and relapses were compared using confidence intervals and confirmed that marbofloxacin was non-inferior to enrofloxacin (P > 0.05). There were no significant treatment differences in live weight gains, adverse events and injection site reactions ( 0.05). Significantly more animals developed concurrent disorders in the enrofloxacin (7.5%) than marbofloxacin (0.0%) group (P

Papillary carcinoma of the thyroid (PTC) is generally a slow growing tumor with favorable prognosis, while anaplastic thyroid carcinoma (ATC) is highly aggressive malignancy. Genetic defects in apoptotic pathways may contribute to differences in their biological behavior. In this study, we analyzed immunohistochemically the expression of apoptosis-related molecules: galectin-3, Bcl-2, survivin (antiapoptotic), and Bax (pro-apoptotic), in archival tissue sections of PTC (n = 69) and ATC (n = 30) and correlated the results with clinicopathological parameters of these tumors. Galectin-3 and Bcl-2 showed a similar trend of down-regulation from high levels of both in PTC to low levels in ATC (p

Notoedric mange (feline scabies) is a rare, but highly contagious disease of cats and kittens caused by Notoedres cati (N. cati), which can infest other animals and also humans. The study objective was to determine the efficacy and safety of 10 % imidacloprid/ 1 % moxidectin (Advocate®/Advantage® Multi spot-on for cats) against natural N. cati infestation in cats. Sixteen cats were randomly assigned to treatment group or negative control using pre-treatment mite counts. The treatment group received a single spot on treatment of the investigational veterinary product (IVP) according to label instructions. The control group stayed untreated. Five cats from the negative control were treated with the IVP at the end of the study and observed for 28 days to increase the treatment group. Skin scrapings and mite counts were performed 28 days post treatment (p.t.). Notoedric skin lesion assessments with clinical scoring were performed regularly. Five animals had to be removed prematurely from the study population due to different reasons. The number of viable N. cati mites in all treated animals 28 days p.t. was zero compared with 2.8 ± 3.0 in the negative control, being significantly lower for treated cats (p = 0.0019, Wilcoxon test). The resulting efficacy was 100 %. Clinical cure based on skin lesion assessment was achieved 28 days p.t. in 100 % of all treated animals completing 28 study days. The IVP was well tolerated and applied at the minimal therapeutic dose (10 mg imidacloprid/1 mg moxidectin/kg body weight) a high therapeutic efficacy in curing N. cati infestations and feline scabies clinical symptoms was recorded.

The most common histological variants of papillary thyroid carcinoma (PTC), classical (CPTC) and follicular (FPTC), have different diagnostic features, molecular biology, and prognosis. Matrix metalloproteinase-9 (MMP-9) endopeptidase which degrades the components of the extracellular matrix is essential in the invasive growth and metastasizing of malignant tumors. The serum copper (Cu)/zinc (Zn) ratios are sensitive diagnostic and prognostic indicators in oncology since Cu- and Zn-dependent enzymes play important roles in the genesis and the progression of tumors. The aim of this study was to examine the expressions of MMP-9 in tissues of CPTC and FPTC, as well as to determine the Cu/Zn ratios in the same samples. MMP-9 was determined immunohistochemically, and the concentrations of copper and zinc in thyroid tissue were determined by means of flame atomic absorption spectrometry. The results obtained revealed significantly higher expressions of MMP-9 in CPTC in comparison with FPTC, as well as higher Cu/Zn ratios in CPTC than in FPTC. Thus, determining MMP-9 activities and the Cu/Zn ratios could improve the accuracy of the standard histopathological diagnosis of these two types of PTC.

The aim of this study was to assess the clinical utility of circulating preoperative Cyfra 21.1 [soluble fragment of cytokeratin (CK) 19] and galectin-3 (gal-3) in patients with thyroid tumors, to compare their serum values with tissue expression and to analyze the prognostic significance of these markers in relation to the clinical status of postsurgical differentiated thyroid carcinoma (DTC) patients.Concentrations of Cyfra 21.1 and gal-3 were evaluated by immunoassays in sera of 9 healthy subjects, 97 preoperative patients with diverse thyroid tumors (10 FTA, 63 PTC, 11 FTC, 5 PDTC, 4 ATC, 4 LNM) and 25 postoperative DTC patients (14 remissions and 11 metastases).Low Cyfra 21.1 values were found in all subgroups, but with a tendency toward higher values in poorly differentiated DTC patients. Compared to the control (0.23 ng/mL), serum levels of gal-3 were significantly elevated in patients with thyroid tumors but with overlapping between adenoma (4.16 ng/mL) and carcinoma (3.85, 4.37, 4.64, 6.07 ng/mL for PTC, PDTC, ATC and LNM, respectively). The tissue expression of CK19 and gal-3 was immunohistochemically determined on 45 matched paraffin-embedded sections. Most thyroid carcinomas showed positive CK19 (27/35) and gal-3 immunostaining (31/35), while adenomas were mostly immunonegative (8/10 and 7/10, respectively). However, there was no significant correlation between their serum and tissue levels. Clinical status of postoperative DTC patients had no influence on serum concentrations of the tested markers.While CK19 and gal-3 are accurate as tissue markers, their serum levels could not be used as reliable markers for identification of thyroid malignancy or in thyroid cancer follow-up. On the other hand, a tendency toward higher serum levels of Cyfra 21.1 in the small number of PDTC patients examined adds weight to previous reports postulating a role for cytokeratins in predicting a high degree of malignancy.

The expression of galectin-8 (gal-8) has been shown to be altered during neoplastic transformation of certain cell types. This is the first study aimed to analyze the expression of this protein in normal and pathological human thyroid tissue. A total of 41 archival thyroid tissue samples (5 follicular adenomas, 31 papillary carcinomas, 5 follicular carcinomas) together with 36 adjacent hyperplastic or normal thyroid tissues were analyzed by immunohistochemistry. Galectin-8 was expressed in the majority of papillary carcinomas (27/31; 87%). Positive but weaker staining was also found in some of the follicular thyroid carcinomas (2/5; 40%) and adenomas (2/5; 40%). This protein was not detectable in five normal thyroid tissue samples, whereas hyperplastic areas adjacent to tumor were weakly positive in 9 out of 31 cases (29%). High gal-8 immunostaining in papillary thyroid carcinoma indicates that gal-8 may potentially serve as a marker of papillary thyroid carcinoma. However, it does not seem to be helpful in the differential diagnostics of follicular carcinoma and adenoma. Further studies are required to determine biological functions and molecular mechanisms underlying the increased expression of gal-8 protein in thyroid lesions, particularly, in papillary thyroid carcinoma.

Thyroperoxidase (TPO) is a thyroid-specific enzyme expressed by differentiated thyroid cells. Initial immunohistochemical studies claimed that TPO expression, detected by the monoclonal antibody mAb 47, may be a potentially important diagnostic tool in differentiating malignant from benign lesions. However, some recent studies have failed to reproduce the earlier results, suggesting the limitations for TPO immunohistochemistry. To assess these observations we have evaluated the immunohistochemical expression of TPO in thyroid tissue from 215 patients. The studied material included 87 nonmalignant thyroid lesions and 128 thyroid carcinomas. TPO expression was investigated using newly available mAb 47 and staining of less than 80% of the follicular cells/specimen as the threshold indicating a malignant lesion. We found that TPO had a sensitivity of 89.9% for cancer and a specificity of 64.4% for nonmalignant lesions, showing that it does not give a sufficient degree of diagnostic certainty that the lesion is benign. In addition, the variability in the degree of TPO expression found within and between follicular carcinomas, and the significant number of benign adenomas having similar immunostaining patterns, assured us that TPO immunostaining is not sufficiently discriminatory in the differential diagnosis of thyroid cancer versus benign lesions.

Gray platelet syndrome (GPS) is a predominantly recessive platelet disorder that is characterized by mild thrombocytopenia with large platelets and a paucity of α-granules; these abnormalities cause mostly moderate but in rare cases severe bleeding. We sequenced the exomes of four unrelated individuals and identified NBEAL2 as the causative gene; it has no previously known function but is a member of a gene family that is involved in granule development. Silencing of nbeal2 in zebrafish abrogated thrombocyte formation.