Benchmarking atlas-level data integration in single-cell genomics.

Single-cell atlases often include samples that span locations, laboratories and conditions, leading to complex, nested batch effects in data. Thus, joint analysis of atlas datasets requires reliable data integration. To guide integration method choice, we benchmarked 68 method and preprocessing combinations on 85 batches of gene expression, chromatin accessibility and simulation data from 23 publications, altogether representing >1.2 million cells distributed in 13 atlas-level integration tasks. We evaluated methods according to scalability, usability and their ability to remove batch effects while retaining biological variation using 14 evaluation metrics. We show that highly variable gene selection improves the performance of data integration methods, whereas scaling pushes methods to prioritize batch removal over conservation of biological variation. Overall, scANVI, Scanorama, scVI and scGen perform well, particularly on complex integration tasks, while single-cell ATAC-sequencing integration performance is strongly affected by choice of feature space. Our freely available Python module and benchmarking pipeline can identify optimal data integration methods for new data, benchmark new methods and improve method development.

Depression, anxiety and PTSD symptoms before and during the COVID-19 pandemic in the UK.

BACKGROUND: The impact of the coronavirus disease 2019 (COVID-19) pandemic on mental health is still being unravelled. It is important to identify which individuals are at greatest risk of worsening symptoms. This study aimed to examine changes in depression, anxiety and post-traumatic stress disorder (PTSD) symptoms using prospective and retrospective symptom change assessments, and to find and examine the effect of key risk factors. METHOD: Online questionnaires were administered to 34 465 individuals (aged 16 years or above) in April/May 2020 in the UK, recruited from existing cohorts or via social media. Around one-third (n = 12 718) of included participants had prior diagnoses of depression or anxiety and had completed pre-pandemic mental health assessments (between September 2018 and February 2020), allowing prospective investigation of symptom change. RESULTS: Prospective symptom analyses showed small decreases in depression (PHQ-9: -0.43 points) and anxiety [generalised anxiety disorder scale - 7 items (GAD)-7: -0.33 points] and increases in PTSD (PCL-6: 0.22 points). Conversely, retrospective symptom analyses demonstrated significant large increases (PHQ-9: 2.40; GAD-7 = 1.97), with 55% reported worsening mental health since the beginning of the pandemic on a global change rating. Across both prospective and retrospective measures of symptom change, worsening depression, anxiety and PTSD symptoms were associated with prior mental health diagnoses, female gender, young age and unemployed/student status. CONCLUSIONS: We highlight the effect of prior mental health diagnoses on worsening mental health during the pandemic and confirm previously reported sociodemographic risk factors. Discrepancies between prospective and retrospective measures of changes in mental health may be related to recall bias-related underestimation of prior symptom severity.

Sleeping with one eye open: loneliness and sleep quality in young adults.

BACKGROUND: Feelings of loneliness are common among young adults, and are hypothesized to impair the quality of sleep. In the present study, we tested associations between loneliness and sleep quality in a nationally representative sample of young adults. Further, based on the hypothesis that sleep problems in lonely individuals are driven by increased vigilance for threat, we tested whether past exposure to violence exacerbated this association. METHOD: Data were drawn from the Environmental Risk (E-Risk) Longitudinal Twin Study, a birth cohort of 2232 twins born in England and Wales in 1994 and 1995. We measured loneliness using items from the UCLA Loneliness Scale, and sleep quality using the Pittsburgh Sleep Quality Index. We controlled for covariates including social isolation, psychopathology, employment status and being a parent of an infant. We examined twin differences to control for unmeasured genetic and family environment factors. RESULTS: Feelings of loneliness were associated with worse overall sleep quality. Loneliness was associated specifically with subjective sleep quality and daytime dysfunction. These associations were robust to controls for covariates. Among monozygotic twins, within-twin pair differences in loneliness were significantly associated with within-pair differences in sleep quality, indicating an association independent of unmeasured familial influences. The association between loneliness and sleep quality was exacerbated among individuals exposed to violence victimization in adolescence or maltreatment in childhood. CONCLUSIONS: Loneliness is robustly associated with poorer sleep quality in young people, underscoring the importance of early interventions to mitigate the long-term outcomes of loneliness. Special care should be directed towards individuals who have experienced victimization.

Bullying victimization in childhood predicts inflammation and obesity at mid-life: a five-decade birth cohort study.

BACKGROUND: We aimed to test whether childhood bullying victimization increases risk for age-related disease at mid-life using biological markers including inflammation and adiposity, independent of other childhood risk factors and key adult variables. METHOD: The present study was a 50-year prospective longitudinal birth cohort study of all births in Britain in 1 week in 1958. Exposure to bullying was assessed prospectively when participants were aged 7 and 11 years (27.7% occasionally bullied; 14.6% frequently bullied). Blood inflammation biomarkers [C-reactive protein (CRP) and fibrinogen] and adiposity [body mass index (BMI) and waist:hip ratio] were measured at age 45 years. RESULTS: Participants who had been frequently bullied in childhood showed increased levels of CRP at mid-life [ß = 0.07, 95% confidence interval (CI) 0.04-0.10] and higher risk for clinically relevant inflammation cut-off [CRP > 3 mg/l: 20.4% v. 15.9%, odds ratio (OR) = 1.35, 95% CI 1.12-1.64]. Women who were bullied in childhood had higher BMI than non-bullied participants and were at increased risk of being obese (BMI ≥ 30 kg/m2: occasionally bullied: 26.0% v. 19.4%, OR = 1.45, 95% CI 1.18-1.77; frequently bullied: 26.2% v. 19.4%, OR = 1.41, 95% CI 1.09-1.83). Findings remained significant when controlling for childhood risk factors (e.g. parental social class; participants' BMI and psychopathology in childhood) and key adult variables (e.g. adult social class, smoking, diet and exercise). CONCLUSIONS: Bullied children show increases in risk factors for age-related disease in middle adulthood, independent of co-occurring childhood and adult risks. Given the high prevalence of bullying victimization in childhood, tackling this form of psychosocial stress early in life has the potential of reducing risk for age-related disease and its associated burden.

Childhood maltreatment and obesity: systematic review and meta-analysis.

Obesity is a prevalent global-health problem associated with substantial morbidity, impairment and economic burden. Because most readily available forms of treatment are ineffective in the long term, it is essential to advance knowledge of obesity prevention by identifying potentially modifiable risk factors. Findings from experimental studies in non-human primates suggest that adverse childhood experiences may influence obesity risk. However, observations from human studies showed heterogeneous results. To address these inconsistencies, we performed Medline, PsycInfo and Embase searches till 1 August 2012 for articles examining the association between childhood maltreatment and obesity. We then conducted a meta-analysis of the identified studies and explored the effects of various possible sources of bias. A meta-analysis of 41 studies (190 285 participants) revealed that childhood maltreatment was associated with elevated risk of developing obesity over the life-course (odds ratio=1.36; 95% confidence interval=1.26-1.47). Results were not explained by publication bias or undue influence of individual studies. Overall, results were not significantly affected by the measures or definitions used for maltreatment or obesity, nor by confounding by childhood or adult socioeconomic status, current smoking, alcohol intake or physical activity. However, the association was not statistically significant in studies of children and adolescents, focusing on emotional neglect, or adjusting for current depression. Furthermore, the association was stronger in samples including more women and whites, but was not influenced by study quality. Child maltreatment is a potentially modifiable risk factor for obesity. Future research should clarify the mechanisms through which child maltreatment affects obesity risk and explore methods to remediate this effect.

Internalizing disorders and leukocyte telomere erosion: a prospective study of depression, generalized anxiety disorder and post-traumatic stress disorder.

There is evidence that persistent psychiatric disorders lead to age-related disease and premature mortality. Telomere length has emerged as a promising biomarker in studies that test the hypothesis that internalizing psychiatric disorders are associated with accumulating cellular damage. We tested the association between the persistence of internalizing disorders (depression, generalized anxiety disorder and post-traumatic stress disorder) and leukocyte telomere length (LTL) in the prospective longitudinal Dunedin Study (n=1037). Analyses showed that the persistence of internalizing disorders across repeated assessments from ages 11 to 38 years predicted shorter LTL at age 38 years in a dose-response manner, specifically in men (ß=-0.137, 95% confidence interval (CI): -0.232, -0.042, P=0.005). This association was not accounted for by alternative explanatory factors, including childhood maltreatment, tobacco smoking, substance dependence, psychiatric medication use, poor physical health or low socioeconomic status. Additional analyses using DNA from blood collected at two time points (ages 26 and 38 years) showed that LTL erosion was accelerated among men who were diagnosed with internalizing disorder in the interim (ß=-0.111, 95% CI: -0.184, -0.037, P=0.003). No significant associations were found among women in any analysis, highlighting potential sex differences in internalizing-related telomere biology. These findings point to a potential mechanism linking internalizing disorders to accelerated biological aging in the first half of the life course, particularly in men. Because internalizing disorders are treatable, the findings suggest the hypothesis that treating psychiatric disorders in the first half of the life course may reduce the population burden of age-related disease and extend health expectancy.

Exposure to violence during childhood is associated with telomere erosion from 5 to 10 years of age: a longitudinal study.

There is increasing interest in discovering mechanisms that mediate the effects of childhood stress on late-life disease morbidity and mortality. Previous studies have suggested one potential mechanism linking stress to cellular aging, disease and mortality in humans: telomere erosion. We examined telomere erosion in relation to children's exposure to violence, a salient early-life stressor, which has known long-term consequences for well-being and is a major public-health and social-welfare problem. In the first prospective-longitudinal study with repeated telomere measurements in children while they experienced stress, we tested the hypothesis that childhood violence exposure would accelerate telomere erosion from age 5 to age 10 years. Violence was assessed as exposure to maternal domestic violence, frequent bullying victimization and physical maltreatment by an adult. Participants were 236 children (49% females; 42% with one or more violence exposures) recruited from the Environmental-Risk Longitudinal Twin Study, a nationally representative 1994-1995 birth cohort. Each child's mean relative telomere length was measured simultaneously in baseline and follow-up DNA samples, using the quantitative PCR method for T/S ratio (the ratio of telomere repeat copy numbers to single-copy gene numbers). Compared with their counterparts, the children who experienced two or more kinds of violence exposure showed significantly more telomere erosion between age-5 baseline and age-10 follow-up measurements, even after adjusting for sex, socioeconomic status and body mass index (B=-0.052, s.e.=0.021, P=0.015). This finding provides support for a mechanism linking cumulative childhood stress to telomere maintenance, observed already at a young age, with potential impact for life-long health.

Increased serotonin transporter gene (SERT) DNA methylation is associated with bullying victimization and blunted cortisol response to stress in childhood: a longitudinal study of discordant monozygotic twins.

BACKGROUND: Childhood adverse experiences are known to induce persistent changes in the hypothalamic-pituitary-adrenal (HPA) axis reactivity to stress. However, the mechanisms by which these experiences shape the neuroendocrine response to stress remain unclear. Method We tested whether bullying victimization influenced serotonin transporter gene (SERT) DNA methylation using a discordant monozygotic (MZ) twin design. A subsample of 28 MZ twin pairs discordant for bullying victimization, with data on cortisol and DNA methylation, were identified in the Environmental Risk (E-Risk) Longitudinal Twin Study, a nationally representative 1994-1995 cohort of families with twins. RESULTS: Bullied twins had higher SERT DNA methylation at the age of 10 years compared with their non-bullied MZ co-twins. This group difference cannot be attributed to the children's genetic makeup or their shared familial environments because of the study design. Bullied twins also showed increasing methylation levels between the age of 5 years, prior to bullying victimization, and the age of 10 years whereas no such increase was detected in non-bullied twins across time. Moreover, children with higher SERT methylation levels had blunted cortisol responses to stress. CONCLUSIONS: Our study extends findings drawn from animal models, supports the hypothesis that early-life stress modifies DNA methylation at a specific cytosine-phosphate-guanine (CpG) site in the SERT promoter and HPA functioning and suggests that these two systems may be functionally associated.

Prevalence of 25(OH)D insufficiency and overweight/obesity in an adult population from the Central Italy.

Background: Nowadays, excess weight is reaching epidemic proportions and it is necessary to identify patients at greater metabolic risk, in order to determine the most suitable pharmacological and dietetic options. On the other hand, vitamin D insufficiency (or hypovitaminosis D) is prevalent in obese patients. It most commonly occurs in people with inadequate sunlight exposure and nutritional intake of vitamin D, disorders limiting vitamin D absorption, and conditions impairing vitamin D conversion into active metabolite, including certain liver, kidney, and hereditary disorders. It can impair bone mineralization, leading to an increased risk of bone fractures. However, the correlation between the hypovitaminosis D and overweight is poorly understood. Aim: This study aims to evaluate the prevalence of vitamin D deficiency, correlating it to the status of body fat and lipid profile in an adult population from the Italian region of Abruzzo. Methods: A total of 135 participants (BMI≥ 18.5 kg/m²) were enrolled in this observational study: face-to-face interview and physical examination were conducted during their initial evaluation, and their serum and anthropometric parameters were assessed. Results: Among study participants higher BMI, WC, WHtR and WHR were associated to lower vitamin D values, especially in females: a comparison between its values and anthropometric indicators is important to guide the preliminary prevention and early detection of vitamin D insufficiency in general population.

Validation of a high-sensitivity assay for C-reactive protein in human saliva.

This study aimed to validate a high-sensitivity assay for C-reactive protein (CRP) in saliva as an alternative medium to study inflammation in large epidemiological cohorts and young people. We measured CRP in saliva and serum in 61 (29.5% males) healthy adult volunteers. We found a moderate-to-strong association between CRP measured in saliva and in serum (r=.72, p<.001). In agreement with the non-steroidal structure and the high molecular weight of CRP, we observed a low saliva-to-serum CRP ratio (1:1633.64). Furthermore, a dichotomous index of salivary CRP, equivalent to a clinically relevant serum CRP cut-off (3mg/l), was associated to known correlates of systemic inflammation (IL-6, BMI and smoking). Finally, we showed that CRP in saliva is stable at room temperature up to 8h after collection. Our study provides initial evidence suggesting that non-invasive assessment of CRP in saliva allows valid prediction of serum CRP. Salivary CRP may thus facilitate and promote research exploring the correlates of low-grade inflammation in epidemiological studies and makes it feasible to expand psychoneuroimmunology research to pediatric populations.

Single-nucleus RNA-seq2 reveals functional crosstalk between liver zonation and ploidy.

Single-cell RNA-seq reveals the role of pathogenic cell populations in development and progression of chronic diseases. In order to expand our knowledge on cellular heterogeneity, we have developed a single-nucleus RNA-seq2 method tailored for the comprehensive analysis of the nuclear transcriptome from frozen tissues, allowing the dissection of all cell types present in the liver, regardless of cell size or cellular fragility. We use this approach to characterize the transcriptional profile of individual hepatocytes with different levels of ploidy, and have discovered that ploidy states are associated with different metabolic potential, and gene expression in tetraploid mononucleated hepatocytes is conditioned by their position within the hepatic lobule. Our work reveals a remarkable crosstalk between gene dosage and spatial distribution of hepatocytes.

Prognostic significance of atrial fibrillation in thrombolysed and non thrombolysed patients.

AIM: Atrial fibrillation (AF) is considered a frequent complication of acute myocardial infarction (AMI). The aim of this study was to examine the incidence and prognostic significance of AF complicating AMI. METHODS: A total of 848 patients with AMI were examined evaluating: age, sex, coronary risk factors, incidence of AF, prior ischemic events, infarct location, electrocardiogram on admission, thrombolytic therapy, in-hospital complications and mortality. RESULTS: AF was recorded in 84 patients (9.9%). They were older (P<0.0001), less frequently smokers (P<0.007), had higher creatinekinase level (P<0.005) and more advanced heart failure (Killip class >or=2). AF was documented in non-thrombolysed more than in thrombolysed patients (11.2% vs 7.5%). Overall mortality resulted significantly higher in patients with AF (P=0.001); nevertheless it did not result as independent predictor of mortality. Instead, independent predictors of mortality have been Killip class >or= II (P<0.0001), age (P<0.0001) and prior infarction (P<0.002 ). CONCLUSIONS: In our experience, AF cannot be considered an independent predictor of mortality. Contrary, advanced heart failure, either in thrombolysed or not-thrombolysed patients, is an independent predictor of AF and mortality. Nevertheless, AF represents an expression of advanced heart failure, that is worsened by the development of arrhythmia with severe consequences on prognosis.

Polio Patients in Northern Italy, a 50 Year Follow-up.

BACKGROUND: Poliomyelitis was before the immunization an important medical problem. Nowadays polio prior patients (PP) suffer from polio sequelae or have developed post-polio-syndrome (PPS) with increasing paresis, pain and fatigue. OBJECTIVES: To analyze the medical situation 50 years after acute polio. The degree of paresis was compared between the recovery 1952-1961 and 2012.The prevalence of patients fulfilling the criteria for PPS was estimated. METHOD: The study was performed in Italy. Included were PP with rehabilitation after acute polio 1952-1961 and in 2012. During the years PP underwent yearly evaluation. A thorough neurological examination was performed in 2012. A telephone interview with questions concerning pain, paresis, fatigue, walking aids and concomitant diseases was performed in 2012. The patients were divided in two groups, if they fulfilled the criteria for PPS or not. RESULTS: Included were 67(94%) patients receiving rehabilitation after acute poliomyelitis and 2012. 78% were walkers, half of the PPS used wheelchair. Eight out of ten suffered from pain. Four out of ten fulfilled the PPS criteria. Pain was slightly more common in PPS. CONCLUSION: Female gender, fatigue and wheelchair dependency were significantly more common in PPS while pain was common in both groups.

Inflammation and clinical response to treatment in depression: A meta-analysis.

The depressive state has been characterised as one of elevated inflammation, which holds promise for better understanding treatment-resistance in affective disorders as well as for future developments in treatment stratification. Aiming to investigate alterations in the inflammatory profiles of individuals with depression as putative biomarkers for clinical response, we conducted meta-analyses examining data from 35 studies that investigated inflammation before and after treatment in depressed patients together with a measure of clinical response. There were sufficient data to analyse IL-6, TNFα and CRP. Levels of IL-6 decreased with antidepressant treatment regardless of outcome, whereas persistently elevated TNFα was associated with prospectively determined treatment resistance. Treatment non-responders tended to have higher baseline inflammation, using a composite measure of inflammatory markers. Our findings suggest that elevated levels of inflammation are contributory to treatment resistance. Combining inflammatory biomarkers might prove a useful tool to improve diagnosis and detection of treatment refractoriness, and targeting persistent inflammation in treatment-resistant depression may offer a potential target for the development of novel intervention strategies.

Diffusion of teicoplanin and vancomycin in agar.

Teicoplanin, although more active than vancomycin [by minimum inhibitory concentration (MIC)], produces smaller inhibition zones in sensitivity testing with 30-microgram disks. Our data support the hypothesis that this is due to lower diffusion of teicoplanin in agar media. After 6 hr of incubation, approximately 70% of vancomycin, but only 20% of teicoplanin entered the agar from a paper disk charged with 30 micrograms of antibiotic. This is due to a difference between the diffusion coefficients: 0.47 mm2/hr for teicoplanin and 0.72 mm2/hr for vancomycin. With the methodology used in this work, it is possible to calculate the range of concentrations of the antibiotic occurring at times likely to include the critical time--the time when the inhibition zone is formed--of most strains at any given distance from the reservoir. One can thus estimate the breakpoint diameter for a given MIC breakpoint; for example, an MIC breakpoint of less than or equal to 4 micrograms/ml would correspond to a greater than or equal to 15-mm breakpoint diameter for vancomycin (30-microgram disk) and a greater than or equal to 13-mm breakpoint diameter for teicoplanin (30-microgram disk).

Plasma levels of endothelin-1 increase in patients with sarcoidosis and fall after disease remission.

BACKGROUND: Sarcoidosis is a chronic systemic disease, characterized by an imbalance of immunity processes and the presence of granuloma. Endothelin-1, a new vasoactive and bronchoconstrictive peptide, is a powerful mitogen for smooth muscle cells and fibroblasts and plays a role in the inflammation state. We postulate that endothelin-1 has a role in sarcoidosis. METHODS: We studied the behaviour of circulating levels of endothelin-1 in 20 patients with sarcoidosis and its correlation with some biochemical parameters of activity disease, such as erythrocyte sedimentation rate (ESR) and serum angiotensin-converting enzyme (SACE). We measured serum levels of ESR, SACE, calcium and plasma endothelin-1 levels in all patients at the beginning of the study and one again in 9 patients with clinical-biochemical remission of disease after steroid treatment. RESULTS: In patients with sarcoidosis, circulating levels of endothelin-1, SACE and ESR were significantly higher (p<0.001) than those of healthy subjects. Moreover, in patients with pulmonary involvement, there was a significant statistical difference (p<0.001) between endothelin-1 levels and radiological stage compared to normal subjects. In the 9 patients with remission of disease, both endothelin-1 levels and parameters of activity disease normalized. CONCLUSIONS: Our results seem to suggest that the increase of plasma endothelin-1 levels in active sarcoidosis can represent an expression of the endothelial dysfunction and reflect the picture of cellular activation.

Model choice for teicoplanin kinetics in man.

Teicoplanin is a new long half life antibiotic, characterized by a polyexponential profile. A pharmacokinetic study was made in healthy volunteers receiving 15, 20 and 25 mg/Kg iv doses of Teicoplanin. Plasma concentration-time data were fitted by a polyexponential equation, consisting of two, three, four and five terms. The software was PCNONLIN, using the Gauss-Newton method with Harley's and Levenberg's modification and 1/Y2 as a weighting factor, where Y is the predicted concentration. The increase of the number of exponential terms from two to five resulted in a continuous minimization of the sum of the weighted squared residuals. To test whether or not this sum had been sufficiently reduced to justify the fitting with additional exponential terms, Akaike, Gallant and F-ratio test criteria were used. The four exponential equation best fit most of the data sets. However, the estimates of the main parameters (AUC, V, Vss, CL, Css min, Css max, number of doses to reach 95%ss) calculated according to tri and four-exponential models did not significantly differ. In the dose range studied teicoplanin pharmacokinetics are linear. In conclusion, an additional exponential term in the equation can significantly improve the best fit of teicoplanin plasma curves according to the above criteria, but it may not lead to a significant variation of the main pharmacokinetic parameters and derived values. This indicated that for clinical purposes a tri exponential model suffices for describing the kinetics of Teicoplanin in man.

Leptin deficiency in maltreated children.

Consistent with findings from experimental research in nonhuman primates exposed to early-life stress, children exposed to maltreatment are at high risk of detrimental physical health conditions, such as obesity and systemic inflammation. Because leptin is a key molecule involved in the regulation of both energy balance and immunity, we investigated abnormalities in leptin physiology among maltreated children. We measured leptin, body mass index and C-reactive protein in 170 12-year-old children members of the Environmental-Risk Longitudinal Twin Study, for whom we had prospectively-collected information on maltreatment exposure. We found that maltreated children exhibited blunted elevation in leptin levels in relation to increasing levels of physiological stimuli, adiposity and inflammation, compared with a group of non-maltreated children matched for gender, zygosity and socioeconomic status. These findings were also independent of key potential artifacts and confounders, such as time of day at sample collection, history of food insecurity, pubertal maturation and depressive symptoms. Furthermore, using birth weight as a proxy measure for leptin, we found that physiological abnormalities were presumably not present at birth in children who went on to be maltreated but only emerged over the course of childhood, after maltreatment exposure. Leptin deficiency may contribute to onset, persistence and progression of physical health problems in maltreated children.

Pharmacokinetics of A40926 in rats after single intravenous and subcutaneous doses.

A40926 is a new glycopeptide antibiotic with unique activity against Neisseria gonorrhoeae and high and prolonged levels in mouse blood (B. P. Goldstein, E. Selva, L. Gastaldo, M. Berti, R. Pallanza, F. Ripamonti, P. Ferrari, M. Denaro, V. Arioli, and G. Cassani, Antimicrob. Agents Chemother., 31:1961-1966, 1987). We studied the pharmacokinetics of A40926 in rats after single intravenous and subcutaneous 10-mg/kg (body weight) doses. Concentrations in plasma and urine were determined by microbiological assay. After intravenous administration, high concentrations of A40926, ranging from 132 mg/liter at 3 min to 0.7 mg/liter at 96 h, were found in plasma. Concentrations declined with a three-exponential decay correlated with a prolonged, biphasic distribution and a slow elimination (terminal half-life, 61.22 h). After completion of the distribution, the compound was widely distributed to the extravascular space. The rate-limiting step in the elimination of A40926 from the body appears to be the slow return from the deep compartment into the central one. A40926 was rapidly absorbed from the injection site after subcutaneous administration, and its availability was close to 90%. The percentage of the dose excreted in urine in 120 h was 35.9%.