A database and deep learning toolbox for noise-optimized, generalized spike inference from calcium imaging

Inference of action potentials (‘spikes’) from neuronal calcium signals is complicated by the scarcity of simultaneous measurements of action potentials and calcium signals (‘ground truth’). In this study, we compiled a large, diverse ground truth database from publicly available and newly performed recordings in zebrafish and mice covering a broad range of calcium indicators, cell types and signal-to-noise ratios, comprising a total of more than 35 recording hours from 298 neurons. We developed an algorithm for spike inference (termed CASCADE) that is based on supervised deep networks, takes advantage of the ground truth database, infers absolute spike rates and outperforms existing model-based algorithms. To optimize performance for unseen imaging data, CASCADE retrains itself by resampling ground truth data to match the respective sampling rate and noise level; therefore, no parameters need to be adjusted by the user. In addition, we developed systematic performance assessments for unseen data, openly released a resource toolbox and provide a user-friendly cloud-based implementation

Diabetes and Co-morbid Depression Among Racially Diverse, Low-Income Adults

Background Research suggests individuals with diabetes are twice as likely as those without diabetes to be clinically depressed. Still unknown is the relationship between diabetes and depression in socioeconomically disadvantaged populations. Purpose We examined the relationship between diabetes and depressive symptoms in a large, racially diverse, low-income cohort in the southeastern USA. Methods A total of 69,068 adults were recruited from community health centers in 12 southeastern states. A fully adjusted polytomous logistic regression model tested the relationship between demographics, lifestyle behaviors, antidepressant use, body mass index, diabetes diagnosis, diabetes duration, diabetes medication compliance, and depressive symptoms using the Centers for Epidemiological Studies Depression scale. Results Diabetes was present in 21.7% of sample. While a diabetes diagnosis was associated with having severe depressive symptoms (AOR, 1.24; 95% CI, 1.14–1.34), demographics, lifestyle behaviors, body mass index and antidepressant use were more strongly associated with severe depressive symptoms than a diabetes diagnosis. Conclusions Having diabetes was associated with the presence and severity of depressive symptoms in a large, low-income sample of racially diverse adults. However, the relationship between diabetes and depressive symptoms was weaker than in other studies with higher socioeconomic groups

Dietary fat intake and lung cancer risk: a pooled analysis

Purpose Dietary fat may play a role in lung carcinogenesis. Findings from epidemiologic studies, however, remain inconsistent. In this pooled analysis of 10 prospective cohort studies from the United States, Europe, and Asia, we evaluated the associations of total and specific types of dietary fat with lung cancer risk. Methods Cox regression was used to estimate hazard ratios (HRs) and 95% CIs in each cohort. Study-specific risk estimates were pooled by random- or fixed-effects meta-analysis. The first 2 years of follow-up were excluded to address potential influence of preclinical dietary changes. Results Among 1,445,850 participants, 18,822 incident cases were identified (mean follow-up, 9.4 years). High intakes of total and saturated fat were associated with an increased risk of lung cancer (for highest v lowest quintile: HR, 1.07 and 1.14, respectively; 95% CI, 1.00 to 1.15 and 1.07 to 1.22, respectively; P for trend for both < .001). The positive association of saturated fat was more evident among current smokers (HR, 1.23; 95% CI, 1.13 to 1.35; P for trend < .001) than former/never smokers (P for interaction = .004), and for squamous cell and small cell carcinoma (HR, 1.61 and 1.40, respectively; 95% CI, 1.38 to 1.88 and 1.17 to 1.67, respectively; P for trend for both < .001) than other histologic types (P for heterogeneity < .001). In contrast, a high intake of polyunsaturated fat was associated with a decreased risk of lung cancer (HR, 0.92; 95% CI, 0.87 to 0.98 for highest v lowest quintile; P for trend = .02). A 5% energy substitution of saturated fat with polyunsaturated fat was associated with a 16% to 17% lower risk of small cell and squamous cell carcinoma. No associations were found for monounsaturated fat. Conclusion Findings from this large, international cohort consortium suggest that modifying dietary fat intake (ie, replacing saturated fat with polyunsaturated fat) may reduce lung cancer risk, particularly among smokers and for squamous cell and small cell carcinoma