Leveraging OpenStack and Ceph for a Controlled-Access Data Cloud

While traditional HPC has and continues to satisfy most workflows, a new generation of researchers has emerged looking for sophisticated, scalable, on-demand, and self-service control of compute infrastructure in a cloud-like environment. Many also seek safe harbors to operate on or store sensitive and/or controlled-access data in a high capacity environment. To cater to these modern users, the Minnesota Supercomputing Institute designed and deployed Stratus, a locally-hosted cloud environment powered by the OpenStack platform, and backed by Ceph storage. The subscription-based service complements existing HPC systems by satisfying the following unmet needs of our users: a) on-demand availability of compute resources, b) long-running jobs (i.e., $> 30$ days), c) container-based computing with Docker, and d) adequate security controls to comply with controlled-access data requirements. This document provides an in-depth look at the design of Stratus with respect to security and compliance with the NIH's controlled-access data policy. Emphasis is placed on lessons learned while integrating OpenStack and Ceph features into a so-called "walled garden", and how those technologies influenced the security design. Many features of Stratus, including tiered secure storage with the introduction of a controlled-access data "cache", fault-tolerant live-migrations, and fully integrated two-factor authentication, depend on recent OpenStack and Ceph features.Comment: 7 pages, 5 figures, PEARC '18: Practice and Experience in Advanced Research Computing, July 22--26, 2018, Pittsburgh, PA, US

Is recurrence in major depressive disorder related to bipolarity and mixed features? Results from the BRIDGE-II-Mix study

Background: Current classifications separate Bipolar (BD) from Major Depressive Disorder (MDD) based on polarity rather than recurrence. We aimed to determine bipolar/mixed feature frequency in a large MDD multinational sample with (High-Rec) and without (Low-Rec) >3 recurrences, comparing the two subsamples. Methods: We measured frequency of bipolarity/hypomanic features during current depressive episodes (MDEs) in 2347 MDD patients from the BRIDGE-II-mix database, comparing High-Rec with Low-Rec. We used Bonferroni-corrected Student's t-test for continuous, and chi-squared test, for categorical variables. Logistic regression estimated the size of the association between clinical characteristics and High-Rec MDD. Results: Compared to Low-Rec (n = 1084, 46.2%), High-Rec patients (n = 1263, 53.8%) were older, with earlier depressive onset, had more family history of BD, more atypical features, suicide attempts, hospitalisations, and treatment resistance and (hypo)manic switches when treated with antidepressants, higher comorbidity with borderline personality disorder, and more hypomanic symptoms during current MDE, resulting in higher rates of mixed depression according to both DSM-5 and research-based diagnostic (RBDC) criteria. Logistic regression showed age at first symptoms < 30 years, current MDE duration ≤ 1 month, hypomania/mania among first-degree relatives, past suicide attempts, treatment-resistance, antidepressant-induced swings, and atypical, mixed, or psychotic features during MDE to associate with High-Rec. Limitations Number of MDEs for defining recurrence was arbitrary; cross-sectionality did not allow assessment of conversion from MDD to BD. Conclusions: High-Rec MDD differed from Low-Rec group for several clinical/epidemiological variables, including bipolar/mixed features. Bipolarity specifier and RBDC were more sensitive than DSM-5 criteria in detecting bipolar and mixed features in MDD

Aggressiveness in depression: a neglected symptom possibly associated with bipolarity and mixed features

OBJECTIVE: To evaluate aggressiveness during a major depressive episode (MDE) and its relationship with bipolar disorder (BD) in a post hoc analysis of the BRIDGE-II-MIX study. METHOD: A total of 2811 individuals were enrolled in this multicenter cross-sectional study. MDE patients with (MDE-A, n = 399) and without aggressiveness (MDE-N, n = 2412) were compared through chi-square test or Student's t-test. A stepwise backward logistic regression model was performed. RESULTS: MDE-A group was more frequently associated with BD (P < 0.001), while aggressiveness was negatively correlated with unipolar depression (P < 0.001). At the logistic regression, aggressiveness was associated with the age at first depressive episode (P < 0.001); the severity of mania (P = 0.03); the diagnosis of BD (P = 0.001); comorbid borderline personality disorder (BPD) (P < 0.001) but not substance abuse (P = 0.63); no current psychiatric treatment (P < 0.001); psychotic symptoms (P = 0.007); the marked social/occupational impairment (P = 0.002). The variable most significantly associated with aggressiveness was the presence of DSM-5 mixed features (P < 0.001, OR = 3.815). After the exclusion of BPD, the variable of lifetime suicide attempts became significant (P = 0.013, OR = 1.405). CONCLUSION: Aggressiveness seems to be significantly associated with bipolar spectrum disorders, independently from BPD and substance abuse. Aggressiveness should be considered as a diagnostic criterion for the mixed features specifier and a target of tailored treatment strategy

The implications of hypersomnia in the context of major depression: Results from a large, international, observational study

According to the DSM-5, 'reduction in the need for sleep' is the only sleep-related criteria for mixed features in depressive episodes. We aimed at studying the prevalence, clinical correlates and the role of hypersomnia in a sample of acutely depressed patients. Secondarily, we factors significantly increasing the odds of hypersomnia were studied. We conducted a post-hoc analysis of the BRIDGE-II-Mix study. Variables were compared between patients with hypersomnia (SLEEP+) and with insomnia (SLEEP-) with standard bivariate tests. A stepwise backward logistic regression model was performed with SLEEP+ as dependent variable. A total of 2514 subjects were dichotomized into SLEEP+ (n = 423, 16.8%) and SLEEP- (n = 2091, 83.2%). SLEEP+ had significant higher rates of obese BMI (p < 0.001), BD diagnosis (p = 0.027), severe BD (p < 0.001), lifetime suicide attempts (p < 0.001), lower age at first depression (p = 0.004) than SLEEP-. Also, SLEEP+ had significantly poorer response to antidepressants (AD) such as (hypo)manic switches, AD resistance, affective lability, or irritability (all 0<0.005). Moreover, SLEEP+ had significantly higher rates of mixed-state specifiers than SLEEP- (all 0 < 0.006). A significant contribution to hypersomnia in our regression model was driven by metabolic-related features, such as 'current bulimia' (OR = 4.21) and 'overweight/obese BMI (OR = 1.42)'. Globally, hypersomnia is associated with poor outcome in acute depression. Hypersomnia is strongly associated with mixed features and bipolarity. Metabolic aspects could influence the expression of hypersomnia, worsening the overall clinical outcome. Along with commonly used screening tools, detection of hypersomnia has potential, costless discriminative validity in the differential diagnosis unipolar and bipolar depression

Post-glacial colonisation of Europe by the wood mouse, Apodemus sylvaticus : evidence of a northern refugium and dispersal with humans

The wood mouse Apodemus sylvaticus is an opportunistic rodent that is found throughout most of the European mainland. It is present on many islands around the margins of the continent and in northern Africa. The species has been the subject of previous phylogeographic studies but these have focussed on the more southerly part of its range. A substantial number of new samples, many of them from the periphery of the species’ range, contribute to an exceptional dataset comprising 981 mitochondrial cytochrome b sequences. These new data provide sufficient resolution to transform our understanding of the species’ survival through the last glaciation and its subsequent re-colonisation of the continent. The deepest genetic split we found is in agreement with previous studies and runs from the Alps to central Ukraine, but we further distinguish two separate lineages in wood mice to the north and west of this line. It is likely that this part of Europe was colonised from two refugia, putatively located in the Iberian peninsula and the Dordogne or Carpathian region. The wood mouse therefore joins the growing number of species with extant populations that appear to have survived the Last Glacial Maximum in northern refugia, rather than solely in traditionally recognised refugial locations in the southern European peninsulas. Furthermore, the existence of a northern refugium for the species was predicted in a study of mitochondrial variation in a specific parasite of the wood mouse, demonstrating the potential value of data from parasites to phylogeographic studies. Lastly, the presence of related haplotypes in widely disparate locations, often on islands or separated by substantial bodies of water, demonstrates the propensity of the wood mouse for accidental human-mediated transport

Factores predictores de éxito en la terapia de cánulas nasales de alto flujo en la insuficiencia respiratoria aguda secundaria a COVID-19 en la unidad de urgencias de adultos

Objetivo: Determinar los factores asociados al éxito de la terapia de cánulas nasales de alto flujo (CNAF) en el manejo de la insuficiencia respiratoria aguda (IRA) secundaria a COVID-19 en una unidad de urgencia de alta complejidad. Método: Estudio descriptivo y transversal. Se incluyeron sujetos mayores de 18 años con IRA secundaria a COVID-19 y requerimientos de CNAF según el protocolo institucional. El éxito o el fracaso de la terapia se definió según la progresión hacia ventilación mecánica invasiva. Se realizó un análisis descriptivo y asociación de variables según grupo de éxito y fracaso. Para evaluar la asociación de variables se utilizó un modelo univariado, un modelo multivariado, el cálculo del poder predictivo mediante curva ROC y el punto de corte de variables asociadas. Resultados: Se incluyeron 181 sujetos, de los cuales el 68% tuvieron éxito en la terapia con CNAF. El 72% fueron hombres y la edad media fue de 65 años. Ambos grupos mostraron homogeneidad en sus características clínicas y sociodemográficas. El análisis multivariado mostró que a mayor saturación de oxígeno a los 5 minutos de iniciada la terapia aumenta la probabilidad de su éxito un 51% (odds ratio: 0.49; intervalo de confianza del 95%: 0.40-0.60). Asimismo, saturaciones sobre el 94% a los 5 minutos de iniciada la terapia podrían determinar el éxito terapéutico (sensibilidad del 67% y especificidad del 39%). Conclusiones: Nuestro estudio sugiere que una mayor saturación de oxígeno a los 5 minutos de inicio de la terapia con CNAF en la unidad de urgencia se asocia a mayor éxito terapéutico y menor probabilidad de intubación orotraqueal en pacientes con IRA por COVID-19

Relationships between recurrence and polarity in major depressive disorders: Pooled analysis of the BRIDGE and BRIDGE-II-MIX cohorts

BACKGROUND current classifications of mood disorders focus on polarity rather than recurrence, separating bipolar disorder from major depressive disorder (MDD). The aim of the present study is to explore the possible relationships between number and frequency of depressive episodes and clinical variables associated to bipolarity, in a large sample of MDD patients. METHODS the clinical characteristics of 7055 patients with MDD were analyzed and compared according to the number and frequency of depressive episodes. Two stepwise backward logistic regression model were used to identify the predictive value of clinical features based on the presence of high number (≥3 episodes) and high frequency (≥3 episodes/year) of depressive episodes. RESULTS high-recurrence and high-frequency MDD patients showed greater family history for bipolar disorder, higher prevalence of psychotic features, more suicide attempts, higher rates of treatment resistance and mood switches with antidepressants (ADs) and higher rates of bipolarity diagnosis according to Angst criteria, compared to low-recurrence and low-frequency patients. Logistic regressions showed that a brief current depressive episode, a previous history of treatment resistance and AD-induced mood switches, a diagnosis of bipolarity and comorbid borderline personality disorder were the variables associated with both high-recurrence and high-frequency depression. LIMITATIONS the study participating centers were not randomly selected and several variables were retrospectively assessed. CONCLUSIONS even in the absence of hypomanic/manic episodes, high-recurrence and high-frequency MDD seem to be in continuity with the bipolar spectrum disorders in terms of clinical features and, perhaps, treatment response

Is recurrence in major depressive disorder related to bipolarity and mixed features? Results from the BRIDGE-II-Mix study

Background Current classifications separate Bipolar (BD) from Major Depressive Disorder (MDD) based on polarity rather than recurrence. We aimed to determine bipolar/mixed feature frequency in a large MDD multinational sample with (High-Rec) and without (Low-Rec) >3 recurrences, comparing the two subsamples. Methods We measured frequency of bipolarity/hypomanic features during current depressive episodes (MDEs) in 2347 MDD patients from the BRIDGE-II-mix database, comparing High-Rec with Low-Rec. We used Bonferroni-corrected Student's t-test for continuous, and chi-squared test, for categorical variables. Logistic regression estimated the size of the association between clinical characteristics and High-Rec MDD. Results Compared to Low-Rec (n = 1084, 46.2%), High-Rec patients (n = 1263, 53.8%) were older, with earlier depressive onset, had more family history of BD, more atypical features, suicide attempts, hospitalisations, and treatment resistance and (hypo)manic switches when treated with antidepressants, higher comorbidity with borderline personality disorder, and more hypomanic symptoms during current MDE, resulting in higher rates of mixed depression according to both DSM-5 and research-based diagnostic (RBDC) criteria. Logistic regression showed age at first symptoms < 30 years, current MDE duration ≤ 1 month, hypomania/mania among first-degree relatives, past suicide attempts, treatment-resistance, antidepressant-induced swings, and atypical, mixed, or psychotic features during MDE to associate with High-Rec. Limitations Number of MDEs for defining recurrence was arbitrary; cross-sectionality did not allow assessment of conversion from MDD to BD. Conclusions High-Rec MDD differed from Low-Rec group for several clinical/epidemiological variables, including bipolar/mixed features. Bipolarity specifier and RBDC were more sensitive than DSM-5 criteria in detecting bipolar and mixed features in MDD

Is recurrence in major depressive disorder related to bipolarity and mixed features? Results from the BRIDGE-II-Mix study

Background: Current classifications separate Bipolar (BD) from Major Depressive Disorder (MDD) based on polarity rather than recurrence. We aimed to determine bipolar/mixed feature frequency in a large MDD multinational sample with (High-Rec) and without (Low-Rec) >3 recurrences, comparing the two subsamples. Methods: We measured frequency of bipolarity/hypomanic features during current depressive episodes (MDEs) in 2347 MDD patients from the BRIDGE-II-mix database, comparing High-Rec with Low-Rec. We used Bonferroni-corrected Student's t-test for continuous, and chi-squared test, for categorical variables. Logistic regression estimated the size of the association between clinical characteristics and High-Rec MDD. Results: Compared to Low-Rec (n = 1084, 46.2%), High-Rec patients (n = 1263, 53.8%) were older, with earlier depressive onset, had more family history of BD, more atypical features, suicide attempts, hospitalisations, and treatment resistance and (hypo)manic switches when treated with antidepressants, higher comorbidity with borderline personality disorder, and more hypomanic symptoms during current MDE, resulting in higher rates of mixed depression according to both DSM-5 and research-based diagnostic (RBDC) criteria. Logistic regression showed age at first symptoms < 30 years, current MDE duration ≤ 1 month, hypomania/mania among first-degree relatives, past suicide attempts, treatment-resistance, antidepressant-induced swings, and atypical, mixed, or psychotic features during MDE to associate with High-Rec. Limitations Number of MDEs for defining recurrence was arbitrary; cross-sectionality did not allow assessment of conversion from MDD to BD. Conclusions: High-Rec MDD differed from Low-Rec group for several clinical/epidemiological variables, including bipolar/mixed features. Bipolarity specifier and RBDC were more sensitive than DSM-5 criteria in detecting bipolar and mixed features in MDD