A DevOps approach to integration of software components in an EU research project

We present a description of the development and deployment infrastructure being created to support the integration effort of HARNESS, an EU FP7 project. HARNESS is a multi-partner research project intended to bring the power of heterogeneous resources to the cloud. It consists of a number of different services and technologies that interact with the OpenStack cloud computing platform at various levels. Many of these components are being developed independently by different teams at different locations across Europe, and keeping the work fully integrated is a challenge. We use a combination of Vagrant based virtual machines, Docker containers, and Ansible playbooks to provide a consistent and up-to-date environment to each developer. The same playbooks used to configure local virtual machines are also used to manage a static testbed with heterogeneous compute and storage devices, and to automate ephemeral larger-scale deployments to Grid5000. Access to internal projects is managed by GitLab, and automated testing of services within Docker-based environments and integrated deployments within virtual-machines is provided by Buildbot

Women are warmer but no less assertive than men: gender and language on Facebook

Using a large social media dataset and open-vocabulary methods from computational linguistics, we explored differences in language use across gender, affiliation, and assertiveness. In Study 1, we analyzed topics (groups of semantically similar words) across 10 million messages from over 52,000 Facebook users. Most language differed little across gender. However, topics most associated with self-identified female participants included friends, family, and social life, whereas topics most associated with self-identified male participants included swearing, anger, discussion of objects instead of people, and the use of argumentative language. In Study 2, we plotted male- and female-linked language topics along two interpersonal dimensions prevalent in gender research: affiliation and assertiveness. In a sample of over 15,000 Facebook users, we found substantial gender differences in the use of affiliative language and slight differences in assertive language. Language used more by self-identified females was interpersonally warmer, more compassionate, polite, and—contrary to previous findings—slightly more assertive in their language use, whereas language used more by self-identified males was colder, more hostile, and impersonal. Computational linguistic analysis combined with methods to automatically label topics offer means for testing psychological theories unobtrusively at large scale.This work was supported by the Templeton Religion Trust

Living in the past, present, and future: measuring temporal orientation with language

OBJECTIVE: Temporal orientation refers to individual differences in the relative emphasis one places on the past, present, or future, and is related to academic, financial, and health outcomes. We propose and evaluate a method for automatically measuring temporal orientation through language expressed on social media. METHOD: Judges rated the temporal orientation of 4,302 social media messages. We trained a classifier based on these ratings, which could accurately predict the temporal orientation of new messages in a separate validation set (accuracy/mean sensitivity = .72; mean specificity = .77). We used the classifier to automatically classify 1.3 million messages written by 5,372 participants (50% female, aged 13-48). Finally, we tested whether individual differences in past, present, and future orientation differentially related to gender, age, Big Five personality, satisfaction with life, and depressive symptoms. RESULTS: Temporal orientations exhibit several expected correlations with age, gender, and Big Five personality. More future-oriented people were older, more likely to be female, more conscientious, less impulsive, less depressed, and more satisfied with life; present orientation showed the opposite pattern. CONCLUSION: Language-based assessments can complement and extend existing measures of temporal orientation, providing an alternative approach and additional insights into language and personality relationships. This article is protected by copyright. All rights reserved.Support for this article was provided by grant #63597 from the Robert Wood Johnson Foundation (M. E. P. Seligman, PI) and by a grant from the Templeton Religion Trust (M.E.P. Seligman, H. A. Schwartz, L. H. Ungar, co-PIs)

Personality, gender, and age in the language of social media: the open-vocabulary approach

We analyzed 700 million words, phrases, and topic instances collected from the Facebook messages of 75,000 volunteers, who also took standard personality tests, and found striking variations in language with personality, gender, and age. In our open-vocabulary technique, the data itself drives a comprehensive exploration of language that distinguishes people, finding connections that are not captured with traditional closed-vocabulary word-category analyses. Our analyses shed new light on psychosocial processes yielding results that are face valid (e.g., subjects living in high elevations talk about the mountains), tie in with other research (e.g., neurotic people disproportionately use the phrase ‘sick of’ and the word ‘depressed’), suggest new hypotheses (e.g., an active life implies emotional stability), and give detailed insights (males use the possessive ‘my’ when mentioning their ‘wife’ or ‘girlfriend’ more often than females use ‘my’ with ‘husband’ or 'boyfriend’). To date, this represents the largest study, by an order of magnitude, of language and personalit

The language of religious affiliation: social, emotional, and cognitive differences

Religious affiliation is an important identifying characteristic for many individuals and relates to numerous life outcomes including health, well-being, policy positions, and cognitive style. Using methods from computational linguistics, we examined language from 12,815 Facebook users in the United States and United Kingdom who indicated their religious affiliation. Religious individuals used more positive emotion words (β = .278, p < .0001) and social themes such as family (β = .242, p < .0001), while nonreligious people expressed more negative emotions like anger (β = −.427, p < .0001) and categories related to cognitive processes, like tentativeness (β = −.153, p < .0001). Nonreligious individuals also used more themes related to the body (β = −.265, p < .0001) and death (β = −.247, p < .0001). The findings offer directions for future research on religious affiliation, specifically in terms of social, emotional, and cognitive differences

Joint effect of phosphorus limitation and temperature on alkaline phosphatase activity and somatic growth in Daphnia magna

Alkaline phosphatase (AP) is a potential biomarker for phosphorus (P) limitation in zooplankton. However, knowledge about regulation of AP in this group is limited. In a laboratory acclimation experiment, we investigated changes in body AP concentration for Daphnia magna kept for 6 days at 10, 15, 20 and 25°C and fed algae with 10 different molar C:P ratios (95–660). In the same experiment, we also assessed somatic growth of the animals since phosphorus acquisition is linked to growth processes. Overall, non-linear but significant relationships of AP activity with C:P ratio were observed, but there was a stronger impact of temperature on AP activity than of P limitation. Animals from the lowest temperature treatment had higher normalized AP activity, which suggests the operation of biochemical temperature compensation mechanisms. Body AP activity increased by a factor of 1.67 for every 10°C decrease in temperature. These results demonstrate that temperature strongly influences AP expression. Therefore, using AP as a P limitation marker in zooplankton needs to consider possible confounding effects of temperature. Both temperature and diet affected somatic growth. The temperature effect on somatic growth, expressed as the Q10 value, responded non-linearly with C:P, with Q10 ranging between 1.9 for lowest food C:P ratio and 1.4 for the most P-deficient food. The significant interaction between those two variables highlights the importance of studying temperature-dependent changes of growth responses to food quality

The Human Polyoma JC Virus Agnoprotein Acts as a Viroporin

Virus infections can result in a range of cellular injuries and commonly this involves both the plasma and intracellular membranes, resulting in enhanced permeability. Viroporins are a group of proteins that interact with plasma membranes modifying permeability and can promote the release of viral particles. While these proteins are not essential for virus replication, their activity certainly promotes virus growth. Progressive multifocal leukoencephalopathy (PML) is a fatal demyelinating disease resulting from lytic infection of oligodendrocytes by the polyomavirus JC virus (JCV). The genome of JCV encodes six major proteins including a small auxiliary protein known as agnoprotein. Studies on other polyomavirus agnoproteins have suggested that the protein may contribute to viral propagation at various stages in the replication cycle, including transcription, translation, processing of late viral proteins, assembly of virions, and viral propagation. Previous studies from our and other laboratories have indicated that JCV agnoprotein plays an important, although as yet incompletely understood role in the propagation of JCV. Here, we demonstrate that agnoprotein possesses properties commonly associated with viroporins. Our findings demonstrate that: (i) A deletion mutant of agnoprotein is defective in virion release and viral propagation; (ii) Agnoprotein localizes to the ER early in infection, but is also found at the plasma membrane late in infection; (iii) Agnoprotein is an integral membrane protein and forms homo-oligomers; (iv) Agnoprotein enhances permeability of cells to the translation inhibitor hygromycin B; (v) Agnoprotein induces the influx of extracellular Ca2+; (vi) The basic residues at amino acid positions 8 and 9 of agnoprotein key are determinants of the viroporin activity. The viroporin-like properties of agnoprotein result in increased membrane permeability and alterations in intracellular Ca2+ homeostasis leading to membrane dysfunction and enhancement of virus release

Evolution of sex-specific pace-of-life syndromes: genetic architecture and physiological mechanisms

Sex differences in life history, physiology, and behavior are nearly ubiquitous across taxa, owing to sex-specific selection that arises from different reproductive strategies of the sexes. The pace-of-life syndrome (POLS) hypothesis predicts that most variation in such traits among individuals, populations, and species falls along a slow-fast pace-of-life continuum. As a result of their different reproductive roles and environment, the sexes also commonly differ in pace-of-life, with important consequences for the evolution of POLS. Here, we outline mechanisms for how males and females can evolve differences in POLS traits and in how such traits can covary differently despite constraints resulting from a shared genome. We review the current knowledge of the genetic basis of POLS traits and suggest candidate genes and pathways for future studies. Pleiotropic effects may govern many of the genetic correlations, but little is still known about the mechanisms involved in trade-offs between current and future reproduction and their integration with behavioral variation. We highlight the importance of metabolic and hormonal pathways in mediating sex differences in POLS traits; however, there is still a shortage of studies that test for sex specificity in molecular effects and their evolutionary causes. Considering whether and how sexual dimorphism evolves in POLS traits provides a more holistic framework to understand how behavioral variation is integrated with life histories and physiology, and we call for studies that focus on examining the sex-specific genetic architecture of this integration