Nanocuration workflows: Establishing best practices for identifying, inputting, and sharing data to inform decisions on nanomaterials

There is a critical opportunity in the field of nanoscience to compare and integrate information across diverse fields of study through informatics (i.e., nanoinformatics). This paper is one in a series of articles on the data curation process in nanoinformatics (nanocuration). Other articles in this series discuss key aspects of nanocuration (temporal metadata, data completeness, database integration), while the focus of this article is on the nanocuration workflow, or the process of identifying, inputting, and reviewing nanomaterial data in a data repository. In particular, the article discusses: 1) the rationale and importance of a defined workflow in nanocuration, 2) the influence of organizational goals or purpose on the workflow, 3) established workflow practices in other fields, 4) current workflow practices in nanocuration, 5) key challenges for workflows in emerging fields like nanomaterials, 6) examples to make these challenges more tangible, and 7) recommendations to address the identified challenges. Throughout the article, there is an emphasis on illustrating key concepts and current practices in the field. Data on current practices in the field are from a group of stakeholders active in nanocuration. In general, the development of workflows for nanocuration is nascent, with few individuals formally trained in data curation or utilizing available nanocuration resources (e.g., ISA-TAB-Nano). Additional emphasis on the potential benefits of cultivating nanomaterial data via nanocuration processes (e.g., capability to analyze data from across research groups) and providing nanocuration resources (e.g., training) will likely prove crucial for the wider application of nanocuration workflows in the scientific community

Survival of icy grains in debris discs. The role of photosputtering

We put theoretical constraints on the presence and survival of icy grains in debris discs. Particular attention is paid to UV sputtering of water ice, which has so far not been studied in detail in this context. We present a photosputtering model based on available experimental and theoretical studies. We quantitatively estimate the erosion rate of icy and ice-silicate grains, under the influence of both sublimation and photosputtering, as a function of grain size, composition and distance from the star. The effect of erosion on the grain's location is investigated through numerical simulations coupling the grain size to its dynamical evolution. Our model predicts that photodesorption efficiently destroy ice in optically thin discs, even far beyond the sublimation snow line. For the reference case of beta Pictoris, we find that only > 5mm grains can keep their icy component for the age of the system in the 50-150AU region. When taking into account the collisional reprocessing of grains, we show that the water ice survival on grains improves (grains down to ~ 20 um might be partially icy). However, estimates of the amount of gas photosputtering would produce on such a hypothetical population of big icy grains lead to values for the OI column density that strongly exceed observational constraints for beta Pic, thus ruling out the presence of a significant amount of icy grains in this system. Erosion rates and icy grains survival timescales are also given for a set of 11 other debris disc systems. We show that, with the possible exception of M stars, photosputtering cannot be neglected in calculations of icy grain lifetimes.Comment: 12 pages, 9 figures. accepted by A&

Unemployment Convergence in Central and Eastern European Countries: Driving Forces and Cluster Behavior

Employing a nonlinear logistic smooth transition autoregression system and comovement analysis, we find that the German business cycle has acted as a common driver affecting the cyclical behavior of unemployment rates in Central and Eastern European countries. In addition, we identify two convergence clubs in unemployment dynamics. The first comprises the Baltic States, Hungary, and Poland, and the second group of countries is composed of the Czech Republic and Slovakia. Interestingly, this classification matches the labor market policies and institutional divergences observed among these countries

Psychometric Properties of the German Version of the Pain Vigilance and Awareness Questionnaire (PVAQ) in Pain-Free Samples and Samples with Acute and Chronic Pain

The way individuals attend to pain is known to have a considerable impact on the experience and chronification of pain. One method to assess the habitual "attention to pain" is the Pain Vigilance and Awareness Questionnaire (PVAQ). With the present study, we aimed to test the psychometric properties of the German version of the PVAQ across pain-free samples and across patients with acute and chronic pain. Two samples of pain-free individuals (student sample (N = 255)/non-student sample (N = 362)) and two clinical pain samples (acute pain patients (N = 105)/chronic pain patients (N = 36)) were included in this cross-sectional evaluation of the German PVAQ. Factor structure was assessed using exploratory and confirmatory factor analyses. Reliability was assessed using internal consistency (Cronbach's alpha). Construct validity was tested by assessing correlations between PVAQ and theoretically related constructs. Exploratory factor analysis (non-student sample) and confirmatory factor analysis (student sample, acute pain patient sample) suggested that a two-factor solution best fitted our data ("attention to pain," "attention to changes in pain"). Internal consistency ranged from acceptable to good in all four samples. As hypothesized, the PVAQ correlated significantly with theoretically related constructs in all four samples, suggesting good construct validity in pain-free individuals and in pain patients. The German PVAQ shows good psychometric properties across samples of pain-free individuals and patients suffering from pain that are comparable to PVAQ versions of other languages. Thus, the German PVAQ seems to be a measure of pain vigilance equally valid as found in other countries

STAT-1 decoy oligodeoxynucleotide inhibition of acute rejection in mouse heart transplants

During acute rejection of cardiac transplants endothelial cell–leukocyte interaction fuelled by co-stimulatory molecules like CD40/CD154 may ultimately lead to graft loss. One key player in up-regulating the expression of such pro-inflammatory gene products is the interferon-γ-dependent transcription factor STAT-1. Hence down-regulating interferon-γ-stimulated pro-inflammatory gene expression in the graft endothelial cells by employing a decoy oligodeoxynucleotide (dODN) neutralising STAT-1 may protect the graft. To verify this hypothesis, heterotopic mouse heart transplantation was performed in the allogeneic B10.A(2R) to C57BL/6 and syngeneic C57BL/6 to C57BL/6 strain combination without immunosuppression. Graft vessels were pre-treated with STAT-1 dODN, mutant control ODN (10 μM each) or vehicle (Ringer solution). Cellular rejection (vascular and interstitial component) was graded histologically and CD40, ICAM-1, VCAM-1, MCP-1, E-selectin and RANTES expression in the graft monitored by real time PCR 24 h and 9 days post-transplantation. Nine days after transplantation both rejection scores were significantly diminished by 85 and 70%, respectively, in STAT-1 dODN-treated allografts as compared to mutant control ODN-treated allografts. According to immunohistochemistry analysis, this was accompanied by a reduced infiltration of monocyte/macrophages and T cells into the graft myocardium. In addition, pro-inflammatory gene expression was strongly impaired by more than 80% in STAT-1 dODN-treated allografts 24 h post-transplantation but not in mutant control ODN or vehicle-treated allografts. This inhibitory effect on pro-inflammatory gene expression was no longer detectable 9 days post-transplantation. Single periprocedural treatment with a STAT-1 dODN thus effectively reduces cellular rejection in mouse heart allografts. This effect is associated both with an early decline in pro-inflammatory gene expression and a later drop in mononuclear cell infiltration

Cancer patients' needs during hospitalisation: a quantitative and qualitative study

BACKGROUND: The evaluation of cancer patients needs, especially during that delicate period when they are hospitalized, allows the identification of those areas of care that require to be improved. Aims of the study were to evaluate the needs in cancer inpatients and to improve the understanding of the meanings of the needs expressed. METHODS: The study was conducted during a "sample day", with all the cancer patients involved having been hospitalized at the Istituto Nazionale Tumori of Milan (INT) for at least 48 hours beforehand. The study was carried out using quantitative and qualitative methodologies. The quantitative part of the study consisted in making use of the Needs Evaluation Questionnaire (NEQ), a standardized questionnaire administered by the INT Psychology Unit members, supported by a group of volunteers from the Milan section of the Italian League Against Cancer. The aim of the qualitative part of the study, by semi-structured interviews conducted with a small sample of 8 hospitalized patients, was to improve our understanding of the meanings, implications of the needs directly described from the point of view of the patients. Such an approach determines the reasons and conditions of the dissatisfaction in the patient, and provides additional information for the planning of improvement interventions. RESULTS: Of the 224 eligible patients, 182 (81%) completed the questionnaire. Four of the top five needs expressed by 40% or more of the responders concerned information needs (diagnosis, future conditions, dialogue with doctors, economic-insurance solutions related to the disease). Only one of the 5 was concerned with improved "hotel" services (bathrooms, meals, cleanliness). Qualitative analysis showed that the most expressed need (to receive more information on their future conditions) has the meaning to know how their future life will be affected more than to know his/her actual prognosis. CONCLUSIONS: Some of the needs which emerged from this investigation could be immediately satisfied (the need for psychological support, the need for economic aid, the need for spiritual support), while others will have to be faced in the longer term; for example, the presence of a high percentage of needs in patient-physician relationships and/or information-communication issues, could be resolved by setting up structured introductory training courses for all clinicians in the institution. On the other hand, the needs related to the living infrastructure (bathrooms, meals, etc...) could encourage the Institution to improve its services

Flow cytometry as a rapid analytical tool to determine physiological responses to changing O2 and iron concentration by Magnetospirillum gryphiswaldense strain MSR-1

Magnetotactic bacteria (MTB) are a diverse group of bacteria that synthesise magnetosomes, magnetic membrane-bound nanoparticles that have a variety of diagnostic, clinical and biotechnological applications. We present the development of rapid methods using flow cytometry to characterize several aspects of the physiology of the commonly-used MTB Magnetospirillum gryphiswaldense MSR-1. Flow cytometry is an optical technique that rapidly measures characteristics of individual bacteria within a culture, thereby allowing determination of population heterogeneity and also permitting direct analysis of bacteria. Scatter measurements were used to measure and compare bacterial size, shape and morphology. Membrane permeability and polarization were measured using the dyes propidium iodide and bis-(1,3-dibutylbarbituric acid) trimethine oxonol to determine the viability and ‘health’ of bacteria. Dyes were also used to determine changes in concentration of intracellular free iron and polyhydroxylakanoate (PHA), a bacterial energy storage polymer. These tools were then used to characterize the responses of MTB to different O2 concentrations and iron-sufficient or iron-limited growth. Rapid analysis of MTB physiology will allow development of bioprocesses for the production of magnetosomes, and will increase understanding of this fascinating and useful group of bacteria