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Abstract Background High-throughput screening of pharmaceutical compound activity in tissue culture experiments requires time-consuming repeated analysis of the large amounts of data generated. Automation of the evaluation procedure and assessment of measurement accuracy can save time and improve the comparability of results. Results We present a tool for simultaneous evaluation of an arbitrary number of compound screens including a standardized statistical validation. It is provided as a novel R package with a Tcl/Tk-based GUI for convenient use in the lab and runs on usual platforms like Linux, Windows and Mac OS. In a compound screen of lung cancer cells, the tool was successfully and efficiently applied for data analysis. Conclusion The package provides an efficient and intuitive platform for automatic evaluation of compound screens, improving the performance and standardization of data analysis.

Workplace integration of undergraduate student nurses through clinical placement remains an integral part of nurse education. The role of clinical facilitators who support this integration is complex and shaped by the expectations of various key stakeholders. These multiple expectations often resulting in the role being blurred and lacking clarity. The research aim is to identify the roles and expectations of clinical facilitators from the perspectives of academics/educators and students and to explore qualities that allow clinical facilitators to conduct their role effectively. A cross-sectional survey was utilised. Exploratory factor analysis, free text data and comparative analysis were used. Findings suggest a discordance in understanding of the clinical facilitator role by educators and students. Students tended to focus on skills and knowledge without consideration of the broader nursing profession. The clinical facilitator’s ability to role model and influence is seen as a “hidden curriculum” that students are largely unaware of. The clinical facilitator role is complex, with education critical in supporting this role and thus the success of students. Illumination of the hidden nursing curriculum would enable better understanding of the clinical facilitator role in engaging students with the varying requirements of the nursing profession.

Rapid changes of the biosphere observed in recent years are caused by both small and large scale drivers, like shifts in temperature, transformations in land-use, or changes in the energy budget of systems. While the latter processes are easily quantifiable, documentation of the loss of biodiversity and community structure is more difficult. Changes in organismal abundance and diversity are barely documented. Censuses of species are usually fragmentary and inferred by often spatially, temporally and ecologically unsatisfactory simple species lists for individual study sites. Thus, detrimental global processes and their drivers often remain unrevealed. A major impediment to monitoring species diversity is the lack of human taxonomic expertise that is implicitly required for large-scale and fine-grained assessments. Another is the large amount of personnel and associated costs needed to cover large scales, or the inaccessibility of remote but nonetheless affected areas.To overcome these limitations we propose a network of Automated Multisensor stations for Monitoring of species Diversity (AMMODs) to pave the way for a new generation of biodiversity assessment centers. This network combines cutting-edge technologies with biodiversity informatics and expert systems that conserve expert knowledge. Each AMMOD station combines autonomous samplers for insects, pollen and spores, audio recorders for vocalizing animals, sensors for volatile organic compounds emitted by plants (pVOCs) and camera traps for mammals and small invertebrates. AMMODs are largely self-containing and have the ability to pre-process data (e.g. for noise filtering) prior to transmission to receiver stations for storage, integration and analyses. Installation on sites that are difficult to access require a sophisticated and challenging system design with optimum balance between power requirements, bandwidth for data transmission, required service, and operation under all environmental conditions for years. An important prerequisite for automated species identification are databases of DNA barcodes, animal sounds, for pVOCs, and images used as training data for automated species identification. AMMOD stations thus become a key component to advance the field of biodiversity monitoring for research and policy by delivering biodiversity data at an unprecedented spatial and temporal resolution.

Agricultural intensification has caused decrease and fragmentation of European semi-natural dry grasslands. While a high biodiversity value of dry grasslands is acknowledged for plants and insects, locally and on landscape level, their relevance for mobile species, such as bats, is unknown. Here we investigate the use of dry grassland fragments by bats in an agriculturally intensified region in Germany and evaluate local and landscape factors influencing bat activity and assemblages. Specifically, we predicted that a combination of local dry grassland structural richness and landscape features as well as their interactions affect bat activity and foraging above dry grasslands. We also expected that these features influence compositions of local bat assemblages. We repeatedly sampled at 12 dry grassland plots with acoustic monitoring and assessed activity and foraging of bat species/sonotypes, which we grouped into guilds known for foraging in open land, at vegetation edges and in narrow spaces. We determined structural richness of the dry grassland plots in field and derived landscape features from digital landscape data. A relatively high proportion of bat species/sonotypes used dry grasslands regularly. The edge space foragers responded positively to higher local structural richness. Their dry grassland use increased when surrounding forests and woody features were less available, but they foraged more on dry grasslands closer to water bodies. Narrow space bat activity on dry grasslands decreased with less landscape connectivity. Open and narrow space foragers responded to local structural richness only in landscape context. For all bat guilds we found increased use of structurally richer dry grasslands when there was more open farmland in the surroundings. This was also the case for edge space foragers, when landscapes were more homogeneous. Lastly, with increasing structural richness, bat assemblages were more dominated by edge space foragers. We show the importance of European dry grassland fragments for the highly mobile group of bats under certain local structural and landscape compositional conditions. Our results underline the value of heterogeneous dry grassland fragments as potential stepping stones in intensively used farmland areas and contribute to evidence based decision making in dry grassland management and bat conservation.

Abstract Background Next-Generation Sequencing (NGS) has been widely accepted as an essential tool in molecular biology. Reduced costs and automated analysis pipelines make the use of NGS data feasible even for small labs, yet the methods for interpreting the data are not sophisticated enough to account for the amount of information. Results We propose s·nr, a Visual Analytics tool that provides simple yet powerful visual interfaces for displaying and querying NGS data. It allows researchers to explore their own data in the context of experimental data deposited in public repositories, as well as to extract specific data sets with similar gene expression signatures. We tested s·nr on 1543 RNA-Seq based mouse differential expression profiles derived from the public ArrayExpress platform. We provide the repository of processed data with this paper. Conclusion s·nr, easily deployable utilizing its containerized implementation, empowers researchers to analyze and relate their own RNA-Seq as well as to provide interactive and contextual crosstalk with data from public repositories. This allows users to deduce novel and unbiased hypotheses about the underlying molecular processes. Demo Login demo/demo: snr.sf.mpg.de (Tested with Google Chrome)

Up to 40% of esophageal carcinomas have a biallelic intact TP53 gene. It is largely unclear how these carcinoma cells prevent apoptosis, what is the kind of pathway alterations, or whether therapeutically relevant alterations exist in this subgroup. We evaluated The Cancer Genome Atlas (TCGA) data to compare TP53-mutated with TP53–wild-type tumors regarding copy number variations, gene mutations, and expression patterns of protein-coding genes and miRNAs. Additionally, we analyzed up to 428 esophageal adenocarcinomas (EACs) in total using an ultra-deep parallel sequencing panel, immunohistochemistry, as well as fluorescence in situ hybridization. In the TCGA cohort, 17.3% has a biallelic intact TP53 gene. This group has a smaller average total size of somatic copy number variations. Some protein coding genes and miRNAs were differentially expressed between the TP53-wild-type and TP53-mutated group to emphasize mdm2, CCND2, TP73, or miRNA 150, 488, or 4662a. In addition, 50% of the TP53–wild-type tumors carry somatic mutations in at least one of the genes involved in the TP53 pathway. Our patient cohort revealed 41.3% TP53–wild-type tumors; 5.6% were MDM2 amplified. In accordance with the TCGA data, we did not find a prognostic relevance of TP53 in our tumor cohort as well. The mutation status of TP53 defines an important subtype in esophageal carcinoma. Our comprehensive molecular analysis revealed important and potentially therapeutically relevant genomic alterations in this subgroup.

Despite the popularity of the flipped classroom, its effectiveness in achieving greater engagement and learning outcomes is currently lacking substantial empirical evidence. This study surveyed 563 undergraduate and postgraduate students (61% female) participating in flipped teaching environments and ten convenors of the flipped courses in which the student sample was enrolled. Results suggest that higher education students can be differentiated based on their preferences for elements of a flipped classroom, resulting in two clusters of students: those who embrace most aspects of a flipped classroom environment as well as prefer it (labelled "Flip endorsers") and those who are close to neutral on some elements of a flipped classroom environment but who especially do not endorse the pre-learning aspects (labelled "Flip resisters"). Flip endorsers were found to have more positive attitudes towards the course activities (both pre-class and in-class) and to have felt more involved and engaged in the content. These findings shed some light on the types of students who might prefer flipped classrooms, but more importantly identify those who are likely to resist a change to a flipped classroom environment. The findings also suggest that although students may find the flipped classroom more difficult, student outcomes and active participation in class activities do improve when course convenors (a) use a theoretical perspective to inform their flipped teaching strategy, (b) integrate assessment into the design of their flipped classroom, and (c) flip the entire course.

While Next-Generation Sequencing (NGS) can now be considered an established analysis technology for research applications across the life sciences, the analysis workflows still require substantial bioinformatics expertise. Typical challenges include the appropriate selection of analytical software tools, the speedup of the overall procedure using HPC parallelization and acceleration technology, the development of automation strategies, data storage solutions and finally the development of methods for full exploitation of the analysis results across multiple experimental conditions. Recently, NGS has begun to expand into clinical environments, where it facilitates diagnostics enabling personalized therapeutic approaches, but is also accompanied by new technological, legal and ethical challenges. There are probably as many overall concepts for the analysis of the data as there are academic research institutions. Among these concepts are, for instance, complex IT architectures developed in-house, ready-to-use technologies installed on-site as well as comprehensive Everything as a Service (XaaS) solutions. In this mini-review, we summarize the key points to consider in the setup of the analysis architectures, mostly for scientific rather than diagnostic purposes, and provide an overview of the current state of the art and challenges of the field.

In the arcuate nucleus of the hypothalamus (ARH) satiety signaling (anorexigenic) pro-opiomelanocortin (POMC)-expressing and hunger signaling (orexigenic) agouti-related peptide (AgRP)-expressing neurons are key components of the neuronal circuits that control food intake and energy homeostasis. Here, we assessed whether the catecholamine noradrenalin directly modulates the activity of these neurons in mice. Perforated patch clamp recordings showed that noradrenalin changes the activity of these functionally antagonistic neurons in opposite ways, increasing the activity of the orexigenic NPY/AgRP neurons and decreasing the activity of the anorexigenic POMC neurons. Cell type-specific transcriptomics and pharmacological experiments revealed that the opposing effect on these neurons is mediated by the activation of excitatory α1A - and β- adrenergic receptors in NPY/AgRP neurons, while POMC neurons are inhibited via α2A – adrenergic receptors. Thus, the coordinated differential modulation of the key hypothalamic neurons in control of energy homeostasis assigns noradrenalin an important role to promote feeding.

Activation of the hypoxia inducible transcription factor HIF and the NF-ĸB pathway promotes inflammation-mediated tumor progression. The cellular transcription factor ZNF395 has repeatedly been found overexpressed in various human cancers, particularly in response to hypoxia, implying a functional relevance. To understand the biological activity of ZNF395, we identified target genes of ZNF395 through a genome-wide expression screen. Induced ZNF395 expression led to the upregulation of genes known to play a role in cancer as well as a subset of interferon (IFN)-stimulated genes (ISG) involved in antiviral responses such as IFIT1/ISG56, IFI44 and IFI16. In cells that lack ZNF395, the IFN-α-mediated stimulation of these factors was impaired, demonstrating that ZNF395 is required for the full induction of these antiviral genes. Transient transfections revealed that ZNF395-mediated activation of the IFIT1/ISG56 promoter depends on the two IFN-stimulated response elements within the promoter and on the DNA-binding domain of ZNF395, a so-called C-clamp. We also show that IĸBα kinase (IKK)-signaling is necessary to allow ZNF395 to activate transcription and simultaneously enhances its proteolytic degradation. Thus, ZNF395 becomes activated at the level of protein modification by IKK. Moreover, we confirm that the expression of ZNF395 is induced by hypoxia. Our results characterize ZNF395 as a novel factor that contributes to the maximal stimulation of a subset of ISGs. This transcriptional activity depends on IKK signaling further supporting a role of ZNF395 in the innate immune response. Given these results it is possible that under hypoxic conditions, elevated levels of ZNF395 may support inflammation and cancer progression by activating the target genes involved in the innate immune response and cancer.

Rapid changes of the biosphere observed in recent years are caused by both small and large scale drivers, like shifts in temperature, transformations in land-use, or changes in the energy budget of systems. While the latter processes are easily quantifiable, documentation of the loss of biodiversity and community structure is more difficult. Changes in organismal abundance and diversity are barely documented. Censuses of species are usually fragmentary and inferred by often spatially, temporally and ecologically unsatisfactory simple species lists for individual study sites. Thus, detrimental global processes and their drivers often remain unrevealed. A major impediment to monitoring species diversity is the lack of human taxonomic expertise that is implicitly required for large-scale and fine-grained assessments. Another is the large amount of personnel and associated costs needed to cover large scales, or the inaccessibility of remote but nonetheless affected areas. To overcome these limitations we propose a network of A utomated M ultisensor stations for Mo nitoring of species D iversity (AMMODs) to pave the way for a new generation of biodiversity assessment centers. This network combines cutting-edge technologies with biodiversity informatics and expert systems that conserve expert knowledge. Each AMMOD station combines autonomous samplers for insects, pollen and spores, audio recorders for vocalizing animals, sensors for volatile organic compounds emitted by plants (pVOCs) and camera traps for mammals and small invertebrates. AMMODs are largely self-containing and have the ability to pre-process data (e.g. for noise filtering) prior to transmission to receiver stations for storage, integration and analyses. Installation on sites that are difficult to access require a sophisticated and challenging system design with optimum balance between power requirements, bandwidth for data transmission, required service, and operation under all environmental conditions for years. An important prerequisite for automated species identification are databases of DNA barcodes, animal sounds, for pVOCs, and images used as training data for automated species identification. AMMOD stations thus become a key component to advance the field of biodiversity monitoring for research and policy by delivering biodiversity data at an unprecedented spatial and temporal resolution. [ABSTRACT FROM AUTHOR]

Abstract Clinical experiences are an essential foundation of nursing education. While there have been many significant investigations into models of clinical education and student learning, how students 'make sense' of their experiences is less well investigated. Senior nursing staff in a tertiary health service partnered with nurse researchers to explore how students can learn more about practice through structured discussions with peers to promote shared understandings. The study aimed to evaluate the contributions to student learning from structured peer discussions about patient care. Exploratory observational study of the effects of learning circle discussions on individual understanding of patient care. A metropolitan health service in southeast Queensland, Australia. 72 Bachelor of Nursing students in Years 2 and 3. Students developed concept maps about patient care prior to peer discussions, and subsequently added further concepts (in another colour of text) after those discussions. Researchers' review of student generated concept maps and coded concepts indicated a five a priori ways of knowing categories: empirical, aesthetic, ethical, personal and socio-political. Descriptive analysis of categories was then conducted. Empirical knowing was high in both groups, with more concepts included in Year 3 student maps. Aesthetic knowing was relatively high in both groups. Socio-political knowing was lower than anticipated overall. Personal and ethical forms of knowing were rarely included on the concept maps. While clinical placement is valued for developing empirical and aesthetic forms of knowing, the other forms of knowing have value for patient and family care and warrant strategies to improve their further development. Developing strategies to support student learning of ethical and personal forms of knowing deserves further investigation. [ABSTRACT FROM AUTHOR]

Abstract Rising numbers of students are required to address the forecast nursing shortage. Health services are challenged to release experienced nursing staff to become supervisors in clinical supervision models and preceptorship models require significant investment in registered nurse education for effectiveness. One health service in southeast Queensland, Australia, developed an innovative clinical education model that draws upon the strengths of supervision and preceptor models, and is consistent with the Dedicated Education Unit model, without the dedicated university and prescribed attendance requirements. Using an iterative qualitative approach and learning circle methods, the aim was to determine feasibility of the model, using information gathered from clinical facilitators, who were the key implementers. Model feasibility was found to be dependent upon three key activities undertaken by the facilitators: align stakeholder expectations with the new model, clarify roles and responsibilities within clusters, and develop strategies for collecting information about student performance. The experience of implementing the model has raised further questions about how students, newly qualified nurses and registered nurses learn in localised work units and what practice pedagogies can be developed to support learning from, as well as improve practice. Highlights • The need for more nurses has increased the number of student and newly qualified nurses. • Traditional clinical supervision and preceptorship are not sustainable. • The Dedicated Education Unit does not work for health services with multiple education partners. • The Clinical Clusters Education Model provides a viable alternative to support learning for higher student numbers. • Learning circles present a useful change management strategy. [ABSTRACT FROM AUTHOR]

The provision of simulation to enhance learning is becoming common practice as clinical placement becomes harder to secure within Bachelor of Nursing programs. The use of simulation videos within a blended learning platform enables students to view best practice and provides relevant links between theory and practice. Four simulation videos depicting family assessment viewed by a cohort of Australian undergraduate nursing students were evaluated. These videos were professionally developed using actors and experienced family nurses. Surveys were used to explore the students' self-assessed knowledge, confidence and learning preferences before and after exposure to blended learning resources. Students' engagement with the simulated videos was captured via the Learning Management System. Time 1 survey was completed by 163 students and Time 2 by 91 students. There was a significant increase in students' perceived knowledge of family theory Item 1 from a mean 4.13 (SD = 1.04) at Time 1 to 4.74 (SD = 0.89) (Z = −4.54 p < 0.001) at Time 2; Item 2- Knowledge of family assessment improved from mean 3.91 (SD = 1.02) at Time 1 to 4.90 (SD = 0.67) (Z = −7.86 p < 0.001) at Time 2. Also a significant increase in their confidence undertaking family assessment Item 5 from a mean 3.55 (SD = 1.14) at Time 1 to 4.44 (SD = 0.85) (Z = −6.12 p < 0.001) at Time 2. The students watched the videos an average of 1.9 times. The simulated videos as a blended learning resource increases the students' understanding of family assessment and is worth incorporating into future development of courses. [ABSTRACT FROM AUTHOR]

Objectives The aim of this review is to inform future educational strategies by synthesising research related to blended learning resources using simulation videos to teach clinical skills for health students. Design An integrative review methodology was used to allow for the combination of diverse research methods to better understand the research topic. This review was guided by the framework described by Whittemore and Knafl (2005), Data Sources Systematic search of the following databases was conducted in consultation with a librarian using the following databases: SCOPUS, MEDLINE, COCHRANE, PsycINFO databases. Keywords and MeSH terms: clinical skills, nursing, health, student, blended learning, video, simulation and teaching. Review Methods Data extracted from the studies included author, year, aims, design, sample, skill taught, outcome measures and findings. After screening the articles, extracting project data and completing summary tables, critical appraisal of the projects was completed using the Mixed Methods Appraisal Tool (MMAT). Results Ten articles met all the inclusion criteria and were included in this review. The MMAT scores varied from 50% to 100%. Thematic analysis was undertaken and we identified the following three themes: linking theory to practice , autonomy of learning and challenges of developing a blended learning model . Blended learning allowed for different student learning styles, repeated viewing, and enabled links between theory and practice. The video presentation needed to be realistic and culturally appropriate and this required both time and resources to create. Conclusions A blended learning model, which incorporates video-assisted online resources, may be a useful tool to teach clinical skills to students of health including nursing. Blended learning not only increases students' knowledge and skills, but is often preferred by students due to its flexibility. [ABSTRACT FROM AUTHOR]