Do Editorial Policies Support Ethical Research? A Thematic Text Analysis of Author Instructions in Psychiatry Journals

Introduction: According to the Declaration of Helsinki and other guidelines, clinical studies should be approved by a research ethics committee and seek valid informed consent from the participants. Editors of medical journals are encouraged by the ICMJE and COPE to include requirements for these principles in the journal's instructions for authors. This study assessed the editorial policies of psychiatry journals regarding ethics review and informed consent. Methods and Findings: The information given on ethics review and informed consent and the mentioning of the ICMJE and COPE recommendations were assessed within author's instructions and online submission procedures of all 123 eligible psychiatry journals. While 54% and 58% of editorial policies required ethics review and informed consent, only 14% and 19% demanded the reporting of these issues in the manuscript. The TOP-10 psychiatry journals (ranked by impact factor) performed similarly in this regard. Conclusions: Only every second psychiatry journal adheres to the ICMJE's recommendation to inform authors about requirements for informed consent and ethics review. Furthermore, we argue that even the ICMJE's recommendations in this regard are insufficient, at least for ethically challenging clinical trials. At the same time, ideal scientific design sometimes even needs to be compromised for ethical reasons. We suggest that features of clinical studies that make them morally controversial, but not necessarily unethical, are analogous to methodological limitations and should thus be reported explicitly. Editorial policies as well as reporting guidelines such as CONSORT should be extended to support a meaningful reporting of ethical research.

Effects of Soil Organic Matter Properties and Microbial Community Composition on Enzyme Activities in Cryoturbated Arctic Soils

Enzyme-mediated decomposition of soil organic matter (SOM) is controlled, amongst other factors, by organic matter properties and by the microbial decomposer community present. Since microbial community composition and SOM properties are often interrelated and both change with soil depth, the drivers of enzymatic decomposition are hard to dissect. We investigated soils from three regions in the Siberian Arctic, where carbon rich topsoil material has been incorporated into the subsoil (cryoturbation). We took advantage of this subduction to test if SOM properties shape microbial community composition, and to identify controls of both on enzyme activities. We found that microbial community composition (estimated by phospholipid fatty acid analysis), was similar in cryoturbated material and in surrounding subsoil, although carbon and nitrogen contents were similar in cryoturbated material and topsoils. This suggests that the microbial community in cryoturbated material was not well adapted to SOM properties. We also measured three potential enzyme activities (cellobiohydrolase, leucine-amino-peptidase and phenoloxidase) and used structural equation models (SEMs) to identify direct and indirect drivers of the three enzyme activities. The models included microbial community composition, carbon and nitrogen contents, clay content, water content, and pH. Models for regular horizons, excluding cryoturbated material, showed that all enzyme activities were mainly controlled by carbon or nitrogen. Microbial community composition had no effect. In contrast, models for cryoturbated material showed that enzyme activities were also related to microbial community composition. The additional control of microbial community composition could have restrained enzyme activities and furthermore decomposition in general. The functional decoupling of SOM properties and microbial community composition might thus be one of the reasons for low decomposition rates and the persistence of 400 Gt carbon stored in cryoturbated material.

Transcriptome-Wide Mapping of Pea Seed Ageing Reveals a Pivotal Role for Genes Related to Oxidative Stress and Programmed Cell Death

Understanding of seed ageing, which leads to viability loss during storage, is vital for ex situ plant conservation and agriculture alike. Yet the potential for regulation at the transcriptional level has not been fully investigated. Here, we studied the relationship between seed viability, gene expression and glutathione redox status during artificial ageing of pea (Pisum sativum) seeds. Transcriptome-wide analysis using microarrays was complemented with qRT-PCR analysis of selected genes and a multilevel analysis of the antioxidant glutathione. Partial degradation of DNA and RNA occurred from the onset of artificial ageing at 60% RH and 50 degrees C, and transcriptome profiling showed that the expression of genes associated with programmed cell death, oxidative stress and protein ubiquitination were altered prior to any sign of viability loss. After 25 days of ageing viability started to decline in conjunction with progressively oxidising cellular conditions, as indicated by a shift of the glutathione redox state towards more positive values (>-190 mV). The unravelling of the molecular basis of seed ageing revealed that transcriptome reprogramming is a key component of the ageing process, which influences the progression of programmed cell death and decline in antioxidant capacity that ultimately lead to seed viability loss.

Cell- and Tissue-Specific Transcriptome Analyses of Medicago truncatula Root Nodules

Legumes have the unique ability to host nitrogen-fixing Rhizobium bacteria as symbiosomes inside root nodule cells. To get insight into this key process, which forms the heart of the endosymbiosis, we isolated specific cells/tissues at different stages of symbiosome formation from nodules of the model legume Medicago truncatula using laser-capture microdissection. Next, we determined their associated expression profiles using Affymetrix Medicago GeneChips. Cells were collected from the nodule infection zone divided into a distal (where symbiosome formation and division occur) and proximal region (where symbiosomes are mainly differentiating), as well as infected cells from the fixation zone containing mature nitrogen fixing symbiosomes. As non-infected cells/tissue we included nodule meristem cells and uninfected cells from the fixation zone. Here, we present a comprehensive gene expression map of an indeterminate Medicago nodule and selected genes that show specific enriched expression in the different cells or tissues. Validation of the obtained expression profiles, by comparison to published gene expression profiles and experimental verification, indicates that the data can be used as digital "in situ''. This digital "in situ'' offers a genome-wide insight into genes specifically associated with subsequent stages of symbiosome and nodule cell development, and can serve to guide future functional studies.

Awareness and Learning in Participatory Noise Sensing

The development of ICT infrastructures has facilitated the emergence of new paradigms for looking at society and the environment over the last few years. Participatory environmental sensing, i.e. directly involving citizens in environmental monitoring, is one example, which is hoped to encourage learning and enhance awareness of environmental issues. In this paper, an analysis of the behaviour of individuals involved in noise sensing is presented. Citizens have been involved in noise measuring activities through the WideNoise smartphone application. This application has been designed to record both objective (noise samples) and subjective (opinions, feelings) data. The application has been open to be used freely by anyone and has been widely employed worldwide. In addition, several test cases have been organised in European countries. Based on the information submitted by users, an analysis of emerging awareness and learning is performed. The data show that changes in the way the environment is perceived after repeated usage of the application do appear. Specifically, users learn how to recognise different noise levels they are exposed to. Additionally, the subjective data collected indicate an increased user involvement in time and a categorisation effect between pleasant and less pleasant environments.

How Psychiatry Journals Support the Unbiased Translation of Clinical Research. A Cross-Sectional Study of Editorial Policies

Introduction: Reporting guidelines (e. g. CONSORT) have been developed as tools to improve quality and reduce bias in reporting research findings. Trial registration has been recommended for countering selective publication. The International Committee of Medical Journal Editors (ICMJE) encourages the implementation of reporting guidelines and trial registration as uniform requirements (URM). For the last two decades, however, biased reporting and insufficient registration of clinical trials has been identified in several literature reviews and other investigations. No study has so far investigated the extent to which author instructions in psychiatry journals encourage following reporting guidelines and trial registration. Method: Psychiatry Journals were identified from the 2011 Journal Citation Report. Information given in the author instructions and during the submission procedure of all journals was assessed on whether major reporting guidelines, trial registration and the ICMJE's URM in general were mentioned and adherence recommended. Results: We included 123 psychiatry journals (English and German language) in our analysis. A minority recommend or require 1) following the URM (21%), 2) adherence to reporting guidelines such as CONSORT, PRISMA, STROBE (23%, 7%, 4%), or 3) registration of clinical trials (34%). The subsample of the top-10 psychiatry journals (ranked by impact factor) provided much better but still improvable rates. For example, 70% of the top-10 psychiatry journals do not ask for the specific trial registration number. Discussion: Under the assumption that better reported and better registered clinical research that does not lack substantial information will improve the understanding, credibility, and unbiased translation of clinical research findings, several stakeholders including readers (physicians, patients), authors, reviewers, and editors might benefit from improved author instructions in psychiatry journals. A first step of improvement would consist in requiring adherence to the broadly accepted reporting guidelines and to trial registration.

Nme Gene Family Evolutionary History Reveals Pre-Metazoan Origins and High Conservation between Humans and the Sea Anemone, Nematostella vectensis

Background: The Nme gene family is involved in multiple physiological and pathological processes such as cellular differentiation, development, metastatic dissemination, and cilia functions. Despite the known importance of Nme genes and their use as clinical markers of tumor aggressiveness, the associated cellular mechanisms remain poorly understood. Over the last 20 years, several non-vertebrate model species have been used to investigate Nme functions. However, the evolutionary history of the family remains poorly understood outside the vertebrate lineage. The aim of the study was thus to elucidate the evolutionary history of the Nme gene family in Metazoans. Methodology/Principal Findings: Using a total of 21 eukaryote species including 14 metazoans, the evolutionary history of Nme genes was reconstructed in the metazoan lineage. We demonstrated that the complexity of the Nme gene family, initially thought to be restricted to chordates, was also shared by the metazoan ancestor. We also provide evidence suggesting that the complexity of the family is mainly a eukaryotic innovation, with the exception of Nme8 that is likely to be a choanoflagellate/metazoan innovation. Highly conserved gene structure, genomic linkage, and protein domains were identified among metazoans, some features being also conserved in eukaryotes. When considering the entire Nme family, the starlet sea anemone is the studied metazoan species exhibiting the most conserved gene and protein sequence features with humans. In addition, we were able to show that most of the proteins known to interact with human NME proteins were also found in starlet sea anemone. Conclusion/Significance: Together, our observations further support the association of Nme genes with key cellular functions that have been conserved throughout metazoan evolution. Future investigations of evolutionarily conserved Nme gene functions using the starlet sea anemone could shed new light on a wide variety of key developmental and cellular processes.

Interview with Dana L. Roth

An interview in four sessions, January and February 2014, with longtime Caltech chemistry librarian Dana L. Roth. Roth received his undergraduate education at Pasadena City College and UCLA (BS in chemistry, 1962). In 1965, he received master’s degrees in chemistry from Caltech and in library science from UCLA; that summer, he became Caltech’s chemistry librarian. After consolidation of Caltech’s division libraries in Millikan Library in 1967, he undertook various administrative responsibilities at Millikan over the years, along with his continuing duties as chemistry librarian. Active in the chemistry division of the Special Libraries Association. In 2008, inducted into the SLA Hall of Fame. That year he also received the Thomas W. Schmitt Staff Prize, presented to a Caltech staff member whose contributions “embody the values and spirit that enable the institute to achieve excellence in research and education.” Retired April 2013. In this interview he discusses his initial education as a chemist, including his graduate education at Caltech, and his switch to library science. He traces the development of library science in general and at Caltech—from the card-catalog days to the growth of the electronic Caltech Library system and the present state of online access and databases.

Future Bloom and Blossom Frost Risk for Malus domestica Considering Climate Model and Impact Model Uncertainties

The future bloom and risk of blossom frosts for Malus domestica were projected using regional climate realizations and phenological (= impact) models. As climate impact projections are susceptible to uncertainties of climate and impact models and model concatenation, the significant horizon of the climate impact signal was analyzed by applying 7 impact models, including two new developments, on 13 climate realizations of the IPCC emission scenario A1B. Advancement of phenophases and a decrease in blossom frost risk for Lower Saxony (Germany) for early and late ripeners was determined by six out of seven phenological models. Single model/single grid point time series of bloom showed significant trends by 2021-2050 compared to 1971-2000, whereas the joint signal of all climate and impact models did not stabilize until 2043. Regarding blossom frost risk, joint projection variability exceeded the projected signal. Thus, blossom frost risk cannot be stated to be lower by the end of the 21st century despite a negative trend. As a consequence it is however unlikely to increase. Uncertainty of temperature, blooming date and blossom frost risk projection reached a minimum at 2078-2087. The projected phenophases advanced by 5.5 d K-1, showing partial compensation of delayed fulfillment of the winter chill requirement and faster completion of the following forcing phase in spring. Finally, phenological model performance was improved by considering the length of day.