Welcome to the New Journal Methods and Protocols.
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ABSTRACT:
SUBMITTER: Albericio F
PROVIDER: S-EPMC6526406 | biostudies-literature | 2017 Jun
REPOSITORIES: biostudies-literature
Publications
Welcome to the New Journal <i>Methods and Protocols</i>.
Methods and protocols 20170627 1
I am pleased to introduce <i>Methods and Protocols</i>, a new multidisciplinary, peer-reviewed, open access journal devoted to providing an open forum to report on new procedural approaches and cutting-edge methodological developments.[...]. ...[more]
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Project description:ObjectiveTo investigate the planning of subgroup analyses in protocols of randomised controlled trials and the agreement with corresponding full journal publications.DesignCohort of protocols of randomised controlled trial and subsequent full journal publications.SettingSix research ethics committees in Switzerland, Germany, and Canada.Data sources894 protocols of randomised controlled trial involving patients approved by participating research ethics committees between 2000 and 2003 and 515 subsequent full journal publications.ResultsOf 894 protocols of randomised controlled trials, 252 (28.2%) included one or more planned subgroup analyses. Of those, 17 (6.7%) provided a clear hypothesis for at least one subgroup analysis, 10 (4.0%) anticipated the direction of a subgroup effect, and 87 (34.5%) planned a statistical test for interaction. Industry sponsored trials more often planned subgroup analyses compared with investigator sponsored trials (195/551 (35.4%) v 57/343 (16.6%), P<0.001). Of 515 identified journal publications, 246 (47.8%) reported at least one subgroup analysis. In 81 (32.9%) of the 246 publications reporting subgroup analyses, authors stated that subgroup analyses were prespecified, but this was not supported by 28 (34.6%) corresponding protocols. In 86 publications, authors claimed a subgroup effect, but only 36 (41.9%) corresponding protocols reported a planned subgroup analysis.ConclusionsSubgroup analyses are insufficiently described in the protocols of randomised controlled trials submitted to research ethics committees, and investigators rarely specify the anticipated direction of subgroup effects. More than one third of statements in publications of randomised controlled trials about subgroup prespecification had no documentation in the corresponding protocols. Definitive judgments regarding credibility of claimed subgroup effects are not possible without access to protocols and analysis plans of randomised controlled trials.
| S-EPMC4100616 | biostudies-literature
Project description:FeRIC (Ferritin iron Redistribution to Ion Channels) is a magnetogenetic technique that uses radiofrequency (RF) alternating magnetic fields to activate the transient receptor potential channels, TRPV1 and TRPV4, coupled to cellular ferritins. In cells expressing ferritin-tagged TRPV, RF stimulation increases the cytosolic Ca2+ levels via a biochemical pathway. The interaction between RF and ferritin increases the free cytosolic iron levels that, in turn, trigger chemical reactions producing reactive oxygen species and oxidized lipids that activate the ferritin-tagged TRPV. In this pathway, it is expected that experimental factors that disturb the ferritin expression, the ferritin iron load, the TRPV functional expression, or the cellular redox state will impact the efficiency of RF in activating ferritin-tagged TRPV. Here, we examined several experimental factors that either enhance or abolish the RF control of ferritin-tagged TRPV. The findings may help optimize and establish reproducible magnetogenetic protocols.
| S-EPMC8479696 | biostudies-literature
Project description:Europe recently experienced a large influx of refugees, spurring much public debate about the admission and integration of refugees and migrants into society. Previous research based on cross-sectional data found that European citizens generally favour asylum seekers with high employability, severe vulnerabilities, and Christians over Muslims. These preferences and attitudes were found to be homogeneous across countries and socio-demographic groups. Here, we do not study the general acceptance of asylum seekers, but the acceptance of refugee and migrant homes in citizens' vicinity and how it changes over time. Based on a repeated stated choice experiment on preferences for refugee and migrant homes, we show that the initially promoted "welcome culture" towards refugees in Germany was not reflected in the views of a majority of a sample of German citizens who rather disapproved refugee homes in their vicinity. Their preferences have not changed between November 2015, the peak of "welcome culture," and November 2016, after political debates, media reporting and public discourse had shifted towards limiting admission of immigrants. A minority of one fifth of the sample population, who were initially rather approving of refugee and migrant homes being established in their vicinity, were more likely to change their preferences towards a rather disapproving position in 2016. Experience of contact with refugees and migrants, higher education, and general pro-immigration attitudes explain acceptance of refugee and migrant homes as well as preference stability over time. Country of origin and religion of refugees and migrants are considered less important than decent housing conditions and whether refugee and migrants arrive as families or single persons. In this respect our results highlight the importance of humanitarian aspects of sheltering and integration of refugees and other migrants into society.
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Project description:Objective: A comprehensive, integrated support programme for new international students of medicine has been developed, implemented and evaluated at the Charité. The objectives of the programme were improved social integration, orientation on the study program and Charité campus, as well as qualification in medical specialist language. Project outline: The "Charité Orientation Module for International Students" (ChOIS) was designed by a working group with a variety of expertise in the field of international students. The programme has three stages: Recruitment (specific invitation on matriculation); Orientation week before semester start; and Parallel events during the first semester. ChoOIS was piloted in the Winter Semester 2015/16 and, following evaluation, continued in a modified form in the Summer Semester 2016. Key features were: Welcome and social integration by faculty welcome-events and student group activities; Orientation on the study program, on teaching infrastructures at the Charité and on student life in Berlin by senior medical students; and Training in language for medical communication and bedside teaching by professional lecturers. Results: Results of evaluations conducted after the orientation weeks, at the end of the semester and retrospectively in the 3rd semester produced high approval ratings of the individual features of the ChOIS-programme and of the programme as a whole by participating students. Discussion: A comprehensive, integrated support programme for new international students of medicine has been developed and implemented. The ChOIS-programme can serve as a practice model to guide other medical faculties. In future, a programme that goes beyond the start of the course and includes more involvement by senior students would be desirable.
| S-EPMC6326404 | biostudies-other
Project description:This SuperSeries is composed of the SubSeries listed below.
2018-08-20 | GSE118767 | GEO
Project description:Single cell RNA sequencing (scRNA-seq) technology has undergone rapid development in recent years and brings new challenges in data processing and analysis. This has led to an explosion of tailored analysis methods for scRNA-seq to address various biological questions. However, the current lack of gold-standard benchmarking datasets makes it difficult for researchers to evaluate the performance of the many methods available in a systematic manner. Here, we designed and generated a cross-platform benchmark dataset that has in-built truth in various forms and varying levels of biological noise. We used this dataset to compare different protocols and data analysis methods. We found that different protocols have different data quality and ERCC spike-in works independently to endogenous RNA. We found significant differences in the results from the methods compared and we associated the results with data characteristics to identify methods that perform well in different situations. Our dataset and analysis provide a valuable resource for algorithm selection in different biological settings.
2019-12-19 | GSE142286 | GEO
Project description: Not available
| S-EPMC8631410 | biostudies-literature
Project description:Nucleocytoplasmic large DNA viruses, or representatives of the proposed order Megavirales, belong to families of giant viruses that infect a broad range of eukaryotic hosts. Megaviruses have been previously described to comprise a fourth monophylogenetic TRUC (things resisting uncompleted classification) together with cellular domains in the universal tree of life. Recently described pandoraviruses have large (1.9-2.5 MB) and highly divergent genomes. In the present study, we updated the classification of pandoraviruses and other reported giant viruses. Phylogenetic trees were constructed based on six informational genes. Hierarchical clustering was performed based on a set of informational genes from Megavirales members and cellular organisms. Homologous sequences were selected from cellular organisms using TimeTree software, comprising comprehensive, and representative sets of members from Bacteria, Archaea, and Eukarya. Phylogenetic analyses based on three conserved core genes clustered pandoraviruses with phycodnaviruses, exhibiting their close relatedness. Additionally, hierarchical clustering analyses based on informational genes grouped pandoraviruses with Megavirales members as a super group distinct from cellular organisms. Thus, the analyses based on core conserved genes revealed that pandoraviruses are new genuine members of the 'Fourth TRUC' club, encompassing distinct life forms compared with cellular organisms.
| S-EPMC4435241 | biostudies-literature
Project description:Single cell RNA sequencing (scRNA-seq) technology has undergone rapid development in recent years and brings new challenges in data processing and analysis. This has led to an explosion of tailored analysis methods for scRNA-seq to address various biological questions. However, the current lack of gold-standard benchmarking datasets makes it difficult for researchers to evaluate the performance of the many methods available in a systematic manner. Here, we designed and generated a cross-platform benchmark dataset that has in-built truth in various forms and varying levels of biological noise. We used this dataset to compare different protocols and data analysis methods. We found that different protocols have different data quality and ERCC spike-in works independently to endogenous RNA. We found significant differences in the results from the methods compared and we associated the results with data characteristics to identify methods that perform well in different situations. Our dataset and analysis provide a valuable resource for algorithm selection in different biological settings.
2018-08-18 | GSE118704 | GEO