Post-Doc Interviews in the Life Sciences: An Often-Overlooked Process that Is Susceptible to Bias.
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ABSTRACT:
SUBMITTER: Burnett NP
PROVIDER: S-EPMC7671148 | biostudies-literature |
REPOSITORIES: biostudies-literature
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Project description:ObjectivesThe purpose of this research is to understand the thought processes that underpin responses to stated preference approaches for eliciting quality of life, in particular the standard gamble.MethodsWe utilize standard gamble preference elicitation survey techniques to elicit quality-adjusted life year weights for two reduced health states: chronic severe depression and total blindness. After the survey, we conduct open-ended qualitative interviews with respondents to determine their thought processes while taking the surveys and to shed light on what their quality-adjusted life year weight is capturing. Survey responses were coded and analyzed for themes in NVivo, the results of which were then formalized in the terminology of decision sciences.ResultsThe qualitative results of the cognitive interviews present systematic evidence for a type of cognitive bias present in standard gamble quality-adjusted life year weight elicitation, which has not been previously highlighted and which we call treatment bias. We define this treatment bias as the consideration of salient treatment alternatives correlated with a reduced health state, when these alternatives are not explicitly posed in the question. Our formalization of this cognitive behavior demonstrates that treatment bias will always bias the elicited health state utility of treating the illness in question downward.ConclusionThe treatment bias highlighted in this study has implications for economic evaluation when comparing treatment for illnesses where alternative treatments are widely publicized versus those that are not. For example, comparing the effectiveness of treating depression versus arthritis may be biased against depression if advertisements for anti-depressants are more widely viewed by survey respondents than advertisements for arthritis treatments. We propose a statement to be imbedded in all questionnaires regarding stated preference elicitation of quality-adjusted life year weights in order to correct for this bias in future stated preference surveys.
| S-EPMC6563399 | biostudies-literature
Project description:Observer bias and other "experimenter effects" occur when researchers' expectations influence study outcome. These biases are strongest when researchers expect a particular result, are measuring subjective variables, and have an incentive to produce data that confirm predictions. To minimize bias, it is good practice to work "blind," meaning that experimenters are unaware of the identity or treatment group of their subjects while conducting research. Here, using text mining and a literature review, we find evidence that blind protocols are uncommon in the life sciences and that nonblind studies tend to report higher effect sizes and more significant p-values. We discuss methods to minimize bias and urge researchers, editors, and peer reviewers to keep blind protocols in mind.
| S-EPMC4496034 | biostudies-literature
Project description:BackgroundThe web has seen an explosion of chemistry and biology related resources in the last 15 years: thousands of scientific journals, databases, wikis, blogs and resources are available with a wide variety of types of information. There is a huge need to aggregate and organise this information. However, the sheer number of resources makes it unrealistic to link them all in a centralised manner. Instead, search engines to find information in those resources flourish, and formal languages like Resource Description Framework and Web Ontology Language are increasingly used to allow linking of resources. A recent development is the use of userscripts to change the appearance of web pages, by on-the-fly modification of the web content. This opens possibilities to aggregate information and computational results from different web resources into the web page of one of those resources.ResultsSeveral userscripts are presented that enrich biology and chemistry related web resources by incorporating or linking to other computational or data sources on the web. The scripts make use of Greasemonkey-like plugins for web browsers and are written in JavaScript. Information from third-party resources are extracted using open Application Programming Interfaces, while common Universal Resource Locator schemes are used to make deep links to related information in that external resource. The userscripts presented here use a variety of techniques and resources, and show the potential of such scripts.ConclusionThis paper discusses a number of userscripts that aggregate information from two or more web resources. Examples are shown that enrich web pages with information from other resources, and show how information from web pages can be used to link to, search, and process information in other resources. Due to the nature of userscripts, scientists are able to select those scripts they find useful on a daily basis, as the scripts run directly in their own web browser rather than on the web server. This flexibility allows the scientists to tune the features of web resources to optimise their productivity.
| S-EPMC2222660 | biostudies-literature
Project description:Freshwater planarian flatworms possess uncanny regenerative capacities mediated by abundant and collectively totipotent adult stem cells. Key functions of these cells during regeneration and tissue homeostasis have been shown to depend on PIWI, a molecule required for piRNA expression in planarians. Nevertheless, the full complement of piRNAs, and microRNAs (miRNAs) in this organism has yet to be defined. Here, we report on the large scale cloning and sequencing of small RNAs from the planarian Schmidtea mediterranea, yielding altogether millions of sequenced unique small RNAs. We show that piRNAs are in part organized in genomic clusters and that they share characteristic features with mammalian and fly piRNAs. We further identify 61 novel miRNA genes and thus double the number of known planarian miRNAs. Sequencing, as well as quantitative PCR of small RNAs uncovered ten miRNAs enriched in planarian stem cells. These miRNAs are down-regulated in animals in which stem cells have been abrogated by irradiation, and thus constitute miRNAs likely associated with specific stem cell functions. Altogether, we present the first comprehensive small RNA analysis in animals belonging to the third animal superphylum, the Lophotrochozoa, and single out a number of miRNAs that may function in regeneration. Several of these miRNAs are deeply conserved in animals.
2009-07-01 | GSE16159 | GEO
Project description:Early-life microbial exposure is of particular importance to growth, immune system development and long-lasting health. Hence, early microbiota composition is a promising predictive biomarker for health and disease but still remains poorly characterized in regards to susceptibility to diarrhoea. In the present study, we aimed to assess if gut bacterial community diversity and composition during the suckling period were associated with differences in susceptibility of pigs to post-weaning diarrhoea. Twenty piglets from 5 sows (4 piglets / litter) were weaned in poor housing conditions to challenge their susceptibility to post-weaning diarrhoea. Two weeks after weaning, 13 pigs exhibited liquid faeces during 2 or 3 days and were defined as diarrhoeic (D) pigs. The other 7 pigs did not have diarrhea during the whole post-weaning experimental periodand were defined as healthy (H) pigs. Using a molecular characterisation of fecal microbiota with CE-SSCP fingerprint, Next Generation Sequencing and qPCR, we show that D and H pigs were mainly discriminated as early as postnatal day (PND) 7, i.e. 4 weeks before post-weaning diarrhoea occurence. At PND 7 H pigs displayed a lower evenness and a higher abundance of Prevotellaceae, Lachnospiraceae, Ruminocacaceae and Lactobacillaceae compared to D pigs. The sPLS regression method indicates that these bacterial families were strongly correlated to a higher Bacteroidetes abundance observed in PND 30 H pigs one week before diarrhoea. These results emphasize the potential of early microbiota diversity and composition as being an indicator of susceptibility to post-weaning diarrhoea. Furthermore, they support the health promoting strategies of pig herds through gut microbiota engineering.
| S-EPMC5225014 | biostudies-literature
Project description:Highlights•Crises present vexing challenges. Understanding what is happening and what therefore to do is for executive leaders.•The POP-DOC Loop links critical situational awareness to appropriate decisions and actions.•The POP-DOC Loop integrates and sequences dynamic functions to enhance leader adaptability and productivity in crisis.•The POP-DOC Loop steps reflect understanding of cognitive functioning and its influence on leader behavior.
| S-EPMC7264025 | biostudies-literature
Project description:BackgroundPatient-reported outcomes (PROs), such as health-related quality of life (HRQL) are increasingly used to evaluate treatment effectiveness in clinical trials, are valued by patients, and may inform important decisions in the clinical setting. It is of concern, therefore, that preliminary evidence, gained from group discussions at UK-wide Medical Research Council (MRC) quality of life training days, suggests there are inconsistent standards of HRQL data collection in trials and appropriate training and education is often lacking. Our objective was to investigate these reports, to determine if they represented isolated experiences, or were indicative of a potentially wider problem.Methods and findingsWe undertook a qualitative study, conducting 26 semi-structured interviews with research nurses, data managers, trial coordinators and research facilitators involved in the collection and entry of HRQL data in clinical trials, across one primary care NHS trust, two secondary care NHS trusts and two clinical trials units in the UK. We used conventional content analysis to analyze and interpret our data. Our study participants reported (1) inconsistent standards in HRQL measurement, both between, and within, trials, which appeared to risk the introduction of bias; (2), difficulties in dealing with HRQL data that raised concern for the well-being of the trial participant, which in some instances led to the delivery of non-protocol driven co-interventions, (3), a frequent lack of HRQL protocol content and appropriate training and education of trial staff, and (4) that HRQL data collection could be associated with emotional and/or ethical burden.ConclusionsOur findings suggest there are inconsistencies in the standards of HRQL data collection in some trials resulting from a general lack of HRQL-specific protocol content, training and education. These inconsistencies could lead to biased HRQL trial results. Future research should aim to develop HRQL guidelines and training programmes aimed at supporting researchers to carry out high quality data collection.
| S-EPMC3790726 | biostudies-literature
Project description:Throughout history, the life sciences have been revolutionised by technological advances; in our era this is manifested by advances in instrumentation for data generation, and consequently researchers now routinely handle large amounts of heterogeneous data in digital formats. The simultaneous transitions towards biology as a data science and towards a 'life cycle' view of research data pose new challenges. Researchers face a bewildering landscape of data management requirements, recommendations and regulations, without necessarily being able to access data management training or possessing a clear understanding of practical approaches that can assist in data management in their particular research domain. Here we provide an overview of best practice data life cycle approaches for researchers in the life sciences/bioinformatics space with a particular focus on 'omics' datasets and computer-based data processing and analysis. We discuss the different stages of the data life cycle and provide practical suggestions for useful tools and resources to improve data management practices.
| S-EPMC6069748 | biostudies-literature
Project description:Although a vast amount of life sciences data is generated in the form of images, most scientists still store images on extremely diverse and often incompatible storage media, without any type of metadata structure, and thus with no standard facility with which to conduct searches or analyses. Here we present a solution to unlock the value of scientific images. The Global Image Database (GID) is a web-based (http://www.gwer.ch/qv/gid/gid.ht m ) structured central repository for scientific annotated images. The GID was designed to manage images from a wide spectrum of imaging domains ranging from microscopy to automated screening. The annotations in the GID define the source experiment of the images by describing who the authors of the experiment are, when the images were created, the biological origin of the experimental sample and how the sample was processed for visualization. A collection of experimental imaging protocols provides details of the sample preparation, and labeling, or visualization procedures. In addition, the entries in the GID reference these imaging protocols with the probe sequences or antibody names used in labeling experiments. The GID annotations are searchable by field or globally. The query results are first shown as image thumbnail previews, enabling quick browsing prior to original-sized annotated image retrieval. The development of the GID continues, aiming at facilitating the management and exchange of image data in the scientific community, and at creating new query tools for mining image data.
| S-EPMC29843 | biostudies-literature