NCBI GEO: archive for gene expression and epigenomics data sets: 23-year update.

The Gene Expression Omnibus (GEO) is an international public repository that archives gene expression and epigenomics data sets generated by next-generation sequencing and microarray technologies. Data are typically submitted to GEO by researchers in compliance with widespread journal and funder mandates to make generated data publicly accessible. The resource handles raw data files, processed data files and descriptive metadata for over 200 000 studies and 6.5 million samples, all of which are indexed, searchable and downloadable. Additionally, GEO offers web-based tools that facilitate analysis and visualization of differential gene expression. This article presents the current status and recent advancements in GEO, including the generation of consistently computed gene expression count matrices for thousands of RNA-seq studies, and new interactive graphical plots in GEO2R that help users identify differentially expressed genes and assess data set quality. The GEO repository is built and maintained by the National Center for Biotechnology Information (NCBI), a division of the National Library of Medicine (NLM), and is publicly accessible at https://www.ncbi.nlm.nih.gov/geo/.

NCBI GEO: archive for functional genomics data sets--update.

The Gene Expression Omnibus (GEO, http://www.ncbi.nlm.nih.gov/geo/) is an international public repository for high-throughput microarray and next-generation sequence functional genomic data sets submitted by the research community. The resource supports archiving of raw data, processed data and metadata which are indexed, cross-linked and searchable. All data are freely available for download in a variety of formats. GEO also provides several web-based tools and strategies to assist users to query, analyse and visualize data. This article reports current status and recent database developments, including the release of GEO2R, an R-based web application that helps users analyse GEO data.

Correction: Behavior Analysts' Use of Treatments for Individuals with Autism: Trends within the Field.

[This corrects the article DOI: 10.1007/s40617-023-00776-2.].

NCBI GEO: archive for functional genomics data sets--10 years on.

A decade ago, the Gene Expression Omnibus (GEO) database was established at the National Center for Biotechnology Information (NCBI). The original objective of GEO was to serve as a public repository for high-throughput gene expression data generated mostly by microarray technology. However, the research community quickly applied microarrays to non-gene-expression studies, including examination of genome copy number variation and genome-wide profiling of DNA-binding proteins. Because the GEO database was designed with a flexible structure, it was possible to quickly adapt the repository to store these data types. More recently, as the microarray community switches to next-generation sequencing technologies, GEO has again adapted to host these data sets. Today, GEO stores over 20,000 microarray- and sequence-based functional genomics studies, and continues to handle the majority of direct high-throughput data submissions from the research community. Multiple mechanisms are provided to help users effectively search, browse, download and visualize the data at the level of individual genes or entire studies. This paper describes recent database enhancements, including new search and data representation tools, as well as a brief review of how the community uses GEO data. GEO is freely accessible at http://www.ncbi.nlm.nih.gov/geo/.

Parents' Emotional Responses to Behavior Analysis Terms: A Comparative Analysis.

Behavior analysts are concerned with developing strong client-therapist relationships. One challenge to the development of such relationships may be a reliance on technical language that stakeholders find unpleasant. Previous research suggests that some behavior analysis terms evoke negative emotional responses. However, most relevant research was conducted with individuals from the general public and not individuals with a history of interaction with behavior analysts. The current study evaluated how parents of individuals with disabilities, who accessed behavior analytic services for their child, rated their emotional responses to 40 behavior analysis terms. We found that half of behavior analysis terms were rated as less pleasant than the majority of English words by parents. Furthermore, word emotion ratings by our stakeholder sample corresponded closely to norms obtained from the general public (Warriner et al. Behavior Research Methods, 45(4), 1191-1207, 2013). Our findings suggest that, while learning history may mediate some emotional responses to words, published word emotion data could be a useful guide to how stakeholders may respond to behavior analysis terminology. A need remains for additional studies examining word emotion responses that may be unique to particular sub-categories of stakeholders and evaluating how emotional responses impact the development of effective relationships.

Behavior Analysts' Use of Treatments for Individuals with Autism: Trends within the Field.

Previous surveys revealed the majority of certified behavior analysts reported using applied behavior analysis (ABA) as a treatment for individuals on the autism spectrum. However, some certificants have also reported using treatments without evidence (Schreck et al. Behavioral Interventions, 31(4), 355-376, 2016; Schreck & Mazur Behavioral Interventions: Theory & Practice in Residential & Community- Based Clinical Programs, 23(3), 201-212, 2008). The field of ABA has undergone many changes in the last five years. This survey evaluated trends in the use and variables influencing the use of autism treatments over that time. Results indicated that study participants (N = 921 BCBA-Ds, BCBAs, BCaBAs, and RBTs) were significantly less likely to report current use of ABA and some unestablished treatments (e.g., DIR Floortime, sensory integration therapy) than participants in 2016 (Schreck et al. Behavioral Interventions, 31(4), 355-376, 2016). Participants frequently cited persuasion by others as an influence for their treatment selections. Because behavior analysts' use of unestablished treatments may be detrimental to client outcomes and the reputation and success of the field of ABA, future research is needed to identify methods for increasing behavior analysts' use of empirically supported treatments.

NCBI GEO: archive for high-throughput functional genomic data.

The Gene Expression Omnibus (GEO) at the National Center for Biotechnology Information (NCBI) is the largest public repository for high-throughput gene expression data. Additionally, GEO hosts other categories of high-throughput functional genomic data, including those that examine genome copy number variations, chromatin structure, methylation status and transcription factor binding. These data are generated by the research community using high-throughput technologies like microarrays and, more recently, next-generation sequencing. The database has a flexible infrastructure that can capture fully annotated raw and processed data, enabling compliance with major community-derived scientific reporting standards such as 'Minimum Information About a Microarray Experiment' (MIAME). In addition to serving as a centralized data storage hub, GEO offers many tools and features that allow users to effectively explore, analyze and download expression data from both gene-centric and experiment-centric perspectives. This article summarizes the GEO repository structure, content and operating procedures, as well as recently introduced data mining features. GEO is freely accessible at http://www.ncbi.nlm.nih.gov/geo/.

Soft Skills: The Case for Compassionate Approaches or How Behavior Analysis Keeps Finding Its Heart.

As the field of behavior analysis expands, our need to develop ourselves as more effective collaborators, particularly with families who may be the primary consumers of our science, becomes paramount. As scientists, our training lies primarily in the behavior analytic technologies that we study and apply. But our ability to disseminate our science, collaborate with non-behavior analysts, and ultimately grow our field hinges on our ability to navigate interpersonal situations in a way that puts forth compassion and humanity. We have the opportunity and capability to use our empirical procedures to implement and assess the effectiveness of interventions that target the soft skills of our field. The current article discusses the benefits of empathic and collaborative approaches in fields related to behavior analysis and provides suggestions for current behavior analysts to incorporate compassionate care into their practices. We provide a checklist for compassionate interactions accompanied by possibilities for its use as a tool for self-evaluation, procedural fidelity, and comprehensive training in the area of collaboration with families. Finally, we discuss areas for future research with respect to assessing and improving behavior analysts' compassionate approaches to treatment.

Initiatives to Address Diversity, Equity, and Inclusion Within a Higher Education ABA Department.

Recent events have highlighted the need for behavior analysis to address issues of diversity, equity, and inclusion (DEI) in service provision and in higher education. There has been a call to action issued, noting the need for cultural humility and cultural responsiveness. An opportunity exists within training programs to ensure that students of behavior analysis are instructed in ways that promote cultural responsiveness and that equip them to serve diverse populations. Additionally, more needs to be done to engineer environments where students of behavior analysis are treated with respect and compassion, and to ensure that educational environments promote the comfort and success of all students. This article outlines the initiatives of an applied behavior analysis department to gather information about DEI on the local level, identify goals, implement change, and evaluate progress toward these goals.

Acute Myocardial Infarction Cohorts Defined by International Classification of Diseases, Tenth Revision Versus Diagnosis-Related Groups: Analysis of Diagnostic Agreement and Quality Measures in an Integrated Health System.

BACKGROUND: Among Medicare value-based payment programs for acute myocardial infarction (AMI), the Hospital Readmissions Reduction Program uses International Classification of Diseases, Tenth Revision (ICD-10) codes to identify the program denominator, while the Bundled Payments for Care Improvement Advanced program uses diagnosis-related groups (DRGs). The extent to which these programs target similar patients, whether they target the intended population (type 1 myocardial infarction), and whether outcomes are comparable between cohorts is not known. METHODS: In a retrospective study of 2176 patients hospitalized in an integrated health system, a cohort of patients assigned a principal ICD-10 diagnosis of AMI and a cohort of patients assigned an AMI DRG were compared according to patient-level agreement and outcomes such as mortality and readmission. RESULTS: One thousand nine hundred thirty-five patients were included in the ICD-10 cohort compared with 662 patients in the DRG cohort. Only 421 patients were included in both AMI cohorts (19.3% agreement). DRG cohort patients were older (70 versus 65 years, P<0.001), more often female (48% versus 30%, P<0.001), and had higher rates of heart failure (52% versus 33%, P<0.001) and kidney disease (42% versus 25%, P<0.001). Comparing outcomes, the DRG cohort had significantly higher unadjusted rates of 30-day mortality (6.6% versus 2.5%, P<0.001), 1-year mortality (21% versus 8%, P<0.001), and 90-day readmission (26% versus 19%, P=0.006) than the ICD-10 cohort. Two observations help explain these differences: 61% of ICD-10 cohort patients were assigned procedural DRGs for revascularization instead of an AMI DRG, and type 1 myocardial infarction patients made up a smaller proportion of the DRG cohort (34%) than the ICD-10 cohort (78%). CONCLUSIONS: The method used to identify denominators for value-based payment programs has important implications for the patient characteristics and outcomes of the populations. As national and local quality initiatives mature, an emphasis on ICD-10 codes to define AMI cohorts would better represent type 1 myocardial infarction patients.

Tooth whitening: current status.

This article reviews the history of tooth whitening and its rapid evolution and briefly discusses tooth whitening agents and protocols. The active ingredients and mode of action during the whitening process are explained. The factors affecting the speed of whitening and its final results are discussed, as well as adverse effects and safety precautions. Protocols are explained in detail, and the predicted outcomes, including those for tetracycline-stained teeth, are covered.

A Redescription of the Bulla, Antennae, and Mouth Parts of Female Clavella sp. (Copepoda: Siphonostomatoida: Lernaeopodidae) Infesting Wild Gadus morhua Using Scanning Electron Microscopy (SEM).

Many members of the Copepod family Lernaeopodidae are well-known parasites of gadids. This study reports on the occurrence of a lernaeopodid infestation of wild-sourced Gadus morhua sampled from separate inshore (Gilbert Bay, NL) and offshore (Virgin Rocks, NL) populations from Newfoundland, Canada. The majority of the parasites were observed to be associated with the buccal cavity, gill filaments, gill arch, and occasionally near the outer edge of the operculum. Anatomical analysis and detailed redescriptions of the parasite's functional anatomy (mouth parts, antennae, and bulla complex) using high-resolution SEM indicated that the parasite was most likely of the genus Clavella. New morphological details of the second antennae ornamentation, first maxillae, bulla complex, and the oral cone are provided and discussed with regard to their potential in taxonomic applications.