REDfly: the transcriptional regulatory element database for Drosophila.

The REDfly database provides a comprehensive curation of experimentally-validated Drosophila transcriptional cis-regulatory elements and includes information on DNA sequence, experimental evidence, patterns of regulated gene expression, and more. Now in its thirteenth year, REDfly has grown to over 23 000 records of tested reporter gene constructs and 2200 tested transcription factor binding sites. Recent developments include the start of curation of predicted cis-regulatory modules in addition to experimentally-verified ones, improved search and filtering, and increased interaction with the authors of curated papers. An expanded data model that will capture information on temporal aspects of gene regulation, regulation in response to environmental and other non-developmental cues, sexually dimorphic gene regulation, and non-endogenous (ectopic) aspects of reporter gene expression is under development and expected to be in place within the coming year. REDfly is freely accessible at http://redfly.ccr.buffalo.edu, and news about database updates and new features can be followed on Twitter at @REDfly_database.

CaringGuidance™ after breast cancer diagnosis eHealth psychoeducational intervention to reduce early post-diagnosis distress.

PURPOSE: Significant cancer-related distress affects 30-60% of women diagnosed with breast cancer. Fewer than 30% of distressed patients receive psychosocial care. Unaddressed distress is associated with poor treatment adherence, reduced quality of life, and increased healthcare costs. This study aimed to evaluate the preliminary efficacy of a new web-based, psychoeducational distress self-management program, CaringGuidance™ After Breast Cancer Diagnosis, on newly diagnosed women's reported distress. METHODS: One-hundred women, in five states, diagnosed with breast cancer within the prior 3 months, were randomized to 12 weeks of independent use of CaringGuidance™ plus usual care or usual care alone. The primary multidimensional outcome, distress, was measured with the Distress Thermometer (DT), the Center for Epidemiologic Studies Depression Scale (CES-D), and the Impact of Events Scale (IES) at baseline and months 1, 2, and 3. Intervention usage was continually monitored by the data analytic system imbedded within CaringGuidance™. RESULTS: Although multilevel models showed no significant overall effects, post hoc analysis showed significant group differences in slopes occurring between study months 2 and 3 on distress (F(1,70) = 4.91, p = .03, η2 = .065) measured by the DT, and depressive symptoms (F(1, 76) = 4.25, p = .043, η2 = .053) favoring the intervention. CONCLUSIONS: Results provide preliminary support for the potential efficacy of CaringGuidance™ plus usual care over usual care alone on distress in women newly diagnosed with breast cancer. This analysis supports and informs future study of this self-management program aimed at filling gaps in clinical distress management.

Feasibility and acceptance of the CaringGuidance web-based, distress self-management, psychoeducational program initiated within 12 weeks of breast cancer diagnosis.

OBJECTIVE: Limited clinical resources create barriers to quality management of cancer-related distress. CaringGuidance After Breast Cancer Diagnosis is a web-based, patient-controlled, psychoeducational program of cognitive-behavioral, coping and problem-solving strategies aimed at early post-diagnosis distress reduction without clinical resources. This study evaluated the feasibility of recruiting and retaining newly diagnosed women to 12 weeks of CaringGuidance and program acceptance. METHODS: Women with stage 0 to II breast cancer diagnosed within the prior 3 months were recruited from clinics and communities in four states, from 2013 to 2015 and randomized to 12 weeks of CaringGuidance plus usual care (n = 57) or usual care alone (n = 43). Recruitment, retention, and program use were tracked. Using standard and study-derived measures, demographic and psychological variables were assessed at baseline and monthly and program satisfaction at 12 weeks. RESULTS: Of 139 women screened, 100 enrolled, five withdrew, and 12 were lost to follow-up (83% retention rate). Total program engagement was positively associated with greater baseline intrusive/avoidant thoughts. Intervention participants (92%) believed CaringGuidance would benefit future women and was easy to use. Sixty-six percent believed CaringGuidance helped them cope. Women used program content to change thoughts (49%) or behaviors (40%). Stress in the previous year was positively associated with reports that CaringGuidance was reassuring and helpful. CONCLUSIONS: Feasibility and acceptance of CaringGuidance was demonstrated pointing to the program's potential as a cancer-distress self-management intervention. Future research will explore program feasibility and acceptability in other regions of the United States, leading to clinical implementation trials.

Effects of social constraints and web-based psychoeducation on cancer-related psychological adjustment early-after breast cancer diagnosis.

Purpose: Social constraints are interactions between individuals that result in preventing one's disclosure of thoughts and emotions needed to facilitate cognitive processing of a traumatic event such as a breast cancer diagnosis. This study explored women's perceived social constraints from spouse/partners (S/P) and family/friends (F/F) in the first months after diagnosis while engaged in a study of CaringGuidance™ After Breast Cancer Diagnosis, a web-based, psychoeducational, self-management intervention aimed at women's psychological adjustment. Design: Randomized, controlled, pilot study. Sample: 100 women within 0-3 months of first, stage 0-II breast cancer diagnosis. Methods: Subjects were randomized to self-guided use of CaringGuidance™ for three months plus usual care or usual care alone. Social constraints (S/P) and (F/F), distress, depressive-symptoms, intrusive/avoidant thoughts, and coping were measured at baseline, 1, 2, and 3 months. Findings: The CaringGuidance™ group experienced a significantly greater decrease in perceived social constraints from S/P and F/F over three months than the usual care group. Change in social constraints from F/F significantly moderated change in depressive-symptoms and intrusive/avoidant thoughts, but the same was not true for change in S/P constraints. Conclusions: CaringGuidance™ holds promise as an intervention for newly diagnosed women to self-manage perceptions of social constraints. Implications for Psychosocial Providers: Providers should assess newly diagnosed women's perceptions of social constraining behavior from F/F, recognizing the potential significant impact of these interactions on psychological adjustment.

Analysis of secondary structural elements in human microRNA hairpin precursors.

BACKGROUND: MicroRNAs (miRNAs) regulate gene expression by targeting complementary mRNAs for destruction or translational repression. Aberrant expression of miRNAs has been associated with various diseases including cancer, thus making them interesting therapeutic targets. The composite of secondary structural elements that comprise miRNAs could aid the design of small molecules that modulate their function. RESULTS: We analyzed the secondary structural elements, or motifs, present in all human miRNA hairpin precursors and compared them to highly expressed human RNAs with known structures and other RNAs from various organisms. Amongst human miRNAs, there are 3808 are unique motifs, many residing in processing sites. Further, we identified motifs in miRNAs that are not present in other highly expressed human RNAs, desirable targets for small molecules. MiRNA motifs were incorporated into a searchable database that is freely available. We also analyzed the most frequently occurring bulges and internal loops for each RNA class and found that the smallest loops possible prevail. However, the distribution of loops and the preferred closing base pairs were unique to each class. CONCLUSIONS: Collectively, we have completed a broad survey of motifs found in human miRNA precursors, highly expressed human RNAs, and RNAs from other organisms. Interestingly, unique motifs were identified in human miRNA processing sites, binding to which could inhibit miRNA maturation and hence function.

Sequence-based design of bioactive small molecules that target precursor microRNAs.

Oligonucleotides are designed to target RNA using base pairing rules, but they can be hampered by poor cellular delivery and nonspecific stimulation of the immune system. Small molecules are preferred as lead drugs or probes but cannot be designed from sequence. Herein, we describe an approach termed Inforna that designs lead small molecules for RNA from solely sequence. Inforna was applied to all human microRNA hairpin precursors, and it identified bioactive small molecules that inhibit biogenesis by binding nuclease-processing sites (44% hit rate). Among 27 lead interactions, the most avid interaction is between a benzimidazole (1) and precursor microRNA-96. Compound 1 selectively inhibits biogenesis of microRNA-96, upregulating a protein target (FOXO1) and inducing apoptosis in cancer cells. Apoptosis is ablated when FOXO1 mRNA expression is knocked down by an siRNA, validating compound selectivity. Markedly, microRNA profiling shows that 1 only affects microRNA-96 biogenesis and is at least as selective as an oligonucleotide.

REDfly v3.0: toward a comprehensive database of transcriptional regulatory elements in Drosophila.

The REDfly database of Drosophila transcriptional cis-regulatory elements provides the broadest and most comprehensive available resource for experimentally validated cis-regulatory modules and transcription factor binding sites among the metazoa. The third major release of the database extends the utility of REDfly as a powerful tool for both computational and experimental studies of transcription regulation. REDfly v3.0 includes the introduction of new data classes to expand the types of regulatory elements annotated in the database along with a roughly 40% increase in the number of records. A completely redesigned interface improves access for casual and power users alike; among other features it now automatically provides graphical views of the genome, displays images of reporter gene expression and implements improved capabilities for database searching and results filtering. REDfly is freely accessible at http://redfly.ccr.buffalo.edu.

Postoperative Restrictive Opioid Protocols and Durable Changes in Opioid Prescribing and Chronic Opioid Use.

Importance: Changes in postsurgical opioid prescribing practices may help reduce chronic opioid use in surgical patients. Objective: To investigate whether postsurgical acute pain across different surgical subspecialties can be managed effectively after hospital discharge with an opioid supply of 3 or fewer days and whether this reduction in prescribed opioids is associated with reduced new, persistent opioid use. Design, Setting, and Participants: In this prospective cohort study with a case-control design, a restrictive opioid prescription protocol (ROPP) specifying an opioid supply of 3 or fewer days after discharge from surgery along with standardized patient education was implemented across all surgical services at a tertiary-care comprehensive cancer center. Participants were all patients who underwent surgery from August 1, 2018, to July 31, 2019. Main Outcomes and Measures: Main outcomes were the rate of compliance with the ROPP in each surgical service, the mean number of prescription days and refill requests, type of opioid prescribed, and rate of conversion to chronic opioid use determined via a state-run opioid prescription program. Postsurgical complications were also measured. Results: A total of 4068 patients (mean [SD] age, 61.0 [13.8] years; 2528 women [62.1%]) were included, with 2017 in the pre-ROPP group (August 1, 2018, to January 31, 2019) and 2051 in the post-ROPP group (February 1, 2019, to July 31, 2019). The rate of compliance with the protocol was 95%. After implementation of the ROPP, mean opioid prescription days decreased from a mean (SD) of 3.9 (4.5) days in the pre-ROPP group to 1.9 (3.6) days in the post-ROPP group (P < .001). The ROPP implementation led to a 45% decrease in prescribed opioids after surgery (mean [SD], 157.22 [338.06] mean morphine milligram equivalents [MME] before ROPP vs 83.54 [395.70] MME after ROPP; P < .001). Patients in the post-ROPP cohort requested fewer refills (367 of 2051 [17.9%] vs 422 of 2017 [20.9%] in the pre-ROPP cohort; P = .02). There was no statistically significant difference in surgical complications. The conversion rate to chronic opioid use decreased following ROPP implementation among both opioid-naive patients with cancer (11.3% [143 of 1267] to 4.5% [118 of 2645]; P < .001) and those without cancer (6.1% [19 of 310] to 2.7% [16 of 600]; P = .02). Conclusions and Relevance: In this cohort study, prescribing an opioid supply of 3 or fewer days to surgical patients after hospital discharge was feasible for most patients, led to a significant decrease in the number of opioids prescribed after surgery, and was associated with a significantly decreased conversion to long-term opioid use without concomitant increases in refill requests or significant compromises in surgical recovery.

Identification of interacting transcription factors regulating tissue gene expression in human.

BACKGROUND: Tissue gene expression is generally regulated by multiple transcription factors (TFs). A major first step toward understanding how tissues achieve their specificity is to identify, at the genome scale, interacting TFs regulating gene expression in different tissues. Despite previous discoveries, the mechanisms that control tissue gene expression are not fully understood. RESULTS: We have integrated a function conservation approach, which is based on evolutionary conservation of biological function, and genes with highest expression level in human tissues to predict TF pairs controlling tissue gene expression. To this end, we have identified 2549 TF pairs associated with a certain tissue. To find interacting TFs controlling tissue gene expression in a broad spatial and temporal manner, we looked for TF pairs common to the same type of tissues and identified 379 such TF pairs, based on which TF-TF interaction networks were further built. We also found that tissue-specific TFs may play an important role in recruiting non-tissue-specific TFs to the TF-TF interaction network, offering the potential for coordinating and controlling tissue gene expression across a variety of conditions. CONCLUSION: The findings from this study indicate that tissue gene expression is regulated by large sets of interacting TFs either on the same promoter of a gene or through TF-TF interaction networks.

REDfly 2.0: an integrated database of cis-regulatory modules and transcription factor binding sites in Drosophila.

The identification and study of the cis-regulatory elements that control gene expression are important areas of biological research, but few resources exist to facilitate large-scale bioinformatics studies of cis-regulation in metazoan species. Drosophila melanogaster, with its well-annotated genome, exceptional resources for comparative genomics and long history of experimental studies of transcriptional regulation, represents the ideal system for regulatory bioinformatics. We have merged two existing Drosophila resources, the REDfly database of cis-regulatory modules and the FlyReg database of transcription factor binding sites (TFBSs), into a single integrated database containing extensive annotation of empirically validated cis-regulatory modules and their constituent binding sites. With the enhanced functionality made possible through this integration of TFBS data into REDfly, together with additional improvements to the REDfly infrastructure, we have constructed a one-stop portal for Drosophila cis-regulatory data that will serve as a powerful resource for both computational and experimental studies of transcriptional regulation. REDfly is freely accessible at http://redfly.ccr.buffalo.edu.

ORegAnno: an open-access community-driven resource for regulatory annotation.

ORegAnno is an open-source, open-access database and literature curation system for community-based annotation of experimentally identified DNA regulatory regions, transcription factor binding sites and regulatory variants. The current release comprises 30 145 records curated from 922 publications and describing regulatory sequences for over 3853 genes and 465 transcription factors from 19 species. A new feature called the 'publication queue' allows users to input relevant papers from scientific literature as targets for annotation. The queue contains 4438 gene regulation papers entered by experts and another 54 351 identified by text-mining methods. Users can enter or 'check out' papers from the queue for manual curation using a series of user-friendly annotation pages. A typical record entry consists of species, sequence type, sequence, target gene, binding factor, experimental outcome and one or more lines of experimental evidence. An evidence ontology was developed to describe and categorize these experiments. Records are cross-referenced to Ensembl or Entrez gene identifiers, PubMed and dbSNP and can be visualized in the Ensembl or UCSC genome browsers. All data are freely available through search pages, XML data dumps or web services at: http://www.oreganno.org.

The NFI-Regulome Database: A tool for annotation and analysis of control regions of genes regulated by Nuclear Factor I transcription factors.

BACKGROUND: Genome annotation plays an essential role in the interpretation and use of genome sequence information. While great strides have been made in the annotation of coding regions of genes, less success has been achieved in the annotation of the regulatory regions of genes, including promoters, enhancers/silencers, and other regulatory elements. One reason for this disparity in annotated information is that coding regions can be assessed using high-throughput techniques such as EST sequencing, while annotation of regulatory regions often requires a gene-by-gene approach. RESULTS: The NFI-Regulome database http://nfiregulome.ccr.buffalo.edu was designed to promote easy annotation of the regulatory regions of genes that contain binding sites for the NFI (Nuclear Factor I) family of transcription factors, using data from the published literature. Binding sites are annotated together with the sequence of the gene, obtained from the UCSC Genome site, and the locations of all binding sites for multiple genes can be displayed in a number of formats designed to facilitate inter-gene comparisons. Classes of genes based on expression pattern, disease involvement, or types of binding sites present can be readily compared in order to assess common "architectural" structures in the regulatory regions. CONCLUSIONS: The NFI-Regulome database allows rapid display of the relative locations and number of transcription factor binding sites of individual or defined sets of genes that contain binding sites for NFI transcription factors. This database may in the future be expanded into a distributed database structure including other families of transcription factors. Such databases may be useful for identifying common regulatory structures in genes essential for organ development, tissue-specific gene expression or those genes related to specific diseases.

REDfly: a Regulatory Element Database for Drosophila.

Bioinformatics studies of transcriptional regulation in the metazoa are significantly hindered by the absence of readily available data on large numbers of transcriptional cis-regulatory modules (CRMs). Even the richly annotated Drosophila melanogaster genome lacks extensive CRM information. We therefore present here a database of Drosophila CRMs curated from the literature complete with both DNA sequence and a searchable description of the gene expression pattern regulated by each CRM. This resource should greatly facilitate the development of computational approaches to CRM discovery as well as bioinformatics analyses of regulatory sequence properties and evolution.