We present a data exploration system equipped with smart drill-down, a novel operator for interactively exploring a relational table to discover and summarize "interesting" groups of tuples. Each such group of tuples is represented by a rule. For instance, the rule (a, b, ★, 1000) tells us that there are a thousand tuples with value a in the first column and b in the second column (and any value in the third column). Smart drill-down presents an analyst with a list of rules that together describe interesting aspects of the table. The analyst can tailor the definition of interesting, and can interactively apply smart drill-down on an existing rule to explore that part of the table. In the demonstration, conference attendees will be able to use the data exploration system equipped with smart drill-down, and will be able to contrast smart drill-down to traditional drill-down, for various interestingness measures, and resource constraints.

We present smart drill-down, an operator for interactively exploring a relational table to discover and summarize "interesting" groups of tuples. Each group of tuples is described by a rule. For instance, the rule (a, b, ⋆, 1000) tells us that there are a thousand tuples with value a in the first column and b in the second column (and any value in the third column). Smart drill-down presents an analyst with a list of rules that together describe interesting aspects of the table. The analyst can tailor the definition of interesting, and can interactively apply smart drill-down on an existing rule to explore that part of the table. We demonstrate that the underlying optimization problems are NP-Hard, and describe an algorithm for finding the approximately optimal list of rules to display when the user uses a smart drill-down, and a dynamic sampling scheme for efficiently interacting with large tables. Finally, we perform experiments on real datasets on our experimental prototype to demonstrate the usefulness of smart drill-down and study the performance of our algorithms.

Objective

We sought to characterize the performance of inpatient and outpatient computerized clinical decision support (CDS) alerts aimed at reducing inappropriate benzodiazepine and nonbenzodiazepine sedative medication prescribing in older adults 18 months after implementation.

Methods

We reviewed the performance of two CDS alerts in the outpatient and inpatient settings in 2019. To examine the alerts' effectiveness, we analyzed metrics including overall alert adherence, provider-level adherence, and reasons for alert trigger and override.

Results

In 2019, we identified a total of 14,534 and 4,834 alerts triggered in the outpatient and inpatient settings, respectively. Providers followed only 1% of outpatient and 3% of inpatient alerts. Most alerts were ignored (68% outpatient and 60% inpatient), while providers selected to override the remaining alerts. In each setting, the top 2% of clinicians were responsible for approximately 25% of all ignored or overridden alerts. However, a small proportion of clinicians (2% outpatient and 4% inpatient) followed the alert at least half of the time and accounted for a disproportionally large fraction of the total followed alerts. Our analysis of the free-text comments revealed that many alerts were to continue outpatient prescriptions or for situational anxiety.

Conclusion

Our findings highlight the importance of evaluation of CDS performance after implementation. We found large variation in response to the inpatient and outpatient alerts, both with respect to follow and ignore rates. Reevaluating the alert design by providing decision support by indication may be more helpful and may reduce alert fatigue.

Integrase-defective lentiviral vectors (IDLVs) have been of limited success in the delivery of zinc finger nucleases (ZFNs) to human cells, due to low expression. A reason for reduced gene expression has been proposed to involve the epigenetic silencing of vector genomes, carried out primarily by histone deacetylases (HDACs). In this study, we tested valproic acid (VPA), a known HDAC inhibitor (HDACi), for its ability to increase transgene expression from IDLVs, especially in the context of ZFN delivery. Using ZFNs targeting the human adenosine deaminase (ADA) gene in K562 cells, we demonstrated that treatment with VPA enhanced ZFN expression by up to 3-fold, resulting in improved allelic disruption at the ADA locus. Furthermore, three other U.S. Food and Drug Administration-approved HDACis (vorinostat, givinostat, and trichostatin-A) exhibited a similar effect on the activity of ZFN-IDLVs in K562 cells. In primary human CD34(+) cells, VPA- and vorinostat-treated cells showed higher levels of expression of both green fluorescent protein (GFP) as well as ZFNs from IDLVs. A major mechanism for the effects of HDAC inhibitors on improving expression was from their modulation of the cell cycle, and the influence of heterochromatinization was determined to be a lesser contributing factor.

Background

Conservative management may be a desirable option for elderly, fragile, or demented patients who reach end-stage renal disease (ESRD), yet some patients with dementia are placed on renal replacement therapy nonetheless.

Methods

From a nationwide cohort of 45,076 US veterans who transitioned to ESRD over 4 contemporary years (October 1, 2007 to September 30, 2011), we identified 1,336 (3.0%) patients with International Classification of Diseases, Ninth Revision, Clinical Modification code-based dementia diagnosis during the prelude (predialysis) period. We examined the association of prelude dementia with all-cause mortality within the first 6 months following transition to dialysis, using a propensity-matched cohort and Cox proportional hazards models.

Results

In the entire cohort, the overall mean ± standard deviation age at baseline was 72 ± 11 years, 95% were male, 23% were African-American, and 66% were diabetic. There were 8,080 (18.5%) deaths (mortality rate, 412; 95% confidence interval [CI], 403-421/1,000 patient-years) in the dementia-negative group, and 396 (29.6%) deaths (mortality rate, 708; 95% CI, 642-782/1,000 patient-years) in the dementia-positive group in the entire cohort in the first 6 months after dialysis initiation. Presence of dementia was associated with higher risk of all-cause mortality (adjusted hazard ratio, 1.25; 95% CI, 1.12-1.38) compared to dementia-free patients in the first 6 months after dialysis initiation.

Conclusion

Pre-ESRD dementia is associated with increased risk of early post-ESRD mortality in veterans transitioning to dialysis.

The next generation of high-power lasers enables repetition of experiments at orders of magnitude higher frequency than what was possible using the prior generation. Facilities requiring human intervention between laser repetitions need to adapt in order to keep pace with the new laser technology. A distributed networked control system can enable laboratory-wide automation and feedback control loops. These higher-repetition-rate experiments will create enormous quantities of data. A consistent approach to managing data can increase data accessibility, reduce repetitive data-software development and mitigate poorly organized metadata. An opportunity arises to share knowledge of improvements to control and data infrastructure currently being undertaken. We compare platforms and approaches to state-of-the-art control systems and data management at high-power laser facilities, and we illustrate these topics with case studies from our community.

CD8⁺ T cells recognize and eliminate tumors in an antigen-specific manner. Despite progress in characterizing the antitumor T cell repertoire and function, the identification of target antigens remains a challenge. Here we describe the use of chimeric receptors called signaling and antigen-presenting bifunctional receptors (SABRs) in a cell-based platform for T cell receptor (TCR) antigen discovery. SABRs present an extracellular complex comprising a peptide and major histocompatibility complex (MHC), and induce intracellular signaling via a TCR-like signal after binding with a cognate TCR. We devised a strategy for antigen discovery using SABR libraries to screen thousands of antigenic epitopes. We validated this platform by identifying the targets recognized by public TCRs of known specificities. Moreover, we extended this approach for personalized neoantigen discovery.

X-linked hyper-immunoglobulin M (hyper-IgM) syndrome (XHIM) is a primary immunodeficiency due to mutations in CD40 ligand that affect immunoglobulin class-switch recombination and somatic hypermutation. The disease is amenable to gene therapy using retroviral vectors, but dysregulated gene expression results in abnormal lymphoproliferation in mouse models, highlighting the need for alternative strategies. Here, we demonstrate the ability of both the transcription activator-like effector nuclease (TALEN) and clustered regularly interspaced short palindromic repeats-associated protein 9 (CRISPR/Cas9) platforms to efficiently drive integration of a normal copy of the CD40L cDNA delivered by Adeno-Associated Virus. Site-specific insertion of the donor sequence downstream of the endogenous CD40L promoter maintained physiologic expression of CD40L while overriding all reported downstream mutations. High levels of gene modification were achieved in primary human hematopoietic stem cells (HSCs), as well as in cell lines and XHIM-patient-derived T cells. Notably, gene-corrected HSCs engrafted in immunodeficient mice at clinically relevant frequencies. These studies provide the foundation for a permanent curative therapy in XHIM.

CD4+ T cells recognize peptide antigens presented on class II major histocompatibility complex (MHC-II) molecules to carry out their function. The remarkable diversity of T cell receptor sequences and lack of antigen discovery approaches for MHC-II make profiling the specificities of CD4+ T cells challenging. We have expanded our platform of signaling and antigen-presenting bifunctional receptors to encode MHC-II molecules presenting covalently linked peptides (SABR-IIs) for CD4+ T cell antigen discovery. SABR-IIs can present epitopes to CD4+ T cells and induce signaling upon their recognition, allowing a readable output. Furthermore, the SABR-II design is modular in signaling and deployment to T cells and B cells. Here, we demonstrate that SABR-IIs libraries presenting endogenous and non-contiguous epitopes can be used for antigen discovery in the context of type 1 diabetes. SABR-II libraries provide a rapid, flexible, scalable and versatile approach for de novo identification of CD4+ T cell ligands from single-cell RNA sequencing data using experimental and computational approaches.