Application of protein lysate microarrays to molecular marker verification and quantification

This study presents the development and application of protein lysate microarray (LMA) technology for verification of presence and quantification of human tissue samples for protein biomarkers. Sub-picogram range sensitivity has been achieved on LMA using a non-enzymatic protein detection methodology. Results from a set of quality control experiments are presented and demonstrate the high sensitivity and reproducibility of the LMA methodology. The optimized LMA methodology has been applied for verification of the presence and quantification of disease markers for atherosclerosis. LMA were used to measure lipoprotein [a] and apolipoprotein B100 in 52 carotid endarterectomy samples. The data generated by LMA were validated by ELISA using the same protein lysates. The correlations of protein amounts estimated by LMA and ELISA were highly significant, with r(2 )≥ 0.98 (p ≤ 0.001) for lipoprotein [a] and with r(2 )≥ 0.94 (p ≤ 0.001) for apolipoprotein B100. This is the first report to compare data generated using proteins microarrays with ELISA, a standard technology for the verification of the presence of protein biomarkers. The sensitivity, reproducibility, and high-throughput quality of LMA technology make it a potentially powerful technology for profiling disease specific protein markers in clinical samples

The Foundation Model Transparency Index

Foundation models have rapidly permeated society, catalyzing a wave of generative AI applications spanning enterprise and consumer-facing contexts. While the societal impact of foundation models is growing, transparency is on the decline, mirroring the opacity that has plagued past digital technologies (e.g. social media). Reversing this trend is essential: transparency is a vital precondition for public accountability, scientific innovation, and effective governance. To assess the transparency of the foundation model ecosystem and help improve transparency over time, we introduce the Foundation Model Transparency Index. The Foundation Model Transparency Index specifies 100 fine-grained indicators that comprehensively codify transparency for foundation models, spanning the upstream resources used to build a foundation model (e.g data, labor, compute), details about the model itself (e.g. size, capabilities, risks), and the downstream use (e.g. distribution channels, usage policies, affected geographies). We score 10 major foundation model developers (e.g. OpenAI, Google, Meta) against the 100 indicators to assess their transparency. To facilitate and standardize assessment, we score developers in relation to their practices for their flagship foundation model (e.g. GPT-4 for OpenAI, PaLM 2 for Google, Llama 2 for Meta). We present 10 top-level findings about the foundation model ecosystem: for example, no developer currently discloses significant information about the downstream impact of its flagship model, such as the number of users, affected market sectors, or how users can seek redress for harm. Overall, the Foundation Model Transparency Index establishes the level of transparency today to drive progress on foundation model governance via industry standards and regulatory intervention.Comment: Authored by the Center for Research on Foundation Models (CRFM) at the Stanford Institute for Human-Centered Artificial Intelligence (HAI). Project page: https://crfm.stanford.edu/fmt

A comparative analysis of data generated using two different target preparation methods for hybridization to high-density oligonucleotide microarrays

BACKGROUND: To generate specific transcript profiles, one must isolate homogenous cell populations using techniques that often yield small amounts of RNA, requiring researchers to employ RNA amplification methods. The data generated by using these methods must be extensively evaluated to determine any technique dependent distortion of the expression profiles. RESULTS: High-density oligonucleotide microarrays were used to perform experiments for comparing data generated by using two protocols, an in vitro transcription (IVT) protocol that requires 5 μg of total RNA and a double in vitro transcription (dIVT) protocol that requires 200 ng of total RNA for target preparation from RNA samples extracted from a normal and a cancer cell line. In both cell lines, about 10% more genes were detected with IVT than with dIVT. Genes were filtered to exclude those that were undetected on all arrays. Hierarchical clustering using the 9,482 genes that passed the filter showed that the variation attributable to biological differences between samples was greater than that introduced by differences in the protocols. We analyzed the behavior of these genes separately for each protocol by using a statistical model to estimate the posterior probability of various levels of fold change. At each level, more differentially expressed genes were detected with IVT than with dIVT. When we checked for genes that had a posterior probability greater than 99% of fold change greater than 2, in data generated by IVT but not dIVT, more than 60% of these genes had posterior probabilities greater than 90% in data generated by dIVT. Both protocols identified the same functional gene categories to be differentially expressed. Differential expression of selected genes was confirmed using quantitative real-time PCR. CONCLUSION: Using nanogram quantities on total RNA, the usage of dIVT protocol identified differentially expressed genes and functional categories consistent with those detected by the IVT protocol. There was a loss in sensitivity of about 10% when detecting differentially expressed genes using the dIVT protocol. However, the lower amount of RNA required for this protocol, as compared to the IVT protocol, renders this methodology a highly desirable one for biological systems where sample amounts are limiting

SUPPORT-AF: Piloting a Multi-Faceted, Electronic Medical Record-Based Intervention to Improve Prescription of Anticoagulation

Background: Only 50% of eligible atrial fibrillation ( AF ) patients receive anticoagulation ( AC ). Feasibility and effectiveness of electronic medical record (EMR)-based interventions to profile and raise provider AC percentage is poorly understood. The SUPPORT-AF (Supporting Use of AC Through Provider Profiling of Oral AC Therapy for AF) study aims to improve rates of adherence to AC guidelines by developing and delivering supportive tools based on the EMR to providers treating patients with AF. Methods and Results: We emailed cardiologists and community-based primary care providers affiliated with our institution reports of their AC percentage relative to peers. We also sent an electronic medical record-based message to these providers the day before an appointment with an atrial fibrillation patient who was eligible but not receiving AC . The electronic medical record message asked the provider to discuss AC with the patient if he or she deemed it appropriate. To assess feasibility, we tracked provider review of our correspondence. We also tracked the change in AC for intervention providers relative to alternate primary care providers not receiving our intervention. We identified 3786, 1054, and 566 patients cared for by 49 cardiology providers, 90 community-based primary care providers, and 88 control providers, respectively. At baseline, the percentage of AC was 71.3%, 63.5%, and 58.3% for these 3 respective groups. Intervention providers reviewed our e-mails and electronic medical record messages 45% and 96% of the time, respectively. For providers responding, patient refusal was the most common reason for patients not being on AC (21%) followed by high bleeding risk (19%). At follow-up 10 weeks later, change in AC was no different for either cardiology or community-based primary care providers relative to controls (0.2% lower and 0.01% higher, respectively). Conclusions: Our intervention profiling AC was feasible, but not sufficient to increase AC in our population

Recent Trends in Oral Anticoagulant Use and Post-Discharge Complications Among Atrial Fibrillation Patients with Acute Myocardial Infarction

Background: Atrial fibrillation (AF) is a common complication of acute myocardial infarction (AMI).The CHA2DS2VAScand CHADS2risk scoresare used to identifypatients with AF at risk for strokeand to guide oral anticoagulants (OAC) use, including patients with AMI. However, the epidemiology of AF, further stratifiedaccording to patients\u27 risk of stroke, has not been wellcharacterized among those hospitalized for AMI. Methods: We examined trends in the frequency of AF, rates of discharge OAC use, and post-discharge outcomes among 6,627 residents of the Worcester, Massachusetts area who survived hospitalization for AMI at 11 medical centers between 1997 and 2011. Results: A total of 1,050AMI patients had AF (16%) andthe majority (91%)had a CHA2DS2VAScscore \u3e 2.AF rates were highest among patients in the highest stroke risk group.In comparison to patients without AF, patients with AMI and AF in the highest stroke risk category had higher rates of post-discharge complications, including higher 30-day re-hospitalization [27 % vs. 17 %], 30-day post-discharge death [10 % vs. 5%], and 1-year post-discharge death [46 % vs. 18 %] (p \u3c 0.001 for all). Notably, fewer than half of guideline-eligible AF patients received an OAC prescription at discharge. Usage rates for other evidence-based therapies such as statins and beta-blockers,lagged in comparison to AMI patients free from AF. Conclusions: Our findings highlight the need to enhance efforts towards stroke prevention among AMI survivors with AF

Development, implementation, and evaluation of a competency-based didactic and simulation-focused boot camp for incoming urology residents: Report of the first three years

Introduction: The Royal College of Physicians and Surgeons of Canada’s Competence by Design (CBD) initiative presents curricula challenges to ensure residents gain proficiency while progressing through training. To prepare first-year urology residents (R1s), we developed, implemented, and evaluated a didactic and simulation-focused boot camp to implement the CBD curriculum. We report our experiences and findings of the first three years. Methods: Urology residents from two Canadian universities participated in the two-day boot camp at the beginning of residency. Eleven didactic and six simulation sessions allowed for instruction and deliberate practice with feedback. Pre-and post-course multiple-choice questionnaires (MCQs) and an objective structured clinical exam (OSCE) evaluated knowledge and skills uptake. For initial program evaluation, three R2s served as historical controls in year 1. Results: Nineteen residents completed boot camp. The mean age was 26.4 (±2.8) and 13 were male. Participants markedly improved on the pre- and post-MCQs (year 1: 62% and 91%; year 2: 55% and 89%; year 3: 58% and 86%, respectively). Participants scored marginally higher than the controls on four of the six OSCE stations. OSCE scores remained \u3e88% over the three cohorts. All participants reported higher confidence levels post-boot camp and felt it was excellent preparation for residency. Conclusions: During its first three years, our urology boot camp has demonstrated high feasibility and utility. Knowledge and technical skills uptake were established via MCQ and OSCE results, with participants’ scores near or above those of R2 controls. This boot camp will remain in our CBD curriculum and can provide a framework for other urology residency programs

miR-21 Plays a Dual Role in Tumor Formation and Cytotoxic Response in Breast Tumors

Breast cancer (BrCa) relies on specific microRNAs to drive disease progression. Oncogenic miR-21 is upregulated in many cancers, including BrCa, and is associated with poor survival and treatment resistance. We sought to determine the role of miR-21 in BrCa tumor initiation, progression and treatment response. In a triple-negative BrCa model, radiation exposure increased miR-21 in both primary tumor and metastases. In vitro, miR-21 knockdown decreased survival in all BrCa subtypes in the presence of radiation. The role of miR-21 in BrCa initiation was evaluated by implanting wild-type miR-21 BrCa cells into genetically engineered mouse models where miR-21 was intact, heterozygous or globally ablated. Tumors were unable to grow in the mammary fat pads of miR-21−/− mice, and grew in ~50% of miR-21+/− and 100% in miR-21+/+ mice. The contribution of miR-21 to progression and metastases was tested by crossing miR-21−/− mice with mice that spontaneously develop BrCa. The global ablation of miR-21 significantly decreased the tumorigenesis and metastases of BrCa, while sensitizing tumors to radio-and chemotherapeutic agents via Fas/FasL-dependent apoptosis. Therefore, targeting miR-21 alone or in combination with various radio or cytotoxic therapies may represent novel and efficacious therapeutic modalities for the future treatment of BrCa patients

Tbata modulates thymic stromal cell proliferation and thymus function

By inhibiting Nedd8, Tbata suppresses thymic epithelial cell proliferation and thymus size in mice.Niche availability provided by stromal cells is critical to thymus function. Thymi with diminished function contain fewer stromal cells, whereas thymi with robust function contain proliferating stromal cell populations. Here, we show that the thymus, brain, and testes–associated gene (Tbata; also known as SPATIAL) regulates thymic epithelial cell (TEC) proliferation and thymus size. Tbata is expressed in thymic stromal cells and interacts with the enzyme Uba3, thereby inhibiting the Nedd8 pathway and cell proliferation. Thymi from aged Tbata-deficient mice are larger and contain more dividing TECs than wild-type littermate controls. In addition, thymic reconstitution after bone marrow transplantation occurred more rapidly in Rag2−/−Tbata−/− mice than in Rag2−/−Tbata+/+ littermate controls. These findings suggest that Tbata modulates thymus function by regulating stromal cell proliferation via the Nedd8 pathway