Comparing the Quality of Domain-Specific Versus General Language Models for Artificial Intelligence-Generated Differential Diagnoses in PICU Patients.

OBJECTIVES: Generative language models (LMs) are being evaluated in a variety of tasks in healthcare, but pediatric critical care studies are scant. Our objective was to evaluate the utility of generative LMs in the pediatric critical care setting and to determine whether domain-adapted LMs can outperform much larger general-domain LMs in generating a differential diagnosis from the admission notes of PICU patients. DESIGN: Single-center retrospective cohort study. SETTING: Quaternary 40-bed PICU. PATIENTS: Notes from all patients admitted to the PICU between January 2012 and April 2023 were used for model development. One hundred thirty randomly selected admission notes were used for evaluation. INTERVENTIONS: None. MEASUREMENTS AND MAIN RESULTS: Five experts in critical care used a 5-point Likert scale to independently evaluate the overall quality of differential diagnoses: 1) written by the clinician in the original notes, 2) generated by two general LMs (BioGPT-Large and LLaMa-65B), and 3) generated by two fine-tuned models (fine-tuned BioGPT-Large and fine-tuned LLaMa-7B). Differences among differential diagnoses were compared using mixed methods regression models. We used 1,916,538 notes from 32,454 unique patients for model development and validation. The mean quality scores of the differential diagnoses generated by the clinicians and fine-tuned LLaMa-7B, the best-performing LM, were 3.43 and 2.88, respectively (absolute difference 0.54 units [95% CI, 0.37-0.72], p < 0.001). Fine-tuned LLaMa-7B performed better than LLaMa-65B (absolute difference 0.23 unit [95% CI, 0.06-0.41], p = 0.009) and BioGPT-Large (absolute difference 0.86 unit [95% CI, 0.69-1.0], p < 0.001). The differential diagnosis generated by clinicians and fine-tuned LLaMa-7B were ranked as the highest quality in 144 (55%) and 74 cases (29%), respectively. CONCLUSIONS: A smaller LM fine-tuned using notes of PICU patients outperformed much larger models trained on general-domain data. Currently, LMs remain inferior but may serve as an adjunct to human clinicians in real-world tasks using real-world data.

Curcumin inhibits Aspergillus flavus infection and aflatoxin production possibly by inducing ROS burst.

Aspergillus flavus contamination is common in various food and feed ingredients, and it poses to serious threats to human and animal health. Curcumin is a plant-derived polyphenol that exhibits antifungal activity. In this study, the antifungal effect of curcumin on A. flavus was evaluated, and the underlying mechanism was investigated. Curcumin effectively decreased aflatoxin B1 synthesis and suppressed A. flavus infection in peanut. Curcumin inhibited the mycelial growth and sporulation of A. flavus. Ergosterol biosynthesis in A. flavus was suppressed, and cell membrane permeability was enhanced. The pathogenicity of A. flavus was also reduced by curcumin treatment. Curcumin induced ROS burst in the hyphae of A. flavus, and those damages could be reversed by exogenous superoxide dismutase, suggesting that curcumin inhibited A. flavus possibly via inducing oxidative stress. These results indicate that curcumin has the potential to be used as a preservative to control A. flavus contamination in food and feedstuff.

Implementation Science in Pediatric Critical Care - Sedation and Analgesia Practices as a Case Study.

Sedation and analgesia (SA) management is essential practice in the pediatric intensive care unit (PICU). Over the past decade, there has been significant interest in optimal SA management strategy, due to reports of the adverse effects of SA medications and their relationship to ICU delirium. We reviewed 13 studies examining SA practices in the PICU over the past decade for the purposes of reporting the study design, outcomes of interest, SA protocols used, strategies for implementation, and the patient-centered outcomes. We highlighted the paucity of evidence-base for these practices and also described the existing gaps in the intersection of implementation science (IS) and SA protocols in the PICU. Future studies would benefit from a focus on effective implementation strategies to introduce and sustain evidence-based SA protocols, as well as novel quasi-experimental study designs that will help determine their impact on relevant clinical outcomes, such as the occurrence of ICU delirium. Adoption of the available evidence-based practices into routine care in the PICU remains challenging. Using SA practice as an example, we illustrated the need for a structured approach to the implementation science in pediatric critical care. Key components of the successful adoption of evidence-based best practice include the assessment of the local context, both resources and barriers, followed by a context-specific strategy for implementation and a focus on sustainability and integration of the practice into the permanent workflow.

Implementation of an Analgesia-Sedation Protocol Is Associated With Reduction in Midazolam Usage in the PICU.

OBJECTIVES: Examine the association of a revised analgesia-sedation protocol with midazolam usage in the PICU. DESIGN: A single-center nonrandomized before-after study. SETTING: PICU at a quaternary pediatric hospital (Boston Children's Hospital, Boston, MA). PATIENTS: Children admitted to the PICU who were mechanically ventilated for greater than 24 hours. The preimplementation cohort included 190 eligible patients admitted between July 29, 2017, and February 28, 2018, and the postimplementation cohort included 144 patients admitted between July 29, 2019, and February 28, 2020. INTERVENTIONS: Implementation of a revised analgesia-sedation protocol. MEASUREMENTS AND MAIN RESULTS: Our primary outcome, total dose of IV midazolam administered in mechanically ventilated patients up to day 14 of ventilation, decreased by 72% (95% CI [61-80%]; p < 0.001) in the postimplementation cohort. Dexmedetomidine usage increased 230% (95% CI [145-344%]) in the postimplementation cohort. Opioid usage, our balancing metric, was not significantly different between the two cohorts. There were no significant differences in ventilator-free days, PICU length of stay, rate of unplanned extubations, failed extubations, cardiorespiratory arrest events, and 24-hour readmissions to the PICU. CONCLUSIONS: We successfully implemented an analgesia-sedation protocol that primarily uses dexmedetomidine and intermittent opioids, and it was associated with significant decrease in overall midazolam usage in mechanically ventilated patients in the PICU. The intervention was not associated with changes in opioid usage or prevalence of adverse events.

A SALL4/MLL/HOXA9 pathway in murine and human myeloid leukemogenesis.

The embryonic self-renewal factor SALL4 has been implicated in the development of human acute myeloid leukemia (AML). Transgenic mice expressing the human SALL4B allele develop AML, which indicates that this molecule contributes to leukemia development and maintenance. However, the underlying mechanism of SALL4-dependent AML progression is unknown. Using SALL4B transgenic mice, we observed that HoxA9 was significantly upregulated in SALL4B leukemic cells compared with wild-type controls. Downregulation of HoxA9 in SALL4B leukemic cells led to decreased replating capacity in vitro and delayed AML development in recipient mice. In primary human AML cells, downregulation of SALL4 led to decreased HOXA9 expression and enhanced apoptosis. We found that SALL4 bound a specific region of the HOXA9 promoter in leukemic cells. SALL4 overexpression led to enhanced binding of histone activation markers at the HOXA9 promoter region, as well as increased HOXA9 expression in these cells. Furthermore, we observed that SALL4 interacted with mixed-lineage leukemia (MLL) and co-occupied the HOXA9 promoter region with MLL in AML leukemic cells, which suggests that a SALL4/MLL pathway may control HOXA9 expression. In summary, our findings revealed a molecular mechanism for SALL4 function in leukemogenesis and suggest that targeting of the SALL4/MLL/HOXA9 pathway would be an innovative approach in treating AML.

SALL4 is a key transcription regulator in normal human hematopoiesis.

BACKGROUND: Stem cell factor SALL4 is a zinc finger transcription factor. It plays vital roles in the maintenance of embryonic stem cell properties, functions as an oncogene in leukemia, and has been recently proposed to use for cord blood expansion. The mechanism(s) by which SALL4 functions in normal human hematopoiesis, including identification of its target genes, still need to be explored. STUDY DESIGN AND METHODS: Chromatin immunoprecipitation followed by microarray hybridization (ChIP-chip) was used for mapping SALL4 global gene targets in normal primary CD34+ cells. The results were then correlated with SALL4 functional studies in the CD34+ cells. RESULTS: More than 1000 potential SALL4 downstream target genes have been identified, and validation of binding by ChIP-quantitative polymerase chain reaction was performed for 5% of potential targets. These include genes that are involving in hematopoietic differentiation and self-renewal, such as HOXA9, RUNX1, CD34, and PTEN. Down regulation of SALL4 expression using small-hairpin RNA in these cells led to decreased in vitro myeloid colony-forming abilities and impaired in vivo engraftment. Furthermore, HOXA9 was identified to be a major SALL4 target in normal human hematopoiesis and the loss of either SALL4 or HOXA9 expression in CD34+ cells shared a similar phenotype. CONCLUSION: Taken together, SALL4 is a key regulator in normal human hematopoiesis and the mechanism of its function is at least in part through the HOXA9. Future study will determine whether modulating the SALL4/HOXA9 pathway can be used in cellular therapy such as cord blood expansion and/or myeloid engraftment.

Akt phosphorylates the transcriptional repressor bmi1 to block its effects on the tumor-suppressing ink4a-arf locus.

The Polycomb group protein Bmi1 is a transcriptional silencer of the Ink4a-Arf locus, which encodes the cell cycle regulator p16(Ink4a) and the tumor suppressor p19(Arf). Bmi1 plays a key role in oncogenesis and stem cell self-renewal. We report that phosphorylation of human Bmi1 at Ser³¹6 by Akt impaired its function by triggering its dissociation from the Ink4a-Arf locus, which resulted in decreased ubiquitylation of histone H2A and the inability of Bmi1 to promote cellular proliferation and tumor growth. Moreover, Akt-mediated phosphorylation of Bmi1 also inhibited its ability to promote self-renewal of hematopoietic stem and progenitor cells. Our study provides a mechanism for the increased abundance of p16(Ink4a) and p19(Arf) seen in cancer cells with an activated phosphoinositide 3-kinase to Akt signaling pathway and identifies crosstalk between phosphorylation events and chromatin structure.

The ability of MLL to bind RUNX1 and methylate H3K4 at PU.1 regulatory regions is impaired by MDS/AML-associated RUNX1/AML1 mutations.

The mixed-lineage leukemia (MLL) H3K4 methyltransferase protein, and the heterodimeric RUNX1/CBFß transcription factor complex, are critical for definitive and adult hematopoiesis, and both are frequently targeted in human acute leukemia. We identified a physical and functional interaction between RUNX1 (AML1) and MLL and show that both are required to maintain the histone lysine 4 trimethyl mark (H3K4me3) at 2 critical regulatory regions of the AML1 target gene PU.1. Similar to CBFß, we show that MLL binds to AML1 abrogating its proteasome-dependent degradation. Furthermore, a subset of previously uncharacterized frame-shift and missense mutations at the N terminus of AML1, found in MDS and AML patients, impairs its interaction with MLL, resulting in loss of the H3K4me3 mark within PU.1 regulatory regions, and decreased PU.1 expression. The interaction between MLL and AML1 provides a mechanism for the sequence-specific binding of MLL to DNA, and identifies RUNX1 target genes as potential effectors of MLL function.

SALL4, a stem cell factor, affects the side population by regulation of the ATP-binding cassette drug transport genes.

Our previous work shows that the stem cell factor SALL4 plays a central role in embryonic and leukemic stem cells. In this study, we report that SALL4 expression was higher in drug resistant primary acute myeloid leukemic patients than those from drug-responsive cases. In addition, while overexpression of SALL4 led to drug resistance in cell lines, cells with decreased SALL4 expression were more sensitive to drug treatments than the parental cells. This led to our investigation of the implication of SALL4 in drug resistance and its role in side population (SP) cancer stem cells. SALL4 expression was higher in SP cells compared to non-SP cells by 2-4 fold in various malignant hematopoietic cell lines. Knocking down of SALL4 in isolated SP cells resulted in a reduction of SP cells, indicating that SALL4 is required for their self-renewal. The SP phenotype is known to be mediated by members of the ATP-binding cassette (ABC) drug transport protein family, such as ABCG2 and ABCA3. Using chromatin-immunoprecipitation (ChIP), quantitative reverse transcription polymerase chain reaction (qRT-PCR) and electrophoretic mobility shift assay(EMSA), we demonstrated that SALL4 was able to bind to the promoter region of ABCA3 and activate its expression while regulating the expression of ABCG2 indirectly. Furthermore, SALL4 expression was positively correlated to those of ABCG2 and ABCA3 in primary leukemic patient samples. Taken together, our results suggest a novel role for SALL4 in drug sensitivity, at least in part through the maintenance of SP cells, and therefore may be responsible for drug-resistance in leukemia. We are the first to demonstrate a direct link between stem cell factor SALL4, SP and drug resistance in leukemia.

Stem cell factor SALL4 represses the transcriptions of PTEN and SALL1 through an epigenetic repressor complex.

BACKGROUND: The embryonic stem cell (ESC) factor, SALL4, plays an essential role in both development and leukemogenesis. It is a unique gene that is involved in self-renewal in ESC and leukemic stem cell (LSC). METHODOLOGY/PRINCIPAL FINDINGS: To understand the mechanism(s) of SALL4 function(s), we sought to identify SALL4-associated proteins by tandem mass spectrometry. Components of a transcription repressor Mi-2/Nucleosome Remodeling and Deacetylase (NuRD) complex were found in the SALL4-immunocomplexes with histone deacetylase (HDAC) activity in ESCs with endogenous SALL4 expression and 293T cells overexpressing SALL4. The SALL4-mediated transcriptional regulation was tested on two potential target genes: PTEN and SALL1. Both genes were confirmed as SALL4 downstream targets by chromatin-immunoprecipitation, and their expression levels, when tested by quantitative reverse transcription polymerase chain reaction (qRT-PCR), were decreased in 293T cells overexpressing SALL4. Moreover, SALL4 binding sites at the promoter regions of PTEN and SALL1 were co-occupied by NuRD components, suggesting that SALL4 represses the transcriptions of PTEN and SALL1 through its interactions with the Mi-2/NuRD complex. The in vivo repressive effect(s) of SALL4 were evaluated in SALL4 transgenic mice, where decreased expressions of PTEN and SALL1 were associated with myeloid leukemia and cystic kidneys, respectively. CONCLUSIONS/SIGNIFICANCE: In summary, we are the first to demonstrate that stem cell protein SALL4 represses its target genes, PTEN and SALL1, through the epigenetic repressor Mi-2/NuRD complex. Our novel finding provides insight into the mechanism(s) of SALL4 functions in kidney development and leukemogenesis.