ATAT: Automated Tissue Alignment and Traversal in Spatial Transcriptomics with Self-Supervised Learning.

Spatial transcriptomics (ST) has enhanced RNA analysis in tissue biopsies, but interpreting these data is challenging without expert input. We present Automated Tissue Alignment and Traversal (ATAT), a novel computational framework designed to enhance ST analysis in the context of multiple and complex tissue architectures and morphologies, such as those found in biopsies of the gastrointestinal tract. ATAT utilizes self-supervised contrastive learning on hematoxylin and eosin (H&E) stained images to automate the alignment and traversal of ST data. This approach addresses a critical gap in current ST analysis methodologies, which rely heavily on manual annotation and pathologist expertise to delineate regions of interest for accurate gene expression modeling. Our framework not only streamlines the alignment of multiple ST samples, but also demonstrates robustness in modeling gene expression transitions across specific regions. Additionally, we highlight the ability of ATAT to traverse complex tissue topologies in real-world cases from various individuals and conditions. Our method successfully elucidates differences in immune infiltration patterns across the intestinal wall, enabling the modeling of transcriptional changes across histological layers. We show that ATAT achieves comparable performance to the state-of-the-art method, while alleviating the burden of manual annotation and enabling alignment of tissue samples with complex morphologies.

Implementation of an opioid reduction toolkit in pancreatectomy patients significantly increases patient awareness of safe practice and decreases amount prescribed and consumed.

BACKGROUND: Postoperative opioid abuse following surgery is a major concern. This study sought to create an opioid reduction toolkit to reduce the number of narcotics prescribed and consumed while increasing awareness of safe disposal in pancreatectomy patients. METHODS: Prescription, consumption, and refill request data for postoperative opioids were collected from patients receiving an open pancreatectomy before and after the implementation of an opioid reduction toolkit. Outcomes included safe disposal practice awareness for unused medication. RESULTS: 159 patients were included in the study: 24 in the pre-intervention and 135 in the post-intervention group. No significant demographic or clinical differences existed between groups. Median morphine milliequivalents (MMEs) prescribed were significantly reduced from 225 (225-310) to 75 (75-113) in the post-intervention group (p < 0.0001). Median MMEs consumed were significantly reduced from 109 (111-207) to 15 (0-75), p < 0.0001), as well. Refill request rates remained equivalent during the study (Pre: 17% v Post: 13%, p = 0.9) while patient awareness of safe disposal increased (Pre: 25% v Post: 62%, p < 0.0001). DISCUSSION: An opioid reduction toolkit significantly reduced the number of postoperative opioids prescribed and consumed after open pancreatectomy, while refill request rates remained the same and patients' awareness of safe disposal increased.

Do On-Table Radiographs Predict Postoperative Sagittal Alignment after Posterior Lumbar Fusion?

OBJECTIVE: To determine if intraoperative on-table lumbar lordosis and segmental lordosis correlate with postoperative lordosis following single-level posterolateral decompression and fusion (PLDF) or transforaminal lumbar interbody fusion (TLIF). METHODS: Electronic medical records were reviewed for patients ≥18 years old who underwent PLDF or TLIF between 2012 and 2020. Lumbar lordosis and segmental lordosis were compared between pre-, intra-, and postoperative radiographs using paired t tests. Significance was set at P < 0.05. RESULTS: A total of 200 patients met inclusion criteria. No significant differences in preoperative, intraoperative, or postoperative measurements were found between groups. Patients who underwent PLDF experienced less disc height loss over 1 year postoperatively (PLDF: 0.45 ± 0.9 mm vs. TLIF: 1.2 ± 1.4 mm, P < 0.001). Lumbar lordosis significantly decreased between intraoperative to postoperative radiographs at 2-6 weeks for PLDF (Δ: -4.0°, P < 0.001) and TLIF (Δ: -5.6°, P < 0.001), but no change was identified between the intraoperative and >6 month postoperative radiographs for PLDF (Δ: -0.3°, P = 0.634) or TLIF (Δ: -1.6°, P = 0.087). Segmental lordosis significantly increased from the preoperative to post-instrumentation intraoperative radiographs for PLDF (Δ: 2.7°, P < 0.001) and TLIF (Δ: 1.8°, P < 0.001), but it subsequently decreased at the final follow up for PLDF (Δ: -1.9°, P < 0.001) and TLIF (Δ: -2.3°, P < 0.001). CONCLUSIONS: Subtle decreases in lumbar lordosis may be noticed in early postoperative radiographs compared with intraoperative images on Jackson operative tables. However, these changes are not present at 1-year follow-up as lumbar lordosis increases to a similar level as intraoperative fixation.

Patient contrastive learning: A performant, expressive, and practical approach to electrocardiogram modeling.

Supervised machine learning applications in health care are often limited due to a scarcity of labeled training data. To mitigate the effect of small sample size, we introduce a pre-training approach, Patient Contrastive Learning of Representations (PCLR), which creates latent representations of electrocardiograms (ECGs) from a large number of unlabeled examples using contrastive learning. The resulting representations are expressive, performant, and practical across a wide spectrum of clinical tasks. We develop PCLR using a large health care system with over 3.2 million 12-lead ECGs and demonstrate that training linear models on PCLR representations achieves a 51% performance increase, on average, over six training set sizes and four tasks (sex classification, age regression, and the detection of left ventricular hypertrophy and atrial fibrillation), relative to training neural network models from scratch. We also compared PCLR to three other ECG pre-training approaches (supervised pre-training, unsupervised pre-training with an autoencoder, and pre-training using a contrastive multi ECG-segment approach), and show significant performance benefits in three out of four tasks. We found an average performance benefit of 47% over the other models and an average of a 9% performance benefit compared to best model for each task. We release PCLR to enable others to extract ECG representations at https://github.com/broadinstitute/ml4h/tree/master/model_zoo/PCLR.

Late onset atrial fibrillation in patients undergoing surgical aortic valve replacement.

OBJECTIVE: Aortic valve disease is a risk factor for atrial fibrillation (AF), and AF is associated with increased late mortality and morbidity after cardiac surgery. The evolution of alternative approaches to AF prophylaxis, including less invasive technologies and medical therapies, has altered the balance between risk and potential benefit for prophylactic intervention at the time of surgical aortic valve replacement (SAVR). Such interventions impose incremental risk, however, making an understanding of predictors of new onset AF that persists beyond the perioperative episode relevant. METHODS: We conducted a retrospective single-institution cohort analysis of patients undergoing SAVR with no history of preoperative AF (n = 1014). These patients were cross-referenced against an institutional electrocardiogram (ECG) database to identify those with ECGs 3-12 months after surgery. Logistic regression was used to identify predictors of late AF. RESULTS: Among the 401 patients (40%), who had ECGs in our institution 3-12 months after surgery, 16 (4%) had late AF. Patients with late AF were older than patients without late AF (73 vs. 65, p = .025), and underwent procedures that were more urgent/emergent (38% vs. 15%, p = .015), with higher predicted risk of mortality (2.2% vs. 1.3%, p = .012). Predictors associated with the development of late AF were advanced age, higher preoperative creatinine level and urgent/emergent surgery. CONCLUSIONS: The incidence of late AF 3-12 months after SAVR, is low. Prophylactic AF interventions at the time of SAVR may not be warranted.

A plasma cell-based pericardial effusion leading to tamponade in a patient with multiple myeloma - a case report and review of the literature.

A rare case of extramedullary multiple myeloma causing cardiac tamponade secondary to a plasma cell-based pericardial effusion is described. A systematic search using PubMed (National Library of Medicine) was used to identify a further 27 cases dating back to 1970. Case characteristics, treatment strategies, and survival time following tamponade are discussed. Linear regression demonstrated a weak but statistically significant correlation between survival time following tamponade and treatment with systemic chemotherapy and steroids (ß=16.8 weeks, P=.009). However, this manifestation of extramedullary multiple myeloma still conveys a dismal prognosis with a median survival following tamponade of only 6 weeks based on our review.

Hydrochlorothiazide vs chlorthalidone, indapamide, and potassium-sparing/hydrochlorothiazide diuretics for reducing left ventricular hypertrophy: A systematic review and meta-analysis.

Left ventricular hypertrophy develops in 36%-41% of hypertensive patients and independently predicts cardiovascular events and total mortality. Moreover, drug-induced reduction in left ventricular mass (LVM) correlates with improved prognosis. The optimal thiazide-type diuretic for reducing LVM is unknown. Evidence regarding potency, cardiovascular events, sodium, and potassium suggested the hypothesis that "CHIP" diuretics (CHlorthalidone, Indapamide, and Potassium-sparing diuretic/hydrochlorothiazide [PSD/HCTZ]) would reduce LVM more than HCTZ. Systematic searches of five databases were conducted. Among the 38 randomized trials, a 1% reduction in systolic blood pressure (SBP) predicted a 1% reduction in LVM, P = 0.00001. CHIP-HCTZ differences in reducing LVM differed across trials (ie, heterogeneity), making interpretation uncertain. However, among the 28 double-blind trials, heterogeneity was undetectable, and HCTZ reduced LVM (percent reduction [95% CI]) by -7.3 (-10.4, -4.2), P < 0.0001. CHIP diuretics surpassed HCTZ in reducing LVM: chlorthalidone -8.2 (-14.7, -1.6), P = 0.015; indapamide -7.5 (-12.7, -2.3), P = 0.005; and all CHIP diuretics combined -7.7 (-12.2, -3.1), P < 0.001. The comparison of PSD/HCTZ with HCTZ had low statistical power but favored PSD/HCTZ: -6.0 (-14.1, +2.1), P = 0.149. Thus, compared to HCTZ, CHIP diuretics had twice the effect on LVM. CHIP diuretics did not surpass HCTZ in reducing systolic or diastolic blood pressure: -0.3 (-5.0, +4.3) and -1.6 (-5.6, +2.4), respectively. The strength of evidence that CHIP diuretics surpass HCTZ for reducing LVM was high (GRADE criteria). In conclusion, these novel results have demonstrated that CHIP diuretics reduce LVM 2-fold more than HCTZ among hypertensive patients. Although generally related to LVM, blood pressure fails to explain the superiority of CHIP diuretics for reducing LVM.

Hydrochlorothiazide and alternative diuretics versus renin-angiotensin system inhibitors for the regression of left ventricular hypertrophy: a head-to-head meta-analysis.

BACKGROUND: Found in 36-41% of hypertension, elevated left ventricular mass (LVM) independently predicts cardiovascular events and total mortality. Conversely, drug-induced regression of LVM predicts improved outcomes. Previous studies have favored renin-angiotensin system inhibitors (RASIs) over other antihypertensives for reducing LVM but ignored differences among thiazide-type diuretics. From evidence regarding potency, cardiovascular events, and electrolytes, we hypothesized a priori that 'CHIP' diuretics [CHlorthalidone, Indapamide and Potassium-sparing Diuretic/hydrochlorothiazide (PSD/HCTZ)] would rival RASIs for reducing LVM. METHOD AND RESULTS: Systematic review yielded 12 relevant double-blind randomized trials. CHIPs were more closely associated with reduced LVM than HCTZ (P = 0.004), indicating that RASIs must be compared with each diuretic separately. Publication bias favoring RASIs was corrected by cumulative analysis. For reducing LVM, HCTZ tended to be less effective than RASIs. However, the following surpassed RASIs: chlorthalidone Hedge's G: -0.37 (95% CI -0.72 to -0.02), P = 0.036; indapamide -0.20 (-0.39 to -0.01), P = 0.035; all CHIPs combined (with 61% of patients in one trial) -0.25 (-0.41to -0.09), P = 0.002. Statistical significance (P < 0.05) did not depend on any one trial. CHIPs reduction in LVM was 37% greater than that from RASIs. CHIPs superiority tended to increase with trial duration, from a negligible effect at 0.5 year to a maximal effect at 0.9-1.0 years: -0.26 (-0.43 to -0.09), P = 0.003. Fifty-eight percent of patients had information on echocardiographic components of LVM: relative to RASIs, CHIPs significantly reduced end-diastolic LV internal dimension (EDLVID): -0.18 (-0.36 to -0.00), P = 0.046. Strength of evidence favoring CHIPs over RASIs was at least moderate. CONCLUSION: In these novel results in patients with hypertension, CHIPs surpassed RASIs for reducing LVM and EDLVID.

Incidental Discovery of Multiorgan Extramedullary Plasmacytomas in the Setting of Newly Diagnosed Multiple Myeloma and Delayed Hemolytic Transfusion Reaction.

Extramedullary plasmacytomas (EMPs) are defined by the presence of clonal plasma cell proliferation outside of the bone marrow, portending an overall poor prognosis. This case highlights extramedullary plasmacytomas as an unusual presenting manifestation of multiple myeloma. Through incidental discovery during a delayed hemolytic transfusion reaction workup, EMPs were found in the liver, spleen, and possibly the lung. Though rare at presentation, this case emphasizes that the presence of EMPs should be considered at the outset as it not only impacts the treatment regimen for such patients but also considerably affects prognosis.

First Reported Case of Hemopericardium Related to Dabigatran Use Reversed by New Antidote Idarucizumab.

Dabigatran, the first novel oral anticoagulant (NOAC) with a reversal agent, heralded a paradigm shift in the treatment of nonvalvular atrial fibrillation. The potential for life-threatening hemorrhagic events with the use of NOACs has been highly debated since the effectiveness of reversal agents such as idarucizumab is based primarily on pharmacologic data. It is known that cancer patients are at an increased risk of bleeding with anticoagulation, though specific studies demonstrating the risks or efficacy of NOACs in this population are lacking. We provide the first report of hemopericardium resulting in multiorgan failure related to dabigatran use that was successfully reversed by idarucizumab in a man with prostate cancer on chemotherapy.

Using Gold Nanoparticles as Delivery Vehicles for Targeted Delivery of Chemotherapy Drug Fludarabine Phosphate to Treat Hematological Cancers.

Nanotechnology is an emerging paradigm for creating functional nanoscale materials for various biomedical applications. In this study, a new nanotechnology-based drug delivery method was developed using gold nanoparticles (GNPs) as a delivery vehicle to reduce adverse drug side effects. Fludarabine Phosphate is a commercial chemotherapy drug used in cancer treatment, and has ability to kill various cancer cells. KG-1 cell, a type of acute cancer leukemia cell, was selected as a proof-of-concept target in this study. Due to the small size of GNPs, they can help Fludarabine Phosphate enter cancer cells more efficiently and better interfere with DNA synthesis in the cancer cells. To enhance targeting ability, folic acid molecules were also covalently linked to GNPs, resulting in GNP-Fludarabine-folic acid (GNP-F/f). Compared to treatments with GNP-F or drugs on its own (Fludarabine Phosphate), the GNP-F/f achieves much improved cell-killing effects. The UV-Vis spectra results also revealed that the drugs had successfully bonded covalently to the GNPs. The higher cell-killing efficiency of GNP-F/f compared with GNP-Fludarabine (GNP-F) or drugs on their own further validates the effectiveness of both the vectors (GNPs) and folic acid in enhancing the drug delivery to the cancer cells. The MTT viability tests showed that the GNPs had no cytotoxicity.

Dendritic cells tolerized with adenosine A2AR agonist attenuate acute kidney injury.

DC-mediated NKT cell activation is critical in initiating the immune response following kidney ischemia/reperfusion injury (IRI), which mimics human acute kidney injury (AKI). Adenosine is an important antiinflammatory molecule in tissue inflammation, and adenosine 2A receptor (A2AR) agonists protect kidneys from IRI through their actions on leukocytes. In this study, we showed that mice with A2AR-deficient DCs are more susceptible to kidney IRI and are not protected from injury by A2AR agonists. In addition, administration of DCs treated ex vivo with an A2AR agonist protected the kidneys of WT mice from IRI by suppressing NKT production of IFN-γ and by regulating DC costimulatory molecules that are important for NKT cell activation. A2AR agonists had no effect on DC antigen presentation or on Tregs. We conclude that ex vivo A2AR-induced tolerized DCs suppress NKT cell activation in vivo and provide a unique and potent cell-based strategy to attenuate organ IRI.

Dendritic cell sphingosine 1-phosphate receptor-3 regulates Th1-Th2 polarity in kidney ischemia-reperfusion injury.

Dendritic cells (DCs) are central to innate and adaptive immunity of early kidney ischemia-reperfusion injury (IRI), and strategies to alter DC function may provide new therapeutic opportunities. Sphingosine 1-phosphate (S1P) modulates immunity through binding to its receptors (S1P1-5), and protection from kidney IRI occurs in S1P3-deficient mice. Through a series of experiments we determined that this protective effect was owing in part to differences between S1P3-sufficient and -deficient DCs. Mice lacking S1P3 on bone marrow cells were protected from IRI, and S1P3-deficient DCs displayed an immature phenotype. Wild-type (WT) but not S1P3-deficient DCs injected into mice depleted of DCs prior to kidney IR reconstituted injury. Adoptive transfer (i.e., i.v. injection) of glycolipid (Ag)-loaded WT but not S1P3-deficient DCs into WT mice exacerbated IRI, suggesting that WT but not S1P3-deficient DCs activated NKT cells. Whereas WT DC transfers activated the Th1/IFN-γ pathway, S1P3-deficient DCs activated the Th2/IL-4 pathway, and an IL-4-blocking Ab reversed protection from IRI, supporting the concept that IL-4 mediates the protective effect of S1P3-deficient DCs. Administration of S1P3-deficient DCs 7 d prior to or 3 h after IRI protected mice from IRI and suggests their potential use in cell-based therapy. We conclude that absence of DC S1P3 prevents DC maturation and promotes a Th2/IL-4 response. These findings highlight the importance of DC S1P3 in modulating NKT cell function and IRI and support development of selective S1P3 antagonists for tolerizing DCs for cell-based therapy or for systemic administration for the prevention and treatment of IRI and autoimmune diseases.

Exploring the cell uptake mechanism of phospholipid and polyethylene glycol coated gold nanoparticles.

Recently, there has been a lot of interest in using gold nanoparticles (GNPs) for biomedical applications due to their biocompatibility. To increase GNP cell uptake and circulation half-life, and to improve its bio-distribution in vivo, we chose to coat GNPs with 1-palmitoyl-2-oleoyl-sn-glycero-3-phospho-(1'-rac-glycerol) (sodium salt) (POPG) and polyethylene glycol (PEG). Two different methods were used to synthesize POPG-GNPs or PEG-GNPs, but the resulting nanoparticle sizes and morphologies were similar. Under the same incubation conditions, POPG-GNPs can be uptaken quicker than PEG-GNPs by cells-specifically, the maximum uptake was 8 h versus 16 h after incubation. In addition, the uptake amount of POPG-GNPs was more than that of PEG-GNPs. The uptake processes were confirmed by SEM and TEM images. The main reason for the greater uptake of POPG-GNPs can be attributed to the structural similarities between the POPG coating and the cell membrane as well as GNP aggregation.

Magnetic gold nanoparticles: synthesis, characterization and its application in the delivery of FITC into KG-1 cells.

In this article, we report a new method-a sonication method to disperse iron oxide nanoparticles into smaller nanoparticles and make gold ions absorb onto the surface or trapped in the micropores of the iron oxide nanoparticles using sonication action. By using quick reduction of ascorbic acid and post-HCI solution treatment, gold covered magnetic nanoparticles (mGNPs) with spherical morphology and uniform size were synthesized in a water solution. The size of the mGNPs was found to be 20-30 nm. Some ideal mGNPs possessed a core-shell structure. The mGNPs were non-cytotoxic and mGNP-fluorescein isothiocyanate (FITC) can enter KG-1 cells when driven by an external magnetic force, which was confirmed by confocal imaging. The confocal image also showed the FITC inside the KG-1 cells was near the nucleus. The fluorescein isothiocyanate (FITC) delivery efficiency is about 100% according to the flow cytometry results.

Regulatory T cell dysfunction in subjects with common variable immunodeficiency complicated by autoimmune disease.

Approximately 25% of subjects with common variable immunodeficiency (CVID) develop autoimmune disease. We analyzed T cell subsets, specifically regulatory T cells along with B cell subsets to determine whether there were changes in regulatory T cells which would correlate with the autoimmune disease clinical phenotype in CVID subjects. We hypothesized that regulatory T cell (CD4+CD25hiCD127lo) suppressive function would be impaired in CVID subjects with autoimmune disease. Using purified, sorted Treg from CVID subjects (n=14) and from healthy controls (HC, n=5) in standard suppression assays, we found the suppressive function of Treg from CVID subjects with autoimmune disease (CVID w/ AI, n=8) to be significantly attenuated compared to CVID subjects with no autoimmune disease (CVID w/o AI, n=6) and to HC (n=5). A number of proteins associated with Treg function were decreased in expression as detected through immunofluorescent antibody via flow cytometry (mean fluorescence intensity (MFI) of FoxP3, Granzyme A, XCL1, pSTAT5, and GITR in Treg was significantly lower (by up to 3 fold) in CVID w/ AI compared to CVID w/o AI and HC. Furthermore, a statistically significant correlation was found between intracellular MFI of FoxP3, Granzyme A, and pSTAT5 in Treg and the degree of Treg dysfunction. These results suggest that attenuation of Treg function is associated with autoimmune disease in CVID subjects and may contribute to autoimmune pathogenesis.

The role of pericytes in blood-vessel formation and maintenance.

Blood vessels are composed of two interacting cell types. Endothelial cells form the inner lining of the vessel wall, and perivascular cells--referred to as pericytes, vascular smooth muscle cells or mural cells--envelop the surface of the vascular tube. Over the last decades, studies of blood vessels have concentrated mainly on the endothelial cell component, especially when the first angiogenic factors were discovered, while the interest in pericytes has lagged behind. Pericytes are, however, functionally significant; when vessels lose pericytes, they become hemorrhagic and hyperdilated, which leads to conditions such as edema, diabetic retinopathy, and even embryonic lethality. Recently, pericytes have gained new attention as functional and critical contributors to tumor angiogenesis and therefore as potential new targets for antiangiogenic therapies. Pericytes are complex. Their ontogeny is not completely understood, and they perform various functions throughout the body. This review article describes the current knowledge about the nature of pericytes and their functions during vessel growth, vessel maintenance, and pathological angiogenesis.

PDGFRbeta+ perivascular progenitor cells in tumours regulate pericyte differentiation and vascular survival.

The microvasculature consists of endothelial cells and their surrounding pericytes. Few studies on the regulatory mechanisms of tumour angiogenesis have focused on pericytes. Here we report the identification of tumour-derived PDGFRbeta (+) (platelet-derived growth factor receptor beta) progenitor perivascular cells (PPCs) that have the ability to differentiate into pericytes and regulate vessel stability and vascular survival in tumours. A subset of PDGFRbeta (+) PPCs is recruited from bone marrow to perivascular sites in tumours. Specific inhibition of PDGFRbeta signalling eliminates PDGFRbeta (+) PPCs and mature pericytes around tumour vessels, leading to vascular hyperdilation and endothelial cell apoptosis in pancreatic islet tumours of transgenic Rip1Tag2 mice.

Benefits of targeting both pericytes and endothelial cells in the tumor vasculature with kinase inhibitors.

Functions of receptor tyrosine kinases implicated in angiogenesis were pharmacologically impaired in a mouse model of pancreatic islet cancer. An inhibitor targeting VEGFRs in endothelial cells (SU5416) is effective against early-stage angiogenic lesions, but not large, well-vascularized tumors. In contrast, a kinase inhibitor incorporating selectivity for PDGFRs (SU6668) is shown to block further growth of end-stage tumors, eliciting detachment of pericytes and disruption of tumor vascularity. Importantly, PDGFRs were expressed only in perivascular cells of this tumor type, suggesting that PDGFR(+) pericytes in tumors present a complimentary target to endothelial cells for efficacious antiangiogenic therapy. Therapeutic regimes combining the two kinase inhibitors (SU5416 and SU6668) were more efficacious against all stages of islet carcinogenesis than either single agent. Combination of the VEGFR inhibitor with another distinctive kinase inhibitor targeting PDGFR activity (Gleevec) was also able to regress late-stage tumors. Thus, combinatorial targeting of receptor tyrosine kinases shows promise for treating multiple stages in tumorigenesis, most notably the often-intractable late-stage solid tumor.