tbuckley/cabot-search huggingface dataset:
Recent Advances in Atherosclerotic Disease Screening Using Pervasive Healthcare
Authors: Jingjing Luo, Zhengrong Yan, Shijie Guo, Wei Chen
Journal: IEEE Reviews in Biomedical Engineering (2021)

Atherosclerosis screening helps the medical model transform from therapeutic medicine to preventive medicine by assessing degree of atherosclerosis prior to the occurrence of fatal vascular events. Pervasive screening emphasizes atherosclerotic monitoring with easy access, quick process, and advanced computing. In this work, we introduced five cutting-edge pervasive technologies including imaging photoplethysmography (iPPG), laser Doppler, radio frequency (RF), thermal imaging (TI), optical fiber sensing and piezoelectric sensor. IPPG measures physiological parameters by using video images that record the subtle skin color changes consistent with cardiac-synchronous blood volume changes in subcutaneous arteries and capillaries. Laser Doppler obtained the information on blood flow by analyzing the spectral components of backscattered light from the illuminated tissues' surface. RF is based on Doppler shift caused by the periodic movement of the chest wall induced by respiration and heartbeat. TI measures vital signs by detecting electromagnetic radiation emitted by blood flow. The working principle of optical fiber sensor is to detect the change of light properties caused by the interaction between the measured physiological parameter and the entering light. Piezoelectric sensors are based on the piezoelectric effect of dielectrics. All these pervasive technologies are noninvasive, mobile, and can detect physiological parameters related to atherosclerosis screening.
Quality of Life and Caregiver Burden in Patients and Their Caregivers Undergoing Outpatient Autologous Stem Cell Transplantation Compared to Inpatient Transplantation
Authors: Anca Prica, Vinita Dhir, Rachel Aitken, Harminder K Paul, Osvaldo Espin-Garcia, Sita Bhella, Christine I. Chen, Michael Crump, Robert Kridel, Vishal Kukreti, John Kuruvilla, Donna E. Reece, Rodger E Tiedemann, Suzanne Trudel
Journal: Blood (2021)
splatPop: simulating population scale single-cell RNA sequencing data
Authors: Christina B. Azodi, Luke Zappia, Alicia Oshlack, Davis J. McCarthy
Journal: Genome biology (2021)

Abstract Population-scale single-cell RNA sequencing (scRNA-seq) is now viable, enabling finer resolution functional genomics studies and leading to a rush to adapt bulk methods and develop new single-cell-specific methods to perform these studies. Simulations are useful for developing, testing, and benchmarking methods but current scRNA-seq simulation frameworks do not simulate population-scale data with genetic effects. Here, we present splatPop, a model for flexible, reproducible, and well-documented simulation of population-scale scRNA-seq data with known expression quantitative trait loci. splatPop can also simulate complex batch, cell group, and conditional effects between individuals from different cohorts as well as genetically-driven co-expression.
Empagliflozin Reverses Late Na <sup>+</sup> Current Enhancement and Cardiomyocyte Proarrhythmia in a Translational Murine Model of Heart Failure With Preserved Ejection Fraction
Authors: Bence Hegyi, Juliana Mira Hernandez, Erin Y. Shen, Nima R. Habibi, Julie Bossuyt, Donald M. Bers
Journal: Circulation (2022)
Using Circulating Tumor DNA for Colon Cancer Adjuvant Therapy: To Be or Not to Be?
Authors: Van K. Morris, Thomas J. George
Journal: Clinical Cancer Research (2021)

Detection of circulating tumor DNA (ctDNA) postoperatively is prognostic for recurrence for patients with stage III colon cancer. Those with sustained undetectable ctDNA will likely be cured. Eradication of minimal residual disease (per ctDNA clearance) with chemotherapy did not occur in most ctDNA-positive patients and led to eventual disease relapse.See related article by Henriksen et al., p. 507.
Phase II Trial of Imatinib Plus Binimetinib in Patients With Treatment-Naive Advanced Gastrointestinal Stromal Tumor
Authors: Ping Chi, Li-Xuan Qin, Bastien Nguyen, Ciara M. Kelly, Sandra P. D'Angelo, Mark A. Dickson, Mrinal M. Gounder, Mary L. Keohan, Sujana Movva, Benjamin A. Nacev, Evan Rosenbaum, Katherine A. Thornton, Aimee M. Crago, Sam Yoon, Gary Ulaner, Randy Yeh, Moriah Martindale, Haley T. Phelan, Matthew D. Biniakewitz, Sarah Warda, Cindy J. Lee, Michael F. Berger, Nikolaus D. Schultz, Samuel Singer, Sinchun Hwang, Yu Chen, Cristina R. Antonescu, William D. Tap
Journal: Journal of Clinical Oncology (2022)

Dual targeting of the gastrointestinal stromal tumor (GIST) lineage-specific master regulators, ETV1 and KIT, by MEK and KIT inhibitors were synergistic preclinically and may enhance clinical efficacy. This trial was designed to test the efficacy and safety of imatinib plus binimetinib in first-line treatment of GIST.
Abstract P058: Comparative Effects Of Different Dietary Patterns On Biomarkers Of Non-Communicable Diseases: A Systematic Review And Network Meta-Analysis
Authors: Shuang Liang, Jovana Mijatovic, Ang Li, Reeja Nasir, Clemence Toniutti, Kim Bell-Anderson, Fiona O'Leary, Michael Skilton
Journal: Circulation (2022)

Each year, there are millions non-communicable diseases (NCDs) related deaths that are attributed to dietary risk factors. Dietary pattern describes the overall combination of dietary components, therefore is a more proximate representation of real-world dietary intake. The comparisons of different dietary patterns have been largely limited by the traditional pair-wise meta-analysis. We conducted a systematic review and network meta-analysis of randomised trials with healthy participants to compare major dietary patterns in NCD prevention, using biomarkers of NCDs as outcomes. For each biomarker outcome, a random effects network meta-analysis was conducted to estimate all possible pair-wise relative effects and to obtain a relative ranking of the dietary patterns in a connected network. The relative effects were estimated by calculating the summary mean differences (MD) with corresponding 95% CI. The relative ranking was assessed using the distribution of the ranking probabilities and the surface under the cumulative ranking curves (SUCRA). Of the 4008 records identified from the systematic literature search, 72 articles met our inclusion criteria and 68 were included in the quantitative synthesis. We compared up to 11 dietary patterns (Mediterranean diet, DASH diet, Paleo diet, dietary guidelines-based diet, low GI / GL diet, plant based diet, low fat diet, low carbohydrate high fat diet, traditional Mexican diet, high GI / GL diet and western habitual diet) for their effects on 11 NCD biomarkers (HDL, TG, LDL, TC, glucose, insulin, hsCRP, apoB, apoA1, HOMA-IR, and IL-6). Compared to western habitual diet, the Mediterranean diet, DASH diet, dietary guidelines based diet, plant based diet and low fat diet reduced LDL, TC, and apoB (MD range: -0.29 to -0.17 mmol/L, -0.36 to -0.24 mmol/L, and -0.11 to -0.07 g/L, respectively, all p&lt;0.05); the Paleo diet, plant based diet and dietary guidelines based diet reduced HOMA-IR (MD range: -0.95 to -0.35, all p&lt;0.05). While no dietary pattern ranked consistently highest across all NCD biomarkers, the Mediterranean diet was best to improve lipid profile (LDL, HDL, TC, TG, apoB and apoA1 combined average SUCRA: 63.1%); low carbohydrate high fat diet was best for glycaemic control (glucose, insulin and HOMA-IR combined average SUCRA: 66.4%); and Paleo diet was best in inflammation reduction (hsCRP and IL-6 combined average SUCRA: 87.0%). The Paleo diet had the highest all-outcomes-combined ranking (average SUCRA: 63.1%), followed by the Mediterranean diet (58.9%) and DASH diet (58.8%), while the western habitual diet (37.8%) and high GI / GL diet (38.5%) received the lowest all-outcomes-combined SUCRAs. Our findings suggest that the Paleo diet may provide potential health benefit and warrants further consideration for NCD prevention.
Circadian rhythms and renal pathophysiology
Authors: Rajesh Mohandas, Lauren G. Douma, Yogesh Scindia, Michelle L. Gumz
Journal: Journal of Clinical Investigation (2022)

The reality of life in modern times is that our internal circadian rhythms are often out of alignment with the light/dark cycle of the external environment. This is known as circadian disruption, and a wealth of epidemiological evidence shows that it is associated with an increased risk for cardiovascular disease. Cardiovascular disease remains the top cause of death in the United States, and kidney disease in particular is a tremendous public health burden that contributes to cardiovascular deaths. There is an urgent need for new treatments for kidney disease; circadian rhythm-based therapies may be of potential benefit. The goal of this Review is to summarize the existing data that demonstrate a connection between circadian rhythm disruption and renal impairment in humans. Specifically, we will focus on chronic kidney disease, lupus nephritis, hypertension, and aging. Importantly, the relationship between circadian dysfunction and pathophysiology is thought to be bidirectional. Here we discuss the gaps in our knowledge of the mechanisms underlying circadian dysfunction in diseases of the kidney. Finally, we provide a brief overview of potential circadian rhythm-based interventions that could provide benefit in renal disease.
FDG PET/CT Image of Soft Tissue Aneurysmal Bone Cyst
Authors: Liu Xiao, Junjun Cheng, Lin Li
Journal: Clinical Nuclear Medicine (2022)

Abstract Soft tissue aneurysmal bone cyst is very rare. Herein, we report FDG PET/CT findings of aneurysmal bone cyst in a 19-year-old man. On conventional image, it presented as a paravertebral soft tissue mass with heterogeneous enhancement and rim eggshell-like calcification. On PET/CT, this solitary lesion had intense FDG uptake with an SUV max of 10.33. The final pathology supported a diagnosis of aneurysmal bone cyst. Our case suggests that soft tissue aneurysmal bone cyst should be regarded as a differential diagnosis of solitary paravertebral mass with intense FDG uptake.
Patterns of Carbon-Bound Exogenous Compounds in Patients with Lung Cancer and Association with Disease Pathophysiology
Authors: Thomas Kunzke, Verena M. Prade, Achim Buck, Na Sun, Annette Feuchtinger, Marco Matzka, Isis E. Fernandez, Wim Wuyts, Maximilian Ackermann, Danny Jonigk, Michaela Aichler, Ralph A. Schmid, Oliver Eickelberg, Sabina Berezowska, Axel Walch
Journal: Cancer Research (2021)

Asymptomatic anthracosis is the accumulation of black carbon particles in adult human lungs. It is a common occurrence, but the pathophysiologic significance of anthracosis is debatable. Using in situ high mass resolution matrix-assisted laser desorption/ionization (MALDI) fourier-transform ion cyclotron resonance (FT-ICR) mass spectrometry imaging analysis, we discovered noxious carbon-bound exogenous compounds, such as polycyclic aromatic hydrocarbons (PAH), tobacco-specific nitrosamines, or aromatic amines, in a series of 330 patients with lung cancer in highly variable and unique patterns. The characteristic nature of carbon-bound exogenous compounds had a strong association with patient outcome, tumor progression, the tumor immune microenvironment, programmed death-ligand 1 (PD-L1) expression, and DNA damage. Spatial correlation network analyses revealed substantial differences in the metabolome of tumor cells compared with tumor stroma depending on carbon-bound exogenous compounds. Overall, the bioactive pool of exogenous compounds is associated with several changes in lung cancer pathophysiology and correlates with patient outcome. Given the high prevalence of anthracosis in the lungs of adult humans, future work should investigate the role of carbon-bound exogenous compounds in lung carcinogenesis and lung cancer therapy. SIGNIFICANCE: This study identifies a bioactive pool of carbon-bound exogenous compounds in patient tissues associated with several tumor biological features, contributing to an improved understanding of drivers of lung cancer pathophysiology.
Immunogenicity and Reactogenicity of SARS-CoV-2 Vaccines in Patients With Cancer: The CANVAX Cohort Study
Authors: Vivek Naranbhai, Claire A. Pernat, Alexander Gavralidis, Kerri J. St Denis, Evan C. Lam, Laura M. Spring, Steven J. Isakoff, Jocelyn R. Farmer, Leyre Zubiri, Gabriela S. Hobbs, Joan How, Andrew M. Brunner, Amir T. Fathi, Jennifer L. Peterson, Mustafa Sakhi, Grace Hambelton, Elyssa N. Denault, Lindsey J. Mortensen, Lailoo A. Perriello, Marissa N. Bruno, Brittany Y. Bertaux, Aleigha R. Lawless, Monica A. Jackson, Elizabeth Niehoff, Caroline Barabell, Christian N. Nambu, Erika Nakajima, Trenton Reinicke, Cynthia Bowes, Cristhian J. Berrios-Mairena, Onosereme Ofoman, Grace E. Kirkpatrick, Julia C. Thierauf, Kerry Reynolds, Henning Willers, Wilfredo-Garcia Beltran, Anand S. Dighe, Rebecca Saff, Kimberly Blumenthal, Ryan J. Sullivan, Yi-Bin Chen, Arthur Kim, Aditya Bardia, Alejandro B. Balazs, A. John Iafrate, Justin F. Gainor
Journal: Journal of Clinical Oncology (2021)

The immunogenicity and reactogenicity of SARS-CoV-2 vaccines in patients with cancer are poorly understood.We performed a prospective cohort study of adults with solid-organ or hematologic cancers to evaluate anti-SARS-CoV-2 immunoglobulin A/M/G spike antibodies, neutralization, and reactogenicity ≥ 7 days following two doses of mRNA-1273, BNT162b2, or one dose of Ad26.COV2.S. We analyzed responses by multivariate regression and included data from 1,638 healthy controls, previously reported, for comparison.Between April and July 2021, we enrolled 1,001 patients; 762 were eligible for analysis (656 had neutralization measured). mRNA-1273 was the most immunogenic (log10 geometric mean concentration [GMC] 2.9, log10 geometric mean neutralization titer [GMT] 2.3), followed by BNT162b2 (GMC 2.4; GMT 1.9) and Ad26.COV2.S (GMC 1.5; GMT 1.4; P < .001). The proportion of low neutralization (< 20% of convalescent titers) among Ad26.COV2.S recipients was 69.9%. Prior COVID-19 infection (in 7.1% of the cohort) was associated with higher responses (P < .001). Antibody titers and neutralization were quantitatively lower in patients with cancer than in comparable healthy controls, regardless of vaccine type (P < .001). Receipt of chemotherapy in the prior year or current steroids were associated with lower antibody levels and immune checkpoint blockade with higher neutralization. Systemic reactogenicity varied by vaccine and correlated with immune responses (P = .002 for concentration, P = .016 for neutralization). In 32 patients who received an additional vaccine dose, side effects were similar to prior doses, and 30 of 32 demonstrated increased antibody titers (GMC 1.05 before additional dose, 3.17 after dose).Immune responses to SARS-CoV-2 vaccines are modestly impaired in patients with cancer. These data suggest utility of antibody testing to identify patients for whom additional vaccine doses may be effective and appropriate, although larger prospective studies are needed.
Lesion-Based Radiomics Signature in Pretherapy 18F-FDG PET Predicts Treatment Response to Ibrutinib in Lymphoma
Authors: Jorge E. Jimenez, Dong Dai, Guofan Xu, Ruiyang Zhao, Tengfei Li, Tinsu Pan, Linghua Wang, Yingyan Lin, Zhangyang Wang, David Jaffray, John D. Hazle, Homer A. Macapinlac, Jia Wu, Yang Lu
Journal: Clinical Nuclear Medicine (2022)

Purpose The aim of this study was to develop a pretherapy PET/CT-based prediction model for treatment response to ibrutinib in lymphoma patients. Patients and Methods One hundred sixty-nine lymphoma patients with 2441 lesions were studied retrospectively. All eligible lymphomas on pretherapy 18 F-FDG PET images were contoured and segmented for radiomic analysis. Lesion- and patient-based responsiveness to ibrutinib was determined retrospectively using the Lugano classification. PET radiomic features were extracted. A radiomic model was built to predict ibrutinib response. The prognostic significance of the radiomic model was evaluated independently in a test cohort and compared with conventional PET metrics: SUV max , metabolic tumor volume, and total lesion glycolysis. Results The radiomic model had an area under the receiver operating characteristic curve (ROC AUC) of 0.860 (sensitivity, 92.9%, specificity, 81.4%; P &lt; 0.001) for predicting response to ibrutinib, outperforming the SUV max (ROC AUC, 0.519; P = 0.823), metabolic tumor volume (ROC AUC, 0.579; P = 0.412), total lesion glycolysis (ROC AUC, 0.576; P = 0.199), and a composite model built using all 3 (ROC AUC, 0.562; P = 0.046). The radiomic model increased the probability of accurately predicting ibrutinib-responsive lesions from 84.8% (pretest) to 96.5% (posttest). At the patient level, the model's performance (ROC AUC = 0.811; P = 0.007) was superior to that of conventional PET metrics. Furthermore, the radiomic model showed robustness when validated in treatment subgroups: first (ROC AUC, 0.916; P &lt; 0.001) versus second or greater (ROC AUC, 0.842; P &lt; 0.001) line of defense and single treatment (ROC AUC, 0.931; P &lt; 0.001) versus multiple treatments (ROC AUC, 0.824; P &lt; 0.001). Conclusions We developed and validated a pretherapy PET-based radiomic model to predict response to treatment with ibrutinib in a diverse cohort of lymphoma patients.
55P The impact of liquid next-generation testing timing on treatment-naïve advanced non-small cell lung cancer: A prospective observational study
Authors: C. Yang, J-Y. Shih, W-Y. Liao, C-C. Ho, C-L. Hsu, T-H. Tsai, S-G. Wu, Y-T. Lin, W-H. Hsu, J.C. Yang, C-J. Yu, P-C. Yang
Journal: Annals of Oncology (2022)
Single-cell multiomics reveals increased plasticity, resistant populations, and stem-cell–like blasts in <i>KMT2A</i>-rearranged leukemia
Authors: Changya Chen, Wenbao Yu, Fatemeh Alikarami, Qi Qiu, Chia-hui Chen, Jennifer Flournoy, Peng Gao, Yasin Uzun, Li Fang, James W. Davenport, Yuxuan Hu, Qin Zhu, Kai Wang, Clara Libbrecht, Alex Felmeister, Isaiah Rozich, Yang-yang Ding, Stephen P. Hunger, Carolyn A. Felix, Hao Wu, Patrick A. Brown, Erin M. Guest, David M. Barrett, Kathrin M. Bernt, Kai Tan
Journal: Blood (2021)

KMT2A-rearranged (KMT2A-r) infant acute lymphoblastic leukemia (ALL) is a devastating malignancy with a dismal outcome, and younger age at diagnosis is associated with increased risk of relapse. To discover age-specific differences and critical drivers that mediate poor outcome in KMT2A-r ALL, we subjected KMT2A-r leukemias and normal hematopoietic cells from patients of different ages to single-cell multiomics analyses. We uncovered the following critical new insights: leukemia cells from patients <6 months have significantly increased lineage plasticity. Steroid response pathways are downregulated in the most immature blasts from younger patients. We identify a hematopoietic stem and progenitor-like (HSPC-like) population in the blood of younger patients that contains leukemic blasts and form an immunosuppressive signaling circuit with cytotoxic lymphocytes. These observations offer a compelling explanation for the ability of leukemias in young patients to evade chemotherapy and immune-mediated control. Our analysis also revealed preexisting lymphomyeloid primed progenitors and myeloid blasts at initial diagnosis of B-ALL. Tracking of leukemic clones in 2 patients whose leukemia underwent a lineage switch documented the evolution of such clones into frank acute myeloid leukemia (AML). These findings provide critical insights into KMT2A-r ALL and have clinical implications for molecularly targeted and immunotherapy approaches. Beyond infant ALL, our study demonstrates the power of single-cell multiomics to detect tumor intrinsic and extrinsic factors affecting rare but critical subpopulations within a malignant population that ultimately determines patient outcome.
Updated Integrated Analysis of the Efficacy and Safety of Entrectinib in Patients With <i>NTRK</i> Fusion-Positive Solid Tumors
Authors: George D. Demetri, Filippo De Braud, Alexander Drilon, Salvatore Siena, Manish R. Patel, Byoung Chul Cho, Stephen V. Liu, Myung-Ju Ahn, Chao-Hua Chiu, Jessica J. Lin, Koichi Goto, Jeeyun Lee, Lyudmila Bazhenova, Thomas John, Marwan Fakih, Sant P. Chawla, Rafal Dziadziuszko, Takashi Seto, Sebastian Heinzmann, Bethany Pitcher, David Chen, Timothy R. Wilson, Christian Rolfo
Journal: Clinical Cancer Research (2022)

Abstract Purpose: Entrectinib potently inhibits tropomyosin receptor kinases (TRKAs)/B/C and ROS1, and previously induced deep [objective response rate (ORR) 57.4%] and durable [median duration of response (DoR) 10.4 months] responses in adults with NTRK fusion-positive solid tumors from three phase I/II trials. This article expands prior reports with additional patients and longer follow-up. Patients and Methods: Patients with locally advanced/metastatic NTRK fusion-positive solid tumors and ≥12 months' follow-up were included. Primary endpoints were ORR and DoR by blinded independent central review (BICR); secondary endpoints included progression-free survival (PFS), intracranial efficacy, and safety. The safety-evaluable populations included all patients who had received ≥1 entrectinib dose. Results: At clinical cut-off (August 31, 2020), the efficacy-evaluable population comprised 121 adults with 14 tumor types and ≥30 histologies. Median follow-up was 25.8 months; 61.2% of patients had a complete (n = 19) or partial response (n = 55). Median DoR was 20.0 months [95% confidence interval (CI), 13.0–38.2]; median PFS was 13.8 months (95% CI, 10.1–19.9). In 11 patients with BICR-assessed measurable central nervous system (CNS) disease, intracranial ORR was 63.6% (95% CI, 30.8–89.1) and median intracranial DoR was 22.1 (95% CI, 7.4–not estimable) months. The safety profile of entrectinib in adults and pediatric patients was aligned with previous reports. Most treatment-related adverse events (TRAEs) were grade 1/2 and manageable/reversible with dose modifications. TRAE-related discontinuations occurred in 8.3% of patients. Conclusions: With additional clinical experience, entrectinib continues to demonstrate durable systemic and intracranial responses and can address the unmet need of a CNS-active treatment in patients with NTRK fusion-positive solid tumors.
Cross-protective immunity following coronavirus vaccination and coronavirus infection
Authors: Tanushree Dangi, Nicole Palacio, Sarah Sanchez, Mincheol Park, Jacob Class, Lavanya Visvabharathy, Thomas Ciucci, Igor J. Koralnik, Justin M. Richner, Pablo Penaloza-MacMaster
Journal: Journal of Clinical Investigation (2021)

Although severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) vaccines have shown efficacy against SARS-CoV-2, it is unknown if coronavirus vaccines can also protect against other coronaviruses that may infect humans in the future. Here, we show that coronavirus vaccines elicited cross-protective immune responses against heterologous coronaviruses. In particular, we show that a severe acute respiratory syndrome coronavirus 1 (SARS-CoV-1) vaccine developed in 2004 and known to protect against SARS-CoV-1 conferred robust heterologous protection against SARS-CoV-2 in mice. Similarly, prior coronavirus infections conferred heterologous protection against distinct coronaviruses. Cross-reactive immunity was also reported in patients with coronavirus disease 2019 (COVID-19) and in individuals who received SARS-CoV-2 vaccines, and transfer of plasma from these individuals into mice improved protection against coronavirus challenges. These findings provide the first demonstration to our knowledge that coronavirus vaccines (and prior coronavirus infections) can confer broad protection against heterologous coronaviruses and establish a rationale for universal coronavirus vaccines.
Efficacy, immunogenicity, and safety of a quadrivalent HPV vaccine in men: results of an open-label, long-term extension of a randomised, placebo-controlled, phase 3 trial
Authors: Stephen E Goldstone, Anna R Giuliano, Joel M Palefsky, Eduardo Lazcano-Ponce, Mary E Penny, Robinson E Cabello, Edson D Moreira, Ezio Baraldi, Heiko Jessen, Alex Ferenczy, Robert Kurman, Brigitte M Ronnett, Mark H Stoler, Oliver Bautista, Rituparna Das, Thomas Group, Alain Luxembourg, Hao Jin Zhou, Alfred Saah
Journal: The Lancet Infectious Diseases (2021)