tbuckley/cabot-search huggingface dataset:
Artificial intelligence, complex system analysis and simulation modeling for early detection of lung cancer
Authors: O. Kshivets
Journal: Journal of Clinical Oncology (2007)

18127 Background: Early detection (ED) of non-small cell lung cancer (LC) is the key to the cancer problem solving and practically regulates effectiveness of surgery. We examined immunologic factors associated with early LC. Methods: In trial (1987–2006) the data of consecutive and monitored 94 LC patients (LCP) after lobectomies (age=58.3±0.8 years; tumor size=2.32±0.07 cm; m=80, f=14) with pathologic stage IA (T1N0M0) (squamous=36, adenocarcinoma=53, large cell=5; G1=32, G2=38, G3=24), 282 patients with lung non-malignant pathology (NMP) (m=188, f=94; pneumonectomies=5, lobectomies=179, segmentectomies=98; non-malignant tumours=100; abscess=112; tuberculoma=70) and 120 healthy donors (HD) (m=69, f=51) were reviewed. Variables selected for ED study were input levels of 64 immunity blood parameters, sex, age. Representativeness of samplings was reached by means of randomisation based on unrepeated random selection. Logistic regression, clustering, discriminant analysis, neural networks computing, structural equation modeling, Monte Carlo and bootstrap simulation were used to determine any significant regularity. Results: Logistic regression modeling displayed that ED of LC significantly depended on: CD8, CD4, CD16, neutrophils, monocytes (P=0.002–0.041). Neural networks computing, genetic algorithm selection and bootstrap simulation discovered relationships between early LC and blood lymphocytes (rank=1), T-lymphocytes (2), CD4 (3), CD16 (4), B- lymphocytes (5), CD1 (6), NST-A2 (7), CD8 (8), NST-SP (9), NST-A1 (10), monocytes (11), eosinophils (12). Conclusions: Correct recognition of LCP with stage IA (T1N0M0) from NMP and HD was 81.7% by logistic regression (odds ratio=6.39), 84.1% by discriminant analysis and 99.2% by neural networks computing (area under ROC curve=0.99; error=0.063). No significant financial relationships to disclose.
Outcome-Related Signatures Identified by Whole Transcriptome Sequencing of Resectable Stage III/IV Melanoma Evaluated after Starting Hu14.18-IL2
Authors: Richard K. Yang, Igor B. Kuznetsov, Erik A. Ranheim, Jun S. Wei, Sivasish Sindiri, Berkley E. Gryder, Vineela Gangalapudi, Young K. Song, Viharkumar Patel, Jacquelyn A. Hank, Cindy Zuleger, Amy K. Erbe, Zachary S. Morris, Renae Quale, KyungMann Kim, Mark R. Albertini, Javed Khan, Paul M. Sondel
Journal: Clinical Cancer Research (2020)

Abstract Purpose: We analyzed whole transcriptome sequencing in tumors from 23 patients with stage III or IV melanoma from a pilot trial of the anti-GD2 immunocytokine, hu14.18-IL2, to identify predictive immune and/or tumor biomarkers in patients with melanoma at high risk for recurrence. Experimental Design: Patients were randomly assigned to receive the first of three monthly courses of hu14.18-IL2 immunotherapy either before (Group A) or after (Group B) complete surgical resection of all known diseases. Tumors were evaluated by histology and whole transcriptome sequencing. Results: Tumor-infiltrating lymphocyte (TIL) levels directly associated with relapse-free survival (RFS) and overall survival (OS) in resected tumors from Group A, where early responses to the immunotherapy agent could be assessed. TIL levels directly associated with a previously reported immune signature, which associated with RFS and OS, particularly in Group A tumors. In Group A tumors, there were decreased cell-cycling gene RNA transcripts, but increased RNA transcripts for repair and growth genes. We found that outcome (RFS and OS) was directly associated with several immune signatures and immune-related RNA transcripts and inversely associated with several tumor growth–associated transcripts, particularly in Group A tumors. Most of these associations were not seen in Group B tumors. Conclusions: We interpret these data to signify that both immunologic and tumoral cell processes, as measured by RNA-sequencing analyses detected shortly after initiation of hu14.18-IL2 therapy, are associated with long-term survival and could potentially be used as prognostic biomarkers in tumor resection specimens obtained after initiating neoadjuvant immunotherapy.
N6‐Methyladenosine Reader Protein YT521‐B Homology Domain‐Containing 2 Suppresses Liver Steatosis by Regulation of mRNA Stability of Lipogenic Genes
Authors: Bing Zhou, Caizhi Liu, Lingyan Xu, Youwen Yuan, Jiejie Zhao, Wenjun Zhao, Yiyan Chen, Jin Qiu, Meiyao Meng, Ying Zheng, Dongmei Wang, Xin Gao, Xiaoying Li, Qihong Zhao, Xiaohui Wei, Duojiao Wu, Huijie Zhang, Cheng Hu, Xiaozhen Zhuo, Minghua Zheng, Hua Wang, Yan Lu, Xinran Ma
Journal: Hepatology (2020)

Nonalcoholic fatty liver disease (NAFLD) is characterized by accumulation of excessive triglycerides (TGs) in hepatocytes. Obesity is a major risk factor for developing fatty liver, although the intracellular molecular basis remains largely unclear. N6 -methyladenosine (m6 A) RNA methylation is the most common internal modification in eukaryotic mRNA. In the present study, by m6 A sequencing and RNA sequencing, we found that both m6 A enrichment and mRNA expression of lipogenic genes were significantly increased in leptin-receptor-deficient db/db mice. Importantly, our results showed that YT521-B homology domain-containing 2 (Ythdc2), an m6 A reader, was markedly down-regulated in livers of obese mice and NAFLD patients. Suppression of Ythdc2 in livers of lean mice led to TG accumulation, whereas ectopic overexpression of Ythdc2 in livers of obese mice improved liver steatosis and insulin resistance. Mechanistically, we found that Ythdc2 could bind to mRNA of lipogenic genes, including sterol regulatory element-binding protein 1c, fatty acid synthase, stearoyl-CoA desaturase 1, and acetyl-CoA carboxylase 1, to decrease their mRNA stability and inhibit gene expression. Our findings describe an important role of the m6 A reader, Ythdc2, for regulation of hepatic lipogenesis and TG homeostasis, which might provide a potential target for treating obesity-related NAFLD.
Assessment of Treatment Cost-effectiveness Using a Colorectal Cancer Mutation Profile
Authors: Timothy J. Yeatman, Michael J. Schell, William Sause
Journal: JAMA Network Open (2020)

Se Ryeong Jang, MPH; Han Truong, BS; Aaron Oh, BA; Jin Choi, BS; Angela C. Tramontano, MPH; Monika Laszkowska, MD; Chin Hur, MD, MPH
Abstract ES6-3: Breast cancer genetic testing: moving from cancer risk assessment to therapeutic biomarker
Authors: J Balmaña
Journal: Cancer Research (2020)

Abstract In the last two decades germline genetic testing for breast cancer (BC) susceptibility has evolved from a single-gene analysis to a multigene cancer panel risk assessment tool. In addition, identifying a mutation in the BRCA1/2 genes may nowadays represent an opportunity for cancer targeted therapy. Current challenges in our routine clinical practice and for public health policies are to reconcile the implications derived from the identification of a hereditary cancer susceptibility that may impact beyond the person who is performing the genetic test, with and increasing and faster access to the test. Assessment of cancer risk was the first reason to incorporate germline BC genetic testing. As a consequence, mutation carriers are recommended specific screening and/or risk reduction options. While prophylactic bilateral salpingoophorectomy has shown a decrease in mortality and ovarian cancer-specific mortality, its role as a risk reduction option for breast cancer remains controversial. Radiologic imaging with magnetic resonance and mammogram has demonstrated beneficial in early detection of breast cancer, but risk reducing mastectomy may also be an option. Recent prospective data has shown that cancer risks differ between BRCA1 and BRCA2 mutation carriers, and that this estimation may be influenced by a combination of single-nucleotide polymorphism that constitute the polygenic risk score (PRS). Whether a more precise accuracy in cancer risk estimation in the short term (ie 5-10 years) may help to tailor screening and/or risk reduction options is unknown. As more BC-associated genes have been identified and technology has evolved, single gene testing has evolved to multigene panel testing. Available data suggests that patients can cope with multigene cancer panels although more research is needed to fully understand the psychosocial implications of multigene cancer panels, especially for those who have variants of unknown significance or moderate penetrance variants. Research is also needed to explore and develop communication models that maximize patients’ understanding and empower them to make informed decisions. The impact on reproductive-decision making will also be explored. Finally, a mutation in the BRCA1/2 genes is a predictive biomarker for targeted therapies in breast, ovarian, pancreatic and prostate cancer. Therefore, knowing the genetic status of our BC patients may influence their therapeutic options. The challenges and opportunities derived from new clinical scenarios that accompany these advances will be addressed during the educational session. Citation Format: J Balmaña. Breast cancer genetic testing: moving from cancer risk assessment to therapeutic biomarker [abstract]. In: Proceedings of the 2019 San Antonio Breast Cancer Symposium; 2019 Dec 10-14; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2020;80(4 Suppl):Abstract nr ES6-3.
Promotion of Mental Health as a Key Element of Pediatric Care
Authors: Ellen C. Perrin
Journal: JAMA Pediatrics (2020)

Our website uses cookies to enhance your experience. By continuing to use our site, or clicking "Continue," you are agreeing to our Cookie Policy | Continue JAMA Pediatrics HomeNew OnlineCurrent IssueFor Authors Podcast Publications JAMA JAMA Network Open JAMA Cardiology JAMA Dermatology JAMA Health Forum JAMA Internal Medicine JAMA Neurology JAMA Oncology JAMA Ophthalmology JAMA Otolaryngology–Head & Neck Surgery JAMA Pediatrics JAMA Psychiatry JAMA Surgery Archives of Neurology & Psychiatry (1919-1959) JN Learning / CMESubscribeJobsInstitutions / LibrariansReprints & Permissions Terms of Use | Privacy Policy | Accessibility Statement 2023 American Medical Association. All Rights Reserved Search All JAMA JAMA Network Open JAMA Cardiology JAMA Dermatology JAMA Forum Archive JAMA Health Forum JAMA Internal Medicine JAMA Neurology JAMA Oncology JAMA Ophthalmology JAMA Otolaryngology–Head & Neck Surgery JAMA Pediatrics JAMA Psychiatry JAMA Surgery Archives of Neurology & Psychiatry Input Search Term Sign In Individual Sign In Sign inCreate an Account Access through your institution Sign In Purchase Options: Buy this article Rent this article Subscribe to the JAMA Pediatrics journal
Practice Paradigms Before and After Introduction of the Diagnosis-Noninvasive Follicular Thyroid Neoplasm with Papillary-Like Nuclear Features (NIFTP): an Institutional Experience
Authors: Levon Katsakhyan, Sharon Song, Marcos Lepe, Hadi Shojaei, Kathleen T. Montone, Virginia A. LiVolsi, Zubair W. Baloch
Journal: Endocrine Pathology (2020)
Abstract 16241: A Clinical, Proteomics, and Artificial Intelligence-Driven Modelto Predict Acute Kidney Injury in Patients Undergoing Coronary Angiography-Results From the Catheter Sampled Blood Archive in Cardiovascular Diseases Study
Authors: Nasrien Ibrahim, Cian P McCarthy, Shrerya Shrestha, Hanna K Gaggin, Renata Mukai, Craig A Megarat, Rhonda F Rhyne, James L Januzzi
Journal: Circulation (2018)

Introduction: Acute kidney injury (AKI) following cardiovascular procedures has substantial impact on patient management and prognosis. Background: Standard measures of kidney function are only mod...
Monitoring effects of imatinib (Ima) plus gemcitabine (Ge) chemotherapy (CT) on functional status of tumors (T) using dynamic contrast enhanced magnetic resonance imaging (DCE-MRI) and magnetic resonance spectroscopy (MRS)
Authors: W. Wolf, C. A. Presant, V. Waluch, H. Kim
Journal: Journal of Clinical Oncology (2007)

13001 Background: The ability to monitor the effect of all interventions on the functional status of tumors is critical in allowing clinicians to optimize/individualize chemotherapy to a given patient (pt). This is especially true when such pts are treated with a combination of targeting agents and cytotoxic anticancer drugs. The present study tested the combination of Ima and Gem to determine T pharmacokinetics (PK) and pharmacodynamics (PD) using DCE-MRI and 19F-MRS. Methods: Pts with measurable and MRI-imagible refractory solid T possibly responsive to Ge were randomized to receive either: one course of Ima with PK/PD, followed by one course of Ge with PK/PD, followed by the combination ImaGe; or one course of Ge with PK/PD followed by one course of Ima with PK/PD, followed by ImaGe. Ge was given at 900 mg/m2 IV over 30 min. for PK/PD and at 10 mg/m2/min. for continued therapy. Ima was given at 400 mg daily for 5 d. with Ge given on day 3. Doses were adjusted for toxicity. T vascularity (V) was measured by the use of DCE-MRI (AACR 95:490,2004). The initial contrast accumulation rate (ICAR) and the delayed contrast accumulation rate (DCAR) were calculated as the slope of the influx and efflux curves. Ge T PK was measured by serial 19F-MRS for ∼ 1hr post Ge administration. Results: 4 pts are evaluable at present: 2 Ca pancreas, 1 Ca breast and 1 Ca ovary. Ge PK are still in analysis. DCE-MRI data indicated an increase in T ICAR 1 week after Ima of 18% and 180% in 2 pts, and a decrease of -14% and -21% in 2 pt. By 2 wk post Ima, ICAR had further decreased to -75% in the latter pt. T size evaluation by RECIST showed progression of Ca in the 2 pt with increased ICAR, and a PR and stable disease in the 2 pt with a decrease in ICAR. Additional correlations with DCAR and Ge T PK will be shown. Conclusions: Ima and Ge CT is associated with a heterogeneous response in DCE-MRI. Ima has an antiangiogenic effect in some pts. This effect may be correlated with T response to Ima plus Ge. Measuring PK and PD using DCE-MRI and MRS may be useful in understanding individual responses to Ima drug combinations. No significant financial relationships to disclose.
‘Good vibrations’: positional treatments for obstructive sleep apnoea
Authors: Raphael Heinzer
Journal: Thorax (2020)

Obstructive sleep apnoea (OSA) is at least twice more severe in the supine position compared with the non-supine positions in about three quarters of patients with OSA.1 About one-third of them even have ‘exclusively positional’ sleep apnoea with normal apnoea–hypopnoea index (AHI) in the non-supine positions, which makes them accessible to positional treatment (PT). Until recently, most PT devices were derived from the traditional ‘tennis ball technique’, which makes the supine position uncomfortable and stimulate patients to sleep on their side. There are plenty of such devices on the market, but they are by essence uncomfortable, and their long-term usage was reported to be very low.2 

A new generation of ‘active’ PT was developed in recent years. It consists of small electronic devices worn either at the neck or at the chest level, which vibrate when the patients are in the supine position until they turn to their side. Several …
Abstract P278: Association of Alcohol Use With Poor Outcomes in Takotsubo Cardiomyopathy
Authors: Temidayo Abe, Samuel Ogbuchi, Taiwo Ajose, Ajibola Babatunde, Chinonyelum Nwagbara, Tolulope Abe, Temitope Tobun, Nicolas Bakinde
Journal: Circulation (2020)

Introduction: Recent studies have demonstrated poor outcomes in patients with takotsubo cardiomyopathy (TCM). It is important to determine the predictors of these outcomes for appropriate risk stratification and to decrease the overall disease burden. Physical stressors and preexisting heart failure have been associated with poorer outcomes, however, the impact of alcohol use (ETOH) has not been discussed. Aim: To determine if underlying alcohol use is associated with poorer outcomes in patients with TCM. Methods: We recruited 6750 patients from 2011, 2012 National Inpatient Sample, 6325 had TCM alone while 425 had TCM and ETOH use. Our outcomes of interest were overall mortality, mechanical hemodynamic support (MHS) acute respiratory failure(ARF), cardiac arrest (SCA), cardiogenic shock, and atrial fibrillation. All clinical characteristics were defined as per the International Classification of Diseases 9th revision (ICD-9) codes. Logistic regression was used to estimate the odds ratio of the outcomes in the study compared to the control group while stratified analysis was used to adjust for age and sex both accounting for underlying comorbidities. Results: There was no significant difference between the two groups in the rates of atrial fibrillation (11.1% vs 10.4%; P= 0.656), cardiogenic shock (6.2% vs 4.7%; P= 0.201), MHS (2.3% vs 1.4%; P= 0.221) and overall mortality (4.1% vs 3.8%; p=0.702). Rates of ARF (29.9%, vs 18.2%; P&lt; 0.0001) and SCA (4.9% vs 3.0%; P=0.025) were higher in patients with TCM+ETOH compared to TCM alone. Table 1 displays the adjusted odds ratios for the outcomes. Compared to the participants with TCM alone, odd ratios of ARF was significantly higher in patients with TCM+ETOH. Table 2 displays the stratified analysis based sex. Compared with TCM alone, female patients with TCM+ETOH are more likely to develop ARF, cardiogenic shock and SCA. Conclusion: Preexisting alcohol use is associated with poorer outcomes in female patients with TCM.
The Skyrocketing Cost of Rectal Indomethacin
Authors: B. Joseph Elmunzer, Inmaculada Hernandez, Walid F. Gellad
Journal: JAMA Internal Medicine (2020)

Our website uses cookies to enhance your experience. By continuing to use our site, or clicking "Continue," you are agreeing to our Cookie Policy | Continue JAMA Internal Medicine HomeNew OnlineCurrent IssueFor Authors Podcast Publications JAMA JAMA Network Open JAMA Cardiology JAMA Dermatology JAMA Health Forum JAMA Internal Medicine JAMA Neurology JAMA Oncology JAMA Ophthalmology JAMA Otolaryngology–Head & Neck Surgery JAMA Pediatrics JAMA Psychiatry JAMA Surgery Archives of Neurology & Psychiatry (1919-1959) JN Learning / CMESubscribeJobsInstitutions / LibrariansReprints & Permissions Terms of Use | Privacy Policy | Accessibility Statement 2023 American Medical Association. All Rights Reserved Search All JAMA JAMA Network Open JAMA Cardiology JAMA Dermatology JAMA Forum Archive JAMA Health Forum JAMA Internal Medicine JAMA Neurology JAMA Oncology JAMA Ophthalmology JAMA Otolaryngology–Head & Neck Surgery JAMA Pediatrics JAMA Psychiatry JAMA Surgery Archives of Neurology & Psychiatry Input Search Term Sign In Individual Sign In Sign inCreate an Account Access through your institution Sign In Purchase Options: Buy this article Rent this article Subscribe to the JAMA Internal Medicine journal
Reprogrammed astrocytes display higher neurogenic competence, migration ability and cell death resistance than reprogrammed fibroblasts
Authors: Xiaohuan Xia, Chunhong Li, Yi Wang, Xiaobei Deng, Yizhao Ma, Lu Ding, Jialin Zheng
Journal: Translational Neurodegeneration (2020)

The direct reprogramming of somatic cells into induced neural progenitor cells (iNPCs) has been envisioned as a promising approach to overcome ethical and clinical issues of pluripotent stem cell transplantation. We previously reported that astrocyte-derived induced pluripotent stem cells (iPSCs) have more tendencies for neuronal differentiation than fibroblast-derived iPSCs. However, the differences of neurogenic potential between astrocyte-derived iNPCs (AiNPCs) and iNPCs from non-neural origins, such as fibroblast-derived iNPCs (FiNPCs), and the underlying mechanisms remain unclear. Our results suggested that AiNPCs exhibited higher differentiation efficiency, mobility and survival capacities, compared to FiNPCs. The whole transcriptome analysis revealed higher activities of TGFβ signaling in AiNPCs, versus FiNPCs, following a similar trend between astrocytes and fibroblasts. The higher neurogenic competence, migration ability, and cell death resistance of AiNPCs could be abrogated using TGFβ signaling inhibitor LY2157299. Hence, our study demonstrates the difference between iNPCs generated from neural and non-neural cells, together with the underlying mechanisms, which, provides valuable information for donor cell selection in the reprogramming approach.
Abstract P298: Racial Differences in Diabetes Care Practices: Prevalence and Determinants in Older Adults
Authors: Michael Fang, B Gwen Windham, James S Pankow, Elizabeth Selvin
Journal: Circulation (2020)

Background: The burden of complications among older adults with diabetes is high and disproportionately affects racial/ethnic minorities. Differences in diabetes care practices may be an important contributor to disparities. Our study examined whether engagement in diabetes care practices varies by race/ethnicity in older adults. Methods: We conducted a cross-sectional analysis of the prevalence of diabetes care practices using data from visit 6 (2016-2017) of the Atherosclerosis Risk in Communities (ARIC) study. Participants with previously diagnosed diabetes self-reported receipt of four annual examinations/tests (HbA1c testing, urine protein testing, eye examination, foot examination) and two types of vaccinations (influenza [annual], pneumonia [ever]). We assessed crude differences across race using chi-square tests. For care practices that differed significantly, we conducted a mediational analysis using logistic regression models to explore potential mechanisms. Results: Among the 886 participants with previously diagnosed diabetes (62% white, 58% female, mean age 79), the receipt of recommended annual tests or examinations (HbA1c and urine protein testing, eye and foot exams) was high (73%-94%) and did not differ significantly across race ( Figure ). In contrast, whites were more likely than blacks to have received vaccinations for influenza (83% versus 69%, P&lt;0.001) and pneumonia (90% versus 73%, P&lt;0.001), respectively ( Figure ). Differences in sociodemographic characteristics and health status explained ~52% and ~15% of the difference in influenza and pneumonia vaccinations, with household income emerging as the most important mediator for both outcomes. Conclusion: Engagement in diabetes care practices among older adults was high, but whites were more likely than blacks to receive recommended vaccinations. Ensuring vaccination coverage among racial/ethnic minorities with diabetes is important and may reduce disparities in development of complications.