tbuckley/cabot-search huggingface dataset:
Integrating machine learning and multiscale modeling—perspectives, challenges, and opportunities in the biological, biomedical, and behavioral sciences
Authors: Mark Alber, Adrian Buganza Tepole, William R. Cannon, Suvranu De, Salvador Dura-Bernal, Krishna Garikipati, George Karniadakis, William W. Lytton, Paris Perdikaris, Linda Petzold, Ellen Kuhl
Journal: npj Digital Medicine (2019)

Fueled by breakthrough technology developments, the biological, biomedical, and behavioral sciences are now collecting more data than ever before. There is a critical need for time- and cost-efficient strategies to analyze and interpret these data to advance human health. The recent rise of machine learning as a powerful technique to integrate multimodality, multifidelity data, and reveal correlations between intertwined phenomena presents a special opportunity in this regard. However, machine learning alone ignores the fundamental laws of physics and can result in ill-posed problems or non-physical solutions. Multiscale modeling is a successful strategy to integrate multiscale, multiphysics data and uncover mechanisms that explain the emergence of function. However, multiscale modeling alone often fails to efficiently combine large datasets from different sources and different levels of resolution. Here we demonstrate that machine learning and multiscale modeling can naturally complement each other to create robust predictive models that integrate the underlying physics to manage ill-posed problems and explore massive design spaces. We review the current literature, highlight applications and opportunities, address open questions, and discuss potential challenges and limitations in four overarching topical areas: ordinary differential equations, partial differential equations, data-driven approaches, and theory-driven approaches. Towards these goals, we leverage expertise in applied mathematics, computer science, computational biology, biophysics, biomechanics, engineering mechanics, experimentation, and medicine. Our multidisciplinary perspective suggests that integrating machine learning and multiscale modeling can provide new insights into disease mechanisms, help identify new targets and treatment strategies, and inform decision making for the benefit of human health.
Genomic characteristics and predicted ancestry of NTRK1/2/3 and ROS1 fusion-positive tumours from &gt;165,000 pan-solid tumours
Authors: T.R. Wilson, E.S. Sokol, S.E. Trabucco, J.Y. Newberg, B. Simmons, T. Riehl, S.L. Maund
Journal: Annals of Oncology (2019)
National Trends in Hepatitis C Infection by Opioid Use Disorder Status Among Pregnant Women at Delivery Hospitalization — United States, 2000–2015
Authors: Jean Y. Ko, Sarah C. Haight, Sarah F. Schillie, Michele K. Bohm, Patricia M. Dietz
Journal: MMWR Morbidity and Mortality Weekly Report (2019)

Hepatitis C virus (HCV) is transmitted primarily through parenteral exposures to infectious blood or body fluids that contain blood (e.g., via injection drug use, needle stick injuries) (1). In the last 10 years, increases in HCV infection in the general U.S. population (1) and among pregnant women (2) are attributed to a surge in injection drug use associated with the opioid crisis. Opioid use disorders among pregnant women have increased (3), and approximately 68% of pregnant women with HCV infection have opioid use disorder (4). National trends in HCV infection among pregnant women by opioid use disorder status have not been reported to date. CDC analyzed hospital discharge data from the 2000-2015 Healthcare Cost and Utilization Project (HCUP) to determine whether HCV infection trends differ by opioid use disorder status at delivery. During this period, the national rate of HCV infection among women giving birth increased >400%, from 0.8 to 4.1 per 1,000 deliveries. Among women with opioid use disorder, rates of HCV infection increased 148%, from 87.4 to 216.9 per 1,000 deliveries, and among those without opioid use disorder, rates increased 271%, although the rates in this group were much lower, increasing from 0.7 to 2.6 per 1,000 deliveries. These findings align with prior ecological data linking hepatitis C increases with the opioid crisis (2). Treatment of opioid use disorder should include screening and referral for related conditions such as HCV infection.
Genomic and clinical characterization of non-small cell lung cancer (NSCLC) patients harboring mutations in FGFR2 and FGFR3
Authors: M. Scheffler, T. Chanra, A. Kron, S. Koleczko, D.S.Y. Abdulla, M.A. Ihle, A. Holzem, R. Riedel, S. Michels, R.N. Fischer, S. Merkelbach-Bruse, R. Büttner, L. Nogova, J. Wolf
Journal: Annals of Oncology (2019)
Neutrophil-to-lymphocyte ratio predicts platinum sensitivity in epithelial ovarian cancer patients: A MITO24 retrospective study
Authors: A. Farolfi, E. Scarpi, F. Greco, A. Bergamini, L. Longo, S. Pignata, C. Casanova, V.l. De Vecchio, A. Bologna, M. Orditura, L. Zavallone, J. Ventriglia, V. Gallà, E. Franzese, E. Pigozzi, V. Loizzi, G. Giorda, D. Giardina, R. Cioffi, U. De Giorgi
Journal: Annals of Oncology (2019)
Updated analysis of the national registry of nervous system tumours in Spain (RETSINE). RETSINE: National registry of nervous system tumours of the Spanish research group in neuro-oncology (GEINO) and Spanish infrequent and orphan tumours group (GETHI)
Authors: I. Ceballos Lenza, P. Perez Segura, M.A.V. Salgado, S. del barco, O. Gallego, T. Quintanar, M.A. Ivars, I. Fernandez Perez, F. García-Piñon, R. de las Penas Bataller
Journal: Annals of Oncology (2019)
Assessment of Survival of Pediatric Patients With Hepatoblastoma Who Received Chemotherapy Following Liver Transplant or Liver Resection
Authors: Jincheng Feng, Ying He, Lai Wei, Dong Chen, Huifang Yang, Rumeng Tan, Zhishui Chen
Journal: JAMA Network Open (2019)

<h3>Importance</h3> The incidence of hepatoblastoma is increasing, and liver transplant (LT) provides a potential cure for pediatric patients with unresectable hepatoblastoma; however, the use of LT for hepatoblastoma has not been examined in a modern cohort. Moreover, data are lacking on the association between the type of surgical management received and overall risk of death among pediatric patients with hepatoblastoma. <h3>Objectives</h3> To examine the receipt of LT among pediatric patients with hepatoblastoma and to assess overall survival of pediatric patients with hepatoblastoma who were treated with chemotherapy after LT or liver resection (LR) using data from a national cancer registry. <h3>Design, Setting, and Participants</h3> This cohort study used data for 443 pediatric patients with histologically confirmed hepatoblastoma who received chemotherapy and surgical therapies, as documented in the Surveillance, Epidemiology, and End Results database of the National Cancer Institute, from 2004 to 2016, with follow-up through December 31, 2018. Multivariable logistic regression was used to determine factors associated with the use of LT. Cox proportional hazards models were used to assess factors associated with overall survival. Data analysis was performed from April 18, 2019, to July 25, 2019. <h3>Main Outcomes and Measures</h3> Overall survival. <h3>Results</h3> Among 443 patients receiving chemotherapy (mean [SD] age, 1.8 [2.6] years; 167 [37.7%] female), 350 (79%) underwent LR and 93 (21%) underwent LT. Multivariable analysis showed that patients with multiple lesions were more likely to undergo LT than LR (31% vs 13%;<i>P</i> &lt; .001) and that patients with higher stage tumors were more likely to undergo LT than LR (local disease, 20% vs 58%; regional disease, 58% vs 24%; distant disease, 22% vs 18%;<i>P</i> &lt; .001). There was a statistically significant 19% increase in the receipt of LT from 8% in 1998 to 27% 2016 (trend test,<i>P</i> = .02). Overall survival at 10 years was not significantly different for the 2 surgical management strategies (87.2% [95% CI, 78.3%-97.1%] for patients undergoing LT vs 87.8% [95% CI, 83.5%-92.4%] for those undergoing LR;<i>P</i> = .92). The overall risk of death was not significantly different for LT compared with LR (hazard ratio, 0.716; 95% CI, 0.309-1.657;<i>P</i> = .44). <h3>Conclusions and Relevance</h3> The use of LT for the management of hepatoblastoma has increased significantly over time. Among pediatric patients with hepatoblastoma receiving chemotherapy, LT was not associated with improved overall survival compared with LR. There was no significant different between treatments with regard to the outcome variable, but this finding cannot be interpreted as indicating equivalence or lack of superiority.
SP0106 Fibroblasts: their roles in matrix and vessels
Authors: J. Distler
Journal: Annals of the Rheumatic Diseases (2018)

<h3></h3> Persistent activation of fibroblasts is a common denominator of fibrotic diseases but mechanistically incompletely defined. In contrast to physiologic tissue repair responses, fibroblasts remain persistently active in fibrotic diseases and continue to release excessive amounts of extracellular matrix. We will discuss novel insights into the molecular mechanisms underlying the uncontrolled activation of fibroblasts in fibrotic diseases and potential implications of those findings for targeted antifibrotic therapies. <h3>Disclosure of Interest</h3> J. Distler Shareholder of: 4D Science, Grant/research support from: Anamar, Active Biotech, Array Biopharma, aTyr, BMS, Bayer Pharma, Boehringer Ingelheim, Celgene, Galapagos, GSK, Inventiva, Novartis, Sanofi-Aventis, RedX, UCB, Consultant for: Actelion, Active Biotech, Anamar, Bayer Pharma, Boehringer Ingelheim, Celgene, Galapagos, GSK, Inventiva, JB Therapeutics, Medac, Pfizer, RuiYi and UCB
An Elderly Bias, Nocturia, and Adverse Effects of Sedative-Hypnotic Medication
Authors: Donald L. Bliwise
Journal: JAMA Internal Medicine (2019)

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
Prognosis of selected triple negative apocrine breast cancer patients who did not receive adjuvant chemotherapy
Authors: G. Cancello, E. Montagna, E. Pagan, V. Bagnardi, E. Munzone, S. Dellapasqua, M. Iorfida, M. Mazza, A.P. De Maio, G. Viale, G. Mazzarol, P. Veronesi, V. Galimberti, G. Santomauro, M.A. Colleoni
Journal: Annals of Oncology (2019)
The use of intravenous ferric carboxymaltose without erythropoiesis-stimulating agents in the treatment of anemia in cancer patients undergoing chemotherapy with or without radiotherapy
Authors: H. Abdel-Razeq, S.S. Saadeh, R. Malhis, O. AL-Natour, S. Yaser, H. Abdulelah, R. Eljaber, G. Khalaf
Journal: Annals of Oncology (2019)
Use of droplet digital polymerase chain reaction for detecting minimal residual disease: A prospective, multi-institutional study
Authors: H. Park, D.-Y. Shin, I. Kim, S.-K. Sohn, Y. Koh, J.-H. Lee, K.-H. Lee, D.-Y. Kim, H.-J. Kim, J.-S. Ahn, J.-O. Lee, S.-M. Bang, J.-W. Cheong, S.-G. Park, S. Park, Y.J. Lee, S.-Y. Ahn
Journal: Annals of Oncology (2019)
Targeting tumour microenvironment, a FAKtual challenge in pancreatic cancer
Authors: Ezequiel J Tolosa, Martín E Fernández-Zapico
Journal: Gut (2019)

In the past two decades, investigators have turned their attention to the development of new approaches to inhibit the aggressive behaviour of the tumour microenvironment (TME) of pancreatic ductal adenocarcinoma (PDAC),1–7 a dismal disease predicted to be the second leading cause of cancer death by 2030. However, complete genetic or pharmacological ablation of stroma results in more aggressive tumours. Furthermore, targeting the TME in patients with PDAC has grown controversial due to failure of clinical trials to improve patient survival.8 9 Together, these findings highlight the need to increase our understanding of the role of TME components (cellular and non-cellular) and their interplay in PDAC pathogenesis. This would better inform development of new treatment approaches not aimed at total stromal depletion, but rather TME reprogramming to ‘activate’ its antitumoural functions or to facilitate sensitivity to specific targeted therapies. In Gut , Jiang and colleagues elegantly report a novel therapeutic approach through partial stromal depletion, employing clinically available focal adhesion kinase (FAK) inhibitors to sensitise PDAC to signal …
DNA methylation-driven genes for constructing diagnostic, prognostic, and recurrence models for hepatocellular carcinoma
Authors: Junyu Long, Peipei Chen, Jianzhen Lin, Yi Bai, Xu Yang, Jin Bian, Yu Lin, Dongxu Wang, Xiaobo Yang, Yongchang Zheng, Xinting Sang, Haitao Zhao
Journal: Theranostics (2019)

In this study, we performed a comprehensively analysis of gene expression and DNA methylation data to establish diagnostic, prognostic, and recurrence models for hepatocellular carcinoma (HCC).Methods: We collected gene expression and DNA methylation datasets for over 1,200 clinical samples.Integrated analyses of RNA-sequencing and DNA methylation data were performed to identify DNA methylation-driven genes.These genes were utilized in univariate, least absolute shrinkage and selection operator (LASSO), and multivariate Cox regression analyses to build a prognostic model.Recurrence and diagnostic models for HCC were also constructed using the same genes.Results: A total of 123 DNA methylation-driven genes were identified.Two of these genes (SPP1 and LCAT) were chosen to construct the prognostic model.The high-risk group showed a markedly unfavorable prognosis compared to the low-risk group in both training (HR = 2.81; P < 0.001) and validation (HR = 3.06; P < 0.001) datasets.Multivariate Cox regression analysis indicated the prognostic model to be an independent predictor of prognosis (P < 0.05).Also, the recurrence model successfully distinguished the HCC recurrence rate between the high-risk and low-risk groups in both training (HR = 2.22; P < 0.001) and validation (HR = 2; P < 0.01) datasets.The two diagnostic models provided high accuracy for distinguishing HCC from normal samples and dysplastic nodules in the training and validation datasets, respectively.Conclusions: We identified and validated prognostic, recurrence, and diagnostic models that were constructed using two DNA methylation-driven genes in HCC.The results obtained by integrating multidimensional genomic data offer novel research directions for HCC biomarkers and new possibilities for individualized treatment of patients with HCC.
Quantitative spatial profiling of lymphocyte-activation gene 3 (LAG-3)/major histocompatibility complex class II (MHC II) interaction in gastric and urothelial tumors
Authors: C.V. Hedvat, G. Lee, V. Baxi, K. Dziuba, D. Locke, B. Li, R. Edwards
Journal: Annals of Oncology (2019)
The efficacy of preoperative breast cancer chemotherapy without anti-HER2-targeted treatment: Single center experience in setting of no reimbursement in Poland (2011-2015)
Authors: A. Badora-Rybicka, A. Polakiewicz-Gilowska, A. Leśniak, W. Bal, M. Kubeczko, K. Świderska, M. Mianowska-Malec, B.D. Grandys, E. Stobiecka, E. Chmielik, A. Kuś, R. Tarnawski, M. Jarzab
Journal: Annals of Oncology (2019)
Early tumour shrinkage (ETS), depth of response (DpR) and associated survival outcomes in patients (pts) with RAS wild type (WT) metastatic colorectal cancer (mCRC) classified according to Köhne prognostic category: Retrospective analysis of the panitumumab (Pmab) PRIME study
Authors: A. Sartore-Bianchi, M. Peeters, M. Geissler, J. Taieb, P. García-Alfonso, T. Price, P. Burdon, Y. Zhang, C.-H. Koehne
Journal: Annals of Oncology (2019)
SAT0450 SENSITIVITY OF DUAL-ENERGY CT SCANNING, ULTRASOUND, AND X-RAY FOR CRYSTAL-PROVEN PSEUDOGOUT
Authors: Sara Tedeschi, Daniel Solomon, Kathleen Vanni, Neal Suh, Stacy Smith
Journal: Annals of the Rheumatic Diseases (2019)

<h3>Background</h3> Advanced imaging modalities such as ultrasound (US) and dual-energy CT (DECT) can help diagnose crystalline arthritis. DECT is highly sensitive and specific in gout and has not been well studied in pseudogout. <h3>Objectives</h3> To compare the sensitivity of DECT, US, and x-ray (XR) in pseudogout. <h3>Methods</h3> We prospectively enrolled patients with crystal-proven pseudogout at a tertiary care center, 3/2018-11/2018. We searched the electronic medical record for synovial fluid crystal lab orders and reviewed the record to identify candidates. Eligible patients were 18 years old with acute monoarthritis, joint aspiration, and synovial fluid calcium pyrophosphate (CPP) crystals on polarized microscopy. Patients with both monosodium urate and CPP crystals were excluded. Subjects provided informed consent and underwent DECT, US, and XR of the aspirated joint and standardized joint (right wrist). All images were interpreted by a musculoskeletal radiologist and a rheumatologist trained in US; consensus was reached on each image. DECT images were post-processed using Siemens Syngo.via software, applying color-coded overlay indicating volume and location of CPP deposits. We considered two volume thresholds (cm<sup>3</sup>) for a positive DECT scan. Imaging abnormalities defining a positive scan were: color-coded changes consistent with CPP (DECT); hyperechoic deposits in hyaline-, fibro-cartilage, or tendon (US); and chondrocalcinosis in hyaline- or fibro-cartilage (XR). We calculated sensitivity and 95% confidence interval (CI) of positive scans in the aspirated joint and prevalence (95% CI) in the standardized joint. <h3>Results</h3> Ten of 27 eligible patients enrolled. Mean (SD) age was 73 (9.7) years; 40% were female. Eight knees and two wrists were aspirated a mean (SD) of 17 (9) days before enrollment. Six subjects received intra-articular steroids before enrollment. Imaging results are shown in Table 1. In the aspirated joint, sensitivity (95% CI) was 90% (71-100%) for DECT volume &gt;0.40 cm<sup>3</sup>, and 100% (100-100%) for DECT volume &gt;0.01 cm<sup>3</sup>; 100% (100-100%) for US; and 70% (42-98%) for XR. In the standardized joint, DECT was positive in 20% (0-45%) for volume &gt;0.40 cm<sup>3</sup>, and 90% (71-100%) for volume &gt;0.01 cm<sup>3</sup>. XR chondrocalcinosis was present in 30% (2-58%) and US was positive in 80% (55-100%) of wrists. <h3>Conclusion</h3> DECT and US had high sensitivity for pseudogout using synovial fluid CPP crystals as the gold standard. Larger studies testing DECT sensitivity and specificity in pseudogout vs. other arthritis and establishing a volume threshold are needed. <h3>References</h3> none <h3>Disclosure of Interests</h3> Sara Tedeschi: None declared, Daniel Solomon Grant/research support from: Abbvie, Amgen, Genentech, Janssen, and Pfizer, Kathleen Vanni: None declared, Neal Suh Grant/research support from: Pfizer, Stacy Smith: None declared
A phase IIa clinical trial combining ALRN-6924 and palbociclib for the treatment of patients with tumours harboring wild-type p53 and MDM2 amplification or MDM2/CDK4 co-amplification
Authors: F. Meric-Bernstam, N. Somaiah, S.G. DuBois, E E Ileana Dumbrava, G.I. Shapiro, M.R. Patel, S. Goel, T. Bauer, D. Pinchasik, A. Annis, M. Aivado, V. Vukovic, M. Saleh
Journal: Annals of Oncology (2019)
Abstract 15849: Exercise Training in Patients With Implantable Cardioverter Defibrillator: A Meta-analysis of Efficacy and Safety Outcomes
Authors: Akhil Parashar, Usman Salahuddin, Ambarish Pandey, Jonathan Piccini, Amar Krishnaswamy, Mandeep Bhargava, Samir Kapadia, Jarett Berry
Journal: Circulation (2015)

Introduction: Implantable cardioverter defibrillators have been shown to improve survival, however, many patients with ICDs experience fear of shocks and avoid physical activity. Little data exist on efficacy and safety of exercise training in heart failure patients with ICDs. We performed a meta-analysis of currently available randomized clinical trials to assess the efficacy and safety of exercise training in this patient population. Methods: Randomized clinical trials that evaluated the efficacy of exercise training in patients with ICDs were included in the pooled meta-analysis. Primary efficacy outcome was change in cardiorespiratory fitness measured as peak oxygen uptake during a maximal treadmill test (CRF, mL/kg/ per minute). Primary safety outcome was difference in proportion of patients experiencing ICD shocks between exercise and control groups. Results: We included study level data from 1,532 patients (812 in exercise group and 720 in control group) derived from 5 studies which met the inclusion criteria. In the pooled analysis (figure panel 1), patients with ICD undergoing exercise training had significantly improved CRF [Weighted mean difference (95% CI): 1.86 ml/kg/min (0.71 to 3.01)]. There was also a significant reduction in the likelihood of ICD shocks (figure panel 2) in the exercise group compared to control group [Pooled odds ratio (95% CI): 0.71 (0.55 to 0.92)]. Conclusion: Exercise training is associated with significant improvements in CRF levels and reduction in the likelihood of ICD shocks among patients with ICDs.
Engaging cancer survivors, healthcare providers and advocates in the development of a colorectal cancer survivorship information resource: A participatory action research study
Authors: A. Drury, N. de Zeeuw, D. Flannery, A. McNamara, A. Nolan, C. O’Brien, K. O’Connor, S. Payne, A.-M. Brady
Journal: Annals of Oncology (2019)
Identification of MET gene amplifications using next-generation sequencing in non-small cell lung cancer patients
Authors: S. Clavé, M. Salido, P. Rocha, M. Hardy-Werbin, J. Gibert, X. Riera, E. Weingartner, G. Cerqueira, D. Nichol, J. Simmons, Á Taus, L. Pijuan, B. Bellosillo, E. Arriola
Journal: Annals of Oncology (2019)
Medicines associated with dependence or withdrawal: a mixed-methods public health review and national database study in England
Authors: John Marsden, Martin White, Fizz Annand, Peter Burkinshaw, Serena Carville, Brian Eastwood, Michael Kelleher, Jonathan Knight, Rosanna O'Connor, Anh Tran, Peter Willey, Felix Greaves, Stephen Taylor
Journal: The Lancet Psychiatry (2019)

Antidepressants, opioids for non-cancer pain, gabapentinoids (gabapentin and pregabalin), benzodiazepines, and Z-drugs (zopiclone, zaleplon, and zolpidem) are commonly prescribed medicine classes associated with a risk of dependence or withdrawal. We aimed to review the evidence for these harms and estimate the prevalence of dispensed prescriptions, their geographical distribution, and duration of continuous receipt using all patient-linked prescription data in England.