tbuckley/cabot-search huggingface dataset:
The Oncology Care Model at 5 Years—Value-Based Payment in the Precision Medicine Era
Authors: Samyukta Mullangi, Stephen M. Schleicher, Ravi B. Parikh
Journal: JAMA Oncology (2021)

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 Oncology 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 Oncology journal
Global burden of acute lower respiratory infection associated with human parainfluenza virus in children younger than 5 years for 2018: a systematic review and meta-analysis
Authors: Xin Wang, You Li, Maria Deloria-Knoll, Shabir A Madhi, Cheryl Cohen, Vina Lea Arguelles, Sudha Basnet, Quique Bassat, W Abdullah Brooks, Marcela Echavarria, Rodrigo A Fasce, Angela Gentile, Doli Goswami, Nusrat Homaira, Stephen R C Howie, Karen L Kotloff, Najwa Khuri-Bulos, Anand Krishnan, Marilla G Lucero, Socorro Lupisan, Maria Mathisen, Kenneth A McLean, Ainara Mira-Iglesias, Cinta Moraleda, Michiko Okamoto, Histoshi Oshitani, Katherine L O'Brien, Betty E Owor, Zeba A Rasmussen, Barbara A Rath, Vahid Salimi, Pongpun Sawatwong, J Anthony G Scott, Eric A F Simões, Viviana Sotomayor, Donald M Thea, Florette K Treurnicht, Lay-Myint Yoshida, Heather J Zar, Harry Campbell, Harish Nair
Journal: The Lancet Global Health (2021)

Human parainfluenza virus (hPIV) is a common virus in childhood acute lower respiratory infections (ALRI). However, no estimates have been made to quantify the global burden of hPIV in childhood ALRI. We aimed to estimate the global and regional hPIV-associated and hPIV-attributable ALRI incidence, hospital admissions, and mortality for children younger than 5 years and stratified by 0-5 months, 6-11 months, and 12-59 months of age.
Bilateral Salpingo-Oophorectomy to Reduce Breast Cancer Risk in Women With Germline <i>BRCA1</i> or <i>BRCA2</i> Pathogenic Variants—Caution Needed—Reply
Authors: Yun-Hee Choi, Mary Beth Terry, Laurent Briollais
Journal: JAMA Oncology (2021)

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Tumor invasion in the hyponychium is associated with distant metastasis and poor prognosis in subungual melanoma: A histologic landscape of 44 cases
Authors: Hyokyung Yoo, Hyeonwoo Kim, Sung Tack Kwon, Seong Jin Jo, Je-Ho Mun, Cheol Lee, Yoonjin Kwak, Byung Jun Kim
Journal: Journal of the American Academy of Dermatology (2021)
The Association Between Breastfeeding and Nonalcoholic Fatty Liver Disease in Parous Women: A Nation‐wide Cohort Study
Authors: Yewan Park, Dong Hyun Sinn, Joo Hyun Oh, Myung Ji Goh, Kyunga Kim, Wonseok Kang, Yong‐Han Paik, Moon Seok Choi, Joon Hyeok Lee, Kwang Cheol Koh, Seung Woon Paik, Geum‐Youn Gwak
Journal: Hepatology (2021)

Breastfeeding has multiple effects on maternal health outcomes. However, the effect of breastfeeding on NAFLD in parous women remains unclear.A total of 6,893 Korean parous women aged 30-50 years who participated in the Korean National Health and Nutrition Examination Survey were assessed for the association between breastfeeding and NAFLD. Duration of lactation was calculated by dividing the total lactation period by the number of breastfed children. NAFLD was defined by the hepatic steatosis index. Of 6,893 women, 1,049 (15.2%) had NAFLD. Prevalence of NAFLD was 18.3%, 14.3%, 12.3%, 14.4%, and 15.8% in women with a breastfeeding period of <1, ≥1-<3, ≥3-<6, ≥6-<12, and ≥12 months, respectively. In a fully adjusted model, breastfeeding (≥1 month) was associated with reduced NAFLD prevalence (OR, 0.67; 95% CI, 0.51-0.89) after adjusting for metabolic, socioeconomic, and maternal risk factors. Fully adjusted ORs (95% CI) decreased with an increase of breastfeeding duration: 0.74 (0.49-1.11), 0.70 (0.47-1.05), 0.67 (0.48-0.94), and 0.64 (0.46-0.89) for women with ≥1-<3, ≥3-<6, ≥6-<12, and ≥12 months of breastfeeding duration, respectively, compared to women with <1 month of breastfeeding duration. Such an association was also observed in all predefined subgroups without interaction.Breastfeeding showed a protective effect against NAFLD in later life of parous women, suggesting a maternal benefit of breastfeeding on NAFLD.
Proteomic, Gene Expression, and Micro-RNA Analysis Of Bone Marrow Mesenchymal Stromal Cells In Acute Myeloid Leukemia Identifies Pro-Inflammatory, Pro-Survival Signatures In Vitro and In Vivo
Authors: Michael Andreeff, Rui-yu Wang, Richard E. Davis, Rodrigo Jacamo, Peter P. Ruvolo, Teresa McQueen, Xielin Huang, Venkata L Battula, Ye Chen, Shonali Majumdar, Juliana M Benito, Zhihong Zeng, Christopher B. Benton, Bing Z Carter, Hong Mu, Wencai Ma, Vivian R Ruvolo, Lauren Hodgson, Sergej Konoplev, Rongqing Pan, Anitha Somanchi, Dirk Strunck, Qiguo Zhang, Steven M. Kornblau, Hagop M Kantarjian, Guido Marcucci, Ramiro Garzon, Johannes Zuber, Scott W. Lowe, Carlo M. Croce, Marina Konopleva
Journal: Blood (2013)
Changes in RT-qPCR Levels during and after TKI Interruptions for Attempted Conceptions in Women with CML
Authors: Louise Caldwell, Simone Claudiani, Dragana Milojkovic, Richard Szydlo, Elisabetta Abruzzese, George Nesr, Michael J. Mauro, Renuka Palanicawander, Aoife Gatenby, Ira Sabli, Jamshid S Khorashad, Letizia Foroni, Jane F. Apperley
Journal: Blood (2017)
Human Somatosensory Processing and Artificial Somatosensation
Authors: Luyao Wang, Lihua Ma, Jiajia Yang, Jinglong Wu
Journal: Cyborg and Bionic Systems (2021)

In the past few years, we have gained a better understanding of the information processing mechanism in the human brain, which has led to advances in artificial intelligence and humanoid robots. However, among the various sensory systems, studying the somatosensory system presents the greatest challenge. Here, we provide a comprehensive review of the human somatosensory system and its corresponding applications in artificial systems. Due to the uniqueness of the human hand in integrating receptor and actuator functions, we focused on the role of the somatosensory system in object recognition and action guidance. First, the low-threshold mechanoreceptors in the human skin and somatotopic organization principles along the ascending pathway, which are fundamental to artificial skin, were summarized. Second, we discuss high-level brain areas, which interacted with each other in the haptic object recognition. Based on this close-loop route, we used prosthetic upper limbs as an example to highlight the importance of somatosensory information. Finally, we present prospective research directions for human haptic perception, which could guide the development of artificial somatosensory systems.
炎症性腸疾患を有する小児における原発性硬化性胆管炎は軽度の臨床活動に関連するが,より頻繁な無症候性炎症および増殖障害に関連する【JST・京大機械翻訳】
Authors: Ricciuto Amanda, E Hansen Bettina, Ngo Brian, Aloi Marina, D Walters Thomas, C Church Peter, Mazurek Abigail, Khan Maryam, Carman Nicholas, Siddiqui Iram, C Nguyen Geoffrey, M Kamath Binita, M Griffiths Anne
Journal: Clinical Gastroenterology and Hepatology (2020)
Correlates of protection against symptomatic and asymptomatic SARS-CoV-2 infection
Authors: Shuo Feng, Daniel J. Phillips, Thomas White, Homesh Sayal, Parvinder K. Aley, Sagida Bibi, Christina Dold, Michelle Fuskova, Sarah C. Gilbert, Ian Hirsch, Holly E. Humphries, Brett Jepson, Elizabeth J. Kelly, Emma Plested, Kathryn Shoemaker, Kelly M. Thomas, Johan Vekemans, Tonya L. Villafana, Teresa Lambe, Andrew J. Pollard, Merryn Voysey, Syed Adlou, Lauren Allen, Brian Angus, Rachel Anslow, Marie-Claude Asselin, Natalie Baker, Philip Baker, Thomas Barlow, Amy Beveridge, Kevin R. Bewley, Phillip Brown, Emily Brunt, Karen R. Buttigieg, Susana Camara, Sue Charlton, Emily Chiplin, Paola Cicconi, Elizabeth A. Clutterbuck, Andrea M. Collins, Naomi S. Coombes, Sue Ann Costa Clemens, Melanie Davison, Tesfaye Demissie, Tanya Dinesh, Alexander D. Douglas, Christopher J. A. Duncan, Katherine R. W. Emary, Katie J. Ewer, Sally Felle, Daniela M. Ferreira, Adam Finn, Pedro M. Folegatti, Ross Fothergill, Sara Fraser, Harriet Garlant, Laura Gatcombe, Kerry J. Godwin, Anna L. Goodman, Christopher A. Green, Bassam Hallis, Thomas C. Hart, Paul T. Heath, Helen Hill, Adrian V. S. Hill, Daniel Jenkin, Mwila Kasanyinga, Simon Kerridge, Chanice Knight, Stephanie Leung, Vincenzo Libri, Patrick J. Lillie, Spyridoula Marinou, Joanna McGlashan, Alastair C. McGregor, Lorna McInroy, Angela M. Minassian, Yama F. Mujadidi, Elizabeth J. Penn, Christos J. Petropoulos, Katrina M. Pollock, Pamela C. Proud, Samuel Provstgaard-Morys, Durga Rajapaska, Maheshi N. Ramasamy, Katherine Sanders, Imam Shaik, Nisha Singh, Andrew Smith, Matthew D. Snape, Rinn Song, Sonu Shrestha, Rebecca K. Sutherland, Emma C. Thomson, David P. J. Turner, Alice Webb-Bridges, Terri Wrin, Christopher J. Williams
Journal: Nature Medicine (2021)

Abstract The global supply of COVID-19 vaccines remains limited. An understanding of the immune response that is predictive of protection could facilitate rapid licensure of new vaccines. Data from a randomized efficacy trial of the ChAdOx1 nCoV-19 (AZD1222) vaccine in the United Kingdom was analyzed to determine the antibody levels associated with protection against SARS-CoV-2. Binding and neutralizing antibodies at 28 days after the second dose were measured in infected and noninfected vaccine recipients. Higher levels of all immune markers were correlated with a reduced risk of symptomatic infection. A vaccine efficacy of 80% against symptomatic infection with majority Alpha (B.1.1.7) variant of SARS-CoV-2 was achieved with 264 (95% CI: 108, 806) binding antibody units (BAU)/ml: and 506 (95% CI: 135, not computed (beyond data range) (NC)) BAU/ml for anti-spike and anti-RBD antibodies, and 26 (95% CI: NC, NC) international unit (IU)/ml and 247 (95% CI: 101, NC) normalized neutralization titers (NF 50 ) for pseudovirus and live-virus neutralization, respectively. Immune markers were not correlated with asymptomatic infections at the 5% significance level. These data can be used to bridge to new populations using validated assays, and allow extrapolation of efficacy estimates to new COVID-19 vaccines.
Exposure to green spaces may strengthen resilience and support mental health in the face of the covid-19 pandemic
Authors: Raf Aerts, Naomi Vanlessen, Olivier Honnay
Journal: BMJ (2021)

<h3>Background</h3> Several recent trials in chronic obstructive pulmonary disease (COPD) have assessed the effectiveness of the fluticasone–salmeterol combination inhaler in preventing COPD exacerbations, while finding an increased risk of pneumonia. The number needed to treat (NNT) is a simple measure to perform the comparative benefit–risk impact, but its calculation involving repeated outcome events such as COPD exacerbations has been incorrect. We describe the proper methods to calculate the NNT and, using data from published trials, apply them to evaluate the relative impact of fluticasone–salmeterol treatment on exacerbations and pneumonias in patients with COPD. <h3>Methods</h3> We review the fundamental definition of NNT and quantify it for situations with varying follow-up times. We review the ‘event-based’ NNT, proposed and used for repeated event outcomes, show its inaccuracy, describe its proper use and provide an approximate formula for its application. <h3>Results</h3> We show that a 1-year trial of the fluticasone–salmeterol combination versus salmeterol used the incorrect event-based approach to calculate the NNT as two patients that need to be treated for 1 year to prevent one COPD exacerbation, when the proper calculation results in a NNT of 14. In contrast, 20 patients need to be treated to induce one pneumonia case. For the TORCH trial, the NNT is 44 patients treated for 3 years with fluticasone–salmeterol versus salmeterol to prevent one exacerbation compared with 16 patients to induce one pneumonia case. <h3>Conclusions</h3> The NNT is a useful measure of the effect of drugs, but its proper calculation is essential to prevent misleading clinical practice guidelines.
Patient-reported survivorship care practices and late effects after treatment of Hodgkin (HL) and non-Hodgkin lymphoma (NHL).
Authors: Melissa Frick, Carolyn Vachani, Margaret K. Hampshire, Christina Bach, Karen Arnold-Korzeniowski, James M. Metz, Christine E. Hill-Kayser
Journal: Journal of Clinical Oncology (2018)

119 Background: Multimodal treatment of HL and NHL yields excellent outcomes, however, survivors are at risk for developing myriad late- and long-term effects (LLTEs). We describe survivorship care practices and LLTEs reported by HL/ NHL survivors. Methods: From a convenience sample of 964 HL (37%) and NHL (63%) cancer survivors using a publicly available Internet-based survivorship care plan (SCP) tool between 2011-2016, we examined cancer care and toxicity profile data. Results: Of all survivors, 67% were female and 84% were Caucasian; median age of diagnosis was 28y for HL and 49y for NHL survivors with median fu of 5y and 2y, respectively. 88% were free of cancer, 9% with recurrent or secondary malignancy, and 3% with metastatic disease. Chemotherapy was delivered to 89% of HL and 94% of NHL survivors, and radiation (RT) to 64% and 28%, respectively. Of those receiving RT, 96% (n = 217) HL and 61% (n = 106) NHL survivors received chest/mantle RT. Few reported receipt of previous SCP (13%) or treatment summary (4%). Most reported continued care from an oncologist (49%) or in combination with a PCP (19%). A shift to PCP management alone was observed, increasing from 2% of survivors if &lt; 2y fu to 30% once ≥2y fu. Survivors who received chest RT reported: hyper- or hypothyroidism (35%), thyroid nodules (8%), speaking/swallowing changes (20%), heart disease (14%), pulmonary fibrosis/pneumonitis (12%), and skin cancers within the RT field (9%). 6 of 321 (2%) who received chest RT reported secondary breast cancers, compared to zero in the group not receiving chest RT with median time to breast cancer 20.5y (R 6-32 years). Receipt of chemotherapy was associated with: chronic fatigue (56%), cognitive change (56%), peripheral neuropathy (35%), sexual changes (15% of males, 35% of females), and heart disease (10%). Conclusions: While this population achieves excellent disease outcomes, survivors report a substantial burden of LLTEs, suboptimal delivery of survivorship information, and transitions of care in follow-up. Multiple opportunities thus exist through which SCPs may be used to improve awareness regarding survivorship/ LLTEs and communicate follow-up care plans between survivors and treatment teams.
Versatile and efficient in vivo genome editing with compact Streptococcus pasteurianus Cas9
Authors: Zhiquan Liu, Siyu Chen, Wanhua Xie, Yuning Song, Jinze Li, Liangxue Lai, Zhanjun Li
Journal: Molecular Therapy (2021)

Compact CRISPR-Cas9 systems that can be packaged into an adeno-associated virus (AAV) show promise for gene therapy. However, the requirement of protospacer adjacent motifs (PAMs) restricts the target scope. To expand this repertoire, we revisited and optimized a small Cas9 ortholog derived from Streptococcus pasteurianus (SpaCas9) for efficient genome editing in vivo. We found that SpaCas9 enables potent targeting of 5′-NNGYRA-3′ PAMs, which are distinct from those recognized by currently used small Cas9s; the Spa-cytosine base editor (CBE) and Spa-adenine base editor (ABE) systems efficiently generated robust C-to-T and A-to-G conversions both in vitro and in vivo. In addition, by exploiting natural variation in the PAM-interacting domain, we engineered three SpaCas9 variants to further expand the targeting scope of compact Cas9 systems. Moreover, mutant mice with efficient disruption of the Tyr gene were successfully generated by microinjection of SpaCas9 mRNA and the corresponding single guide RNA (sgRNA) into zygotes. Notably, all-in-one AAV delivery of SpaCas9 targeting the Pcsk9 gene in adult mouse liver produced efficient genome-editing events and reduced its serum cholesterol. Thus, with distinct PAMs and a small size, SpaCas9 will broaden the CRISPR-Cas9 toolsets for efficient gene modifications and therapeutic applications. Compact CRISPR-Cas9 systems that can be packaged into an adeno-associated virus (AAV) show promise for gene therapy. However, the requirement of protospacer adjacent motifs (PAMs) restricts the target scope. To expand this repertoire, we revisited and optimized a small Cas9 ortholog derived from Streptococcus pasteurianus (SpaCas9) for efficient genome editing in vivo. We found that SpaCas9 enables potent targeting of 5′-NNGYRA-3′ PAMs, which are distinct from those recognized by currently used small Cas9s; the Spa-cytosine base editor (CBE) and Spa-adenine base editor (ABE) systems efficiently generated robust C-to-T and A-to-G conversions both in vitro and in vivo. In addition, by exploiting natural variation in the PAM-interacting domain, we engineered three SpaCas9 variants to further expand the targeting scope of compact Cas9 systems. Moreover, mutant mice with efficient disruption of the Tyr gene were successfully generated by microinjection of SpaCas9 mRNA and the corresponding single guide RNA (sgRNA) into zygotes. Notably, all-in-one AAV delivery of SpaCas9 targeting the Pcsk9 gene in adult mouse liver produced efficient genome-editing events and reduced its serum cholesterol. Thus, with distinct PAMs and a small size, SpaCas9 will broaden the CRISPR-Cas9 toolsets for efficient gene modifications and therapeutic applications.
mbImpute: an accurate and robust imputation method for microbiome data
Authors: Ruochen Jiang, Wei Vivian Li, Jingyi Jessica Li
Journal: Genome biology (2021)

A critical challenge in microbiome data analysis is the existence of many non-biological zeros, which distort taxon abundance distributions, complicate data analysis, and jeopardize the reliability of scientific discoveries. To address this issue, we propose the first imputation method for microbiome data-mbImpute-to identify and recover likely non-biological zeros by borrowing information jointly from similar samples, similar taxa, and optional metadata including sample covariates and taxon phylogeny. We demonstrate that mbImpute improves the power of identifying disease-related taxa from microbiome data of type 2 diabetes and colorectal cancer, and mbImpute preserves non-zero distributions of taxa abundances.
Dietary interventions and nutritional supplements for heart failure: a systematic appraisal and evidence map
Authors: Muhammad Shahzeb Khan, Fiza Khan, Gregg C. Fonarow, Jayakumar Sreenivasan, Stephen J. Greene, Safi U. Khan, Muhammad Shariq Usman, Muthiah Vaduganathan, Marat Fudim, Stefan D. Anker, Javed Butler
Journal: European Journal of Heart Failure (2021)
SNO and EANO practice guideline update: Anticonvulsant prophylaxis in patients with newly diagnosed brain tumors
Authors: Tobias Walbert, Rebecca A Harrison, David Schiff, Edward K Avila, Merry Chen, Padmaja Kandula, Jong Woo Lee, Emilie Le Rhun, Glen H J Stevens, Michael A Vogelbaum, Wolfgang Wick, Michael Weller, Patrick Y Wen, Elizabeth R Gerstner
Journal: Neuro-Oncology (2021)

To update the 2000 American Academy of Neurology (AAN) practice parameter on anticonvulsant prophylaxis in patients with newly diagnosed brain tumors.Following the 2017 AAN methodologies, a systematic literature review utilizing PubMed, EMBASE Library, Cochrane, and Web of Science databases was performed. The studies were rated based on the AAN therapeutic or causation classification of evidence (class I-IV).Thirty-seven articles were selected for final analysis. There were limited high-level, class I studies and mostly class II and III studies. The AAN affirmed the value of these guidelines.In patients with newly diagnosed brain tumors who have not had a seizure, clinicians should not prescribe antiepileptic drugs (AEDs) to reduce the risk of seizures (level A). In brain tumor patients undergoing surgery, there is insufficient evidence to recommend prescribing AEDs to reduce the risk of seizures in the peri- or postoperative period (level C). There is insufficient evidence to support prescribing valproic acid or levetiracetam with the intent to prolong progression-free or overall survival (level C). Physicians may consider the use of levetiracetam over older AEDs to reduce side effects (level C). There is insufficient evidence to support using tumor location, histology, grade, molecular/imaging features when deciding whether or not to prescribe prophylactic AEDs (level U).