tbuckley/cabot-search huggingface dataset:
Calculating the sample size required for developing a clinical prediction model
Authors: Richard D Riley, Joie Ensor, Kym I E Snell, Frank E Harrell, Glen P Martin, Johannes B Reitsma, Karel G M Moons, Gary Collins, Maarten van Smeden
Journal: BMJ (2020)

Clinical prediction models aim to predict outcomes in individuals, to inform diagnosis or prognosis in healthcare. Hundreds of prediction models are published in the medical literature each year, yet many are developed using a dataset that is too small for the total number of participants or outcome events. This leads to inaccurate predictions and consequently incorrect healthcare decisions for some individuals. In this article, the authors provide guidance on how to calculate the sample size required to develop a clinical prediction model.
Benchmarking of computational error-correction methods for next-generation sequencing data
Authors: Keith Mitchell, Jaqueline J. Brito, Igor Mandric, Qiaozhen Wu, Sergey Knyazev, Sei Chang, Lana S. Martin, Aaron Karlsberg, Ekaterina Gerasimov, Russell Littman, Brian L. Hill, Nicholas C. Wu, Harry Taegyun Yang, Kevin Hsieh, Linus Chen, Eli Littman, Taylor Shabani, German Enik, Douglas Yao, Ren Sun, Jan Schroeder, Eleazar Eskin, Alex Zelikovsky, Pavel Skums, Mihai Pop, Serghei Mangul
Journal: Genome biology (2020)

Abstract Background Recent advancements in next-generation sequencing have rapidly improved our ability to study genomic material at an unprecedented scale. Despite substantial improvements in sequencing technologies, errors present in the data still risk confounding downstream analysis and limiting the applicability of sequencing technologies in clinical tools. Computational error correction promises to eliminate sequencing errors, but the relative accuracy of error correction algorithms remains unknown. Results In this paper, we evaluate the ability of error correction algorithms to fix errors across different types of datasets that contain various levels of heterogeneity. We highlight the advantages and limitations of computational error correction techniques across different domains of biology, including immunogenomics and virology. To demonstrate the efficacy of our technique, we apply the UMI-based high-fidelity sequencing protocol to eliminate sequencing errors from both simulated data and the raw reads. We then perform a realistic evaluation of error-correction methods. Conclusions In terms of accuracy, we find that method performance varies substantially across different types of datasets with no single method performing best on all types of examined data. Finally, we also identify the techniques that offer a good balance between precision and sensitivity.
Cognitively bounded rational analyses and the crucial role of theories of subjective utility
Authors: Richard L. Lewis, Andrew Howes
Journal: Behavioral and Brain Sciences (2020)

Abstract We agree that combining rational analysis with cognitive bounds, what we previously introduced as Cognitively Bounded Rational Analysis , is a promising and under-used methodology in psychology. We further situate the framework in the literature, and highlight the important issue of a theory of subjective utility, which is not addressed sufficiently clearly in the framework or related previous work.
Assessment of the Efficacy of Therapies Following Venetoclax Discontinuation in CLL Reveals BTK Inhibition as an Effective Strategy
Authors: Anthony R. Mato, Lindsey E. Roeker, Ryan Jacobs, Brian T. Hill, Nicole Lamanna, Danielle Brander, Mazyar Shadman, Chaitra S. Ujjani, Maryam Sarraf Yazdy, Guilherme Fleury Perini, Javier A. Pinilla-Ibarz, Jacqueline Barrientos, Alan P. Skarbnik, Pallawi Torka, Jeffrey J. Pu, John M. Pagel, Satyen Gohil, Bita Fakhri, Michael Choi, Catherine C. Coombs, Joanna Rhodes, Paul M. Barr, Craig A. Portell, Helen Parry, Christine A. Garcia, Kate J. Whitaker, Allison M. Winter, Andrea Sitlinger, Sirin Khajavian, Ariel F. Grajales-Cruz, Krista M. Isaac, Pratik Shah, Othman S. Akhtar, Rachael Pocock, Kentson Lam, Timothy J. Voorhees, Stephen J. Schuster, Thomas D. Rodgers, Christopher P. Fox, Nicolas Martinez-Calle, Talha Munir, Erica B. Bhavsar, Neil Bailey, Jason C. Lee, Hanna B. Weissbrot, Chadi Nabhan, Julie M. Goodfriend, Amber C. King, Andrew D. Zelenetz, Colleen Dorsey, Kayla Bigelow, Bruce D. Cheson, John N. Allan, Toby A. Eyre
Journal: Clinical Cancer Research (2020)

Venetoclax-based therapy is a standard-of-care option in first-line and relapsed/refractory chronic lymphocytic leukemia (CLL). Patient management following venetoclax discontinuation remains nonstandard and poorly understood.To address this, we conducted a large international study to identify a cohort of 326 patients who discontinued venetoclax and have been subsequently treated. Coprimary endpoints were overall response rate (ORR) and progression-free survival for the post-venetoclax treatments stratified by treatment type [Bruton's tyrosine kinase inhibitor (BTKi), PI3K inhibitor (PI3Ki), and cellular therapies].We identified patients with CLL who discontinued venetoclax in the first-line (4%) and relapsed/refractory settings (96%). Patients received a median of three therapies prior to venetoclax; 40% were BTKi naïve (n = 130), and 81% were idelalisib naïve (n = 263). ORR to BTKi was 84% (n = 44) in BTKi-naïve patients versus 54% (n = 30) in BTKi-exposed patients. We demonstrate therapy selection following venetoclax requires prior novel agent exposure consideration and discontinuation reasons.For BTKi-naïve patients, selection of covalently binding BTKis results in high ORR and durable remissions. For BTKi-exposed patients, covalent BTK inhibition is not effective in the setting of BTKi resistance. PI3Kis following venetoclax do not appear to result in durable remissions. We conclude that BTKi in naïve or previously responsive patients and cellular therapies following venetoclax may be the most effective strategies.See related commentary by Rogers, p. 3501.
Characteristics of pediatric SARS-CoV-2 infection and potential evidence for persistent fecal viral shedding
Authors: Yi Xu, Xufang Li, Bing Zhu, Huiying Liang, Chunxiao Fang, Yu Gong, Qiaozhi Guo, Xin Sun, Danyang Zhao, Jun Shen, Huayan Zhang, Hongsheng Liu, Huimin Xia, Jinling Tang, Kang Zhang, Sitang Gong
Journal: Nature Medicine (2020)
Long-duration chemotherapy, switch to endocrine therapy, or watch only? A single-center retrospective study of metastasis breast cancer with ER/PR(+) and CerbB2(-).
Authors: Huang Jian, zhan-Hong Chen, Wenming Cao, Wei-Wu Ye, Huang Ping, Shao Xiying
Journal: Journal of Clinical Oncology (2013)

e11589 Background: To evaluate the efficiency of long-duration chemotherapy used Capecitabine or switch to endocrine therapy in metastasis breast cancer (MBC) patients with ER/PR(+) and CerbB2(-). Methods: We retrospective analysis 112 patients of our center from 01/Jan/2009 to 30/April/2012, who with ER/PR(+) and CerbB2(-) MBC. All these patients accepted capecitabine -based regimen as first-line or 2nd-line chemotherapy. Three regimens included long-duration chemotherapy(LC) used capecitabine, switch to endocrine therapy(STET) or watch only(WO) were given after capecitabine-based regimen. We compared the differences among these three regimens. Results: 70/112 were first-line chemotherapy,52/112 were 2 nd -line chemotherapy. All these patients used capecitabine-based regimen (include single-agent or in combination with another chemotherapy drug), and the response were: CR, PR, SD≥24 weeks. 29 patients were LC,28 patients were STET and 55 patients were WO after capecitabine-based regimen. The median progression-free survival (mPFS) was 7 months, one year survival rate was 32.0%, response rate(RR) was 35.7% in all these patients. The mPFS were 22 months, 12 months and 5 months in LC group, STET group and WO group respectively. The one year survival rate were 67.6%,46.5% and 5.1% in these three groups respectively. WO group was significantly worse than LC and STET groups on mPFS (p&lt;0.0001) and one year survival rate (p&lt;0.05). LC group and STET group was no significant difference in mPFS(p=0.1832) and one year survival rate (p=0.5012). The RR were 51.7%, 39.3% and 25.5% in these three groups respectively. LC group was significantly better than WO group (p=0.0287). No significant difference between LC and STET groups (p=0.4287) or STET groups and WO group (p=0.2145). Conclusions: Long-duration treatment is better than watch only(WO).Patients with ER/PR(+) and CerbB2(-) MBC used capecitabine-based regimen (include single-agent or in combination with another chemotherapy drug), and the response were: CR, PR, SD≥24 weeks maybe get more benefits from long-duration chemotherapy used capecitabine. A multicenter prospective study is going on.
Mobile messaging with patients
Authors: Laura Martinengo, Pier Spinazze, Josip Car
Journal: BMJ (2020)

What you need to know• Mobile messaging has the potential to support clinical practice and should be offered as an optional service• Before engaging in mobile messaging with your patients, develop a policy that includes the scope of communication, roles, and expected response time• Offer other communication channels to patients who choose to opt out of mobile messaging• Document all communications in patients' electronic health records• Engage a mobile messaging provider compliant with your country's data protection lawsCommunication has been transformed by the mobile phone.Today, mobile messaging is widely used across all age groups, 1 2 exceeding voice calls in people under 50. 3 Healthcare providers worldwide are increasingly adopting digital integrated management systems that include messaging functions.This practice pointer offers an overview of mobile messaging to communicate with patients and carers, and offers suggestions for how to introduce these systems.
Questionable Survival Benefit of Aspirin Use in Patients With Biliary Tract Cancer—Reply
Authors: Sarah S. Jackson, Ruth M. Pfeiffer, Jill Koshiol
Journal: JAMA Oncology (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 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
TEMPORARY MECHANICAL CIRCULATORY SUPPORT USE IN TERTIARY CARDIAC INTENSIVE CARE UNITS BEFORE AND AFTER THE UNOS HEART TRANSPLANTATION ALLOCATION SYSTEM UPDATE: INSIGHTS FROM THE CRITICAL CARE CARDIOLOGY TRIALS NETWORK (CCCTN) REGISTRY
Authors: Anubodh Varshney, David Berg, Erin Ann Bohula, Vivian M. Baird-Zars, Jason Katz, Sean Van Diepen, David A. Morrow
Journal: Journal of the American College of Cardiology (2020)
Phase II study of extended schedule temozolomide in refractory gliomas
Authors: A. Berrocal, P. Perez-Segura, M. Gil, C. Balaña, R. Yaya-Tur, R. Yaya-Tur, J. Rodriguez, G. Reynes, J. Garcia-Lopez, O. Gallego
Journal: Journal of Clinical Oncology (2006)

1516 Background: Temozolomide resistance is mainly mediated by the enzyme AGT that repair DNA damage in a suicide way. Inhibition of this enzyme is greater when temozolomide is administered in a extended schedule that also obtains higher exposure to the drug. Methods: Primary objective is to assess is extended schedule temozolomide can revert resistance. Patients with bidimensionally measurable high grade glioma refractory to temozolomide defined as either progression during treatment or in the following tree months of drug withdrawal were included. Temozolomide was administered at a dose of 85 mg/m 2 daily for 21 consecutive days every 28 days until unacceptable toxicity or progression. Results: Up to now we have included 41 patients, 29 of them available for the first analysis. Mean age is 51.3 (23–77), male 22 (76%), ECOG 0/1/2 7 (24%)/13 (45%)/9 (31%), histology is glioblastoma 18 (61%), anaplastic astrocytoma 9 (31%), anaplastic oligodendroglioma 1 (3.4%) other high grade glioma 1. Fourteen patients received more than one line of chemotherapy before study entrance. 65% were on anticonvulsant therapy mainly with phenytoin 56% or valproic acid 42%. Response to treatment was partial in 2 (6.7%), stable in 9 (31%) progression in 13% (45%) and not assessed in 5. Response only in assessable patients was PR/SD/P 2 (8.3%)/9 (37.5%)/13 (54%). Responses were seen in oligodendroglioma and anaplastic astrocytoma. Median survival has been 5.9 months and time to progression 2 months. 80 courses have been administered with a mean per patient of 2 (1–7). Toxicity has been very mild mainly haematological and grade I and II. 7% of the patients experienced platelet toxicity grade III and 3.5% neutropenia grade III. Non haematological toxicity was mainly transaminase elevation grade I to II in 24% of patients and nausea and vomiting grade I to II in 31%. Conclusions: Extended schedule temozolomide is an active regimen in resistant patients with moderate toxicity. Resistance to temozolomide may be reverted by extended schedule of administration [Table: see text]
Effect of partially hydrolyzed whey infant formula and prolonged breast-feeding on the risk of allergic disease in high-risk children Reply
Authors: David J Hill, Adrian J Lowe, Clifford S Hosking, Catherine M Bennett, Katrina J Allen, Christine Axelrad, John B Carlin, Michael J Abramson, Shyamali C Dharmage
Journal: Journal of Allergy and Clinical Immunology (2011)
Coronary microvascular disease: the next frontier for Cardiovascular Research
Authors: Colin Berry, Dirk J Duncker
Journal: Cardiovascular Research (2020)

Ischaemic heart disease (IHD) persists as the leading cause of premature death and disability worldwide.1 IHD may present as acute myocardial infarction (MI) or a chronic coronary syndrome.2 IHD is increasingly recognized as a concomitant problem in systemic health problems, such as rheumatoid arthritis. Coronary atherosclerosis is a major cause of IHD. The historical primacy of coronary artery disease (CAD) leads some clinicians to view coronary heart disease (CHD) and IHD as synonymous, interchangeable terms. Emerging clinical evidence indicates this is far from being the case and a major reappraisal is warranted.3 CHD represents a subset of IHD, and these terms should not be used interchangeably.

Under-recognition of coronary microvascular disease: time for a reappraisal
Coronary microvascular dysfunction (CMD) has, historically, been under-recognized, not least since the microvessels are invisible to currently available clinical imaging techniques. This simple issue has underpinned key misconceptions about IHD and major knowledge gaps relating to CMD.3 Atherosclerosis is the major cause of CHD and the pathogenesis, prognosis, and treatment of these problems are well-established.2 In recent years, new insights into the causes and consequences of IHD have called into question the CAD stenosis-centred/CHD paradigm.

Most recently, the ISCHEMIA trial results were reported at the Scientific Sessions of the American Heart Association (16 November 2019) (https://professional.heart.org/professional/ScienceNews/UCM_505226_ISCHEMIA-Clinical-Trial-Details.jsp).4 The central hypothesis of the ISCHEMIA trial was that in patients with angina and moderate–severe myocardial ischaemia, compared with initial non-invasive, medical management, a routine invasive strategy with cardiac catheterization followed by coronary revascularization plus optimal medical therapy, would improve prognosis. After 3.3 years of follow-up, there was no difference in the primary endpoint between the randomized groups.4 This trial did have limitations. Under-recruitment and a lower than expected event rate reduced the statistical power for analysis of the primary outcome that ultimately led to a belated, yet prespecified change in the primary composite outcome. Longer-term follow-up with accrual of more events may provide new insights. Nonetheless, ISCHEMIA is the largest study of its kind, and the results call into question the benefits of coronary revascularization in patients with myocardial ischaemia. Crucially, it questions the stenosis-centred pathophysiology of IHD and warrants reassessment of the role of CMD in IHD.
TRANSIENT EFFUSIVE CONSTRICTIVE PERICARDITIS CAUSED BY E.COLI AND E.FAECIUM IN A PATIENT WITH A HISTORY OF ESOPHAGEAL ADENOCARCINOMA TREATED WITH SURGERY, CHEMOTHERAPY AND RADIATION
Authors: Rohini Manaktala, Andrew Elagizi, Aamir Gilani, Sangeeta Shah, Yvonne Gilliland, Allan Klein, Salima Qamruddin
Journal: Journal of the American College of Cardiology (2020)
LONG-TERM OUTCOMES OF PERCUTANEOUS CORONARY INTERVENTION FOR ACUTE MYOCARDIAL INFARCTION IN THE VERY ELDERLY
Authors: Derek Phan, Ming-Sum Lee, Malini Nadadur, Maereg Wassie, Jesse Goitia, Vicken Aharonian, Prakash Mansukhani, Naing Moore, Somjot Brar, Ray Zadegan
Journal: Journal of the American College of Cardiology (2020)
Does the preoperative platelet-to-lymphocyte ratio and neutrophil-to-lymphocyte ratio predict morbidity after gastrectomy for gastric cancer?
Authors: İbrahim Mungan, Çilem Bayındır Dicle, Şerife Bektaş, Sema Sarı, Serdar Yamanyar, Mine Çavuş, Sema Turan, Erdal Birol Bostancı
Journal: Military Medical Research (2020)

Abstract Background Gastric cancer is the 2nd most common cause of cancer-related deaths, and the morbidity rate after surgery is reported to be as high as 46%. The estimation of possible complications, morbidity, and mortality and the ability to specify patients at high risk have become substantial for an intimate follow-up and for proper management in the intensive care unit. This study aimed to determine the prognostic value of the preoperative platelet-to-lymphocyte ratio (PLR) and neutrophil-to-lymphocyte ratio (NLR) and their relations with clinical outcomes and complications after gastrectomy for gastric cancer. Methods This single-center, retrospective cohort study evaluated the data of 292 patients who underwent gastrectomy with curative intent between January 2015 and June 2018 in a tertiary state hospital in Ankara, Turkey. A receiver operating characteristic curve was generated to evaluate the ability of laboratory values to predict clinically relevant postoperative complications. The area under the curve was computed to compare the predictive power of the NLR and PLR. Then, the cutoff points were selected as the stratifying values for the PLR and NLR. Results The area under the curve values of the PLR (0.60, 95% CI 0.542–0.657) and NLR (0.556, 95% CI 0.497–0.614) were larger than those of the other preoperative laboratory values. For the PLR, the diagnostic sensitivity and specificity were 50.00 and 72.22%, respectively, whereas for the NLR, the diagnostic sensitivity and specificity were 37.50 and 80.16%, respectively. The PLR was related to morbidity, whereas the relation of the NLR with mortality was more prominent. This study demonstrated that the PLR and NLR may predict mortality and morbidity via the Clavien-Dindo classification in gastric cancer patients. The variable was grade ≥ 3 in the Clavien-Dindo classification, including complications requiring surgical or endoscopic interventions, life-threatening complications, and death. Both the PLR and NLR differed significantly according to Clavien-Dindo grade ≥ 3. In this analysis, the PLR was related to morbidity, while the NLR relation with mortality was more intense. Conclusion Based on the results of the study, the PLR and NLR could be used as independent predictive factors for mortality and morbidity in patients with gastric cancer.
ALL THAT GLITTERS IS NOT GOLD; DUE DILIGENCE WHEN INTERPRETING PYROPHOSPHATE CARDIAC SCANS TO AVOID MISDIAGNOSIS OF TRANSTHYRETIN CARDIAC AMYLOIDOSIS
Authors: Brian Butera, Brian Butera, Krishna Modi, Diane Klingler, James McCord, Karthikeyan Ananthasubramaniam
Journal: Journal of the American College of Cardiology (2020)
BICUSPID AORTIC VALVE, LEFT VENTRICULAR NONCOMPACTION AND MITRAL ANNULAR DISJUNCTION: A RARE COMBINATION OF VALVULAR AND ARRHYTHMOGENIC CONGENITAL ANOMALIES
Authors: Bryan E-Xin Tan, Mallory Balmer-Swain, Mohan Rao, Bipul Baibhav
Journal: Journal of the American College of Cardiology (2020)
Unmatched Level of Molecular Convergence among Deeply Divergent Complex Multicellular Fungi
Authors: Zsolt Merényi, Arun N Prasanna, Zheng Wang, Károly Kovács, Botond Hegedüs, Balázs Bálint, Balázs Papp, Jeffrey P Townsend, László G Nagy
Journal: Molecular Biology and Evolution (2020)

Convergent evolution is pervasive in nature, but it is poorly understood how various constraints and natural selection limit the diversity of evolvable phenotypes. Here, we analyze the transcriptome across fruiting body development to understand the independent evolution of complex multicellularity in the two largest clades of fungi-the Agarico- and Pezizomycotina. Despite >650 My of divergence between these clades, we find that very similar sets of genes have convergently been co-opted for complex multicellularity, followed by expansions of their gene families by duplications. Over 82% of shared multicellularity-related gene families were expanding in both clades, indicating a high prevalence of convergence also at the gene family level. This convergence is coupled with a rich inferred repertoire of multicellularity-related genes in the most recent common ancestor of the Agarico- and Pezizomycotina, consistent with the hypothesis that the coding capacity of ancestral fungal genomes might have promoted the repeated evolution of complex multicellularity. We interpret this repertoire as an indication of evolutionary predisposition of fungal ancestors for evolving complex multicellular fruiting bodies. Our work suggests that evolutionary convergence may happen not only when organisms are closely related or are under similar selection pressures, but also when ancestral genomic repertoires render certain evolutionary trajectories more likely than others, even across large phylogenetic distances.
COVID-19: consider cytokine storm syndromes and immunosuppression
Authors: Puja Mehta, Daniel F McAuley, Michael Brown, Emilie Sanchez, Rachel S Tattersall, Jessica J Manson
Journal: The Lancet (2020)

As of March 12, 2020, coronavirus disease 2019 (COVID-19) has been confirmed in 125 048 people worldwide, carrying a mortality of approximately 3·7%,1 compared with a mortality rate of less than 1% from influenza. There is an urgent need for effective treatment. Current focus has been on the development of novel therapeutics, including antivirals and vaccines. Accumulating evidence suggests that a subgroup of patients with severe COVID-19 might have a cytokine storm syndrome. We recommend identification and treatment of hyperinflammation using existing, approved therapies with proven safety profiles to address the immediate need to reduce the rising mortality.