tbuckley/cabot-search huggingface dataset:
Peeling the Onion of Brain Representations
Authors: Nikolaus Kriegeskorte, Jörn Diedrichsen
Journal: Annual Review of Neuroscience (2019)

The brain's function is to enable adaptive behavior in the world. To this end, the brain processes information about the world. The concept of representation links the information processed by the brain back to the world and enables us to understand what the brain does at a functional level. The appeal of making the connection between brain activity and what it represents has been irresistible to neuroscience, despite the fact that representational interpretations pose several challenges: We must define which aspects of brain activity matter, how the code works, and how it supports computations that contribute to adaptive behavior. It has been suggested that we might drop representational language altogether and seek to understand the brain, more simply, as a dynamical system. In this review, we argue that the concept of representation provides a useful link between dynamics and computational function and ask which aspects of brain activity should be analyzed to achieve a representational understanding. We peel the onion of brain representations in search of the layers (the aspects of brain activity) that matter to computation. The article provides an introduction to the motivation and mathematics of representational models, a critical discussion of their assumptions and limitations, and a preview of future directions in this area.
Self- and clinician-collected cervical samples for HPV screening did not differ for detection of CIN+ lesions
Authors: Joe Kabukoba
Journal: Annals of Internal Medicine (2019)

Source Citation Polman NJ, Ebisch RMF, Heideman DAM, et al. Performance of human papillomavirus testing on self-collected versus clinician-collected samples for the detection of cervical intraepithelial neoplasia of grade 2 or worse: a randomised, paired screen-positive, non-inferiority trial. Lancet Oncol. 2019;20:229-38. 30658933
Impact of time to treatment initiation (TTI) on survival of patients with newly diagnosed non-small cell lung cancer (NSCLC).
Authors: Abdel-Ghani Azzouqa, Ruqin Chen, Yanyan Lou, Sikander Ailawadhi, Rami Manochakian
Journal: Journal of Clinical Oncology (2019)

9058 Background: Lung Cancer is the leading cause of cancer related deaths in the USA. NSCLC comprises about 85% of lung cancer cases. Although timeliness of care in patients with NSCLC is considered an important aspect of quality care, there are conflicting data about its impact on clinical outcomes. The primary objective of this study is to determine if there is an association between TTI and survival in patients with NSCLC. Methods: In this retrospective study, we reviewed data from our multi-site Mayo Clinic Cancer Center registry and identified patients with newly diagnosed NSCLC from 2000 to 2016. TTI was calculated from time of diagnosis to time of first treatment (surgery, radiation therapy or systemic therapy). Analyses were performed by SAS software 9.4. Log-Rank test was used to compare survival. Cox regression multivariate model was used to evaluate the prognostic value of variables to survival. Results: 10010 patients (53% males and 47%) were reviewed. Median age at diagnosis was 70. Median TTI was 12 days for stage I, and 20 days for stage II, III and IV. We compared outcomes of patients with TTI &gt; 20 days to TTI ≤20 days. Outcomes were stratified based on age, gender, grade, and stage. Median Overall Survival (OS) was significantly better for patients with TTI ≤20 days compared to TTI &gt; 20 days (39.1 vs 28.6 months P-value &lt; 0.0001). Further stratification, based on stage, showed significantly better OS for stage I and II patients with TTI ≤20 days compared to TTI &gt; 20 days (103.4 vs. 63.9 months P-value &lt; 0.0001 and 72.3 vs. 46.8 months P-value 0.0014 respectively). OS for stage III patients with TTI ≤20 days was not significantly different from patients with TTI &gt; 20 days (30.6 vs. 28.5 months P-value 0.118). Interestingly, stage IV patients had worse OS if TTI ≤20 days compared to TTI &gt; 20 days (8.3 vs. 12.8 months P-value &lt; 0.0001). Conclusions: Our study showed an association between TTI and survival of patients with NSCLC. Shorter TTI was associated with better survival in stage I and II patients and worse survival in stage IV patients. Our study further highlights the controversy surrounding the topic of impact of timeliness of care on survival in patients with cancer, specifically NSCLC across different stages.
On using machine learning algorithms to define clinically meaningful patient subgroups
Authors: Rachel Knevel, Tom WJ Huizinga
Journal: Annals of the Rheumatic Diseases (2019)

Improved taxonomy will drive our efforts to personalise medicine over time. Ideally improved taxonomy is fueled by our detailed insight in pathogenesis leading to subgrouping syndrome’s into more homogeneous diseases. An alternative is to cluster subgroups of patients based on similar manifestations and prognosis. So, the recent publication of Spielman et al 1 as well as the correspondence on that study written by Pinal-Fernandez and Mammen2 is very timely and interesting. Spielman et al 1 identified three clinical clusters in patient with anti-Ku-positive myositis by applying hierarchical clustering analysis on both clinical and biological features.

Pinal-Fernandez and Mammen suggest that the results of Spielman’s work might be flawed as they disagree with the method of number of cluster selection. Indirectly they also challenge the idea of using (hierarchical) clustering techniques to identify clinically meaningful patient populations. Of course, we agree that improper use of analytical methods can lead to incorrect conclusions. Therefore, we applaud the ongoing discussion on how to reliably use ‘big-data techniques’ partly fueled by EULAR’s point to consider for the use of …
Effects of acute inhibition of nitric oxide synthase in the lung mechanics on a model of chronic airway inflammation in guinea pigs treated with capsaicin
Authors: I. F. L. C. Tibério, C. M. Prado, E. A. Maldonado-Leick, D. I. Kasahara, V. Arata, F. T. Fernandes, V. C. Ruiz, Mílton de Arruda Martins
Journal: American Journal of Respiratory and Critical Care Medicine (2002)
MicroRNA let-7 Downregulates Ligand-Independent Estrogen Receptor–mediated Male-Predominant Pulmonary Fibrosis
Authors: Sharon Elliot, Simone Periera-Simon, Xiaomei Xia, Paola Catanuto, Gustavo Rubio, Shahriar Shahzeidi, Fadi El Salem, Josh Shapiro, Karoline Briegel, Kenneth S. Korach, Marilyn K. Glassberg
Journal: American Journal of Respiratory and Critical Care Medicine (2019)

The relevance of hormones in idiopathic pulmonary fibrosis (IPF), a predominantly male lung disease, is unknown.
Flu: Australia sees early start to season
Authors: Nigel Hawkes
Journal: BMJ (2019)

The flu season in Australia has started early, prompting some alarming headlines. But it is too soon to say whether 2019 will truly prove a “horror season,” as some press reports have it, or simply a typical year shifted in time by several weeks.

Cases of flu-like illness reported by the GP surveillance system began rising around the end of March, about two months earlier than over the past five years. Had they continued rising at a similar rate, the peak that was reached in 2017—the highest for this period—would soon have been exceeded.

The most recent figures, covering the fortnight to the end of June, in fact show a decline, to around 11 reports of flu-like illness in every 1000 GP consultations, less than half the 2017 peak. The proportion of patients with …
Diabetes During Pregnancy Modifies the Association Between Birth Weight and Education: A Whole-of-Population Study
Authors: Lisa G. Smithers, Murthy N. Mittinty, Gustaaf Dekker, Ben W. Mol, John Lynch
Journal: Diabetes Care (2019)

Higher birth weights usually reflect better intrauterine health, nutrition, and growth. Higher birth weights are also associated with better cognitive outcomes for children (1). However, among pregnancies complicated by diabetes, being born large for gestational age may reflect different intrauterine disease processes, and it is unclear whether this carries the same benefits for education. Our objective is to examine whether diabetes during pregnancy modifies the association between birth weight and school achievement.

This whole-of-population study was conducted using deidentified administrative data that linked perinatal data to children’s school assessments. School assessments were obtained from the National Assessment Program – Literacy and Numeracy (NAPLAN), which involves assessments of reading, writing, spelling, grammar, and numeracy in grade three (age ∼8 years). Scores were dichotomized at performing above the national minimum standard or not. Children who perform at or below the standard typically require classroom learning support. Z scores of birth weight for gestational age (BWGA) were calculated using Australian norms. Diabetes was recorded as either preexisting (i.e., prior to pregnancy, including all types of diabetes) or gestational diabetes mellitus. Preexisting and gestational diabetes mellitus were combined for analyses due to small numbers.

The analysis explored whether the effect of BWGA on NAPLAN was modified by maternal diabetes. BWGA was categorized into the lowest (<20th), middle (20–79th), and highest (≥80th) quintiles. Risk ratios (RR) were calculated from log-Poisson regression models with robust errors …
Capsaicin treatment in a model of chronic airway inflammation in guinea pigs: modulation by nitric oxide synthase inhibitor
Authors: C. M. Prado, V. Arata, E. A. Maldonado-Leick, D. J. Kasahara, F. T. Fernandes, M. G. Pires, A. S. Leme, Mílton de Arruda Martins, I. F. L. C. Tiberio
Journal: American Journal of Respiratory and Critical Care Medicine (2002)
The Sciency Stuff
Authors: Kelly C. Paradis
Journal: JAMA Oncology (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 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
Hamstring rehabilitation in elite track and field athletes: applying the British Athletics Muscle Injury Classification in clinical practice
Authors: Ben Macdonald, Stephen McAleer, Shane Kelly, Robin Chakraverty, Michael Johnston, Noel Pollock
Journal: British Journal of Sports Medicine (2019)

Hamstring injuries are common in elite sports. Muscle injury classification systems aim to provide a framework for diagnosis. The British Athletics Muscle Injury Classification (BAMIC) describes an MRI classification system with clearly defined, anatomically focused classes based on the site of injury: (a) myofascial, (b) muscle-tendon junction or (c) intratendinous; and the extent of the injury, graded from 0 to 4. However, there are no clinical guidelines that link the specific diagnosis (as above) with a focused rehabilitation plan.We present an overview of the general principles of, and rationale for, exercise-based hamstring injury rehabilitation in British Athletics. We describe how British Athletics clinicians use the BAMIC to help manage elite track and field athletes with hamstring injury. Within each class of injury, we discuss four topics: clinical presentation, healing physiology, how we prescribe and progress rehabilitation and how we make the shared decision to return to full training. We recommend a structured and targeted diagnostic and rehabilitation approach to improve outcomes after hamstring injury.
Abstract 18959: Mesp1 Marked Cardiac Progenitor Cells Repair Infarcted Mouse Hearts
Authors: Yu Liu, Li Chen, Andrea A Diaz, Xueping Xu, Austin J Cooney, Bradley K McConnell, Robert J Schwartz
Journal: Circulation (2013)

Mesp1 directs multipotential cardiovascular cell fates, even though it’s transiently induced prior to the appearance of the cardiac progenitor program. Because of Mesp1’s transitory nature, Mesp1-CPC lineages were traced by following EYFP expression in murine Mesp1Cre/+; Rosa26EYFP/+ ES cells. These earliest CPCs strongly expressed cardiac mesoderm markers (Flk1, PDGFRα, Hand2), cardiac transcription factors (Nkx2-5, Tbx5, Mef2c), but not pluripotent markers (Oct4, Sox2, Nanog) nor nascent mesoderm markers (T, Fgf8). These CPCs expressed miRNAs involved in early cell fate decisions but not those in terminal cardiomyocytes. The early EYFP+ cells represented a sub-population of the Flk1+/PDGFRα+ cells, which were widely used to isolate CPCs. BMPs, canonical Wnts and Activin were required for induction and accumulation of Mesp1-CPCs, but extended BMP4 was not compatible with cardiomyocyte formation. Meantime, canonical Wnt inhibitor IWR1 was sufficient to drive CPCs toward cardiomyocyte, suggesting drastic change of extracellular cues is essential for the switch from CPC specification to differentiation. In a post-myocardium infarction mouse model, injected Mesp1-CPCs differentiated into cardiac muscle cells, vascular smooth muscle cells and endothelial cells, with evident neovascularization in both infarct and border zones. Mesp1-CPC proliferation remained evident 12 weeks after injection into the post-MI murine hearts. Injected mouse pre-contractile Mesp-1/EYFP+ CPCs improved the survivability of injured mice and restored the functional performance of infarcted hearts for at least 3 months. In summary, Mesp1-EYFP+ cells are bona fide CPCs and they integrated well in infarcted hearts and emerged de novo into terminally differentiated cardiac myocytes, smooth muscle and vascular endothelial cells.
Smoking history and PD-1/PDL-1 pathway blockade: Predicting response to treatment in metastatic cancer.
Authors: Caitlin Marie Sullivan, Jonathan Lu, John Ross Kucharczyk, Diana Vesselinovitch, Neharika Khurana, Madhav KC, Marc Ryan Matrana
Journal: Journal of Clinical Oncology (2019)

95 Background: Identifying patients who will benefit from immune-checkpoint inhibitor therapy is a challenge as proven predicative indicators remain to be elucidated. High tumor mutational burden (TMB) represents a possible biomarker for response to PD1 blockade such as in nivolumab or pembrolizumab. Genomic analyses have shown that patients with heavy smoking history are more likely to have high TMB. However smoking status alone has not been examined independently in relation to treatment response. We sought to determine whether a relationship existed between smoking history and response to treatment in metastatic non-small cell lung cancer (NSCLC), metastatic renal cell carcinoma (mRCC) and metastatic melanoma (mMelanoma). Methods: A retrospective analysis was conducted of Ochsner Health System patients with mRCC, mMelanoma, and NSCLC receiving a minimum of two cycles of nivolumab or pembrolizumab between 12/2014 and 01/2018. Pre- and post-treatment target lesions were analyzed using RECIST criteria to calculate best response to treatment. Patient demographic information was gathered including age, sex, smoking history, and performance status pre and post treatment. Kaplan-Meier method was used to estimate progression free survival (PFS) and overall survival (OS) outcomes. Results: Heavy smokers (&gt;10 pack-years) had a higher response to immunotherapy than light (&lt; 10 years) and never smokers (p = 0.0500). Heavy smokers with NSCLC treated with immuno-therapy also had significantly improved OS compared to light smokers with NSCLC (p=0.003). mRCC immuno-therapy patients with heavy smoking history showed increased PFS compared to light/never smokers (p=0.026). Conclusions: In summary, in response to PD-1 blockade heavy smokers showed improved survival compared to light and never smokers suggesting smoking history may represent a potential predictor of treatment response to PD-1 inhibitor therapy.[Table: see text]
Incidental Finding of Benign Trichilemmal Cysts on 99mTc-Octreotide Scan
Authors: Isa Neshandar Asli, Ghazal Norouzi
Journal: Clinical Nuclear Medicine (2019)

Abstract A 63-year-old woman with neuroendocrine carcinoma of the colon was referred to our department for staging with 99m Tc-octreotide scan. Two focal, highly intense, superficial lesions were detected in patient's scalp and paralumbar region, medial to the right kidney. Pathology correlation was recommended, revealing them both to be benign trichilemmal cysts. This unexpected finding strengthens the hypothesis of Merkel cell carcinoma and trichilemmal cysts originating from pluripotent stem cells of adnexal epithelium, making a neuroendocrine differentiation for the latter plausible.
Annals Graphic Medicine - An Abbreviated History of My Medical Training
Authors: Jesse Powell
Journal: Annals of Internal Medicine (2019)

Web Exclusives16 July 2019Annals Graphic Medicine - An Abbreviated History of My Medical TrainingFREEJesse Powell, MDJesse Powell, MDProvidence Portland Medical Center, Portland, Oregon (J.P.)Search for more papers by this authorAuthor, Article, and Disclosure Informationhttps://doi.org/10.7326/G18-0014 SectionsAboutVisual AbstractPDF ToolsAdd to favoritesDownload CitationsTrack CitationsPermissions ShareFacebookTwitterLinkedInRedditEmail Download figure Download PowerPoint Download figure Download PowerPoint Download figure Download PowerPoint Comments0 CommentsSign In to Submit A Comment Daniel NorfleetPMG Gateway Internal Medicine, Portland, OR10 July 2019 Stellar Cartoon Contribution! Jesse!--This is great! Thanks for sharing your journey in such a fun format! :) Author, Article, and Disclosure InformationAffiliations: Providence Portland Medical Center, Portland, Oregon (J.P.)Disclosures: The author has disclosed no conflicts of interest. The form can be viewed at www.acponline.org/authors/icmje/ConflictOfInterestForms.do?msNum=G18-0014.Author/Illustrator Information: Jesse Powell, MD, is a member of the teaching faculty at Providence Portland Medical Center Internal Medicine residency program in Portland, Oregon (e-mail, jesse.[email protected]org).This article was published at Annals.org on 9 July 2019. PreviousarticleNextarticle Advertisement FiguresReferencesRelatedDetails Metrics 16 July 2019Volume 171, Issue 2Page: W5-W8KeywordsConflicts of interestDisclosureHealth careHistory of medicineResidency ePublished: 16 July 2019 Issue Published: 16 July 2019 Copyright & PermissionsCopyright © 2019 by American College of Physicians. All Rights Reserved.PDF downloadLoading ...
Abstract 19603: Bone Morphogenetic Protein 6 and Oxidized Low-density Lipoprotein Synergistically Recruit Osteogenic Differentiation in Endothelial Cells
Authors: Lai-Ming Yung, Gonzalo Sánchez-Duffhues, Peter ten Dijke, Paul B Yu
Journal: Circulation (2015)

Introduction: Vascular calcification contributes to mortality and morbidity in atherosclerosis, chronic kidney disease, and diabetes. Vascular calcific lesions contain osteoblast-like and chondroblast-like cells, suggesting a process of endochondral or membranous ossification thought to result from the phenotypic plasticity of vascular cells. Bone morphogenetic protein (BMP) signaling potentiates atherosclerotic calcification, whereas BMP inhibition attenuates vascular inflammation and calcification in atherogenic mice. Hypothesis: We hypothesized endothelial cells may undergo osteogenic differentiation in response to BMP signaling and pro-atherogenic stimuli. Methods and Results: Among various BMP ligands tested, BMP6 and BMP9 elicited the most potent signaling in bovine aortic endothelial cells, however, only BMP6 induced osteogenic differentiation. BMP6 and oxLDL independently and synergistically induced osteogenic differentiation and mineralization, in a manner consistent with endothelial-to-mesenchymal transition. Treatment of endothelial cells with BMP6 or oxidized low-density lipoprotein (oxLDL) individually induced osteogenic and chondrogenic transcription factors Runx2 and Msx2, whereas treatment with BMP6 and oxLDL synergistically up-regulated Osterix and Osteopontin. Production of H2O2 was necessary for oxLDL-induced regulation of Runx2, Msx2, and Osterix in BAEC, and H2O2 was sufficient by itself to up-regulate these genes. Mineralization of endothelial cells in response to BMP6 or oxLDL was abrogated by scavenging reactive oxygen species or inhibiting BMP type I receptor kinases. Similar synergistic effects of BMP and oxLDL upon osteogenic and chondrogenic transcription and phenotypic plasticity in human aortic endothelial cells were observed. Conclusion: These findings provide a potential mechanism for the observed interactions of BMP signaling, oxidative stress, and inflammation in recruiting vascular calcification associated with atherosclerosis.
Propionibacterium acnes Pacemaker Endocarditis in a Patient With a Redundant Loop of the Ventricular Lead
Authors: Luis Gorospe, Javier Miguelena-Hycka, Miren Martín-García, Odile Ajuria-Illarramendi, Nicolás Alejandro Almeida-Aróstegui
Journal: Clinical Nuclear Medicine (2019)

Abstract A 59-year-old man with a pacemaker who was admitted for evaluation of fever was found to have a redundant loop of the ventricular lead and a vegetation attached to it. An FDG PET/CT revealed a focus of FDG uptake at the ventricular lead loop. Surgical extraction of the pacemaker device confirmed a Propionibacterium acnes pacemaker endocarditis. We hypothesize that the redundant loop of the ventricular lead induced a chronic mechanical stress both to the tricuspid valve and to the lead itself, facilitating the bacterial colonization of the lead.
Mutational landscape of patients with acute promyelocytic leukemia at diagnosis and relapse
Authors: Licia Iaccarino, Tiziana Ottone, Valentina Alfonso, Laura Cicconi, Mariadomenica Divona, Serena Lavorgna, Serena Travaglini, Aleandra Ferrantini, Giulia Falconi, Constance Baer, Monica Usai, Fabio Forghieri, Adriano Venditti, Maria Ilaria Del Principe, William Arcese, Maria Teresa Voso, Torsten Haferlach, Francesco Lo‐Coco
Journal: American Journal of Hematology (2019)

Abstract Despite the high probability of cure of patients with acute promyelocytic leukemia (APL), mechanisms of relapse are still largely unclear. Mutational profiling at diagnosis and/or relapse may help to identify APL patients needing frequent molecular monitoring and early treatment intervention. Using an NGS approach including a 31 myeloid gene‐panel, we tested BM samples of 44 APLs at the time of diagnosis, and of 31 at relapse. Mutations in PML and RARA genes were studied using a customized‐NGS‐RNA panel. Patients relapsing after ATRA‐chemotherapy rarely had additional mutations ( P = .009). In patients relapsing after ATRA/ATO, the PML gene was a preferential mutation target. We then evaluated the predictive value of mutations at APL diagnosis. A median of two mutations was detectable in 9/11 patients who later relapsed, vs one mutation in 21/33 patients who remained in CCR ( P = .0032). This corresponded to a significantly lower risk of relapse in patients with one or less mutations (HR 0.046; 95% CI 0.011‐0.197; P &lt; .0001). NGS‐analysis at the time of APL diagnosis may inform treatment decisions, including alternative treatments for cases with an unfavorable mutation profile.