tbuckley/cabot-search huggingface dataset:
Will chairing societies and being on committees strengthen my portfolio when applying for jobs?
Authors: Sophia Bourne
Journal: BMJ (2017)

Dear Sophia

Will chairing societies and being on committees strengthen my portfolio when applying for jobs?

Adnan D’Cunha Kamath, third year medical student, University of Bristol

Although your studies must be your central focus, medical school provides many opportunities to pursue extracurricular activities. These offer respite from the hard slog of preparation for exams, and they can broaden your development as a professional. Medical practice has changed over the …
Welcome to the tea party
Authors: Prizzi Zarsadias, Oliver Ellis
Journal: BMJ (2010)

> “‘I want a clean cup,’ interrupted the Hatter: ‘let’s all move one place on.’
> 
> He moved on as he spoke, and the Dormouse followed him: the March Hare moved into the Dormouse’s place, and Alice rather unwillingly took the place of the March Hare.”

The time of year for medical students to move one place on in their studies has come around yet again. And, as every year, we welcome the new Alices in the first year and wave goodbye to the Mad Hatters who are graduating from the medical school tea party and heading straight for the realities of being a junior doctor.

A brand new …
FDA issues black box warnings on common insomnia drugs
Authors: Owen Dyer
Journal: BMJ (2019)

The US Food and Drug Administration (FDA) is giving black box warnings—its strongest—to the common sleep drugs eszopiclone (Lunesta), zaleplon (Sonata), and zolpidem (Ambien, Ambien CR, Edluar, Intermezzo, and Zolpimist).

It said that it had found 66 examples of patients who took one of these nonbenzodiazepine hypnotics for insomnia and suffered serious injury or death from an activity they performed unconsciously.

The “complex sleep behaviours” exhibited by patients included turning on ovens, driving cars, and shooting themselves with guns.

The FDA has reports of 46 serious injuries from causes as varied as …
Reference equation for the incremental shuttle walk test in Portuguese children and adolescents
Authors: T. Pinho, C. Jácome, J. Pinto, A. Marques
Journal: Pulmonology (2019)

The incremental shuttle walk test (ISWT) is one of the most widely used field tests to assess cardiorespiratory fitness in clinical and research settings. Reference equations to predict ISWT distance in different populations and age cohorts have been established. However, an equation for the Portuguese pediatric population is not available. This study aimed to develop a reference equation for predicting ISWT in Portuguese children and adolescents. Healthy children and adolescents aged between 5 and 17 years old were recruited. Sociodemographic (sex, age), anthropometric (height, weight) and physical activity (Physical Activity Index) data were collected. Lung function was assessed through spirometry and quadriceps muscular strength through hand-held dynamometry. The ISWT was performed twice. A reference equation was established with a multiple linear regression. 130 (60 male; 13.66 ± 2.61y) participants with normal lung function (forced expiratory volume in one second 102.73 ± 15.09% predicted), body mass index (BMI) (20.27 ± 3.59 kg/m2) and quadriceps muscular strength (19.75 ± 6.84 kgf), completed the assessment. 50.8% (n = 66) of the participants were moderately active. Participants walked on average 1165.08 ± 327.19 m in the ISWT. Sex, age and BMI were independent contributors to the ISWT, explaining 54% of its variability (p < 0.001). The derived reference equation was: ISWT = 342.06 + (283.07 × sex) + (83.61 × age) − (22.22 × BMI), with female = 0 and male = 1. Sex, age and BMI were found to be contributors to the ISWT predictive equation for pediatric population, providing a simple reference to assess their cardiorespiratory fitness.
Abstract P3-11-09: Not presented
Authors: RJ Bownes, A Turbull, C Martínez-Pérez, AH Sims, O Oikonomidou
Journal: Cancer Research (2019)

Abstract This abstract was not presented at the conference. Citation Format: Bownes RJ, Turbull A, Martínez-Pérez C, Sims AH, Oikonomidou O. Not presented [abstract]. In: Proceedings of the 2018 San Antonio Breast Cancer Symposium; 2018 Dec 4-8; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2019;79(4 Suppl):Abstract nr P3-11-09.
The stigma of taking a year out from medical school
Authors: Bethan Conrad
Journal: BMJ (2014)

I have never felt as nervous as I did when I requested my year out from medical school. I’d never met anyone who had taken time out, and I wasn’t sure it was possible. You are supposed to put your head down and get on with it, aren’t you?

My first reason for taking time out after my second year of medical school was financial hardship. I had a job throughout the first two years of medical school, but as the third year approached I knew the spare time to earn some cash would get shorter, and my student loan would get bigger. I had overdrafts, no savings, and did not want part time work to hinder my clinical studies. I thought that a year out would enable me to earn and save enough to get through the final three years without working or building up any more debt.

But there was another reason—burnout. By the end of my second …
Abstract P1-19-06: The prognostic value of HER2, YKL-40 and IL-6 in cerebrospinal fluid in trastuzumab naïve breast cancer patients diagnosed with meningeal carcinomatosis
Authors: M Ryberg, JS Johansen, TL Grantzau, C Dehlendorff, DL Nielsen
Journal: Cancer Research (2019)

Abstract Background With the improvements in treatment of patients with metastatic HER2-positive breast cancer (BC) the development of CNS metastases has become a major limitation of life expectancy and quality of life for many patients. Meningeal carcinomatosis represents approximately 10-20% of CNS metastases. The prognosis of meningeal carcinomatosis remains extremely poor. In the present study, we analysed the prognostic value of HER2, YKL-40 and IL-6 in cerebrospinal fluid (CSF) of meningeal carcinomatosis. Methods Between June 1985 and August 1992 sixty-nine CSF samples were collected at Herlev Hospital from trastuzumab naïve BC patients suspected of meningeal carcinomatosis. The cohort was composed of BC patients from two previous studies. Meningeal carcinomatosis was confirmed by tumour cells in CSF (or autopsy/scans). The samples were centrifuged, frozen and kept at -80oC. The concentrations of YKL-40, IL-6 and HER2 in CSF were measured by commercial ELISA (Quidel and R&amp;D) or Luminez (HER2 in second study). Overall survival in meningeal carcinomatosis was analysed with Kaplan-Meier curves and log rank tests using the median CSF value of HER2, YKL40 and IL-6 as cut off. Results 20 patients (29%) had meningeal carcinomatosis (18 patients had tumour cells in CFS, one was diagnosed by autopsy and one by CT scan; 13 of these patients participated in the first study and 7 in the second).10 patients had concomitant brain metastasis. The median survival was 35 days (4-305 days). The median [IQR] CSF concentration of YKL-40 was 284 ng/ml (187-597), IL-6 was15.9 pg/ml (6.5-51.0) and HER2 was 1.5 (0.36-8.70) in the patients with meningeal carcinomatosis. The survival was significantly shorter in patients with high levels of YKL-40 (p=0.03) and IL-6 (p=&amp;lt;0.01). The CSF HER2 level (p=0.51) or presence of brain metastasis (p=0.77) were not associated with survival. Conclusion In this cohort high levels of YKL-40 and IL-6 in CSF were associated with short survival in patients with BC and meningeal carcinomatosis. This was not found for HER2 in CSF or concomitant brain metastasis. Citation Format: Ryberg M, Johansen JS, Grantzau TL, Dehlendorff C, Nielsen DL. The prognostic value of HER2, YKL-40 and IL-6 in cerebrospinal fluid in trastuzumab naïve breast cancer patients diagnosed with meningeal carcinomatosis [abstract]. In: Proceedings of the 2018 San Antonio Breast Cancer Symposium; 2018 Dec 4-8; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2019;79(4 Suppl):Abstract nr P1-19-06.
Response to Open Peer Commentaries: When Is It Ethical for Physician-Investigators to Seek Consent From Their Own Patients?
Authors: Stephanie R. Morain, Steven Joffe, Emily A. Largent
Journal: The American Journal of Bioethics (2019)

"Response to Open Peer Commentaries: When Is It Ethical for Physician-Investigators to Seek Consent From Their Own Patients?." The American Journal of Bioethics, 19(5), pp. W3–W4
Abstract PD6-05: Withdrawn
Authors: RD Kehm, K-A Phillips, MB Daly, IL Andrulis, Y Liao, X Ma, N Zeinomar, RJ MacInnis, GS Dite, EM John, SS Buys, RL Milne, JL Hopper, MB Terry
Journal: Cancer Research (2019)

Abstract This abstract was withdrawn by the authors. Citation Format: Kehm RD, Phillips K-A, Daly MB, Andrulis IL, Liao Y, Ma X, Zeinomar N, MacInnis RJ, Dite GS, John EM, Buys SS, Milne RL, Hopper JL, Terry MB. Withdrawn [abstract]. In: Proceedings of the 2018 San Antonio Breast Cancer Symposium; 2018 Dec 4-8; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2019;79(4 Suppl):Abstract nr PD6-05.
His Corrective Pacing or Biventricular Pacing for Cardiac Resynchronization in Heart Failure
Authors: Gaurav A. Upadhyay, Pugazhendhi Vijayaraman, Hemal M. Nayak, Nishant Verma, Gopi Dandamudi, Parikshit S. Sharma, Moeen Saleem, John Mandrola, Davide Genovese, Roderick Tung
Journal: Journal of the American College of Cardiology (2019)
Abstract PD1-02: Withdrawn
Authors: J Cortes, M Martin, S Pernas, P Gomez Pardo, S Lopez-Tarruella, M Gil-Martin, L Manso, E Ciruelos, JA Perez-Fidalgo, C Hernando, FO Ademuyiwa, K Weilbaecher, I Mayer, TJ Pluard, M Martinez Garcia, L Vahdat, A Wach, D Barker, B Romagnoli, PA Kaufman
Journal: Cancer Research (2019)

Abstract This abstract was withdrawn by the authors. Citation Format: Cortes J, Martin M, Pernas S, Gomez Pardo P, Lopez-Tarruella S, Gil-Martin M, Manso L, Ciruelos E, Perez-Fidalgo JA, Hernando C, Ademuyiwa FO, Weilbaecher K, Mayer I, Pluard TJ, Martinez Garcia M, Vahdat L, Wach A, Barker D, Romagnoli B, Kaufman PA. Withdrawn [abstract]. In: Proceedings of the 2018 San Antonio Breast Cancer Symposium; 2018 Dec 4-8; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2019;79(4 Suppl):Abstract nr PD1-02.
Airway inflammation in COPD: progress to precision medicine
Authors: Christopher Brightling, Neil Greening
Journal: European Respiratory Journal (2019)

Chronic obstructive pulmonary disease (COPD) is a significant cause of morbidity and mortality worldwide, and its prevalence is increasing. Airway inflammation is a consistent feature of COPD and is implicated in the pathogenesis and progression of COPD, but anti-inflammatory therapy is not first-line treatment. The inflammation has many guises and phenotyping this heterogeneity has revealed different patterns. Neutrophil-associated COPD with activation of the inflammasome, T1 and T17 immunity is the most common phenotype with eosinophil-associated T2-mediated immunity in a minority and autoimmunity observed in more severe disease. Biomarkers have enabled targeted anti-inflammatory strategies and revealed that corticosteroids are most effective in those with evidence of eosinophilic inflammation, whereas, in contrast to severe asthma, response to anti-interleukin-5 biologicals in COPD has been disappointing, with smaller benefits for the same intensity of eosinophilic inflammation questioning its role in COPD. Biological therapies beyond T2-mediated inflammation have not demonstrated benefit and in some cases increased risk of infection, suggesting that neutrophilic inflammation and inflammasome activation might be largely driven by bacterial colonisation and dysbiosis. Herein we describe current and future biomarker approaches to assess inflammation in COPD and how this might reveal tractable approaches to precision medicine and unmask important host–environment interactions leading to airway inflammation.
Free apps for preclinical medical students
Authors: Tom Lewis
Journal: BMJ (2012)

So you have arrived at medical school, signed up to all the societies, bought all your textbooks, and realised that you have to study some science before you get to touch a patient. Some free apps are available that will help you manage your documents and note taking in your preclinical years.

Evernote is the best free note taking app, and great for keeping track of preclinical medical notes and more. It is available on a wide range of devices, and allows you to “capture anything.” You can make and save notes while you’re on the go and add a variety of media, including text, photos, attachments, and audio …
Association of Treatment With 5α-Reductase Inhibitors With Time to Diagnosis and Mortality in Prostate Cancer
Authors: Reith R. Sarkar, J. Kellog Parsons, Alex K. Bryant, Stephen T. Ryan, Andrew K. Kader, Rana R. McKay, Anthony V. D’Amico, Paul L. Nguyen, Benjamin J. Hulley, John P. Einck, Arno J. Mundt, Christopher J. Kane, James D. Murphy, Brent S. Rose
Journal: JAMA Internal Medicine (2019)

5α-Reductase inhibitors (5-ARIs), commonly used to treat benign prostatic hyperplasia, reduce serum prostate-specific antigen (PSA) concentrations by 50%. The association of 5-ARIs with detection of prostate cancer in a PSA-screened population remains unclear.To test the hypothesis that prediagnostic 5-ARI use is associated with a delayed diagnosis, more advanced disease at diagnosis, and higher risk of prostate cancer-specific mortality and all-cause mortality than use of other or no PSA-decreasing drugs.This population-based cohort study linked the Veterans Affairs Informatics and Computing Infrastructure with the National Death Index to obtain patient records for 80 875 men with American Joint Committee on Cancer stage I-IV prostate cancer diagnosed from January 1, 2001, to December 31, 2015. Patients were followed up until death or December 31, 2017. Data analysis was performed from March 2018 to May 2018.Prediagnostic 5-ARI use.The primary outcome was prostate cancer-specific mortality (PCSM). Secondary outcomes included time from first elevated PSA (defined as PSA≥4 ng/mL) to diagnostic prostate biopsy, cancer grade and stage at time of diagnosis, and all-cause mortality (ACM). Prostate-specific antigen levels for 5-ARI users were adjusted by doubling the value, consistent with previous clinical trials.Median (interquartile range [IQR]) age at diagnosis was 66 (61-72) years; median [IQR] follow-up was 5.90 (3.50-8.80) years. Median time from first adjusted elevated PSA to diagnosis was significantly greater for 5-ARI users than 5-ARI nonusers (3.60 [95% CI, 1.79-6.09] years vs 1.40 [95% CI, 0.38-3.27] years; P < .001) among patients with known prostate biopsy date. Median adjusted PSA at time of biopsy was significantly higher for 5-ARI users than 5-ARI non-users (13.5 ng/mL vs 6.4 ng/mL; P < .001). Patients treated with 5-ARI were more likely to have Gleason grade 8 or higher (25.2% vs 17.0%; P < .001), clinical stage T3 or higher (4.7% vs 2.9%; P < .001), node-positive (3.0% vs 1.7%; P < .001), and metastatic (6.7% vs 2.9%; P < .001) disease than 5-ARI nonusers. In a multivariable regression, patients who took 5-ARI had higher prostate cancer-specific (subdistribution hazard ratio [SHR], 1.39; 95% CI, 1.27-1.52; P < .001) and all-cause (HR, 1.10; 95% CI, 1.05-1.15; P < .001) mortality.Results of this study demonstrate that prediagnostic use of 5-ARIs was associated with delayed diagnosis and worse cancer-specific outcomes in men with prostate cancer. These data highlight a continued need to raise awareness of 5-ARI-induced PSA suppression, establish clear guidelines for early prostate cancer detection, and motivate systems-based practices to facilitate optimal care for men who use 5-ARIs.
Abstract PD6-11: Withdrawn
Authors: DP Cronin-Fenton, AM Falstie-Jensen, A Kjaersgaard, J Dupont Jensen, EL Lorenzen, KV Reinertsen, OM Dekkers, M Ewertz
Journal: Cancer Research (2019)

Abstract This abstract was withdrawn by the authors. Citation Format: Cronin-Fenton DP, Falstie-Jensen AM, Kjaersgaard A, Dupont Jensen J, Lorenzen EL, Reinertsen KV, Dekkers OM, Ewertz M. Withdrawn [abstract]. In: Proceedings of the 2018 San Antonio Breast Cancer Symposium; 2018 Dec 4-8; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2019;79(4 Suppl):Abstract nr PD6-11.
VetTag: improving automated veterinary diagnosis coding via large-scale language modeling
Authors: Yuhui Zhang, Allen Nie, Ashley Zehnder, Rodney L. Page, James Zou
Journal: npj Digital Medicine (2019)

Unlike human medical records, most of the veterinary records are free text without standard diagnosis coding. The lack of systematic coding is a major barrier to the growing interest in leveraging veterinary records for public health and translational research. Recent machine learning effort is limited to predicting 42 top-level diagnosis categories from veterinary notes. Here we develop a large-scale algorithm to automatically predict all 4577 standard veterinary diagnosis codes from free text. We train our algorithm on a curated dataset of over 100 K expert labeled veterinary notes and over one million unlabeled notes. Our algorithm is based on the adapted Transformer architecture and we demonstrate that large-scale language modeling on the unlabeled notes via pretraining and as an auxiliary objective during supervised learning greatly improves performance. We systematically evaluate the performance of the model and several baselines in challenging settings where algorithms trained on one hospital are evaluated in a different hospital with substantial domain shift. In addition, we show that hierarchical training can address severe data imbalances for fine-grained diagnosis with a few training cases, and we provide interpretation for what is learned by the deep network. Our algorithm addresses an important challenge in veterinary medicine, and our model and experiments add insights into the power of unsupervised learning for clinical natural language processing.
Prediabetes and Risk for Cardiac Death Among Patients With Coronary Artery Disease: The ARTEMIS Study
Authors: Antti M. Kiviniemi, E. Samuli Lepojärvi, Mikko P. Tulppo, Olli-Pekka Piira, Tuomas V. Kenttä, Juha S. Perkiömäki, Olavi H. Ukkola, Robert J. Myerburg, M. Juhani Junttila, Heikki V. Huikuri
Journal: Diabetes Care (2019)

OBJECTIVE To compare cardiac mortality in patients with CAD and prediabetes with that in CAD patients with normal glycemic status and type 2 diabetes. RESEARCH DESIGN AND METHODS The Innovation to Reduce Cardiovascular Complications of Diabetes at the Intersection (ARTEMIS) study included patients with CAD after revascularization (79%), optimal medical therapy, or both. Patients had type 2 diabetes (n = 834), impaired glucose tolerance (IGT; n = 314), impaired fasting glucose (IFG; n = 103), or normal glycemic status (n = 697) as defined on the basis of the results of an oral glucose tolerance test. The primary end point was cardiac death. Major adverse cardiac event (MACE: cardiac death, heart failure, or acute coronary syndrome) and all-cause mortality were secondary end points. RESULTS During a mean ± SD follow-up of 6.3 ± 1.6 years, 101 cardiac deaths, 385 MACEs, and 208 deaths occurred. Patients with IGT tended to have 49% lower adjusted risk for cardiac death (P = 0.069), 32% lower adjusted risk for all-cause mortality (P = 0.076), and 36% lower adjusted risk for MACE (P = 0.011) than patients with type 2 diabetes. The patients with IFG had 82% lower adjusted risk for all-cause mortality (P = 0.015) than the patients with type 2 diabetes, whereas risks for cardiac death and MACE did not differ significantly between the two groups. The adjusted risks for cardiac death, MACE, and all-cause mortality among patients with IGT and IFG did not significantly differ from those risks among patients with normal glycemic status. CONCLUSIONS Cardiac mortality or incidence of MACE in patients with CAD with prediabetes (i.e., IGT or IFG after revascularization, optimal medical therapy, or both) does not differ from those values in patients with normal glycemic status.
Abstract MS1-3: Artificial intelligence to optimize the accuracy and predictiveness of breast cancer pathology
Authors: A Beck
Journal: Cancer Research (2019)

Abstract Pathologic analysis of patient tissue specimens plays a central role in breast oncology. Recent advances in artificial intelligence and computer vision offer tremendous potential for discovering new pathologic mechanisms of cancer treatment response and identifying new diagnostics for matching patients and therapies. We will discuss these new advances and their potential for accelerating progress in the diagnosis and treatment of breast cancer. Citation Format: Beck A. Artificial intelligence to optimize the accuracy and predictiveness of breast cancer pathology [abstract]. In: Proceedings of the 2018 San Antonio Breast Cancer Symposium; 2018 Dec 4-8; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2019;79(4 Suppl):Abstract nr MS1-3.
Abstract OT1-01-01: The NEO-LET-EXE-trial: An intra-patient cross-over trial to explore the "lack of cross-resistance" between steroidal and non-steroidal aromatase inhibitors
Authors: N Bahrami, T Sauer, M Loeng, B Gravdehaug, SS Engebretsen, B Aljabri, V Bemanian, JC Lindstrøm, T Lüders, VN Kristensen, J Geisler
Journal: Cancer Research (2019)

Abstract Background. The aromatase inhibitor letrozole and the aromatase inactivator exemestane currently belong to the most widely used antihormonal drugs for breast cancer worldwide. Both compounds are strongly suppressing estradiol levels in postmenopausal patients with breast cancer. However, in the metastatic setting, these drugs may be used after another, causing new responses in selected patients following switching to the alternative drug after progressing on the first choice. This well-known “lack of cross resistance” has been recognized for some time and is documented by several trials. However, the precise explanation for this clinical observation is still unknown. The solution may potentially lead us to a novel strategy to treat hormone-sensitive breast cancer. Trial design. NEO-LET-EXE is a neoadjuvant, randomized, open-label, intra-patient cross-over trial . Eligibility criteria. Postmenopausal patients suffering from estrogen receptor (ER) positive (&amp;gt;50%), HER-2 negative, locally advanced breast cancer, suitable for neoadjuvant/presurgical antihormonal therapy, may be enrolled. Age: 18+ (no upper limit). Specific aims. To explain the phenomenon of a lack of cross-resistance between steroidal and non-steroidal aromatase inhibitors in vivo. Sequential tumor biopsies and blood samples, obtained at baseline and following 2 months of therapy with each drug given in sequence, will be used to perform a comprehensive exploration of the consequences of each drug therapy. The influence on plasma and tissue steroids (estrogens, androgens, etc.) will be compared. In addition, whole genome sequencing, whole exome sequencing, epigenetics, proteomics and plasma analysis (cytokines, tumor DNA fragments, etc.) will be performed. Statistical methods. Data will be analyzed using mixed effects models. Present accrural and target accrural. 49 out of planned 100 patients have been enrolled so far. The last patient is expected to enter the trial in Q4 2019. Citation Format: Bahrami N, Sauer T, Loeng M, Gravdehaug B, Engebretsen SS, Aljabri B, Bemanian V, Lindstrøm JC, Lüders T, Kristensen VN, Geisler J. The NEO-LET-EXE-trial: An intra-patient cross-over trial to explore the "lack of cross-resistance" between steroidal and non-steroidal aromatase inhibitors [abstract]. In: Proceedings of the 2018 San Antonio Breast Cancer Symposium; 2018 Dec 4-8; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2019;79(4 Suppl):Abstract nr OT1-01-01.