tbuckley/cabot-search huggingface dataset:
Genetic diversity and delineation of Salmonella Agona outbreak strains by next generation sequencing, Bavaria, Germany, 1993 to 2018
Authors: Alexandra Dangel, Anja Berger, Ute Messelhäußer, Regina Konrad, Stefan Hörmansdorfer, Nikolaus Ackermann, Andreas Sing
Journal: Eurosurveillance (2019)

Background In 2017, a food-borne Salmonella Agona outbreak caused by infant milk products from a French supplier occurred in Europe. Simultaneously, S. Agona was detected in animal feed samples in Bavaria. Aim Using next generation sequencing (NGS) and three data analysis methods, this study’s objectives were to verify clonality of the Bavarian feed strains, rule out their connection to the outbreak, explore the genetic diversity of Bavarian S. Agona isolates from 1993 to 2018 and compare the analysis approaches employed, for practicality and ability to delineate outbreaks caused by the genetically monomorphic Agona serovar. Methods In this observational retrospective study, three 2017 Bavarian feed isolates were compared to a French outbreak isolate and 48 S. Agona isolates from our strain collections. The later included human, food, feed, veterinary and environmental isolates, of which 28 were epidemiologically outbreak related. All isolates were subjected to NGS and analysed by: (i) a publicly available species-specific core genome multilocus sequence typing (cgMLST) scheme, (ii) single nucleotide polymorphism phylogeny and (iii) an in-house serovar-specific cgMLST scheme. Using additional international S. Agona outbreak NGS data, the cluster resolution capacity of the two cgMLST schemes was assessed. Results We could prove clonality of the feed isolates and exclude their relation to the French outbreak. All approaches confirmed former Bavarian epidemiological clusters. Conclusion Even for S. Agona, species-level cgMLST can produce reasonable resolution, being standardisable by public health laboratories. For single samples or homogeneous sample sets, higher resolution by serovar-specific cgMLST or SNP genotyping can facilitate outbreak investigations.
Three steps closer to a polio free Africa
Authors: Andrew Moscrop
Journal: BMJ (2001)

Last month witnessed the final effort in a massive three stage polio vaccination campaign in war torn central Africa. Tens of thousands of door to door teams will complete the last of three synchronised rounds of national immunisation days in Angola, Congo, the Democratic Republic of the Congo (formerly Zaire), and Gabon.

The campaign has been coordinated by the Global Polio Eradication Initiative, a collaborative group comprising members of WHO, Unicef, Rotary International, and …
Make medical education more transparent
Authors: David Jason Holt
Journal: BMJ (2006)

Why is it that important information-important enough to appear on an examination-is often withheld from medical students? As a student having just completed the two year didactic component of medical education, I have accrued countless examples of this absurdity.

At the end of the year, our practical skills in medicine are assessed by an objective structured clinical examination, an observed examination of clinical skills. We have to interview a patient, ask all the relevant questions about the presenting problem, and perform a physical exam. Examiners have a list and check off the questions as they are asked, and the physical exam manoeuvres as they are performed. The examination is worth half of our mark for the entire year, but lasts for only two and a half hours. These precious checklists, the criteria by which we are evaluated, are heavily guarded, tightly held secrets. If it were up to the faculty that runs the course, we would never see a checklist throughout all of our time at medical school. How useful would the lists be, however, if they were integrated into our lessons, and the importance of their questions and physical exam manoeuvres were emphasised? To me, the lack of transparency is an injustice and a disservice to our education.

Understanding medical students can help shed some light on a possible reason behind this practice. Applicants to medical school are already intelligent, hardworking, resourceful, and well rounded individuals. The application process further selects from these already highly competent people using various criteria, such as scores in the medical college admission test; essays; …
Cost of AIDS drug slashed in Brazil
Authors: Jonas Souza
Journal: BMJ (2001)

The Swiss pharmaceutical giant Hoffman-La Roche has agreed to reduce the price of its AIDS drug, Viracept, by 40% after pressure from the Brazilian government. The agreement comes after the government said that it would declare AIDS a “national emergency,” triggering a law that would allow domestic production of cheaper, generic versions of drugs when the government judges that a manufacturer's prices are …
<i>Notes from the Field:</i> Outbreak of Multidrug-Resistant <i>Shigella sonnei</i> Infections in a Retirement Community — Vermont, October–November 2018
Authors: Jonathan Strysko, Veronica Fialkowski, Zachary Marsh, Ashutosh Wadhwa, Jennifer Collins, Radhika Gharpure, Patsy Kelso, Cindy R. Friedman, Kathleen E. Fullerton
Journal: MMWR Morbidity and Mortality Weekly Report (2019)
Labyrinth: A Search for the Hidden Meaning of Science
Authors: Lok Bin Yap
Journal: BMJ (2000)

In many ways nature is like the shape changing mythical figure Proteus. It will avoid revealing secrets unless interrogated extensively. This book explores the history of scientific study, drawing on the experiences of scientists and philosophers from the 17th to the 20th centuries.

The author begins the book with a doctor in the early 1600s. William Gilbert studied magnetic rocks and conjectured about the earth's rotation. This leads on to Francis …
Get the most out of your PRN orders
Authors: Teresa Pun
Journal: BMJ (2008)

PRN (also known as “pro re nata” also known “as needed”) orders, I think, were designed to let house officers sleep through the night—not that there's anything wrong with that. Common PRN orders include paracetamol (acetaminophen) for pain, lorazepam for insomnia, and docusate sodium for constipation. One resident also included a variety of routes of administration in his PRN orders to avoid being woken up by the nurse at 0300 because she couldn't give the patient morphine by mouth and needed him to OK an intravenous order for morphine.



A problem with the PRN order is that once it's entered, it tends to go unnoticed by …
Global Snapshots - Sri Lanka: social values mean good health care
Authors: Arany Nerminathan
Journal: BMJ (2003)

In the second of two parts, international health students give an insight to the highs and lows of health around the world

Despite economic constraints, Sri Lanka has achieved impressive health indicators, comparable to those in developed countries, by placing high value on the right of each individual to health and education. Sri Lanka's traditional system of values has always been highly oriented to welfare, and the Buddhist ethos reinforces social egalitarianism and collective responsibility to help the poorest in society.1

Sri Lanka's political system has also supported the …
Picture quiz: Chest trauma
Authors: Chetan S Modi, A Alani, Gwyn S Williams, Patrick Yiu
Journal: BMJ (2007)

A 35 year old man presented at the emergency department with a penetrating chest injury. He was involved in an alleged assault that resulted in a screwdriver being thrust into his sternum. He had no other associated injuries. Initial assessment showed that he was haemodynamically stable with no signs of respiratory distress. The screwdriver was left in place. Chest radiographs taken in the emergency department confirmed the penetrating chest injury (fig 1). Fig 1 Chest radiograph taken in the emergency department
Abstract 12490: Class I Indications for Statin Therapy in Primary Prevention by Three Cholesterol Guidelines and Risk of Incident Cardiovascular Outcomes: Multi-ethnic Study of Atherosclerosis (MESA)
Authors: Peter Flueckiger, Waqas Qureshi, Michael Blaha, Gregory Burke, Veit Sandfort, Erin D Michos, David Herrington, Joseph Yeboah
Journal: Circulation (2015)

Introduction: The major societal guidelines on cholesterol treatment (2013 ACC/AHA, 2004 NCEP/ATP III, and the 2011 ESC/EAS) differ in identifying patients with a class 1 recommendation for statin therapy for atherosclerotic cardiovascular disease (ASCVD). ACC/AHA emphasizes a need for clinician-patient dialogue on the risks/benefits of statins in primary prevention of ASCVD. Limited data exist on the accuracy of statin-eligibility (Class I) for ASCVD events to inform this dialogue. We assessed the accuracy of class I statin eligibility with incident ASCVD events by ACC/AHA compared with NCEP/ATP III and ESC/EAS guidelines. Methods: We evaluated the sensitivity (SN), specificity (SP), positive predictive value (PPV), negative predictive value (NPV) of class I recommendation for statin therapy by each guideline for respective 10 yr. adjudicated incident ASCVD outcomes [NCEP/ATP III- MI, CHD death; ACC/AHA- MI, CHD death, fatal/non-fatal strokes; ESC/EAS: ASCVD death] in participants of the Multi Ethnic Study of Atherosclerosis. We stratified analysis by age, sex, and race. 4723 out of 6814 persons, not on statins at baseline, had complete data. Results: Mean age was 59±9 yrs., 47% male, 37% white, 28% African American (AA), 23% Hispanic, and 12% Asian, 7.5% T2DM, 15%/35% current/former smokers, and mean BMI of 28±6 kg/m2. 7.3% had ASCVD, 5.2% ASCVD death and 5.1% had a CHD event after 10 yrs. See Table 1 for results. Subgroup analysis shows AHA/ACC had a higher SN and lower SP in men vs. women (SN = 76% vs. 46%, SP = 54% vs. 77%) and in those &gt;60 vs. &lt;60 yrs (SN = 79% vs. 40%, SP = 41% vs. 85%). For AHA/ACC, SN was highest in Asians (75%) followed by AA (74%), Hispanics (56%), whites (56%). SP in whites (70%), Hispanics (68%), Asians (68%), AA (60%) Conclusions: Class I statin indication by all 3 guidelines have relatively low sensitivities for a good screening tool. ACC/AHA has higher SN, lower SP, similar NPV and higher PPV compared with NCEP/ATP III and ESC/EAS for primary ASCVD events.
Estimation of the Percentage of US Patients With Cancer Who Are Eligible for and Respond to Checkpoint Inhibitor Immunotherapy Drugs
Authors: Alyson Haslam, Vinay Prasad
Journal: JAMA Network Open (2019)

Immunotherapy checkpoint inhibitors have generated considerable interest because of durable responses in a number of hitherto intractable tumor types.To estimate the percentage of patients with cancer in the United States who are eligible for and respond to checkpoint inhibitor drugs approved for oncology indications by the US Food and Drug Administration (FDA).Retrospective cross-sectional study performed from June 2018 through October 2018 using publicly available data to determine (1) demographic characteristics of patients with advanced or metastatic cancer, (2) FDA data on checkpoint inhibitors approved from January 2011 through August 2018, (3) measures of response from drug labels, and (4) published reports estimating the frequency of various inclusion criteria.The estimated percentages of US patients with cancer who are eligible for and who respond to immunotherapy checkpoint inhibitor drugs, by year.Six checkpoint inhibitor drugs were approved for 14 indications between March 25, 2011, and August 17, 2018. The estimated percentage of patients with cancer who were eligible for checkpoint inhibitor drugs increased from 1.54% (95% CI, 1.51%-1.57%) in 2011 to 43.63% (95% CI, 43.51%-43.75%) in 2018. The percentage of patients with cancer estimated to respond to checkpoint inhibitor drugs was 0.14% (95% CI, 0.13%-0.15%) in 2011 when ipilimumab was approved for unresectable or metastatic melanoma and increased to 5.86% (95% CI, 5.80%-5.92%) by 2015. By 2018, the estimated percentage of responders increased to 12.46% (95% CI, 12.37%-12.54%).The estimated percentages of patients who are eligible for and who respond to checkpoint inhibitor drugs are higher than reported estimates for drugs approved for genome-driven oncology but remain modest. Future research should explore biomarkers to maximize the benefit of immunotherapy among patients receiving it.
Book review: Man and Boy
Authors: Amlan Basu
Journal: BMJ (2000)

Harry Silver “makes a mistake” with a girl at work. He then loses his wife and his job and becomes a single parent-all in the space of a few days. As he learns to bring up his son alone he starts to appreciate, among other things, the father-son bond, and he begins to realise what makes his own father so special. Indeed, the relationship they have is both extremely moving and …
Minerva: June 2001
Authors: I Grant, A Pandya, M G Dickson, C M Quartey–Papafio
Journal: BMJ (2001)

Minerva wonders if there is a conspiracy afoot to phase out doctors altogether. Readers of the Postgraduate Medical Journal (2001; 77:337–9) are reminded this month about the chief nursing officer's 10 key roles for nurses in the NHS Plan. It seems that in future nurses will be required to order diagnostic tests, to make and receive referrals to particular specialists, to admit and discharge patients with specified conditions, and to run clinics. Minerva wonders if the PMJ will be renamed the PNJ in future.

We hear and read a lot about violence among children and teenagers in the United States but far less about bullying. When almost 16 000 children completed the World Health Organization's health behaviour in school aged children survey in 1998 a shocking 30% admitted that they been involved in moderate or frequent bullying (JAMA 2001;285:2094–100). A fifth described themselves as bullies, while 17% claimed they had been the victims of bullying. Not surprisingly, both perpetrating and experiencing bullying was associated with poor psychosocial adjustment.

The most common …
Discussion: studies of LHRH analogs in the human male.
Authors: Coutinho Em, Hong Cy, Turner P, Prasad M, Coale Aj, Kalla Nr, Vasudev M, Anderson Dj, Hill Ja, Haimovici F, Xu C, Zaneveld Lj, Kaminski Jm, Waller Dp, Quigg J, Anderson Ra, Mack, Bauer L, Griffin Pd, Shieh Cc, Wu P, Chiang Bn
Journal: BMJ (1981)

The clinical trials with LHRH (luteinizing hormone receptors hormone) have confirmed the expected effects on the secretion of pituitary gonadotropins and secondary effects of gonadal steroidogenesis.  Discussion focused primarily on the significance of the endocrine changes resulting from down-regulation of the pituitary and alterations in gonadotropins and testosterone secretions.  1 investigator reported that LHRH treatment results in variable decline in basal gonadotropin levels while testosterone is markedly depressed throughout treatment.  The question that arises is how does hCG work.  Some evidence exists of desensitization of acute testicular response to hCG in terms of testosterone production.  If hCG levels remain elevated serum testosterone levels will eventually decline to prepubertal levels.  In speculating on species differences in the various responses of male animals to GnRH agonists 1 investigator reported that the administration of GnRH agonists in rates was accompanied by lowered prolactin secretion and elevated progesterone levels.  Those changes might mediate some of the antagonistic effect of the agonist.  A study in humans showed no elevation of progesterone during the 30-week treatment period.  A Swedish investigator found that LH responses to GnRH tests increased following the discontinuation of treatment with Buserelin.  Thus GnRH agonists may induce the down-regulation of receptor levels in the target organ and in this aspect they differ from steroids.  Major conclusions of the discussion were that investigators with considerable clinical experience involving men have learned that the most pressing question to be raised is whether and in what manner the treatment affects sexual behavior.  From the presentations considered in this section it appears that LHRH analogs have the same potential and the same undesirable side-effects displayed by previous candidates for a male contraceptive.  Some LHRH analogs may effectively suppress spermatogenesis and render a man infertile for as long as the treatment lasts but loss of libido will be common because of the inhibition of gonadotropin secretion and lowered testosterone levels.  None of the analogs discussed which are the 1st compounds to reach the clinical trial stage presents long-acting possibilities.
Correction to: NSAID use and somatic exomic mutations in Barrett’s esophagus
Authors: Patricia C. Galipeau, Kenji M. Oman, Thomas G. Paulson, Carissa A. Sanchez, Qing Zhang, Jerry A. Marty, Jeffrey J. Delrow, Mary K. Kuhner, Thomas L. Vaughan, Brian J. Reid, Xiaohong Li
Journal: Genome Medicine (2019)

It was highlighted that in the original article [1] the Availability of data and materials section was incorrect.
Self directed learning or DIY education?
Authors: Mary Seabrook
Journal: BMJ (2000)

Independent learning has real advantages in the long term One of the latest educational crazes has been to encourage “self directed” (also known as “independent” or “autonomous”) learning for students. Is this based on sound educational theory? Or is it, as some students perceive, a case of lecturers neglecting their duty by expecting students to do it all themselves?

The main characteristic of such learning is that “students take some significant responsibility for their own learning over and above responding to instruction.”1 The approach stems from an inspiring book by the humanist Carl Rogers, who argued that learners should be encouraged to develop their own interests and learning free from fear or external direction.2 Of course this approach has to be modified in a medical school, where graduates will be licensed to practise medicine.

An important benefit of the self directed approach is that it can tackle one of the most enduring problems in medical education: the exponential growth in knowledge. It has long been recognised that the course cannot teach everything that doctors consider relevant, and continued additions can lead to …
Rigorous Trial Design Is Essential to Understand the Role of Opioid Receptors in Ketamine’s Antidepressant Effect
Authors: Boris D. Heifets, Nolan R. Williams, Brandon S. Bentzley, Alan F. Schatzberg
Journal: JAMA Psychiatry (2019)

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A level results are reliable measure of success in medical careers, report says
Authors: Upasana Tayal
Journal: BMJ (2003)

A level results can predict long term career success in medicine, according to a paper recently published in the BMJ by researchers at University College London (2003;327:00-00).

Professor I C McManus and colleagues followed up over 500 doctors who had studied at Westminster medical school, London, between 1975 and 1982 and measured how successful their careers had been. They looked at dropout rates, how long it took students to get to different career grades, the number of research publications they had, and at measures of their stress and burnout levels. The students had …
Chimeric peptide engineered exosomes for dual-stage light guided plasma membrane and nucleus targeted photodynamic therapy
Authors: Hong Cheng, Jing-Hao Fan, Lin-Ping Zhao, Gui-Ling Fan, Rong-Rong Zheng, Xiao-Zhong Qiu, Xi-Yong Yu, Shi-Ying Li, Xian-Zheng Zhang
Journal: Biomaterials (2019)
Obstetrics and Gynaecology
Authors: Nick Jenkins
Journal: BMJ (2000)

Undergraduates in obstetrics and gynaecology have been crying out for a new textbook for years. This was one of the subjects where there was nothing that was quite suited to the needs of medical students. Books for the Diploma Royal College of Obstetrics and Gynaecology were all words, no pictures, and a bit more than we needed to know. Others, such as Ten Teachers, did not always contain enough detail.

Then came Impey, and, in the manner of the London bus, James et al arrived at the same time. Suddenly there are two good texts for undergraduates. Impey's book is my favourite - 100 pages of gynaecology followed by 120 pages of obstetrics. All the big topics are covered systematically, and plenty of boxes provide the answer to the “five causes of vaginal …
Sodium–glucose co‐transporter 2 inhibition with empagliflozin improves cardiac function in non‐diabetic rats with left ventricular dysfunction after myocardial infarction
Authors: Salva R. Yurista, Herman H.W. Silljé, Silke U. Oberdorf‐Maass, Elisabeth‐Maria Schouten, Mario G. Pavez Giani, Jan‐Luuk Hillebrands, Harry van Goor, Dirk J. van Veldhuisen, Rudolf A. de Boer, B. Daan Westenbrink
Journal: European Journal of Heart Failure (2019)

Aims Sodium–glucose co‐transporter 2 (SGLT2) inhibition reduces heart failure hospitalizations in patients with diabetes, irrespective of glycaemic control. We examined the effect of SGLT2 inhibition with empagliflozin (EMPA) on cardiac function in non‐diabetic rats with left ventricular (LV) dysfunction after myocardial infarction (MI). Methods and results Non‐diabetic male Sprague–Dawley rats underwent permanent coronary artery ligation to induce MI, or sham surgery. Rats received chow containing EMPA that resulted in an average daily intake of 30 mg/kg/day or control chow, starting before surgery (EMPA‐early) or 2 weeks after surgery (EMPA‐late). Cardiac function was assessed using echocardiography and histological and molecular markers of cardiac remodelling and metabolism were assessed in the left ventricle. Renal function was assessed in metabolic cages. EMPA increased urine production by two‐fold without affecting creatinine clearance and serum electrolytes. EMPA did not influence MI size, but LV ejection fraction (LVEF) was significantly higher in the EMPA‐early and EMPA‐late treated MI groups compared to the MI group treated with vehicle (LVEF 54%, 52% and 43%, respectively, all P &lt; 0.05). EMPA also attenuated cardiomyocyte hypertrophy, diminished interstitial fibrosis and reduced myocardial oxidative stress. EMPA treatment reduced mitochondrial DNA damage and stimulated mitochondrial biogenesis, which was associated with the normalization of myocardial uptake and oxidation of glucose and fatty acids. EMPA increased circulating ketone levels as well as myocardial expression of the ketone body transporter and two critical ketogenic enzymes, indicating that myocardial utilization of ketone bodies was increased. Together these metabolic changes were associated with an increase in cardiac ATP production. Conclusion Empagliflozin favourably affects cardiac function and remodelling in non‐diabetic rats with LV dysfunction after MI, associated with substantial improvements in cardiac metabolism and cardiac ATP production. Importantly, it did so without renal adverse effects. Our data suggest that EMPA might be of benefit in heart failure patients without diabetes.