tbuckley/cabot-search huggingface dataset:
Practical issues in implementing whole-genome-sequencing in routine diagnostic microbiology
Authors: J.W.A. Rossen, A.W. Friedrich, J. Moran-Gilad
Journal: Clinical Microbiology and Infection (2017)

<h2>Abstract</h2><h3>Background</h3> Next generation sequencing (NGS) is increasingly being used in clinical microbiology. Like every new technology adopted in microbiology, the integration of NGS into clinical and routine workflows must be carefully managed. <h3>Aim</h3> To review the practical aspects of implementing bacterial whole genome sequencing (WGS) in routine diagnostic laboratories. <h3>Sources</h3> Review of the literature and expert opinion. <h3>Content</h3> In this review, we discuss when and how to integrate whole genome sequencing (WGS) in the routine workflow of the clinical laboratory. In addition, as the microbiology laboratories have to adhere to various national and international regulations and criteria for their accreditation, we deliberate on quality control issues for using WGS in microbiology, including the importance of proficiency testing. Furthermore, the current and future place of this technology in the diagnostic hierarchy of microbiology is described as well as the necessity of maintaining backwards compatibility with already established methods. Finally, we speculate on the question of whether WGS can entirely replace routine microbiology in the future and the tension between the fact that most sequencers are designed to process multiple samples in parallel whereas for optimal diagnosis a one-by-one processing of the samples is preferred. Special reference is made to the cost and turnaround time of WGS in diagnostic laboratories. <h3>Implications</h3> Further development is required to improve the workflow for WGS, in particular to shorten the turnaround time, reduce costs, and streamline downstream data analyses. Only when these processes reach maturity will reliance on WGS for routine patient management and infection control management become feasible, enabling the transformation of clinical microbiology into a genome-based and personalized diagnostic field.
Indagine ed intervento su un focolaio epidemico di Legionellosi nei Paesi Bassi: le prime 48 ore
Authors: J. E. van Steenbergen, F. A.N. Slijkerman, P Speelman
Journal: Eurosurveillance (1999)

La ' Westfriese Flora' e una fiera floreale, che dura una settimana e si tiene ogni anno a Bovenkarspel, nei Paesi Bassi nordoccidentali, a cui affluiscono sia agricoltori sia consumatori. La manifestazione di quest'anno, tenutasi dal 19 al 28 Febbraio, ha richiamato 80.000 visitatori da tutto il paese. In seguito all'esposizione, 181 persone che sono intervenute nella seconda meta della settimana, hanno contratto una polmonite da legionella e 21 sono decedute (1,2). Il presente articolo descrive le indagini e gli interventi, intrapresi immediatamente, nei primi due giorni, che hanno condotto ad un allarme su scala nazionale e alla formulazione di interrogativi metodologici utili per le successive indagini.
Kinetics of Human Mutant Tau Prion Formation in the Brains of 2 Transgenic Mouse Lines
Authors: Amanda L. Woerman, Smita Patel, Sabeen A. Kazmi, Abby Oehler, Yevgeniy Freyman, Lloyd Espiritu, Robert Cotter, Julian A. Castaneda, Steven H. Olson, Stanley B. Prusiner
Journal: JAMA Neurology (2017)

Accumulation of the protein tau is a defining characteristic of several neurodegenerative diseases. Thorough assessment of transgenic (Tg) mouse lines that replicate this process is critical for establishing the models used for testing anti-tau therapeutics in vivo.To define a consistent mouse model of disease for use in future compound efficacy studies.In this time course study, cohorts of Tg and control mice were euthanized at defined intervals. Collected brains were bisected down the midline. One half was frozen and used to measure the tau prion content, while the other half was fixed for immunostaining with anti-tau antibodies. All mice were maintained at the Hunters Point Animal Facility at the University of California, San Francisco, and all experiments were performed at the Mission Bay Campus of the University of California, San Francisco. Study animals were PS19, homozygous and hemizygous Tg(MAPT*P301S), and B6/J mice. The study dates were August 9, 2010, to October 3, 2016.Tau prions were measured using a cell-based assay. Neuropathology was measured by determining the percentage area positive for immunostaining in defined brain regions. A separate cohort of mice was aged until each mouse developed neurological signs as determined by trained animal technicians to assess mortality.A total of 1035 mice were used in this time course study. These included PS19 mice (51.2% [126 of 246] male and 48.8% [120 of 246] female), Tg(MAPT*P301S+/+) mice (52.3% [216 of 413] male, 43.8% [181 of 413] female, and 3.9% [16 of 413] undetermined), Tg(MAPT*P301S+/-) mice (51.8% [101 of 195] male and 48.2% [94 of 195] female), and B6/J mice (49.7% [90 of 181] male and 50.3% [91 of 181] female). While considerable interanimal variability in neuropathology, disease onset, and tau prion formation in the PS19 mice was observed, all 3 measures of disease were more uniform in the Tg(MAPT*P301S+/+) mice. Comparing tau prion formation in Tg(MAPT*P301S+/+) mice with B6/J controls, the 95% CIs for the 2 mouse lines diverged before age 5 weeks, and significant (P < .05) neuropathology in the hindbrain of 24-week-old mice was quantifiable.The assessment of disease progression using 3 criteria showed that disease onset in PS19 mice is too variable to obtain reliable measurements for drug discovery research. However, the reproducibility of tau prion formation in young Tg(MAPT*P301S+/+) mice establishes a rapid assay for compound efficacy in vivo.
Abstract MP82: Associations of Positive Psychological Well-being on Changes in Allostatic Load: Multi-Ethnic Study of Atherosclerosis (MESA)
Authors: Rosalba Hernandez, Kiarri Kershaw, Teresa Seeman, Julia Boehm, Thanh-Huyen Vu, Hongyan Ning, Donald Lloyd-Jones
Journal: Circulation (2015)

Background:  Cumulative multi-system physiological dysregulation may represent an important pathway linking psychological well-being to cardiovascular disease (CVD) risk but this relationship is poorly understood. This study examines the cross-sectional associations of psychological well-being (positive affect and dispositional optimism) with allostatic load (AL), i.e., cumulative multi-system physiologic burden.   Methods:  We used data collected from approximately 4,000 adults aged 45-84 who participated in the Multi-Ethnic Study of Atherosclerosis (MESA) with initial baseline enrollment in 2000-2002. Positive affect was calculated by summing four positively-worded items included in the Center for Epidemiologic Studies Depression Scale Revised. The Life Orientation Test-Revised was used to assess levels of dispositional optimism. A composite score for AL was derived from the following physiological components: wait-to-hip ratio, triglycerides, LDL and HDL cholesterol, glucose, systolic blood pressure, resting heart rate, and pulse pressure. Multiple linear regression was used to examine cross-sectional associations of positive affect and AL at baseline (2000-2002) and optimism and AL at the first follow-up visit (2002-2004).   Results:  In models adjusted for socio-demographic factors, psychological well-being was not significantly related to AL for the total sample. However, effect modification was evident by sex and race/ethnicity when examining the association of optimism and AL. Optimism was inversely associated with AL for Caucasian men, after adjustment for socio-demographic factors (Table 1), with a 1-unit increase in optimism associated with a 0.07 reduction in AL ( p  = 0.03).   Conclusion:  The current study offers preliminary evidence for an inverse association between dispositional optimism and AL among Caucasian men. Prospective analyses to come.
Evaluación de la frecuencia de las donaciones sanguíneas contaminadas por VHB, VHC y VIH en los bancos de sangre en el Reino-Unido, 1996-2003
Authors: K Soldan, K Davison, B Dow
Journal: Eurosurveillance (2005)

Recientemente se han introducido varias nuevas pruebas en los servicios ingleses de transfusion sanguinea para mejorar la seguridad de los hemoderivados. La frecuencia (o el riesgo) de introduccion de hemodonaciones infectadas por el virus de la hepatitis B (VHB), el virus de la hepatitis C (VHC) o el VIH en los bancos de sangre, se estimo sobre el periodo 1996-2003. En estos anos fueron puestas en marcha la prueba de acidos nucleicos (NAT) para el VHC, y la prueba combinada VIH antigeno-anticuerpo y NAT para el VIH. 
Se evaluo la frecuencia de introduccion de una donacion contaminada en los bancos de sangre ligada 1) al periodo ventana,2) al fallo de la prueba, y 3) a los errores humanos y tecnicos durante el cribado. El riesgo debido al periodo ventana se ha estimado basandose en la incidencia de la infeccion en los donantes y la duracion del periodo ventana para las pruebas utilizadas, con un ajuste por los intervalos entre donaciones atipicos en donantes seroconvertores. 
La frecuencia de las donaciones infecciosas presentes en los bancos de sangre entre 1996 y 2003 se estimo en 1,66; 0,80 y 0,14 por millon para el VHB, el VHC y el VIH respectivamente. Los resultados del NAT han mostrado una reduccion de un 95% del riesgo de VHC. En cuanto al riesgo estimado para el VIH, se redujo un 10% despues de la introduccion de la prueba combinada VIH antigeno-anticuerpo y del NAT. En el Reino-Unido, el riesgo de transmision del VHB, VHC y HIV por transfusion disminuyo desde 1996 gracias a los progresos en el cribado de las hemodonaciones, aunque la reduccion de los riesgos sea escasa. La mejora de la seguridad de los hemoderivados respecto al VHB, VHC y VIH se conseguira con la reduccion del periodo ventana de las pruebas y posiblemente todavia mas con un refuerzo de la vigilancia de los errores tecnicos y de la seleccion de los donantes.
Retraction notice to “Fast track for elderly patients: Is it feasible for colorectal surgery?” [International Journal of Surgery 12 (2014) S20 – S22]
Authors: Rita Compagna, Giovanni Aprea, Davide De Rosa, Maurizio Gentile, Giovanni Cestaro, Gabriele Vigliotti, Tommaso Bianco, Guido Massa, Maurizio Amato, Salvatore Massa, Bruno Amato
Journal: International Journal of Surgery (2017)
TCT-849 In-stent restenosis treated with everolimus-eluting bioresorbable scaffold: 1-year angiographic results
Authors: Ivan Gomez-Blazquez, Victor Jimenez Diaz, Saleta Fernandez-Barbeira, Guillermo Bastos Fernández, Antonio De Miguel Castro, Jose Antonio Baz Alonso, Alberto Ortiz, Andres Iñiguez
Journal: Journal of the American College of Cardiology (2017)
Reply to: “HBV RNA virion-like particles produced under nucleos(t)ide analogues treatment are mainly replication-deficient”
Authors: Jing Wang, Yiqi Yu, Zhefeng Meng, Chuan Shen, Miaoqu Zhang, Peiyu Qian, Caiyan Zhao, Xuanyi Wang, Yuxian Huang, Jiming Zhang, Chao Qiu, Wenhong Zhang
Journal: Journal of Hepatology (2017)
Abstract 12818: First Experience of Three-dimensional Rotational Angiography Image Integration With Electroanatomical Mapping System to Guide Catheter Ablation of Atrial Fibrillation
Authors: Satoshi Fujita, Eitaro Fujii, Yoshihiko Kagawa, Katsuhiro Inoue, Tsuyoshi Yamada, Norikazu Yamada, Masaaki Ito
Journal: Circulation (2016)

Introduction: Rotational angiography of the left atrium with three-dimensional (3D) reconstruction (3D-ATG) represents a modern method enabling to create computed tomography (CT) like 3D images on a standard X-ray machine. Recently, electroanatomical mapping system can import 3D images reconstructed by 3D-ATG. Hypothesis: We assessed the hypothesis that atrial fibrillation (AF) ablation using 3D-ATG would be feasible with a significant reduction in effective dose without compromising image quality compared with 3D CT image. Methods: 3D-ATG was performed by using the Philips Allura Xper FD 10 system operated at a low-frame pulsed fluoroscopy (7.5 frames per second). Effective radiation dose was calculated from dose area product (DAP) measurements in 103 patients (mean age of 65 years, 71% men) undergoing AF ablation guided by 3D-ATG. Organ dose was measured at 37 points with a radiophotoluminescence glass dosimeter inserted in the position of an anthropomorphic Rando Phantom. Effective dose was calculated by multiplying organ dose by tissue weighting factor. The DAP to effective dose conversion factor was calculated by measurement of DAP at the same time of radiation exposure. Effective dose at CT examination was estimated from dose length product and conversion factor of 0.014. Left atrial dimensions and vertical ostial pulmonary vein (PV) diameters for each imaging method were compared. Results: The DAP to effective dose conversion factor of 3D-ATG was 2.4x10 -4 mSv/mGy•cm 2 by using the Philips Allura Xper FD 10 system in our hospital. Mean DAP for all patients was 7777±1488mGy•cm 2 for rotational angiography of the left atrium. The corresponding effective radiation doses for 3D-ATG were 1.9±0.4mSv. The effective doses for CT examinations were 13.6±4.2mSv (p&lt;0.001). The correlations of left atrial dimension were r=0.73 for sagittal plane, 0.76 for coronal, and 0.80 for vertical (p&lt;0.005). The correlation coefficient between 3D-ATG and 3D-CT for the ostial PV diameters was r=0.72 for left superior PV, 0.88 for left inferior PV, 0.60 for right superior PV, and 0.65 for right inferior PV (p&lt;0.005). Conclusions: AF ablation using 3D-ATG is possible with a significant reduction in effective dose without compromising image quality.
Abstract 13029: Longitudinal Association of Cardiorespiratory Fitness and Physical Activity With Left Ventricular Structure and Function: The Coronary Artery Risk Development In Young Adults (CARDIA) Study
Authors: Timothy M Markman, Michael Blaha, Bharath A Venkatesh, Ravi Shah, Laura Colangelo, Donald M Lloyd-Jones, Venkatesh L Murthy, Joao A Lima, Chintan Desai
Journal: Circulation (2016)

Introduction: Physical activity (PA) and cardiorespiratory fitness (CRF) are related but distinct markers of cardiovascular risk. We aim to characterize the association of PA and CRF with left ventricular (LV) structure and function. Methods: CARDIA enrolled adults age 18 to 30 years in 1985-86 (Year 0). We assessed the relationship between PA (exercise units, {EU}) and CRF (treadmill minutes) from Year 0 with LV structure and function by echocardiography at Year 25. For PA, 200 EU represents a 70-kilogram man expending 300 kilocalories in three 50-minute walks. We used multivariable linear regression to determine if change in PA and CRF were independent predictors of LV structure and function at Year-25. Results: We included 3,339 participants (44% male, 46% black) stratified by the median of PA and CRF. As shown in the Table, participants with CRF above the median had more favorable LV structure and function, including lower LV mass (LVM), higher septal and lateral mitral annular velocity (e’), and more negative global longitudinal strain (GLS). Participants with PA above the median also had more negative GLS and greater septal e’ than those below the median, but the association was not significant in multivariable regression with CRF in the model. CRF remained significantly associated with more negative GLS even when PA was included (β = -0.09, P &lt; 0.001). Compared to participants who remained below the median CRF from Year 0 to Year 20, those who moved from below the median in CRF at Year 0 to above the median at Year 20 had more favorable Year 25 GLS (-14.9% and -15.4%, P = 0.01) and Year 25 LVM (160 gm and 167 gm, P = 0.01). Those who moved above the median in PA also had favorable LV remodeling; however, the association was attenuated with multivariable adjustment. Conclusions: CRF in young adulthood is more closely associated with favorable parameters of LV structure and function 25 years later than PA. Improvement in CRF was associated with more favorable GLS and LV mass 20 years later.
Japan subset of Phase III study KEYNOTE-024: Pembrolizumab for PD-L1 TPS &gt; =50%, treatment-naïve NSCLC
Authors: Miyako Satouchi, Katsuyuki Hotta, Kaname Nosaki, Toshiaki Takahashi, Kazuhiko Nakagawa, Keisuke Aoe, Kazuo Noguchi, Takashi Shimamoto, Reshma Rangwala, Julie Brahmer
Journal: Annals of Oncology (2017)
Assessment of quality of life (QOL), cognitive function and depression in a randomized phase II study of abiraterone acetate (ABI) plus prednisone (P) vs enzalutamide (ENZA) for metastatic castrate-resistant prostate cancer (mCRPC).
Authors: Daniel Khalaf, Katherine Sunderland, Bernhard J. Eigl, Daygen L. Finch, Conrad D. Oja, Joanna Vergidis, Sunil Parimi, Muhammad Zulfiqar, Martin Gleave, Kim N. Chi
Journal: Journal of Clinical Oncology (2017)

5036 Background: ABI + P and ENZA treatments are associated with side effects that may impair QOL. ENZA has been associated with cognitive and memory impairment. There has been no direct comparison between these agents and their effect on these domains. Methods: Randomized phase II trial of ABI + P vs ENZA as 1st-line therapy for mCRPC (ClinicalTrials.gov: NCT02125357). FACT-P QOL questionnaire, patient health questionnaire (PHQ-9) and Montreal Cognitive Assessment (MoCA) were completed throughout the study. The proportion of patients with a clinically significant change in FACT-P (10 points total FACT-P score, 3 points FACT-P subscales), worsening of PHQ-9 depression symptom severity (none = 0-4, mild = 5-9, moderate = 10-14, moderate-severe = 15-19, severe ≥20) and decline in MoCA cognitive impairment level (normal = 27-30, mild = 18-26, moderate = 10-17, severe ˂ 10) at week 12 was compared between study arms for this analysis. Results: From 202 patients (pts) accrued, there were 162, 145 and 142 pts with baseline and 12-week FACT-P, PHQ-9 and MoCA assessment. Median baseline FACT-P, PHQ-9 and MoCA scores were similar in both arms. From baseline to 12 weeks, the median total FACT-P score improved in the ABI + P arm (115 to 128, P = 0.02), but there was no change in the ENZA arm (114 to 114, P = 1.00). There was a higher rate of significant worsening for the physical well-being (PWB) subscale for ENZA vs ABI + P (TABLE), but not for the other FACT-P subscales. There was a higher rate of worsening in depression severity in the ENZA arm (TABLE), although worsening to a moderate-severe/severe level occurred in only 2 patients. There was also a trend for worsening in cognitive impairment for the ENZA arm (TABLE). Conclusions: These data suggest there are distinct differences between ABI + P vs ENZA and their effects on QOL, mood symptoms and cognitive function. Clinical trial information: NCT02125357. [Table: see text]
What Level of Health Spending Is “Affordable”?
Authors: Uwe Reinhardt
Journal: JAMA (2017)

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 HomeNew OnlineCurrent IssueFor Authors Podcasts Clinical Reviews Editors' Summary Medical News Author Interviews More 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 journal
Reactive Neutrophil Responses Dependent on the Receptor Tyrosine Kinase c-MET Limit Cancer Immunotherapy
Authors: Nicole Glodde, Tobias Bald, Debby van den Boorn-Konijnenberg, Kyohei Nakamura, Jake S. O’Donnell, Sabrina Szczepanski, Maria Brandes, Sarah Eickhoff, Indrajit Das, Naveen Shridhar, Daniel Hinze, Meri Rogava, Tetje C. van der Sluis, Janne J. Ruotsalainen, Evelyn Gaffal, Jennifer Landsberg, Kerstin U. Ludwig, Christoph Wilhelm, Monika Riek-Burchardt, Andreas J. Müller, Christoffer Gebhardt, Richard A. Scolyer, Georgina V. Long, Viktor Janzen, Michele W.L. Teng, Wolfgang Kastenmüller, Massimiliano Mazzone, Mark J. Smyth, Thomas Tüting, Michael Hölzel
Journal: Immunity (2017)
Variedad de intoxicaciones alimentarias y fuentes de contaminación
Authors: N Noah
Journal: Eurosurveillance (1999)

Las tres formas, completamente diferentes, de intoxicaciones alimentarias descritas en este numero de Eurosurveillance ilustran la extraordinaria capacidad de los microorganismos a sobrevivir y causar una enfermedad. Clostridium botulinum es un organismo que produce una toxina (por otra parte, facil de destruir por calor) en ciertas condiciones ambientales poco habituales y muy precisas. El articulo sobre el botulismo en Polonia, junto con los publicados en el numero de enero, muestran como estas condiciones, aunque poco frecuentes, siguen estando bastante generalizadas. En los brotes de infeccion por Salmonella enteritidis, suele culparse a los huevos o a las aves de corral utilizadas. La investigacion del brote de Grecia concluyo que la mayonesa elaborada con huevos crudos y almacenada a 15o C fue el vehiculo de infeccion mas probable, y muestra el grado de contaminacion con este microorganismo que presentan los huevos de gallinas en Europa.
Abstract 13458: Survival After Out-of-hospital Cardiac Arrests and Arterial Oxygen Partial Pressure During Cardiopulmonary Resuscitation: The CRITICAL Study in Osaka, Japan
Authors: Junichi Izawa, Tetsuhisa Kitamura, Koichi Hayakawa, Tomoki Yamada, Kazuhisa Yoshiya, Yoshio Abe, Toshifumi Uejima, Yasuo Ohishi, Takeyuki Kiguchi, Masashi Kishi, Masafumi Kishimoto, Shota Nakao, Tetsuro Nishimura, Yasuyuki Hayashi, Takaya Morooka, Taku Sokabe, Tasuku Matsuyama, Takeshi Shimazu, Takashi Kawamura, Taku Iwami
Journal: Circulation (2016)

Introduction: The current resuscitation guidelines recommend the use of the highest possible inspired oxygen concentration during cardiopulmonary resuscitation (CPR). On the other hand, there are conflicting results that PaO 2 after return of spontaneous circulation might be harmful to better outcome. Hypothesis: The objective of this study is to investigate the association between PaO 2 during CPR and survival after out-of-hospital cardiac arrests (OHCA). Methods: Study design: Multicenter cohort study. In Osaka Prefecture, Japan, we registered all consecutive OHCA patients who were transported to institutions participating in our CRITICAL registry since July 1, 2012. From this registry, we included non-traumatic adult OHCA patients with arterial blood gas sampled at the hospitals during CPR. The main exposure was PaO 2 in arterial blood gas analysis during CPR. We classified PaO 2 values as three categories (hypoxemia: 0-60 mmHg; normoxemia: 60-300 mmHg; and hyperoxemia: ≥300 mmHg), referring to previous studies. The primary outcome was survival at one-month after OHCA. Multivariable logistic regression analysis was used to adjust confounders. Results: We analyzed 710 patients. Among them, 4.5% (N = 32) survived at one month and 1.5% (N = 11) had a neurologically favorable outcome. As PaO 2 categories during CPR became higher, one-month survival increased (3.0% [16/528] in hypoxemia, 6.6% [11/166] in normoxemia, and 31.2% [5/16] in hyperoxemia). The adjusted odds ratio (AOR) for one-month survival, controlling for first documented rhythm and bystander witness, reffered to the hypoxemia group was 1.98 (95%CI 0.83-4.69, P=0.120 ) in normoxemia and 8.03 (95%CI 2.16-29.80, P=0.002) in hyperoxemia group. Conclusions: Higher PaO 2 categories during CPR were associated with better survival at one-month in non-traumatic adult OHCA patients. During CPR, maintaining high PaO 2 might be useful for improving outcomes of OHCA patients.