tbuckley/cabot-search huggingface dataset:
<i>Chlamydia trachomatis</i> among Patients Infected with and Treated for <i>Neisseria gonorrhoeae</i> in Sexually Transmitted Disease Clinics in the United States
Authors: Sheryl B. Lyss, Mary L. Kamb, Thomas A. Peterman, John S. Moran, Daniel R. Newman, Gail Bolan, John M. Douglas, Michael Iatesta, C Kevin Malotte, Jonathan M. Zenilman, Josephine Ehret, Charlotte Gaydos, Wilbert J. Newhall
Journal: Annals of Internal Medicine (2003)

Background: For two decades, treatment guidelines for sexually transmitted diseases (STDs) have recommended empirical co-treatment for chlamydia when patients are treated for gonorrhea. Because the epidemiology of and diagnostic testing for STDs have changed over time, co-treatment may no longer be needed as a clinical or public health strategy. Objective: To assess the prevalence of chlamydia among patients at STD clinics who are infected with and treated for Neisseria gonorrhoeae and to determine whether co-treatment recommendations are still justified. Design: Cross-sectional analysis of data from a multisite study. Setting: Five public STD clinics (Baltimore, Maryland; Denver, Colorado; Long Beach, California; Newark, New Jersey; and San Francisco, California), July 1993 through October 1995. Patients: 3885 heterosexual patients (2184 men and 1701 women) who agreed to participate in a trial of counseling interventions and had conclusive results from diagnostic tests for gonorrhea and chlamydia performed routinely as part of the trial. Measurements: Infection with Chlamydia trachomatis as determined by polymerase chain reaction. Results: Chlamydia trachomatis was detected in 20% (95% CI, 16% to 24%) of 411 men and 42% (CI, 35% to 50%) of 151 women with laboratory-confirmed N. gonorrhoeae. Chlamydia trachomatis was detected in 19% (CI, 15% to 22%) of 410 men and 35% (CI, 28% to 43%) of 154 women with treatment indications for gonorrhea who would not otherwise have been treated for chlamydia: chlamydia prevalence among these patients was significantly higher than among patients without treatment indications for either gonorrhea or chlamydia: 7% in men and 9% in women (relative risk, 2.58 [CI, 1.92 to 3.47] and 4.12 [CI, 3.05 to 5.57], respectively). Conclusion: The frequent presence of chlamydia among patients at STD clinics who received treatment for gonorrhea, including sex partners of gonorrhea-infected patients, supports continuing current recommendations for co-treatment. *For members of the Project RESPECT Study Group, see the Appendix.
Abstract P315: Tomato Consumption by Form and Its Relationship to Total Vegetable Intake in the US: Implications for Healthier Dietary Patterns
Authors: Kristin J Reimers, Debra R Keast
Journal: Circulation (2015)

Despite public health efforts to decrease risk of cardiovascular disease by promoting healthier dietary patterns, Americans persistently under-consume vegetables. Discovering feasible, achievable strategies to increase vegetable intake can contribute to improved dietary patterns and health outcomes. Tomatoes are the most consumed non-starchy vegetable in the US and also contribute the greatest porportion of vegetables to the USDA Food Pattern (MyPlate). Despite tomatoes’ dietary importance, little is known about tomato consumption by form. Tomato forms and amounts consumed in the US were determined by examining the intakes of adults 19 years and older (n = 16,252) in the National Health and Nutrition Examination Survey, 2005-06, 2007-08, and 2009-10. The forms of tomatoes in foods participants reported were divided into two categories: tomato products and raw. Foods containing tomato products were further divided into four subgroups: 1) canned tomatoes as main ingredients, 2) canned tomatoes as minor ingredients, 3) juice and 4) condiments. Tomato products comprised approximately 63% of total tomato consumption, primarily as main ingredients (33%) of foods such as pasta with tomato sauce, with smaller amounts contributed from minor ingredients (12%), condiments (10%) and juice (7%). Raw tomatoes accounted for the remaining 37%. Participants who consumed the most tomatoes, defined as those who met or exceeded the MyPlate tomato target amount (0.65 cup equivalents/d), consumed 67% of their tomatoes as tomato products and 33% as raw. These heavy tomato consumers’ total vegetable intake was 2.48 cup equivalents/d, which approximated the 2.5 cup equivalent MyPlate total vegetable target amount. Increasing the awareness and importance of the contribution of tomato intake by form, and the relationship between tomato intake and total vegetable intake targets can inform future strategies to achieve greater vegetable intake and thus improve dietary patterns for Americans.
Abstract P018: Calibration of Analytes Over Twenty-Five Years in the Atherosclerosis Risk in Communities Study
Authors: Christina M Parrinello, Morgan E Grams, David Couper, Christie M Ballantyne, Ron C Hoogeveen, John H Eckfeldt, Elizabeth Selvin, Josef Coresh
Journal: Circulation (2014)

Background: Comparability of laboratory measures over time is important for studies of disease prevalence and progression. While a small amount of bias may seem negligible on an individual level, it can result in substantial misclassification of disease in the population. We conducted a calibration study of important biomarkers across five study visits (25 years) in ARIC. Methods: We re-measured 15 analytes in 200 blood samples to calibrate original measurements at each time point using Bland-Altman plots and Deming regression. We also assessed the impact of calibration on the prevalence of chronic kidney disease (CKD), defined by estimated glomerular filtration rate using creatinine (eGFRcr), and on trends over time. Results: Assays in samples frozen 12-27 years were highly correlated with original values (median r=0.95) after removing outliers (median 4% of values). The range of bias (% difference in means) across visits for each original analyte compared to its reference were: creatinine: 13-49%; uric acid: 3-24%; C-reactive protein: 3-9%; total cholesterol: 1-6%; high density lipoprotein cholesterol: 4-8% (but new methods differed); low density lipoprotein cholesterol: 1-5%; triglycerides: 2-4%; glucose: 1-4%; N-terminal prohormone of brain natriuretic peptide: 2-12%; high sensitivity cardiac troponin T: 1-9%; alanine transaminase (ALT): 21%; aspartate transaminase (AST): 17%; gamma glutamyl transpeptidase: 0.2%; ß2-microglobulin: 1%; beta-trace protein: 13%. Four analytes met calibration criteria: creatinine, uric acid, ALT and AST. The impact on CKD prevalence was substantial and similar to previous statistical calibration (22% uncalibrated, 1.9% previously and 1.3% current laboratory calibration). Trends in eGFRcr over time were better aligned after calibration ( Figure ). Conclusions: Repeat assay of samples shows high correlation with original values. Calibration enables application of absolute cutoffs (required for defining CKD and other conditions) and improves longitudinal analyses.
Women and Alcohol: Contemporary and Historical Perspectives, by Moira Plant
Authors: A. Paton
Journal: BMJ (1997)

Moira Plant Free Association Books, £15.95, pp 388 ISBN 1 85343 364 0

The macho Romans meted out severe punishments to women (the traditional producers and retailers of alcohol) if they touched a drop of the stuff; the fun loving Etruscans made sure that women as well as men were provided with wine in the afterlife. Nowadays men drink alcohol in some Islamic countries, but women on the whole do not; we enlightened Europeans boast that we …
Abstract 15730: Ankle-Brachial Index and Physical Function in Community-Based Older Adults: The Atherosclerosis Risk in Communities (ARIC) Study
Authors: Kunihiro Matsushita, Shoshana Ballew, Yingying Sang, Corey Kalbaugh, Laura Loehr, Alan Hirsch, Hirofumi Tanaka, Gerardo Heiss, B. Gwen Windham, Elizabeth Selvin, Josef Coresh
Journal: Circulation (2014)

Background: Lower extremity peripheral artery disease (PAD), commonly defined by an ankle-brachial index (ABI) &lt;0.9, increases mortality risk and also reduces physical function. All prior studies of the impact of PAD on objectively measured physical function have been in restricted populations with known PAD or physical inactivity, leaving uncertainty regarding its impact in the community. Methods: We studied 5,351 ARIC participants (age 71-90 years during 2011-2013) who underwent the assessment of ABI and the Short Physical Performance Battery (SPPB, 0-12 scale), a summary measure of physical function based on three domains (4-meter walk velocity, timed chair stands, and standing balance). Logistic regression models examined the association of ABI with poor physical function (SPPB score &lt;6), adjusting for potential confounders including a history of other cardiovascular diseases. Results: There were 463 participants (8.2%) with ABI &lt;0.9 and 506 participants (9.0%) with ABI ≥1.3, a potential manifestation of PAD reflecting noncompressible pedal arteries. Both ABI &lt;0.9 and ≥1.3 were significantly and independently associated with higher odds of having poor physical function compared to those with a normal ABI (1.1-1.2). The 469 participants (8.8%) with a “borderline” low ABI (0.9-1.0) also demonstrated significantly poor physical function. Low ABI was significantly associated with poor performance in every SPPB domain, whereas none were statistically significant for high ABI. The results were largely consistent among those without a history of stroke or heart failure. Conclusion: In our population of community-dwelling older adults, ~25% had low, borderline low, or high ABI suggestive of PAD and demonstrated poorer physical function compared to those with normal ABI. Since physical function is a key element for independent living in older adults and several therapeutic options for PAD exist, our findings may have broad and important implications.
867. Correction of Glycogen Storage Disease Type II by Intramuscular Administration of an Adeno-Associated Virus 6 (AAV2/6) Vector Containing a Muscle-Specific Promoter
Authors: Haoyue Zhang, Baodong Sun, Luis Franco, Andrew Bird, Ayn Schneider, Dwight D. Koeberl
Journal: Molecular Therapy (2004)

Severe glycogen storage disease type II (GSD II; Pompe disease; MIM 232300) typically causes death in childhood from cardiomyopathy and cardiorespiratory failure. The underlying deficiency of acid a-glucosidase (GAA) in heart and skeletal muscle has been corrected by enzyme replacement in clinical trials. An AAV2/2 vector containing the hybrid CMV enhancer/chicken beta-actin promoter (CB promoter) to drive hGAA expression was administered by intramuscular injection in GAA-knockout (GAA-KO) mice, and GAA activity increased to normal levels at 6 weeks following vector administration. However, an AAV2/6 vector produced high-level hGAA at 10 days following intramuscular injection in GAA-KO mice that disappeared by 6 weeks. In contrast, an AAV2/6 vector persistently elevated hGAA to approximately 10-fold above normal in the injected gastrocnemius in immunodeficient, GAA-KO/SCID mice 6-weeks following vector administration, and reduced glycogen content to normal levels. AAV2/6 vectors have elicited an immune response in other mouse models for muscular dystrophy, and a CD4+ lympocytic infiltrate was observed in response to the AAV2/6 vector in immunocompetent GAA-KO mice. Therefore, a muscle-specific muscle creatine kinase (MCK) promoter was substituted for the CB promoter in an AAV vector encoding hGAA (AAV-MCKGAApA). The AAV2/6 vector containing the MCK promoter produced high levels of hGAA for longer than 6 weeks in immunocompetent hGAA mice, up to approximately 100-fold greater than GAA levels observed in skeletal muscle for normal mice. Glycogen content was reduced to normal in the injected muscle with AAV-MCKGAApA. However, no secretion of hGAA and uptake in distal tissues was observed, since GAA activity was not elevated in the contralateral gastrocnemius muscle, heart or diaphragm of GAA-KO mice following intramuscular injection of AAV-MCKGAApA. Thus, the threshold for GAA secretion from transduced skeletal muscle exceeds the normal GAA level by > 100-fold (> 4000 nmole/hr/mg). In summary, we demonstrated persistent correction of glycogen storage with an AAV2/6 vector containing a muscle-specific promoter in GSD II mice, and this approach should be considered for muscle-targeted gene therapy in Pompe disease.
Twin fluorophore near infrared KRAS peptide nucleic acid molecular beacons
Authors: Nariman Amirkhanov, Eric Wickstrom
Journal: Clinical Cancer Research (2008)

A7   Most pancreas cancer patients die within a year because they are diagnosed at an advanced incurable stage. However, even before an enlarged mass can be seen by MRI or CT, early stage pancreatic intraepithelial neoplasia (PanIN-1) pancreas cells contain high levels of mRNAs copied from hyperactive cancer genes such as KRAS and HER2. However, PanIN-1 does not always progress. Later stage PanIN-3 pancreas cells, which do progress to frank cancer, contain high levels of mRNAs overproduced by activated CCND1 or BRCA2 oncogenes. Specific detection of PanIN-3 would enable resection of ductal pancreas cancer at a survivable stage. We hypothesized that developing pancreas cancer can be imaged externally in live cells and animals by near infrared hybridization fluorescence (NIRF) imaging of overexpressed cancer gene mRNAs basepaired to molecular beacons. We designed a 12 base peptide nucleic acid (PNA) without a hairpin stem. We hypothesized that twin NIR664 fluorophores at the N and C termini could stack upon each other, mutually quenching their fluorescence, unless the PNA were hybridized to a complementary RNA. No quencher chromophore or hairpin stem is required in this case, unlike typical molecular beacons. Incubation of human AsPC1 KRAS G12D+ pancreas cancer cells with NIR664-KRAS G12D PNA-NIR664 for 24 h incubation, followed by 24 h of efflux, yielded bright NIRF images in the AsPC1 cells. Base mismatch, peptide mismatch, and cell mismatch control experiments are necessary before proceeding to animal experiments. This work was supported in part by NCI contract N01 CO27175 and NCI grant U54 CA105008.
Perioperative Safety in the Longitudinal Assessment of Bariatric Surgery
Authors: David Reed Flum, Steven H. Belle, Wendy C. King, Abdus S. Wahed, Paul Berk, William Chapman, Walter Pories, Anita Courcoulas, Carol McCloskey, James Mitchell, Emma Patterson, Alfons Pomp, Myrlene A. Staten, Susan Z. Yanovski, Richard Thirlby, Bruce Wolfe
Journal: New England Journal of Medicine (2009)

To improve decision making in the treatment of extreme obesity, the risks of bariatric surgical procedures require further characterization.
LSC 2014 abstract - Phenotypic, transcriptomic and epigenetic plasticity of dendritic cells in the lung tumor microenvironment reflects imprinting by hypoxia exposure
Authors: Lotte Pyfferoen, Simon Tavernier, Pieter Mestdagh, Kim Deswarte, Hamida Hammad, Jo Vandesompele, Bart Lambrecht, Karim Vermaelen
Journal: European Respiratory Journal (2014)

Deeper insights into the influence of the lung cancer environment on dendritic cell biology may guide the development of more effective immunotherapy against this lethal tumor.  We developed a preclinical model of lung cancer featuring orthotopic tumour growth in syngeneic, immunocompetent hosts. Lung tumours were found to be preferentially infiltrated by CD11c+/MHCII+/CD11b+/CD103- tumour-infiltrating DCs (TIDCs), which, compared to their peritumoural counterparts, displayed a dramatic overexpression of PD-L1 along with markers associated with tumour-associated macrophages (TAM). Transcriptomic analysis of these CD11b+ TIDCsvsperitumoural CD11b+ DCs showed upregulation of transcripts related to immunosuppressive TAMs and exposure to hypoxia. Global miRNA profiling of CD11b+TIDCs revealed a signature whose predicted targets were concordant with macrophage functions and hypoxic response. We show for the first time that mir-31, a known oncomir, is prominently upregulated in CD11b+TIDCs, and that its expression in DCs is driven by hypoxia. PET-CT imaging of orthotopic lung tumors showed tumoural areas with intense avidity for 18-fluorodeoxyglucose, indicating hypoxia-driven enhanced glucose uptake. In addition, confocal microscopy of intrapulmonary tumors revealed hypoxic regions which were heavily infiltrated with CD11c+ leukocytes.  We conclude that lung tumour-infiltrating DCs display considerable plasticity at the level of phenotype, transcriptome and microRNome, in a pattern that reflects acquisition of immunosuppressive macrophage features as well as exposure to intratumoural hypoxia.
Protective Effects of Amphotericin B Against Spontaneous and Transplantable Murine Tumors 2
Authors: Frederick Valeriote, Richard Lynch, Gerald Medoff, B. Vijaya Kumar
Journal: JNCI Journal of the National Cancer Institute (1976)

Journal Article Protective Effects of Amphotericin B Against Spontaneous and Transplantable Murine Tumors Get access Frederick Valeriote, Frederick Valeriote 3Section of Cancer Biology, Department of Radiology, Washington University School of Medicine, St. Louis, Mo. 63110. Search for other works by this author on: Oxford Academic PubMed Google Scholar Richard Lynch, Richard Lynch 4Department of Pathology, Washington University School of Medicine. Search for other works by this author on: Oxford Academic PubMed Google Scholar Gerald Medoff, Gerald Medoff 5Division of Infectious Diseases, Department of Medicine, Washington University School of Medicine. Search for other works by this author on: Oxford Academic PubMed Google Scholar B. Vijaya Kumar B. Vijaya Kumar 5Division of Infectious Diseases, Department of Medicine, Washington University School of Medicine. 6We thank Ms. Julia Ryan and Ms. Sandra Tolen for their technical assistance. Search for other works by this author on: Oxford Academic PubMed Google Scholar JNCI: Journal of the National Cancer Institute, Volume 56, Issue 3, March 1976, Pages 557–560, https://doi.org/10.1093/jnci/56.3.557 Published: 01 March 1976 Article history Received: 26 June 1975 Accepted: 21 October 1975 Published: 01 March 1976
Tramadol Abuse and Dependence Among Physicians—Reply
Authors: Gregory E. Skipper, David A. Brase
Journal: JAMA (2005)

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Abstract 12072: Predictors of Cardiovascular and Non-Cardiovascular Death: From the Clinic to the Lab
Authors: Maria M Brooks, Bernard R Chaitman, Mandeep Singh, Helen Vlachos, George Steiner, Ashok Krishnaswami, Trevor J Orchard, Frederick Feit, Charanjit Rihal, Oscar Marroquin
Journal: Circulation (2014)

Introduction:  Mortality risk estimates are often limited by the availability of individual patient risk factor data. We developed a series of prediction models for cardiovascular (CV) and non-cardiovascular (non-CV) death using increasing levels of information starting with the 1) standard history and physical examination, with incremental addition of 2) ECG and common lab values, 3) catheterization variables, and 4) research lab values.   Methods:  BARI 2D enrolled 2368 patients with type 2 diabetes and documented stable coronary artery disease from 6 countries. Patients were treated according to national diabetes, hypertension and cholesterol guidelines. Average follow-up was 5.4 years, and an independent adjudication committee classified 149 deaths as cardiovascular and 167 as non-cardiovascular. A series of four multivariable Cox regression models corresponding to the above levels of information were generated for CV and non-CV death, and Harrell c-statistics were used to evaluate model discrimination.   Results:  A history of heart failure, COPD and eGFR were significant independent predictors of both types of death. Classic cardiac risk factors including history of hypertension, ST depression, number of vessels with ≥50% stenosis, and reduced LV function were predictors of death due to cardiovascular causes whereas elevated CRP and total number of lesions were associated with death due to non-cardiovascular causes. Model discrimination for CV death improved with the addition of lab, ECG and angiographic information (c-statistic=0.720 with demographic and clinical predictors only, c-statistics=0.770 with all candidate variables). Improvement in model discrimination across the four models for non-CV death was less marked (c-statistics 0.740 to 0.766).   Conclusion:  Incremental prediction models provide clinically useful information as a patient is sequentially evaluated from the clinical to the lab.
Abstract 231: Preliminary Experience with Prehospital Pupillometry: A Prospective, Observational Study in Out-of-Hospital Cardiac Arrest
Authors: Joshua C Reynolds, Todd Chassee, Mark D Fankhauser, Amy Uber
Journal: Circulation (2014)

Objective: Physiologic monitoring &amp; neuroprognostication during resuscitation are relatively crude. Real time assessment of neurophysiology could be useful to guide resuscitative efforts. Objective assessment of the pupillary light reflex [PLR] is feasible during IHCA with a portable pupillometer, &amp; PLR is associated with survival &amp; neurologic outcome. We are conducting a prospective, observational study to assess the translational potential of pupillometry in the prehospital setting for OHCA. Hypotheses: Prehospital pupillometry is feasible &amp; qualitative assessment of PLR is associated with patient outcomes. Methods: Portable pupillometers (NeurOptics, Inc) were deployed for subjects with EMS treated OHCA. Serial recordings were obtained during routine pulse checks until ROSC, termination, or hospital arrival. We qualified PLR as normal/abnormal/absent with Neurologic Pupillary Index (NPiTM), a continuous scale that combines facets of PLR (e.g. % change, velocity, latency). We reviewed prehospital &amp; hospital records to identify patient characteristics &amp; outcomes, tabulated data as means/medians/proportions, &amp; estimated test performance characteristics. Results: From 2/14 - 6/14, a pupillometer was deployed to 38/58 (66%) patients with EMS treated OHCA (63 ± 16 years, 66% male, 33% witnessed, 54% bystander CPR, 11% shockable rhythm). Of 38 subjects, 21 (56%) were transported (19 ROSC &amp; 2 CPR). At the time of submission, follow-up data were available on 27 (71%) patients (6 survived to admission, 4 had therapeutic hypothermia, 3 had cardiac catheterization, 1 survived to discharge with excellent neurologic recovery). In total, 385 readings were attempted (median 8.5 attempts/patient; IQR 6-12). Median 47% (IQR 25%, 67%) readings had usable data. Most (92%) patients had ≥1 usable reading and 9/38 (24%) had any PLR during resuscitation. Conclusion: Prehospital pupillometry is feasible &amp; may yield prognostic information during resuscitation.