tbuckley/cabot-search huggingface dataset:
The Phylogenetic Analysis of Variable-Length Sequence Data: Elongation Factor–1α Introns in European Populations of the Parasitoid Wasp Genus Pauesia (Hymenoptera: Braconidae: Aphidiinae)
Authors: Ana Sanchis, Jose M. Michelena, Amparo Latorre, Donald L. J. Quicke, Ulf Gärdenfors, Robert Belshaw
Journal: Molecular Biology and Evolution (2001)

Elongation factor-1alpha (EF-1alpha) is a highly conserved nuclear coding gene that can be used to investigate recent divergences due to the presence of rapidly evolving introns. However, a universal feature of intron sequences is that even closely related species exhibit insertion and deletion events, which cause variation in the lengths of the sequences. Indels are frequently rich in evolutionary information, but most investigators ignore sites that fall within these variable regions, largely because the analytical tools and theory are not well developed. We examined this problem in the taxonomically problematic parasitoid wasp genus Pauesia (Hymenoptera: Braconidae: Aphidiinae) using congruence as a criterion for assessing a range of methods for aligning such variable-length EF-1alpha intron sequences. These methods included distance- and parsimony-based multiple-alignment programs (CLUSTAL W and MALIGN), direct optimization (POY), and two "by eye" alignment strategies. Furthermore, with one method (CLUSTAL W) we explored in detail the robustness of results to changes in the gap cost parameters. Phenetic-based alignments ("by eye" and CLUSTAL W) appeared, under our criterion, to perform as well as more readily defensible, but computationally more demanding, methods. In general, all of our alignment and tree-building strategies recovered the same basic topological structure, which means that an underlying phylogenetic signal remained regardless of the strategy chosen. However, several relationships between clades were sensitive both to alignment and to tree-building protocol. Further alignments, considering only sequences belonging to the same group, allowed us to infer a range of phylogenetic relationships that were highly robust to tree-building protocol. By comparing these topologies with those obtained by varying the CLUSTAL parameters, we generated the distribution area of congruence and taxonomic compatibility. Finally, we present the first robust estimate of the European Pauesia phylogeny by using two EF-1alpha introns and 38 taxa (plus 3 outgroups). This estimate conflicts markedly with the traditional subgeneric classification. We recommend that this classification be abandoned, and we propose a series of monophyletic species groups.
BULLAE AND PARAESTHESIAE WITH ABSENT PATELLAR AND ACHILLES REFLEXES: A CLINICAL RECORD
Authors: F. PARKES WEBER
Journal: British Journal of Dermatology (1942)

Journal Article BULLAE AND PARAESTHESIAE WITH ABSENT PATELLAR AND ACHILLES REFLEXES: A CLINICAL RECORD Get access F. PARKES WEBER, M.D., F.R.C.P. F. PARKES WEBER, M.D., F.R.C.P. Senior Physician to the German Hospital, London Search for other works by this author on: Oxford Academic Google Scholar British Journal of Dermatology and Syphilis, Volume 54, Issue 3, 1 March 1942, Pages 69–71, https://doi.org/10.1111/j.1365-2133.1942.tb10616.x Published: 01 March 1942
Validation of the Lewis score for the evaluation of small-bowel Crohn’s disease activity
Authors: José Cotter, Francisca Dias de Castro, Joana Magalhães, Maria Moreira, Bruno Rosa
Journal: Endoscopy (2014)

The Lewis score was developed to measure mucosal inflammatory activity as detected by small-bowel capsule endoscopy (SBCE). The aim of the current study was to validate the Lewis score by assessing interobserver correlation and level of agreement in a clinical setting.This was a retrospective, single-center, double-blind study including patients with isolated small-bowel Crohn's disease who underwent SBCE. The Lewis score was calculated using a software application, based on the characteristics of villous edema, ulcers, and stenoses. The Lewis score was independently calculated by one of three investigators and by a central reader (gold standard). Interobserver agreement was assessed using intraclass correlation (ICC) coefficient and Bland - Altman plots.A total of 70 patients were consecutively included (mean age 33.9 ± 11.7 years). The mean Lewis score was 1265 and 1320 for investigators and the central reader, respectively. There was a high correlation, both for scores obtained for each tertile (first tertile r = 0.659 - 0.950, second tertile r = 0.756 - 0.906, third tertile r = 0.750 - 0.939), and for the global score (r = 0.745 - 0.928) (P < 0.0001). Interobserver agreement was almost perfect between the investigators and the central reader (first tertile ICC = 0.788 - 0.971, second tertile ICC = 0.824 - 0.943, third tertile ICC = 0.857 - 0.968, global score ICC = 0.852 - 0.960; P < 0.0001). The inflammatory activity was classified as normal (score < 135) in 2.9 % vs. 2.9 %, mild (score ≥ 135 - < 790) in 51.4 % vs. 55.7 %, and moderate to severe (score ≥ 790) in 45.8 % vs. 41.4 % of patients, respectively (P < 0.001).A strong interobserver agreement was demonstrated for the determination of the Lewis score in a practical clinical setting, validating this score for the reporting of small-bowel inflammatory activity. The Lewis score might be used for diagnosing, staging, follow-up, and therapeutic assessment of patients with isolated small-bowel Crohn's disease.
The association of vitamin D receptor gene polymorphisms and serum 25-hydroxyvitamin D levels with generalized vitiligo
Authors: K. Li, Q. Shi, L. Yang, X. Li, L. Liu, L. Wang, Q. Li, G. Wang, C.-Y. Li, T.-W. Gao
Journal: British Journal of Dermatology (2012)

Vitiligo is an acquired depigmentation autoimmune disorder that has been described as being associated with lower levels of 25-hydroxyvitamin D [25(OH)D]. Genetic variations within the vitamin D receptor (VDR) gene could lead to significant receptor dysfunction, and could further affect the formation of the biologically active 25(OH)D. Therefore, we hypothesized that VDR polymorphisms might be involved in vitiligo by affecting the formation of 25(OH)D.To evaluate the potential association between VDR polymorphisms and vitiligo susceptibility and the serum levels of 25(OH)D.We performed a hospital-based study of 749 patients with vitiligo and 763 matched controls. We investigated four VDR polymorphisms (FokI, BsmI, ApaI and TaqI) to determine whether they are associated with vitiligo susceptibility in the Chinese population. In addition, the levels of 25(OH)D were measured to evaluate possible associations between the VDR polymorphic variants and clinical and laboratory findings of vitiligo.A significantly decreased risk of developing vitiligo was found to be associated with the BsmI-B, ApaI-A and TaqI-t alleles. According to the genotype distribution, 25(OH)D concentrations were significantly higher in patients carrying the FokI ff or ApaI AA genotypes compared with those carrying the FF or aa genotypes. Logistic regression analysis also showed a dose-response relationship between decreased risk of vitiligo and increased 25(OH)D levels in ApaI-A variant genotype carriers.Our findings suggest that these VDR polymorphisms are associated with 25(OH)D levels and that there exists a genetic predisposition for vitiligo in the Chinese population.
New-Onset Diabetes After Renal Transplantation
Authors: Lidia Ghisdal, Steven Van Laecke, Marc J. Abramowicz, Raymond Vanholder, Daniel Abramowicz
Journal: Diabetes Care (2011)

New-onset diabetes after transplantation (NODAT) is a serious and frequent metabolic complication after renal transplantation. This entity is currently well defined since the publication of the International Consensus Guidelines in 2003. Here, we review the factors contributing to the risk of NODAT and the strategies related to modifiable factors, with emphasis on practical issues. Recognizing these factors may help clinicians to evaluate prospectively appropriate prevention strategies to minimize the risk of NODAT.

Over the past 50 years, the concept of NODAT has evolved in terms of name and definition. Before 2003, de novo diabetes that developed after transplantation was described in various terms, most frequently “posttransplantation diabetes mellitus,” and suffered from a lack of consensus regarding its definition. The most commonly used clinical definition was the requirement of insulin for a minimum period posttransplantation (often 30 days). This definition, however, identified only the most severe cases, leaving out the majority of patients with glucose metabolism disorders. International Consensus Guidelines on NODAT were published in 2003. They recommended that the diagnosis of NODAT should be based on the American Diabetes Association (ADA) criteria for type 2 diabetes published in 2003 (1,2). Since then, a follow-up report from the International Expert Committee further lowered the inferior limit of fasting plasma glucose (FPG) (100 mg/dL) that corresponds to impaired fasting glucose (IFG), based on epidemiologic predictive data (3). In addition, since 2009, the International Expert Committee recommended the use of a standardized A1C assay for diabetes diagnosis (A1C level ≥6.5%), a position that has been endorsed by ADA in 2010 (4). The Expert Committee stated that A1C assay cannot be used in conditions that change red cell turnover. This is the case of end-stage renal disease (ESRD) patients and newly transplanted kidney patients. For instance, the posttransplant period is frequently associated …
Tobacco-Specific Nitrosamines: Formation From Nicotine In Vitro and During Tobacco Curing and Carcinogenicity in Strain A Mice 2 3
Authors: Stephen S. Hecht, Chi-hong B. Chen, Norio Hirota, Raphael M. Ornaf, T. C. Tso, Dietrich Hoffmann
Journal: JNCI Journal of the National Cancer Institute (1978)

The formation of tobacco-specific nitrosamines from the major tobacco alkaloid nicotine was examined. Detached leaf tobacco was fed either [2′-14C]nicotine or [2′-14C]nornicotine and air cured. The cured leaf was then analyzed for [2′-14C]N′-nitrosonornicotine ([2′-14C]NNN). The yield of [2′-14C]NNN was 0.007% from nornicotine and 0.009% from nicotine. Because the ratio of nicotine to nornicotine in conventional nicotine-type tobacco is 20-100:1, nicotine is considered to be the major precursor for the carcinogen NNN in tobacco. The formation of other nitrosamines from nicotine in vitro was then studied. Reaction of nicotine with NaNO2 gave rise to NNN, as well as to two other nitrosamines, 4-(N-methyl-N-nitrosamino)-1- (3-pyridyl)-1-butanone (NNK) and 4-(N-methyl-N-nitrosamino)-4- (3-pyridyl)butanal (NNA). Analysis of market products revealed the presence of NNK (0.6–2.4 μg/g) in chewing tobacco and snuff. The tumorigenic activity of NNN, NNK, and NNA in strain A mice was studied. NNK induced more lung adenomas per mouse than did NNN, whereas NNA was less active than NNN. In addition, two cases of undifferentiated carcinoma of the salivary glands occurred in the NNN experimental groups.
A Comparison of Aprotinin and Lysine Analogues in High-Risk Cardiac Surgery
Authors: Dean A. Fergusson, Paul C. Hébert, C. David Mazer, Stephen Fremes, Charles MacAdams, John M. Murkin, Kevin Teoh, Peter C. Duke, Ramiro Arellano, Morris A. Blajchman, Jean S. Bussières, Dany Côté, Jacek Karski, Raymond Martineau, James A. Robblee, Marc Rodger, George Wells, Jennifer Clinch, Roanda Pretorius
Journal: New England Journal of Medicine (2008)

Antifibrinolytic agents are commonly used during cardiac surgery to minimize bleeding and to reduce exposure to blood products. We sought to determine whether aprotinin was superior to either tranexamic acid or aminocaproic acid in decreasing massive postoperative bleeding and other clinically important consequences.In this multicenter, blinded trial, we randomly assigned 2331 high-risk cardiac surgical patients to one of three groups: 781 received aprotinin, 770 received tranexamic acid, and 780 received aminocaproic acid. The primary outcome was massive postoperative bleeding. Secondary outcomes included death from any cause at 30 days.The trial was terminated early because of a higher rate of death in patients receiving aprotinin. A total of 74 patients (9.5%) in the aprotinin group had massive bleeding, as compared with 93 (12.1%) in the tranexamic acid group and 94 (12.1%) in the aminocaproic acid group (relative risk in the aprotinin group for both comparisons, 0.79; 95% confidence interval [CI], 0.59 to 1.05). At 30 days, the rate of death from any cause was 6.0% in the aprotinin group, as compared with 3.9% in the tranexamic acid group (relative risk, 1.55; 95% CI, 0.99 to 2.42) and 4.0% in the aminocaproic acid group (relative risk, 1.52; 95% CI, 0.98 to 2.36). The relative risk of death in the aprotinin group, as compared with that in both groups receiving lysine analogues, was 1.53 (95% CI, 1.06 to 2.22).Despite the possibility of a modest reduction in the risk of massive bleeding, the strong and consistent negative mortality trend associated with aprotinin, as compared with the lysine analogues, precludes its use in high-risk cardiac surgery. (Current Controlled Trials number, ISRCTN15166455 [controlled-trials.com].).
MECHANISMS OF DIGESTION AND ABSORPTION OF DIETARY VITAMIN A
Authors: Earl H. Harrison
Journal: Annual Review of Nutrition (2005)

Mechanisms involved in the digestion and absorption of dietary vitamin A require the participation of several proteins. Dietary retinyl esters are hydrolyzed in the intestine by the pancreatic enzyme, pancreatic triglyceride lipase, and intestinal brush border enzyme, phospholipase B. Unesterified retinol taken up by the enterocyte is complexed with cellular retinol-binding protein type 2 and the complex serves as a substrate for reesterification of the retinol by the enzyme lecithin:retinol acyltransferase (LRAT). The retinyl esters are then incorporated into chylomicrons, intestinal lipoproteins containing other dietary lipids, such as triglycerides, phospholipids, and free and esterified cholesterol, and apolipoprotein B. Chylomicrons containing newly absorbed retinyl esters are then secreted into the lymph. Although under normal dietary conditions much of the dietary vitamin A is absorbed via the chylomicron/lymphatic route, it is also clear that under some circumstances there is substantial absorption of unesterified retinol via the portal route. Evidence supports the idea that the cellular uptake and efflux of unesterified retinol by enterocytes is mediated by lipid transporters, but the exact number, identity, and role of these proteins is not known and is an active area of research.
Effect of Hormones and Epidermal Growth Factor on the Growth of the Hormone-Responsive 13762NF Rat Mammary Tumor in Collagen Gel Culture2
Authors: James E. Richards, Marc Edery, Rebecca C. Osborn, Lisa N. Larson, Satyabrata Nandi
Journal: JNCI Journal of the National Cancer Institute (1986)

The hormone-responsive mammary tumor 13762NF of the F344 rat was cultured in a collagen gel matrix with the use of a serum-free medium supplemented with hormones and epidermal growth factor (EGF). Hydrocortisone (F) had the greatest effect on cell growth. EGF had no growth-promoting activity when used alone, but it had a significant effect when used with F. There was also a population of cells responsive to progesterone (P) and prolactin (PRL). P synergized with EGF as well as with PRL to promote growth. 17 beta-Estradiol alone or in combination with other hormones had no growth-promoting activity. Receptor levels in the tumor were high for glucocorticoids, intermediate for P and EGF, and low for estrogens. Metastasis in the lung and lymph node showed the same basic hormonal responses as the parent tumor. Cultured cells produced tumors with the same histopathology as the parent tumor when transplanted back into female rats; they had the same receptor levels and when placed back in culture showed a growth response to the same set of hormones. The tumor cells formed colonies that were spherical, which was different from the branching structures formed by normal mammary cells in collagen gel.
Mucocutaneous manifestations of helminth infections
Authors: Omar Lupi, Christopher Downing, Michael Lee, Livia Pino, Francisco Bravo, Patricia Giglio, Aisha Sethi, Sidney Klaus, Omar P. Sangueza, Claire Fuller, Natalia Mendoza, Barry Ladizinski, Laila Woc-Colburn, Stephen K. Tyring
Journal: Journal of the American Academy of Dermatology (2015)
Improving Quality of Care Through Disease Management
Authors: David P. Faxon, Lee H. Schwamm, Richard C. Pasternak, Eric D. Peterson, Barbara Joyce McNeil, Vincent Bufalino, Clyde W. Yancy, Lawrence M. Brass, David W. Baker, Robert O. Bonow, Lynn A. Smaha, Daniel W. Jones, Sidney C. Smith, Gray Ellrodt, Jerilyn Allen, Sanford J. Schwartz, Gregg Fonarow, Pam Duncan, Katie Horton, Renee Smith, Steve Stranne, Kenneth Shine
Journal: Circulation (2004)

P rivate and public policymakers and health insurance plans increasingly are examining and introducing disease management programs to help treat chronic illnesses such as cardiovascular disease and stroke.The term disease management programs typically refers to multidisciplinary efforts to improve the quality and cost-effectiveness of care for select patients with chronic illness.This trend highlights the importance of assessing the clinical and public policy implications of this phenomenon from the perspectives of patients' best interests and quality of care.To address the complex issues surrounding disease management, the American Heart Association (AHA) assembled a multidisciplinary Advisory Working Group on Disease Management in 2002 to offer ongoing guidance in this evolving area.The Advisory Working Group developed a working definition of disease management and established core principles for the application of disease management to cardiovascular disease and stroke, which are the subject of this report.The American Heart Association makes every effort to avoid any actual or potential conflicts of interest that may arise as a result of an outside relationship or a personal, professional, or business interest of a member of the writing panel.Specifically, all members of the writing group are required to complete and submit a Disclosure Questionnaire showing all such relationships that might be perceived as real or potential conflicts of interest.
Ventral Tegmental Area Neurons in Learned Appetitive Behavior and Positive Reinforcement
Authors: Howard L. Fields, Gregory O. Hjelmstad, Elyssa B. Margolis, Saleem M. Nicola
Journal: Annual Review of Neuroscience (2007)

Ventral tegmental area (VTA) neuron firing precedes behaviors elicited by reward-predictive sensory cues and scales with the magnitude and unpredictability of received rewards. These patterns are consistent with roles in the performance of learned appetitive behaviors and in positive reinforcement, respectively. The VTA includes subpopulations of neurons with different afferent connections, neurotransmitter content, and projection targets. Because the VTA and substantia nigra pars compacta are the sole sources of striatal and limbic forebrain dopamine, measurements of dopamine release and manipulations of dopamine function have provided critical evidence supporting a VTA contribution to these functions. However, the VTA also sends GABAergic and glutamatergic projections to the nucleus accumbens and prefrontal cortex. Furthermore, VTA-mediated but dopamine-independent positive reinforcement has been demonstrated. Consequently, identifying the neurotransmitter content and projection target of VTA neurons recorded in vivo will be critical for determining their contribution to learned appetitive behaviors.
Three palonosetron regimens to prevent CINV in myeloma patients receiving multiple-day high-dose melphalan and hematopoietic stem cell transplantation
Authors: S.A. Giralt, K.F. Mangan, R.T. Maziarz, J.S. Bubalo, R. Beveridge, D.D. Hurd, F.L. Mendoza, E.B. Rubenstein, T.J. DeGroot, M.W. Schuster
Journal: Annals of Oncology (2010)
Hospitals fear that GPs will invite tenders on services to avoid legal challenges from private sector
Authors: A. O'Dowd
Journal: BMJ (2013)

<h3>OBJECTIVE:</h3> To assess the possible use of hyaluronic acid (HA) and interleukin-6 (IL-6) together as a biochemical marker of liver damage in mushroom poisoning (MP). <h3>METHODS:</h3> We prospectively studied patients with MP who were admitted to the emergency service, between April 2005 and April 2007, Samsun, Turkey. Twenty-seven patients with MP were included in the study. Serum HA and IL-6 levels of the patients were determined using enzyme-linked immunosorbent assay daily for a total of 3 days. Ten healthy adults were included in the study to serve as controls. The patients were divided into survivors, and non-survivors. <h3>RESULTS:</h3> There was no significant difference between the patients and controls with respect to serum HA levels on admission (p&gt;0.05). However, IL-6 levels on admission were significantly higher in the patients than the control group (p&lt;0.01). Serum HA and IL-6 levels on admission, and the following days were significantly higher in non-surviving patients (n=5) than in surviving patients (n=22) (p&lt;0.05). There was a significant correlation between HA and IL-6 (r=0.42, p&lt;0.05) on admission. The HA concentration was also significantly correlated with aspartate aminotransferase, alanine aminotransferase, and creatinine levels during the observation period. Serum HA and IL-6 levels increased in non-surviving patients throughout the period of observation. <h3>CONCLUSION:</h3> Increased serum HA and IL-6 levels are associated with hepatic damage in acute MP. Hyaluronic acid may be a useful marker in the assessment of MP-induced acute liver failure in clinical practice.
CD14 is a coreceptor of Toll-like receptors 7 and 9
Authors: Christoph L. Baumann, Irene M. Aspalter, Omar Sharif, Andreas Pichlmair, Stephan Blüml, Florian Grebien, Manuela Bruckner, Pawel Pasierbek, Karin Aumayr, Melanie Planyavsky, Keiryn L. Bennett, Jacques Colinge, Sylvia Knapp, Giulio Superti-Furga
Journal: The Journal of Experimental Medicine (2010)

Recognition of pathogens by the innate immune system requires proteins that detect conserved molecular patterns. Nucleic acids are recognized by cytoplasmic sensors as well as by endosomal Toll-like receptors (TLRs). It has become evident that TLRs require additional proteins to be activated by their respective ligands. In this study, we show that CD14 (cluster of differentiation 14) constitutively interacts with the MyD88-dependent TLR7 and TLR9. CD14 was necessary for TLR7- and TLR9-dependent induction of proinflammatory cytokines in vitro and for TLR9-dependent innate immune responses in mice. CD14 associated with TLR9 stimulatory DNA in precipitation experiments and confocal imaging. The absence of CD14 led to reduced nucleic acid uptake in macrophages. Additionally, CD14 played a role in the stimulation of TLRs by viruses. Using various types of vesicular stomatitis virus, we showed that CD14 is dispensable for viral uptake but is required for the triggering of TLR-dependent cytokine responses. These data show that CD14 has a dual role in nucleic acid–mediated TLR activation: it promotes the selective uptake of nucleic acids, and it acts as a coreceptor for endosomal TLR activation.