bluuebunny/crossref_metadata_2025_split huggingface dataset:
Incidence and predictors of cetuximab hypersensitivity reactions in a North Carolina academic medical center
Authors: Hansen Nicole L , Chandiramani Divya V , Morse Michael A , Wei David , Hedrick Nancy E , Hansen Richard A 
Published: February 2010

Objectives. Previous research has indicated a high incidence of cetuximab hypersensitivity reactions in the southern US. This study documents the incidence of hypersensitivity reactions in North Carolina, and explores whether factors such as patient demographics, allergy history, premedications, and cancer type are potential predictors for cetuximab reactions. Methods. This retrospective chart review consisted of 72 consecutively treated patients from Duke University’s Morris Oncology treatment center between September 2005 and August 2007. Data regarding stage of malignancy, premedications, and hypersensitivity reactions were collected from electronic databases. The number and type of reactions were characterized. Patients with and without hypersensitivity reactions were compared using bivariate statistics and multivariate logistic regression. Results. Of the 72 patients, 21 (29%) experienced hypersensitivity reactions. The majority of reactions (62%) were grades III or IV. Of the 21 patients having a reaction, 9 (43%) were sent to the emergency room and 5 (24%) had an overnight hospitalization. Three hospitalized patients were admitted to the intensive care unit. Both male gender (p = 0.039) and head/neck cancer (p = 0.014) were related to an increased likelihood of hypersensitivity reaction in bivariate analyses. In multivariate analyses, controlling for demographics, allergy history, premedications, and cancer type/stage, only type of cancer was predictive of hypersensitivity reaction (colon vs head/neck OR = 0.177; 95% CI 0.036—0.858). Conclusion. This study confirms a high rate of cetuximab hypersensitivity reactions in a southern region of the US. Patients with head/neck cancers were significantly more likely to have hypersensitivity reactions than patients with colon cancers. J Oncol Pharm Practice (2011) 17: 125—130.
LINNAEUS: A species name identification system for biomedical literature
Authors: Gerner Martin , Nenadic Goran , Bergman Casey M 
Published: February 2010

Abstract

Background
The task of recognizing and identifying species names in biomedical literature has recently been regarded as critical for a number of applications in text and data mining, including gene name recognition, species-specific document retrieval, and semantic enrichment of biomedical articles.

Results
In this paper we describe an open-source species name recognition and normalization software system, LINNAEUS, and evaluate its performance relative to several automatically generated biomedical corpora, as well as a novel corpus of full-text documents manually annotated for species mentions. LINNAEUS uses a dictionary-based approach (implemented as an efficient deterministic finite-state automaton) to identify species names and a set of heuristics to resolve ambiguous mentions. When compared against our manually annotated corpus, LINNAEUS performs with 94% recall and 97% precision at the mention level, and 98% recall and 90% precision at the document level. Our system successfully solves the problem of disambiguating uncertain species mentions, with 97% of all mentions in PubMed Central full-text documents resolved to unambiguous NCBI taxonomy identifiers.

Conclusions
LINNAEUS is an open source, stand-alone software system capable of recognizing and normalizing species name mentions with speed and accuracy, and can therefore be integrated into a range of bioinformatics and text-mining applications. The software and manually annotated corpus can be downloaded freely at http://linnaeus.sourceforge.net/.
Identification of genes involved in the mutualistic colonization of the nematode Heterorhabditis bacteriophora by the bacterium Photorhabdus luminescens
Authors: Easom Catherine A , Joyce Susan A , Clarke David J 
Published: February 2010

Abstract

Background

Photorhabdus are Gram negative entomopathogenic bacteria that also have a mutualistic association with nematodes from the family Heterorhabditis. An essential part of this symbiosis is the ability of the bacterium to colonize the gut of the freeliving form of the nematode called the infective juvenile (IJ). Although the colonization process (also called transmission) has been described phenomonologically very little is known about the underlying molecular mechanisms. Therefore, in this study, we were interested in identifying genes in Photorhabdus that are important for IJ colonization.

Results
In this work we genetically tagged P. luminescens TT01 with gfp and constructed a library containing over 3200 mutants using the suicide vector, pUT-Km2. Using a combination of in vitro symbiosis assays and fluorescent microscopy we screened this library for mutants that were affected in their ability to colonize the IJ i.e. with decreased transmission frequencies. In total 8 mutants were identified with transmission frequencies of ≤ 30% compared to wild-type. These mutants were mapped to 6 different genetic loci; the pbgPE operon, galE, galU, proQ, asmA and hdfR. The pbgPE, galE and galU mutants were all predicted to be involved in LPS biosynthesis and, in support of this, we have shown that these mutants are avirulent and sensitive to the cationic antimicriobial peptide, polymyxin B. On the other hand the proQ, asmA and hdfR mutants were not affected in virulence and were either as resistant (proQ) or slightly more sensitive (asmA, hdfR) to polymyxin B than the wild-type (WT).

Conclusions
This is the first report describing the outcome of a comprehensive screen looking for transmission mutants in Photorhabdus. In total 6 genetic loci were identified and we present evidence that all of these loci are involved in the assembly and/or maintenance of LPS and other factors associated with the cell surface. Interestingly several, but not all, of the transmission mutants identified were also avirulent suggesting that there is a significant, but not complete, genetic overlap between pathogenicity and mutualism. Therefore, this study highlights the importance of the cell surface in mediating the symbiotic and pathogenic interactions of Photorhabdus.
Training of patient and consumer representatives in the basic competencies of evidence-based medicine: a feasibility study
Authors: Berger Bettina , Steckelberg Anke , Meyer Gabriele , Kasper Jürgen , Mühlhauser Ingrid 
Published: February 2010

Abstract

Background
Evidence-based medicine (EBM) has become standard approach in medicine. Patients and health authorities increasingly claim active patient roles in decision making. Education to cope with these roles might be useful. We investigated the feasibility, acceptability and possible impact of EBM training courses for patient and consumer representatives.

Methods
We designed a generic one-week EBM course based on previous experience with EBM courses for non-medical health professionals. A course specific competence test has been developed and validated to measure EBM skills. Formative and summative evaluation of the course comprised: 1) EBM skills; 2) individual learning goals; 3) self-reported implementation after six months using semi-structured interviews; 4) group-based feedback by content analysis. EBM skills' achievement was compared to results gathered by a group of undergraduate University students of Health Sciences and Education who had attended a comparable EBM seminar.

Results
Fourteen EBM courses were conducted including 161 participants without previous EBM training (n = 54 self-help group representatives, n = 64 professional counsellors, n = 36 patient advocates, n = 7 others); 71% had a higher education degree; all but five finished the course. Most participants stated personal learning goals explicitly related to practicing EBM such as acquisition of critical appraisal skills (n = 130) or research competencies (n = 67). They rated the respective relevance of the course on average with 80% (SD 4) on a visual analogue scale ranging from 0 to 100%.
Participants passed the competence test with a mean score of 14.7 (SD 3.0, n = 123) out of 19.5 points. The comparison group of students achieved a mean score of 14.4 (SD 3.3, n = 43). Group-based feedback revealed increases of self confidence, empowerment through EBM methodology and statistical literacy, and acquisition of new concepts of patient information and counselling. Implementation of EBM skills was reported by 84 of the 129 (65%) participants available for follow-up interviews. Barriers included lack of further support, limited possibilities to exchange experiences, and feeling discouraged by negative reactions of health professionals.

Conclusions
Training in basic EBM competencies for selected patient and consumer representatives is feasible and accepted and may affect counselling and advocacy activities. Implementation of EBM skills needs support beyond the training course.
Flow cytometry for the evaluation of anti-plasmodial activity of drugs on Plasmodium falciparum gametocytes
Authors: Chevalley Séverine , Coste Agnès , Lopez Alexandrine , Pipy Bernard , Valentin Alexis 
Published: February 2010

Abstract

Background
The activity of promising anti-malarial drugs against Plasmodium gametocytes is hard to evaluate even in vitro. This is because visual examination of stained smears, which is commonly used, is not totally convenient. In the current study, flow cytometry has been used to study the effect of established anti-malarial drugs against sexual stages obtained from W2 strain of Plasmodium falciparum. Gametocytes were treated for 48 h with different drug concentrations and the gametocytaemia was then determined by flow cytometry and compared with visual estimation by microscopy.

Results and conclusions
Initially gametocytaemia was evaluated either using light microscopy or flow cytometry. A direct correlation (r2 = 0.9986) was obtained. Two distinct peaks were observed on cytometry histograms and were attributed to gametocyte populations. The activities of established anti-malarial compounds were then measured by flow cytometry and the results were equivalent to those obtained using light microscopy. Primaquine and artemisinin had IC50 of 17.6 μM and 1.0 μM, respectively.
Gametocyte sex was apparently distinguishable by flow cytometry as evaluated after induction of exflagellation by xanthurenic acid. These data form the basis of further studies for developing new methods in drug discovery to decrease malaria transmission.
Leukotriene B4, administered via intracerebroventricular injection, attenuates the antigen-induced asthmatic response in sensitized guinea pigs
Authors: Zhu Yi-Liang , Zhang Shui-Jun , Deng Yang-Mei , Dong Xin-Wei , Jiang Jun-Xia , Xie Qiang-Min 
Published: February 2010

Abstract

Background
Despite intensive studies focused on the pathophysiology of asthmatic inflammation, little is known about how cross-talk between neuroendocrine and immune systems regulates the inflammatory response during an asthmatic attack. We recently showed corresponding changes of cytokines and leukotriene B4 (LTB4) in brain and lung tissues of antigen-challenged asthmatic rats. Here, we investigated how LTB4 interacts with the neuroendocrine-immune system in regulating antigen-induced asthmatic responses in sensitized guinea pigs.

Methods
Ovalbumin-sensitized guinea pigs were challenged by inhalation of antigen. Vehicle, LTB4 or U75302 (a selective LTB4 BLT1 receptor inhibitor) was given via intracerebroventricular injection (i.c.v.) 30 min before challenge. Airway contraction response was evaluated using Penh values before and after antigen challenge. The inflammatory response in lung tissue was evaluated 24 h after challenge. The LTB4 content of lung and brain homogenate preparations was detected by reversed phase high-performance liquid chromatography (RP-HPLC). Plasma levels of adrenocorticotropic hormone (ACTH) and corticosterone (CORT) were measured using ELISA kits.

Results
Antigen challenge impaired pulmonary function and increased inflammatory cell infiltration in lung tissue. These responses could be significantly suppressed by LTB4, 30 ng i.c.v., in ovalbumin-sensitized guinea pigs. LTB4 content of lung and brain homogenates from antigen-challenged guinea pigs was significantly increased. In addition, administration of LTB4 via i.c.v. markedly increased CORT and ACTH level in plasma before antigen challenge, and there were further increases in CORT and ACTH levels in plasma after antigen challenge. U75302, 100 ng i.c.v., completely blocked the effects of LTB4. In addition, U75302, 100 ng via i.c.v. injection, markedly decreased LTB4 content in lung homogenates, but not in brain homogenates.

Conclusions
Increased LTB4 levels in brain during asthmatic attacks down-regulates airway contraction response and inflammation through the BLT1 receptor. Stimulation of the hypothalamic-pituitary-adrenal axis by LTB4 may result in an increase in systemic glucocorticoids which, in turn, would feed back to suppress the asthmatic response.
Is Duhuo Jisheng Tang containing Xixin safe? A four-week safety study
Authors: Hsieh Shu-Ching , Lai Jung-Nien , Chen Pau-Chung , Chen Chao-Chung , Chen Huey-Jen , Wang Jung-Der 
Published: February 2010

Abstract

Background
Though the nephrotoxicity and carcinogenicity of aristolochic acid (AA) are known, its safety in clinical usage is not clear. This study aims to evaluate the safety of Duhuo Jisheng Tang (DJT) in a four-week study to treat osteoarthritis (OA) of the knee.

Methods
A qualitative and quantitative investigations on DJT were conducted. A list of adverse events (AEs), complete blood counts, and liver and kidney function tests were measured for participants with knee OA at their scheduled hospital visits. Each detected AEs was independently assessed for severity and causality by site investigators (Chinese medical doctors) and study nurses.

Results
A total of 71 eligible subjects were included in the clinical study where 287 AEs were reported. DJT did not contain detectable aristolochic acid (AA) under thin-layer chromatography (TLC) analysis and gas chromatography coupled with mass spectrometry (GC-MS). There were no significant changes in liver or kidney functions.

Conclusion
In four-week use of DJT, no renal tubular damage, no severe incidences of AEs and adverse drug reactions (ADRs) were observed. The present study obtained safety data from active surveillance of DJT.
Decreased response inhibition in middle-aged male patients with type 2 diabetes
Authors: Ishizawa Kaya T , Kumano Hiroaki , Sato Atsushi , Sakura Hiroshi , Iwamoto Yasuhiko 
Published: February 2010

AbstractBackgroundThis study was performed to examine whether patients with type 2 diabetes have cognitive deficits associated with the prefrontal cortex (PFC).MethodsTwenty-seven middle-aged patients with newly diagnosed type 2 diabetes and 27 healthy controls underwent physical measurements and neuropsychological tasks. Response inhibition, reward prediction, and executive function were assessed by the Go/NoGo task, the reversal and extinction tasks, and the Wisconsin Card Sorting Test (WCST). To examine the interactions of being overweight with diabetes on cognitive performance, performance data were analysed by two-way ANCOVA with diabetes and overweight as factors and age as a covariate.ResultsPatients with type 2 diabetes showed significantly decreased response inhibition in the Go/NoGo task (discriminability index:P= 0.001). There was an interaction of being overweight with diabetes on reaction time in the Go trials of the Go/NoGo task (P= 0.009). Being overweight was related to retained responses to the presentiment of reward in the extinction task (P= 0.029). The four groups showed normal cognitive performance in the WCST.ConclusionsOur results showed that middle-aged, newly diagnosed and medication-free patients with type 2 diabetes have a particular neuropsychological deficit in inhibitory control of impulsive response, which is an independent effect of diabetes apart from being overweight.
Comparative kinetic analysis of two fungal β-glucosidases
Authors: Chauve Marie , Mathis Hugues , Huc Delphine , Casanave Dominique , Monot Frédéric , Lopes Ferreira Nicolas 
Published: February 2010

Abstract

Background
The enzymatic hydrolysis of cellulose is still considered as one of the main limiting steps of the biological production of biofuels from lignocellulosic biomass. It is a complex multistep process, and various kinetic models have been proposed. The cellulase enzymatic cocktail secreted by Trichoderma reesei has been intensively investigated. β-glucosidases are one of a number of cellulolytic enzymes, and catalyze the last step releasing glucose from the inhibitory cellobiose. β-glucosidase (BGL1) is very poorly secreted by Trichoderma reesei strains, and complete hydrolysis of cellulose often requires supplementation with a commercial β-glucosidase preparation such as that from Aspergillus niger (Novozymes SP188). Surprisingly, kinetic modeling of β-glucosidases lacks reliable data, and the possible differences between native T. reesei and supplemented β-glucosidases are not taken into consideration, possibly because of the difficulty of purifying BGL1.

Results
A comparative kinetic analysis of β-glucosidase from Aspergillus niger and BGL1 from Trichoderma reesei, purified using a new and efficient fast protein liquid chromatography protocol, was performed. This purification is characterized by two major steps, including the adsorption of the major cellulases onto crystalline cellulose, and a final purification factor of 53. Quantitative analysis of the resulting β-glucosidase fraction from T. reesei showed it to be 95% pure. Kinetic parameters were determined using cellobiose and a chromogenic artificial substrate. A new method allowing easy and rapid determination of the kinetic parameters was also developed. β-Glucosidase SP188 (Km = 0.57 mM; Kp = 2.70 mM) has a lower specific activity than BGL1 (Km = 0.38 mM; Kp = 3.25 mM) and is also more sensitive to glucose inhibition. A Michaelis-Menten model integrating competitive inhibition by the product (glucose) has been validated and is able to predict the β-glucosidase activity of both enzymes.

Conclusions
This article provides a useful comparison between the activity of β-glucosidases from two different fungi, and shows the importance of fully characterizing both enzymes. A Michaelis-Menten model was developed, including glucose inhibition and kinetic parameters, which were accurately determined and compared. This model can be further integrated into a cellulose hydrolysis model dissociating β-glucosidase activity from that of other cellulases. It can also help to define the optimal enzymatic cocktails for new β-glucosidase activities.
Estrogen receptor positive breast cancers in BRCA1 mutation carriers: clinical risk factors and pathologic features
Authors: Tung Nadine , Wang Yihong , Collins Laura C , Kaplan Jennifer , Li Hailun , Gelman Rebecca , Comander Amy H , Gallagher Bridget , Fetten Katharina , Krag Karen , Stoeckert Kathryn A , Legare Robert D , Sgroi Dennis , Ryan Paula D , Garber Judy E , Schnitt Stuart J 
Published: February 2010

Abstract
Introduction
Most breast cancers that occur in women with germline BRCA1 mutations are estrogen receptor-negative (ER-) and also typically lack expression of progesterone receptor (PR) and HER2 overexpression. We undertook a study to assess the clinical factors that predict for an estrogen receptor positive (ER+) breast cancer in BRCA1 mutation carriers and to characterize the pathologic features of these tumors.

Methods
Clinical characteristics of BRCA1 carriers with 58 ER+ and 114 ER- first invasive breast cancers were compared. Pathologic features of BRCA1 ER+ cancers were compared to those of BRCA1 ER- cancers and to age-matched ER+ sporadic cancers.

Results
BRCA1 carriers aged ≥ 50 at diagnosis of first invasive breast cancer were more likely to have an ER+ cancer compared to those aged < 50 (57% vs 29%, P = 0.005). ER+ BRCA1 cancers were less likely than ER- BRCA1 cancers to have "BRCA-associated" features such as high mitotic activity, geographic necrosis/fibrotic focus, and pushing margins (RR 0.06, 0.22, 0.24; P < 0.001, 0.02, 0.03 respectively). When compared to sporadic ER+ cancers, ER+ BRCA1 cancers were more often of invasive ductal type (RR 2.4, P = 0.03), with a high mitotic rate (RR 5.0, P = 0.006) and absent or mild lymphocytic infiltrate (RR 10.2, P = 0.04).

Conclusions
BRCA1 carriers who are older at first breast cancer diagnosis are more likely to have ER+ tumors than younger BRCA1 carriers. These ER+ cancers appear pathologically "intermediate" between ER- BRCA1 cancers and ER+ sporadic breast cancers raising the possibility that either some ER+ BRCA1 cancers are incidental or that there is a unique mechanism by which these cancers develop.
An Inflammatory Gene-Expression Fingerprint in Monocytes of Autoimmune Thyroid Disease Patients
Authors: van der Heul-Nieuwenhuijsen Leonie , Padmos Roos C. , Drexhage Roosmarijn C. , de Wit Harm , Berghout Arie , Drexhage Hemmo A. 
Published: February 2010

Abstract
Context: In monocytes of patients with autoimmune diabetes, we recently identified a gene expression fingerprint of two partly overlapping gene clusters, a PDE4B-associated cluster (consisting of 12 core proinflammatory cytokine/compound genes), a FABP5-associated cluster (three core genes), and a set of nine overlapping chemotaxis, adhesion, and cell assembly genes correlating to both PDE4B and FABP5.
Objective: Our objective was to study whether a similar monocyte inflammatory fingerprint as found in autoimmune diabetes is present in autoimmune thyroid disease (AITD).
Design and Patients: Quantitative PCR was used for analysis of 28 genes in monocytes of 67 AITD patients and 70 healthy controls. The tested 28 genes were the 24 genes previously found abnormally expressed in monocytes of autoimmune diabetes patients plus four extra genes found in whole-genome analysis of monocytes of AITD patients reported here.
Results: Monocytes of 24% of AITD and 50% of latent autoimmune diabetes of adults (LADA) patients shared an inflammatory fingerprint consisting of the set of 24 genes of the PDE4B, FABP5, and overlapping gene sets. This study in addition revealed that FCAR, the gene for the Fcα receptor I, and PPBP, the gene for CXCL7, were part of this proinflammatory monocyte fingerprint.
Conclusions: Our study provides an important tool to determine a shared, specific proinflammatory state of monocytes in AITD and LADA patients, enabling further research into the role of such proinflammatory cells in the failure to preserve tolerance in these conditions and of key fingerprint genes involved.
Cost and Impact of a Quality Improvement Programme in Mental Health Services
Authors: Beecham Jennifer , Ramsay Angus , Gordon Kate , Maltby Sophie , Walshe Kieran , Shaw Ian , Worrall Adrian , King Sarah 
Published: February 2010

Objective To estimate the cost and impact of a centrally-driven quality improvement initiative in four UK mental health communities. Methods Total costs in year 1 were identified using documentation, a staff survey, semi-structured interviews and discussion groups. Few outcome data were collected within the programme so thematic analysis was used to identify the programme's impact within its five broad underlying principles. Results The survey had a 40% response. Total costs ranged between £164,000 and £458,000 per site, plus staff time spent on workstreams. There was a very hazy view of the resources absorbed and poor recording of expenditure and activity. The initiative generated little demonstrable improvements in service quality but some participants reported changes in attitudes. Conclusions Given the difficult contexts, short time-scales and capacity constraints, the programme's lack of impact is not surprising. It may, however, represent a worthwhile investment in cultural change which might facilitate improvements in how services are delivered.