bluuebunny/crossref_metadata_2025_split huggingface dataset:
Estimation and correction of non-specific binding in a large-scale spike-in experiment
Authors: Schuster Eugene F , Blanc Eric , Partridge Linda , Thornton Janet M 
Published: June 2007

Abstract
Background
The availability of a recently published large-scale spike-in microarray dataset helps us to understand the influence of probe sequence in non-specific binding (NSB) signal and enables the benchmarking of several models for the estimation of NSB. In a typical microarray experiment using Affymetrix whole genome chips, 30% to 50% of the probes will apparently have absent target transcripts and show only NSB signal, and these probes can have significant repercussions for normalization and the statistical analysis of the data if NSB is not estimated correctly.

Results
We have found that the MAS5 perfect match-mismatch (PM-MM) model is a poor model for estimation of NSB, and that the Naef and Zhang sequence-based models can reasonably estimate NSB. In general, using the GC robust multi-array average, which uses Naef binding affinities, to calculate NSB (GC-NSB) outperforms other methods for detecting differential expression. However, there is an intensity dependence of the best performing methods for generating probeset expression values. At low intensity, methods using GC-NSB outperform other methods, but at medium intensity, MAS5 PM-MM methods perform best, and at high intensity, MAS5 PM-MM and Zhang's position-dependent nearest-neighbor (PDNN) methods perform best.

Conclusion
A combined statistical analysis using the MAS5 PM-MM, GC-NSB and PDNN methods to generate probeset values results in an improved ability to detect differential expression and estimates of false discovery rates compared with the individual methods. Additional improvements in detecting differential expression can be achieved by a strict elimination of empty probesets before normalization. However, there are still large gaps in our understanding of the Affymetrix GeneChip technology, and additional large-scale datasets, in which the concentration of each transcript is known, need to be produced before better models of specific binding can be created.
The bending of plate using a three-roll pyramid type plate bending machine
Authors: Bassett M B , Johnson W 
Published: June 2007

An experimental three-roll pyramid type plate bending machine was constructed and measurements were made of the upper roll vertical force, the driving torque and the relaxed radius of curvature for a given disposition of the top and bottom rolls. Two methods of analysing the plate bending process in the machine are given: (1) a geometrical analysis based on the assumption that the deflected form of the plate is in the arc of a circle and (2) a load analysis using the uniaxial stress-strain relationship for the material. The experimental results for an aluminium alloy (N.P.8) were best accounted for by the geometrical analysis whilst the load analysis gave disappointing predictions. In Part 2 experiments are reported on the bending of mild steel. In most of the experiments the two lower rolls were driven, but to determine the effect of plate roll friction, some were carried out in which the lower exit roll only was driven. A discussion of the various theoretical analyses which have been proposed is given and they are compared with the results of the authors' experiments.
The design and construction of a new apparatus for measuring the vertical forces exerted in walking: A gait machine
Authors: Skorecki J 
Published: June 2007

A device has been designed and constructed which produces permanent records of the variation with time of the vertical components of forces exerted on the ground by both feet of a human being when walking over a distance of about eleven feet. The device makes use of the elastic displacement of steel diaphragms, the viscous damping of air-free oil and the deflection of collimated beams of ultra-violet light by surface-silvered mirrors actuated by the diaphragms. The records are obtained on photo-sensitive paper. The accuracy of the device, both static and dynamic, is within one per cent. The device, known as a gait machine, has been installed at the Wrightington Hospital (near Wigan) where it replaces a primitive prototype. The machine, which is believed to be the only one of its kind, will be used as a clinical, diagnostic and research tool.
Transcending Operating Barriers Online for Disabled Bodies
Authors: Bowker Natilene I. , Tuffin Keith 
Published: June 2007

AbstractPeople with disabilities often face physical, social, and psychological barriers in daily life because of inaccessible structures and disability prejudice. The online medium's physically, nontaxing capacity for participation as well as a lack of visually mediated cues can potentially eliminate such barriers. This study discursively explored the psychological meaning of what it meant to be online for people with disabilities, focusing on possibilities for operating beyond their standard practices in daily life. Participants were recruited from various disability organisations in New Zealand and were invited to take part in an online interview. The notion of transcending barriers to participation formed a broad pattern in participants' data. This talk comprised 3 linguistic resources: life-altering, overcoming physical barriers, and disconnecting disability. Each resource offered participants a highly positive and significant transformation in subjectivity, enabling people with disabilities to be positioned as equal members of society.
Factors Associated With Exercise Participation and Attitudes to Exercise Among Pregnant Smokers
Authors: Ussher Michael , Ah-Yoon Michael , West Robert , Straus Lianne 
Published: June 2007

AbstractObjective: We assessed exercise levels and psychosocial aspects of exercise among pregnant smokers. Methods: A cross-sectional telephone survey of 88 pregnant smokers assessed levels of participation in exercise and psychosocial aspects of exercise; namely, self-efficacy, beliefs, perceived social support, perceived barriers, intentions and stage of change. Results: The women reported slightly higher levels of physical activity than for the general population of young women. The vast majority of women interviewed reported that exercise was important in their pregnancy, that they intended exercising regularly during pregnancy and were interested in exercise classes as an aid to smoking cessation. Fatigue was the most commonly reported barrier to physical activity during pregnancy, followed by ‘it takes too much time’, ‘uncomfortable when I exercise’ or ‘not sure what to do’. The vast majority of women expressed very little confidence and social support towards exercising. Conclusion: The results suggest that there is potential for using physical activity as an aid to smoking cessation during pregnancy. However, such interventions would need to be sufficiently intensive to address perceived barriers to exercise, lack of social support, low self-efficacy and be tailored to different stages of pregnancy.
Tobacco Interventions Delivered by Pharmacists: A Summary and Systematic Review
Authors: Dent Larry A. , Harris Kari Jo , Noonan Curtis W. 
Published: June 2007

Background. As one of the most accessible health care professionals, pharmacists are in an ideal position to provide tobacco‐cessation and prevention services. Although there is growing interest in expanding the pharmacist's role in tobacco treatment, few published studies have assessed the efficacy or effectiveness of tobacco‐cessation services delivered by pharmacists in the United States.Objective. To summarize and critique studies that examined pharmacist‐delivered tobacco‐cessation services.Methods. Articles written in English that appeared in peer‐reviewed journals were identified from a systematic review of literature published from 1980–2006. Publications were selected for review if the interventions were delivered by pharmacists, if the intervention included United States Food and Drug Administration—approved drugs (if drug therapy was used), and if smoking‐cessation rates could be calculated.Results. Fifteen studies met inclusion criteria. Fourteen of the studies targeted smoking, and one targeted spit (chewing) tobacco. Five studies were controlled, and 10 were uncontrolled. One of the controlled studies (chewing tobacco) and eight of the uncontrolled studies were conducted in the United States. Findings of the uncontrolled U.S. studies suggest that pharmacists can deliver smoking‐cessation services. Three of the controlled studies found statistically significant differences between the pharmacist‐based intervention and the control group, and the trend in the other two studies was toward the effectiveness of the pharmacist‐delivered intervention. Only six of the 15 studies reviewed used biochemical measures to verify self‐reported cessation.Conclusion. The uncontrolled and controlled studies reviewed demonstrate that pharmacists can deliver tobacco‐cessation interventions, and the evidence strongly suggests that they are effective in helping smokers to quit. Future studies conducted in the United States that are well controlled and include biochemical verification of smoking status are needed to provide definitive confirmation that pharmacist‐delivered interventions are effective for smoking cessation. With the availability and expanded training of pharmacists, this is an opportune time for testing and disseminating evidence‐based research evaluating the effectiveness of pharmacist‐delivered tobacco‐cessation services.
Health Outcomes and Economic Impact of Therapy Conversion to a Biphasic Insulin Analog Pen Among Privately Insured Patients with Type 2 Diabetes Mellitus
Authors: Cobden David , Lee Won Chan , Balu Sanjeev , Joshi Ashish V. , Pashos Chris L. 
Published: June 2007

Study Objective. To evaluate claims‐related treatment adherence, health care resource utilization, and associated costs of therapy conversion from an insulin vial and syringe to a premixed biphasic insulin analog pen device among privately insured patients with type 2 diabetes mellitus.Design. Retrospective, longitudinal, intrapatient (before and after) analysis.Data Source. PharMetrics database of medical and pharmaceutical claims from 57 commercial health plans across the United States.Patients. Four hundred eighty‐six adult patients with a confirmed diagnosis of type 2 diabetes who converted from an insulin analog vial and syringe (233 patients) or a human insulin vial and syringe (253 patients) to a biphasic insulin analog pen device between July 1, 2001 and December 31, 2002.Measurements and Main Results. All patients had no previous use of the pen device. Primary end points were medication possession ratio (MPR), a measure of adherence; hypoglycemic events; associations between treatment adherence and hypoglycemic events, and adherence and all‐cause health care costs; and all‐cause—attributable, hypoglycemia‐attributable, and other diabetes‐attributable costs. After conversion, MPR increased significantly from 59% to 68% (p<0.01). A significant decrease in the likelihood of experiencing a hypoglycemic event was also observed after conversion (odds ratio [OR] 0.40, 95% confidence interval [CI] 0.27–0.61, p<0.05), with hypoglycemic occurrences reduced nearly two thirds among subjects with optimal adherence indicated by an MPR of 80% or greater (incidence rate ratio 0.36, 95% CI 0.11–0.76, p<0.05). Significant decreases in hypoglycemia‐attributable emergency department visits (OR 0.36, 95% CI 0.16–0.84, p<0.05) and physician visits (OR 0.39, 95% CI 0.20–0.77, p<0.05) were observed. Total mean all‐cause annual treatment costs were reduced by $1748/patient (p<0.01), hypoglycemia‐attributable costs were reduced by $908/patient (p<0.01), and other diabetes‐attributable costs were reduced by $643/patient (p<0.01). Patients with an MPR of 80% or greater were associated with significant reductions in all‐cause health care costs (OR 0.55, 95% CI 0.31–0.80, p<0.05).Conclusion. Privately insured patients with type 2 diabetes may exhibit considerable improvements in clinical and economic outcomes after insulin therapy conversion from vial and syringe to a premixed biphasic insulin analog pen device.
Institutional Experience with Voriconazole Compared with Liposomal Amphotericin B as Empiric Therapy for Febrile Neutropenia
Authors: Shehab Nadine , DePestel Daryl D. , Mackler Emily R. , Collins Curtis D. , Welch Kathleen , Erba Harry P. 
Published: June 2007

Study Objective. To assess the effectiveness, safety, and cost of empiric treatment of febrile neutropenia before and after implementing an algorithm in which voriconazole was substituted for liposomal amphotericin B (L‐AmB).Design. Retrospective cohort analysis.Setting. An 850‐bed tertiary care hospital, which is also a referral site for patients with acute leukemia.Patients. Fifty‐five adult patients who started empiric antifungal therapy for febrile neutropenia between January 1, 2002, and December 31, 2003, encompassing 58 treatment episodes (defined as a hospitalization during which empiric antifungal therapy was administered).Measurements and Main Results. Medical charts, including patients' pharmacy and laboratory data, were reviewed. Twenty‐six and 32 episodes of L‐AmB and voriconazole use, respectively, were identified. No significant differences between the L‐AmB and voriconazole groups were noted at baseline. Rates of fever resolution (54% vs 59%, p=0.791) and breakthrough invasive fungal infections (11% vs 12%, p>0.999) were similar for the L‐AmB and voriconazole episodes. Premature drug discontinuation due to the prescriber's perceived lack of efficacy occurred most frequently in the voriconazole group (25% vs 8%, p=0.160). Survival was significantly higher in the voriconazole than in the L‐AmB group (100% vs 77%, p=0.006). Adverse effects that were significantly more common in the L‐AmB group than in the voriconazole group were elevated serum creatinine levels (27% vs 3%, p=0.017) and electrolyte disturbances (19% vs 0%, p=0.014). Adverse effects reported more frequently in the voriconazole group than in the L‐AmB group were visual disturbances (9% vs 0%, p=0.245) and elevated hepatic enzyme levels (9% vs 8%, p>0.999). Mean drug expenditures/episode for initial empiric antifungal therapy were lower for voriconazole than for L‐AmB ($1593 vs $4144, or $153 vs $380/day).Conclusion. Our institution's algorithm incorporating voriconazole into the empiric management of febrile neutropenia was associated with effectiveness outcomes comparable to those observed with L‐AmB as well as a lower frequency of adverse effects and overall expenditures for antifungal drugs.
Aprotinin Use in Cardiac Surgery Patients at Low Risk for Requiring Blood Transfusion
Authors: Kristeller Judith L. , Stahl Russell F. , Roslund Brian P. , Roke‐Thomas Marie 
Published: June 2007

Study Objectives. To determine if aprotinin is safe and effective in patients at low risk for requiring blood transfusion after cardiac surgery by evaluating whether there is any significant difference in blood product use or other significant clinical outcomes between patients who received aprotinin versus those who did not.Design. Retrospective review.Setting. Inpatient community nonteaching hospital.Patients. Three hundred thirty‐five patients who underwent primary cardiac surgery involving cardiopulmonary bypass between November 1, 2003, and December 31, 2005, and were considered at low risk for requiring postoperative blood transfusion; 162 patients received aprotinin and 173 patients received aminocaproic acid (control).Measurements and Main Results. Comparison of patients in the aprotinin group versus those in the aminocaproic acid group revealed no difference in total donor exposures to blood products (1.86 vs 1.16 units/patient, p=0.07), total packed red blood cells (PRBCs) received (1.25 vs 0.86 units/patient, p=0.09), postoperative donor exposures to blood products (0.91 vs 0.48 unit/patient, p=0.13), or postoperative PRBCs received (0.61 vs 0.40 unit/patient, p=0.23). No difference was noted in any other clinical outcome in the aprotinin group versus the aminocaproic acid group, including postoperative azotemia (13.0% vs 10.4%, p=0.46), new onset of atrial fibrillation (14.8% vs 15.0%, p=0.95), myocardial infarction, stroke, or death. Mean ± SD total hospital length of stay was similar in the aprotinin group versus the aminocaproic acid group (8.1 ± 3.8 vs 7.4 ± 2.8 days, p=0.08), but length of stay from surgery to discharge was longer in the aprotinin group than in the aminocaproic acid group (5.9 ± 0.17 vs 5.4 ± 0.12 days, p=0.032).Conclusion. Although aprotinin appeared to be safe in this low‐risk patient population, it was not more effective than aminocaproic acid in reducing blood product use after cardiac surgery. More robust evidence is needed from a controlled randomized trial to demonstrate the safety, efficacy, and pharmacoeconomic benefit of aprotinin.
Capitalisation, Commoditisation and Obligation among Ethiopia's Afar Pastoralists
Authors: Davies Jonathan 
Published: June 2007

Abstract
This paper on the Afar pastoralists of north-eastern Ethiopia examines their livelihood goals to understand how they view the institutions that are central to their existence. The paper examines the choices made in allocating livestock resources to accumulate different forms of capital. Using qualitative and quantitative research the paper considers the value of internal livestock exchange for accruing insurance and the impact that such value has on the commoditisation of livestock.
Characterization of Histaminergic Receptors
Authors: Strakhova Marina , Esbenshade Timothy A. 
Published: June 2007

AbstractThis unit describes radioligand binding protocols for histamine H1, H2, H3, and H4receptors. Because these receptors demonstrate low amino acid sequence homology and divergent pharmacological characteristics, assay conditions vary for each. These protocols can be employed in high‐throughput screening programs aimed at identifying selective agonists and antagonists for these sites.
Murine and Canine Models of Appendicular Osteosarcoma
Authors: Fan Timothy M. 
Published: June 2007

AbstractAppendicular osteosarcoma (OSA) is a primary bone sarcoma affecting humans during their second decade of life. Despite aggressive surgical and chemotherapeutic interventions, 30% of patients will experience progressive metastatic disease within 5 years of diagnosis. Understanding the biology of pediatric OSA and potential targets for therapeutic development remains an area of focus for both basic scientists and clinical oncologists. The identification and study of relevant comparative tumor models in mice and canines may allow for a better understanding of OSA biology, and permit the rapid investigation of novel therapeutic strategies for managing this metastatic bone sarcoma. This unit provides a protocol for using an orthotopic, syngeneic murine model of appendicular OSA as an investigative tool for the study of OSA biology. Additionally, the comparative relevance of spontaneously occurring appendicular OSA in canines for the study of pediatric bone sarcomas is discussed.
Carcinogen‐Induced Animal Models of Head and Neck Squamous Cell Carcinoma
Authors: Bassi Daniel E. , Klein‐Szanto A.J.P. 
Published: June 2007

AbstractThis unit provides two models of oral carcinogenesis (hamster cheek pouch and rat tongue), as well as more simple procedures to induce squamous cell carcinomas (SCCs) in mouse skin. The most significant usage of these models has been their application in studying the molecular pathology of the genesis and multi‐step progression of tobacco‐associated SCC. Nevertheless, these protocols have been used frequently as in vivo bioassays to demonstrate the chemopreventive and, to a lesser extent, the chemotherapeutic effects of numerous compounds. Several examples, using four different carcinogenesis protocols, are presented with detailed steps on how to elicit squamous lesions and when and how to apply test compounds that could have either cancer chemopreventive or chemotherapeutic effects.
Orthotopic Model of Human Pancreatic Ductal Adenocarcinoma and Cancer Cachexia in Nude Mice
Authors: Jones‐Bolin Susan , Ruggeri Bruce 
Published: June 2007

AbstractPancreatic ductal adenocarcinoma (PDAC) represents the fourth leading cause of cancer‐related deaths in the United States, with a 5‐year survival rate of only 2% to 10%. This tumor is aggressive, often metastasizing to distant sites (liver, lung, and adjacent intestines) by the time of diagnosis. Treatment options are limited, and the disease carries a grave prognosis for most patients. An orthotopic model of human PDAC in nude mice provides an excellent way to evaluate the pathogenesis of tumor growth and metastasis in order to develop therapies, to better define the underlying biology of tumor growth and metastasis, and to identify new molecular targets. This unit describes an orthotopic model of human PDAC in athymic nude mice that closely mimics the human condition. It is characterized by diffuse peritoneal, lymphatic, and hepatic metastatic spread and manifestations of a cancer cachexic phenotype.
Orthotopic Models of Human Gastric Carcinoma in Nude Mice: Applications for Study of Tumor Growth and Progression
Authors: Jones‐Bolin Susan , Ruggeri Bruce 
Published: June 2007

AbstractGastric carcinoma (GC) remains a leading cause of cancer related deaths worldwide with the 5‐year survival rate in the U.S. at ∼5% to 15% with existing therapies. This tumor is aggressive and has often metastasized to distant sites (liver, lung, and adjacent intestine) by the time of diagnosis. Treatment options (surgery, radiation, and chemotherapy) are limited and the disease carries a grave prognosis for most patients (50% 5‐year survival for distal GC; 10% 5‐year survival for proximal GC). An orthotopic model of human GC in nude mice provides an excellent way to evaluate the pathogenesis of tumor growth and metastasis in order to develop effective therapies, as well as to better understand the underlying biology of gastric tumor growth and metastasis. The protocol described in this unit details the development and characterization of an orthotopic model of human GC in athymic nude mice with diffuse lymphatic and hepatic metastatic spread. This model closely mimics the course of the human disease.
Solid‐Phase Oligonucleotide Labeling with DOTA
Authors: Jaakkola Lassi , Ylikoski Alice , Hovinen Jari 
Published: June 2007

AbstractThis unit describes a method to construct oligonucleotide conjugates labeled with 1,4,7,10‐tetraazacyclododecane‐1,4,7,10‐tetraacetic acid (DOTA) on a solid support. A nucleosidic phosphoramidite that contains a protected DOTA ligand compatible with normal chain assembly is prepared first. As the chain assembly is completed, the oligonucleotide is deprotected and converted to the corresponding gadolinium(III) chelate, resulting in an oligonucleotide conjugate containing the chelate at the 5′‐terminus.
Biophysical Analysis of Triple‐Helix Formation
Authors: Boutorine Alexandre S. , Escudé Christophe 
Published: June 2007

AbstractTwo methods for DNA triple‐helix analysis are described in this unit: a gel‐shift assay based on the slower electrophoretic migration of a triplex in a polyacrylamide gel under nondenaturing conditions, and an optical method in which the thermal denaturation of the triple helix is followed by UV spectrophotometry. Both methods give valuable information on the characteristics of DNA triple‐helix formation and triplex stability under different conditions.