bluuebunny/crossref_metadata_2025_split huggingface dataset:
A study of inter-lab and inter-platform agreement of DNA microarray data
Authors: Wang Huixia , He Xuming , Band Mark , Wilson Carole , Liu Lei 
Published: May 2005

AbstractAs gene expression profile data from DNA microarrays accumulate rapidly, there is a natural need to compare data across labs and platforms. Comparisons of microarray data can be quite challenging due to data complexity and variability. Different labs may adopt different technology platforms. One may ask about the degree of agreement we can expect from different labs and different platforms. To address this question, we conducted a study of inter-lab and inter-platform agreement of microarray data across three platforms and three labs. The statistical measures of consistency and agreement used in this paper are the Pearson correlation, intraclass correlation, kappa coefficients, and a measure of intra-transcript correlation. The three platforms used in the present paper were Affymetrix GeneChip, custom cDNA arrays, and custom oligo arrays. Using the within-platform variability as a benchmark, we found that these technology platforms exhibited an acceptable level of agreement, but the agreement between two technologies within the same lab was greater than that between two labs using the same technology. The consistency of replicates in each experiment varies from lab to lab. When there is high consistency among replicates, different technologies show good agreement within and across labs using the same RNA samples. On the other hand, the lab effect, especially when confounded with the RNA sample effect, plays a bigger role than the platform effect on data agreement.
Using the ecology model to describe the impact of asthma on patterns of health care
Authors: Yawn Barbara P , Fryer George E , Phillips Robert L , Dovey Susan M , Lanier David , Green Larry A 
Published: May 2005

Abstract
Background
Asthma changes both the volume and patterns of healthcare of affected people. Most studies of asthma health care utilization have been done in selected insured populations or in a single site such as the emergency department. Asthma is an ambulatory sensitive care condition making it important to understand the relationship between care in all sites across the health service spectrum. Asthma is also more common in people with fewer economic resources making it important to include people across all types of insurance and no insurance categories. The ecology of medical care model may provide a useful framework to describe the use of health services in people with asthma compared to those without asthma and identify subgroups with apparent gaps in care.

Methods
This is a case-control study using the 1999 U.S. Medical Expenditure Panel Survey. Cases are school-aged children (6 to 17 years) and young adults (18 to 44 years) with self-reported asthma. Controls are from the same age groups who have no self-reported asthma. Descriptive analyses and risk ratios are placed within the ecology of medical care model and used to describe and compare the healthcare contact of cases and controls across multiple settings.

Results
In 1999, the presence of asthma significantly increased the likelihood of an ambulatory care visit by 20 to 30% and more than doubled the likelihood of making one or more visits to the emergency department (ED). Yet, 18.8% of children and 14.5% of adults with asthma (over a million Americans) had no ambulatory care visits for asthma. About one in 20 to 35 people with asthma (5.2% of children and 3.6% of adults) were seen in the ED or hospital but had no prior or follow-up ambulatory care visits. These Americans were more likely to be uninsured, have no usual source of care and live in metropolitan areas.

Conclusion
The ecology model confirmed that having asthma changes the likelihood and pattern of care for Americans. More importantly, the ecology model identified a subgroup with asthma who sought only emergent or hospital services.
Java Web Start based software for automated quantitative nuclear analysis of prostate cancer and benign prostate hyperplasia
Authors: Singh Swaroop S , Kim Desok , Mohler James L 
Published: May 2005

Abstract

Background
Androgen acts via androgen receptor (AR) and accurate measurement of the levels of AR protein expression is critical for prostate research. The expression of AR in paired specimens of benign prostate and prostate cancer from 20 African and 20 Caucasian Americans was compared to demonstrate an application of this system.

Methods
A set of 200 immunopositive and 200 immunonegative nuclei were collected from the images using a macro developed in Image Pro Plus. Linear Discriminant and Logistic Regression analyses were performed on the data to generate classification coefficients. Classification coefficients render the automated image analysis software independent of the type of immunostaining or image acquisition system used. The image analysis software performs local segmentation and uses nuclear shape and size to detect prostatic epithelial nuclei. AR expression is described by (a) percentage of immunopositive nuclei; (b) percentage of immunopositive nuclear area; and (c) intensity of AR expression among immunopositive nuclei or areas.

Results
The percent positive nuclei and percent nuclear area were similar by race in both benign prostate hyperplasia and prostate cancer. In prostate cancer epithelial nuclei, African Americans exhibited 38% higher levels of AR immunostaining than Caucasian Americans (two sided Student's t-tests; P < 0.05). Intensity of AR immunostaining was similar between races in benign prostate.

Conclusion
The differences measured in the intensity of AR expression in prostate cancer were consistent with previous studies. Classification coefficients are required due to non-standardized immunostaining and image collection methods across medical institutions and research laboratories and helps customize the software for the specimen under study. The availability of a free, automated system creates new opportunities for testing, evaluation and use of this image analysis system by many research groups who study nuclear protein expression.
Predicting Inhibitory Drug—Drug Interactions and Evaluating Drug Interaction Reports Using Inhibition Constants
Authors: Bachmann Kenneth A , Lewis Jeffrey D 
Published: May 2005

OBJECTIVE: To review the use of inhibitory constants (Ki) determined from in vitro experiments in the prediction of the significance of inhibitory drug—drug interactions (DDIs). DATA SOURCES: Searches of MEDLINE (1966—August 2004) and manual review of journals, conference proceedings, reference textbooks, and Web sites were performed using the key search terms cytochrome P450, drug—drug interaction, inhibition constant, and Ki. STUDY SELECTION AND DATA EXTRACTION: All articles identified from the data sources were evaluated, and information deemed relevant was included for this review. DATA SYNTHESIS: The cytochrome P450 isoenzymes factor prominently in the explanation of numerous DDIs. Although the regulation of these enzymes by one drug can affect the pharmacokinetics of other drugs, the consequences may not necessarily be significant either in terms of pharmacokinetic or clinical outcomes. Yet, many DDI monographs originate as unconfirmed case reports that implicate the influence of one drug on the CYP-mediated metabolism of another, and these often uncorroborated mechanisms can eventually become regarded as dogma. One consequence of this process is the overprediction of potentially important DDIs. The pharmaceutical industry, Food and Drug Administration, and pharmaceutical scientists have developed a strategy for predicting the significance of inhibitory DDIs at the earliest possible stages of drug development based on a new chemical entity's Ki value, determined in vitro. CONCLUSIONS: We suggest that the use of Ki values of drugs purported to behave as CYP inhibitors be incorporated in the assessment of case reports that ascribe DDIs to inhibition of metabolism of one drug by another.
Phenazopyridine-Induced Sulfhemoglobinemia
Authors: Gopalachar Anuradha S , Bowie Venita L , Bharadwaj Parag 
Published: May 2005

OBJECTIVE: To report a case of sulfhemoglobinemia in a patient receiving phenazopyridine for a urinary tract infection. CASE SUMMARY: A 63-year-old white woman presented to the emergency department with complaints of fatigue and bluish discoloration of her body that had gradually progressed over the previous 6–8 weeks. About 4 months prior to presenting to the emergency department, she had started taking phenazopyridine, an over-the-counter medication for symptoms of dysuria. Because the cyanosis did not improve after the patient received oxygen and methylene blue, sulfhemoglobinemia was suspected and confirmed by spectrophotometer analysis. DISCUSSION: Sulfhemoglobin is a green-pigmented molecule containing a sulfur atom in one or more of the porphyrin rings. It is a rare cause of cyanosis, which is usually drug induced. Sulfhemoglobinemia is suspected when a cyanotic patient has normal to near-normal oxygen tension, laboratory reports of elevated methemoglobin, and does not respond to methylene blue therapy. Sulfhemoglobinemia is relatively rare, despite the widespread use of drugs that have been reported to cause it. Predisposing factors, such as chronic constipation, present in our patient, have been suggested as a source of hydrogen sulfide. CONCLUSIONS: This case of sulfhemoglobinemia, which occurred after the patient took phenazopyridine, is considered a probable adverse event according to the Naranjo probability scale.
Comparison of the Effects of Nitroglycerin and Nitroprusside on Transmitral Doppler Flow Parameters in Patients with Hypertensive Urgency
Authors: Eryonucu Beyhan , Güler Niyazi , Güntekin Ünal , Tuncer Mustafa 
Published: May 2005

BACKGROUND: Sodium nitroprusside (NIP) and nitroglycerin (NIT) are frequently selected agents for acutely reducing blood pressure. However, it is not clear which agent is more efficacious in improving left ventricular filling pressure in hypertensive crises. OBJECTIVE: To compare the acute effects of nitroglycerin (NIT) and nitroprusside (NIP) on transmitral Doppler filling parameters in patients with hypertensive urgency. METHODS: We identified 37 patients from our emergency department with hypertensive urgency and left ventricular filling abnormalities. Hypertensive urgency was defined as a severe blood pressure elevation without evidence of progressive end-organ injury. Patients were randomized to receive an infusion of NIT or NIP. NIT was infused at a starting dose of 10 μg/min; NIP was infused at a starting dose of 0.25 μg/kg/min. The infusion rates were adjusted to decrease mean arterial pressure by 25%, and this reduction was obtained within 2 hours in all patients. Diastolic filling parameters were measured by using echocardiography before and after treatment. Pulsed-wave Doppler transmitral flow velocities were used. Early diastolic flow, atrial contraction signal, early diastolic flow/atrial contraction signal, deceleration time, and isovolumetric relaxation time (IVRT) were measured. RESULTS: There were no differences between groups in baseline demographic and echocardiographic parameters. Blood pressure decreased significantly in both treatment groups. In posttreatment echocardiographic examinations, atrial contraction signal, deceleration time, and IVRT were significantly decreased in both treatment groups. Early diastolic flow was significantly decreased in the NIT group. There were no significant differences between the groups in terms of posttreatment early diastolic flow, atrial contraction signal, deceleration time, and IVRT values. CONCLUSIONS: In hypertensive urgency with left ventricular filling abnormalities, reduction of blood pressure associated with NIT or NIP treatment may improve transmitral Doppler filling parameters. There were no differences demonstrated between the 2 agents.
The Effect of Creatine Intake on Renal Function
Authors: Pline Kurt A , Smith Curtis L 
Published: May 2005

OBJECTIVE: To examine the effect of creatine supplementation on renal function and estimates of creatinine clearance. DATA SOURCES: A MEDLINE search was conducted (1966—September 2004) using the key terms creatine, creatinine, kidney function tests, drug toxicity, and exercise. Relevant articles were cross-referenced to screen for additional information. DATA SYNTHESIS: Supplementation with creatine, an unregulated dietary substance, is increasingly common in young athletes. To date, few studies have evaluated the impact of creatine on renal function and estimates of creatinine clearance. Because creatine is converted to creatinine in the body, supplementation with large doses of creatine may falsely elevate creatinine concentrations. Five studies have reported measures of renal function after acute creatine ingestion and 4 after chronic ingestion. All of these studies were completed in young healthy populations. Following acute ingestion (4–5 days) of large amounts of creatine, creatinine concentrations increased slightly, but not to a clinically significant concentration. Creatinine is also only minimally affected by longer creatine supplementation (up to 5.6 y). CONCLUSIONS: Creatine supplementation minimally impacts creatinine concentrations and renal function in young healthy adults. Although creatinine concentrations may increase after long periods of creatine supplementation, the increase is extremely limited and unlikely to affect estimates of creatinine clearance and subsequent dosage adjustments. Further studies are required in the elderly and patients with renal insufficiency.
Hypersensitivity Reactions to Oxaliplatin in Two Asian Patients
Authors: Ng Christina VT 
Published: May 2005

OBJECTIVE: To report 2 cases of hypersensitivity reactions associated with oxaliplatin treatment in Asian patients. CASE SUMMARIES: A 33-year-old Chinese woman received adjuvant oxaliplatin in combination with fluorouracil and leucovorin. Shortly during her sixth infusion, she developed a severe hypersensitivity reaction. Despite prophylactic measures, she developed another reaction of similar severity during her subsequent infusion and was not further rechallenged with oxaliplatin. The second case involved a 45-year-old Malay woman who received oxaliplatin, fluorouracil, and leucovorin for metastatic colorectal cancer. Shortly during her ninth infusion, she developed a mild hypersensitivity reaction. With prophylactic measures, she developed less marked reactions with her subsequent 3 infusions. DISCUSSION: Hypersensitivity reactions to oxaliplatin have been reported to be between 12% and 16% in the Western population. As of April 20, 2005, there are only 2 previously published reports of hypersensitivity reactions to oxaliplatin in 6 Asian patients. The incidence rates of such reactions in different Asian ethnic groups could vary. The cumulative dose, time of exposure to oxaliplatin, and clinical features were variable and unpredictable in all of the reported Asian patients who developed hypersensitivity reactions. An objective causality assessment using the Naranjo probability scale revealed that oxaliplatin was the highly probable cause of hypersensitivity in the 2 Asian patients reported by our center. CONCLUSIONS: Patients who develop mild to moderate reactions can be rechallenged with the drug administered as a slow infusion with prophylactic measures. Desensitization may allow patients who experience severe hypersensitivity reactions to oxaliplatin to further receive effective therapy for their colorectal cancer.
Extensive Prolongation of aPTT with Argatroban in an Elderly Patient with Improving Renal Function, Normal Hepatic Enzymes, and Metastatic Lung Cancer
Authors: Kubiak David W , Szumita Paul M , Fanikos John R 
Published: May 2005

OBJECTIVE: To report a case of an elderly male with improving renal function and normal hepatic function who sustained an elevated activated partial thromboplastin time (aPTT) after an infusion of argatroban was discontinued. CASE SUMMARY: A 77-year-old white male with a history of heparin-induced thrombocytopenia (HIT) and metastatic lung disease was started on argatroban for treatment of a right upper-extremity deep vein thrombosis (DVT). The infusion was initiated at 2.0 μg/kg/min and was titrated to a goal aPTT of 60–80 seconds. Argatroban was discontinued due to an aPTT elevated to >100 seconds; the aPTT remained elevated for 130 hours after discontinuation of the infusion. DISCUSSION: Argatroban dose reductions in patients with impaired liver and renal function test values have been reported. Elderly subjects may have a prolonged clearance compared with young healthy subjects, although the duration of effect has not been established. As of April 18, 2005, the effect of liver metastasis on argatroban pharmacokinetics in the setting of normal liver function enzyme levels has not been reported. An objective causality assessment using the Naranjo probability scale showed that the prolonged aPTT was probably attributable to argatroban. CONCLUSIONS: Clinicians should exercise caution when initiating argatroban at a dose of 2.0 μg/kg/min in elderly patients with underlying comorbidities, such as metastatic disease and renal impairment, since this may lead to excessive and prolonged anticoagulation and increased risk of bleeding.
trkA Is Expressed in Nociceptive Neurons and Influences Electrophysiological Properties via Nav1.8 Expression in Rapidly Conducting Nociceptors
Authors: Fang Xin , Djouhri Laiche , McMullan Simon , Berry Carol , Okuse Kenji , Waxman Stephen G. , Lawson Sally N. 
Published: May 2005

To test the hypothesis that trkA (the high-affinity NGF receptor) is selectively expressed in nociceptive dorsal root ganglion (DRG) neurons, we examined the intensity of trkA immunoreactivity in single dye-injected rat DRG neurons, the sensory receptor properties of which were identifiedin vivowith mechanical and thermal stimuli. We provide the first evidence in single identified neurons that strong trkA expression in DRGs is restricted to nociceptive neurons, probably accounting for the profound influence of NGF on these neurons. Furthermore, we demonstrate that trkA expression is as high in rapidly conducting (Aα/β) as in more slowly conducting (Aδ and C) nociceptors. All Aα/β low-threshold mechanoreceptors (LTMs) are trkA negative, although weak but detectable trkA is present in some C and Aδ LTMs.NGF can influence electrophysiological properties of DRG neurons, probably by binding to trkA. We found positive correlations for single identified Aα/β (but not C or Aδ) nociceptors between trkA immunocytochemical intensity and electrophysiological properties typical of nociceptors, namely long action potential and afterhyperpolarization durations and large action potential amplitudes. Furthermore, for Aα/β (notCorAδ) nociceptors, trkA intensity is inversely correlated with conduction velocity. Similar relationships, again only in Aα/β nociceptors, between electrophysiological properties and trkA expression exist for sodium channel Nav1.8 but not Nav1.9 immunoreactivities. These findings suggest that in Aα/β nociceptors, influences of NGF on expression levels of Nav1.8 are related to, and perhaps limited by, expression levels of trkA. This view is supported by a positive correlation between immuno-intensities of trkA and Nav1.8 in A-fiber, but not C-fiber, nociceptors.
Otx2 Regulates Subtype Specification and Neurogenesis in the Midbrain
Authors: Vernay Bertrand , Koch Muriel , Vaccarino Flora , Briscoe James , Simeone Antonio , Kageyama Ryoichiro , Ang Siew-Lan 
Published: May 2005

The transcription factor Otx2 is required to determine mesencephalic versus metencephalic (cerebellum/pons) territory during embryogenesis. This function ofOtx2primarily involves positioning and maintaining the mid-hindbrain organizer at the border between midbrain and anterior hindbrain.Otx2expression is maintained long after this organizer is established. We therefore generated conditional mutants ofOtx2using the Cre/loxPsystem to study later roles during rostral brain development. For inactivation ofOtx2in neuronal progenitor cells, we crossedOtx2flox/floxanimals withNestin-Cretransgenic animals. InNestin-Cre/+; Otx2flox/floxembryos, Otx2 activity was lost from the ventral midbrain starting at embryonic day 10.5 (E10.5). In these mutant embryos, the mid-hindbrain organizer was properly positioned at E12.5, although Otx2 is absent from the midbrain. Hence, theNestin-Cre/+; Otx2flox/floxanimals represent a novel mouse model for studying the role ofOtx2in the midbrain, independently of abnormal development of the mid-hindbrain organizer.Our data demonstrate thatOtx2controls the development of several neuronal populations in the midbrain by regulating progenitor identity and neurogenesis. Dorsal midbrain progenitors ectopically expressedMath1and generate an ectopic cerebellar-like structure. Similarly,Nkx2.2ectopic expression ventrally into tegmentum progenitors is responsible for the formation of serotonergic neurons and hypoplasia of the red nucleus in the midbrain. In addition, we discovered a novel role forOtx2in regulating neurogenesis of dopaminergic neurons. Altogether, these results demonstrate thatOtx2is required from E10.5 onward to regulate neuronal subtype identity and neurogenesis in the midbrain.
Fall Chinook Salmon Spawning Activity versus Daylight and Flow in the Tailrace of a Large Hydroelectric Dam
Authors: McMichael Geoffrey A. , McKinstry C. A. , Vucelick J. A. , Lukas J. A. 
Published: May 2005

Abstract
We deployed an acoustic system during the spawning season for fall Chinook salmon Oncorhynchus tshawytscha in 2001 to determine whether fall Chinook salmon spawning activity in a hydroelectric dam tailrace area was affected by daylight or river flow. Our study design allocated sampling effort nearly equally between hours of darkness and hours of daylight throughout each 24-h period. The acoustic system recorded sounds of fall Chinook salmon spawning activity in two index areas downstream of Wanapum Dam on the Columbia River in Washington State. One index area was a deepwater spawning site located in 9–11 m of water. The other index area was a moderate-depth midchannel bar, where water depths ranged from 2.5 to 6 m. We defined the rate of spawning activity in digs per minute. Fall Chinook salmon spawning activity rates in the Wanapum Dam tailrace were influenced by both daylight and river discharge, which had a pronounced nonlinear effect on spawning activity rates. To account for nonlinearity, a generalized additive model was used to characterize the combined effects of river flow and daylight. The final model also suggested that both flow and daylight influenced spawning activity. Spawning activity occurred during both daylight and darkness, significantly more activity occurring during daylight in both index areas. Spawning activity was generally highest at project discharges between 1,700 and 2,266 m3/s in both spawning areas; spawning activity diminished as discharge increased from 3,400 to 4,250 m3/s. We concluded that fall Chinook salmon spawning activity in this regulated discharge environment was affected more by flow (and velocity) than by daylight.