bluuebunny/crossref_metadata_2025_split huggingface dataset:
A meta‐analysis of clinical trials involving different classifications of response into ordered categories
Authors: Whitehead Anne , Jones Nicola M. B. 
Published: April 2007

AbstractStatistical methods are available for performing a meta‐analysis when the response variable of interest is the same in each study. Problems arise when studies exploring a common therapeutic question use different patient response types. This article presents statistical methods for combining studies which involve different classifications of response into ordered categories. The assumptions required for the stratified proportional odds model, on which the analysis is based, are discussed. The approach is illustrated using results from a series of studies investigating the prevention of gastrointestinal damage induced by non‐steroidal anti‐inflammatory drugs.
Multistate modelling of liver transplantation data
Authors: Hansen B. E. , Thorogood J. , Hermans J. , Ploeg R. J. , Van Bockel J. H. , Van Houwelingen J. C. 
Published: April 2007

AbstractThis paper concerns the survival analysis of liver transplant patients when patients with a potentially fatal rejection of the transplanted organ may receive a retransplant. A multistate model, analysing the states ‘alive with first graft’ and ‘alive with second graft’ separately, is suggested. Proportional hazards models and logistic regression models are used to evaluate which risk factors related to donor, preservation and recipient, influence the transition intensities. The complete model is used to predict overall survival of a patient and to study the influence of the risk factors on total survival.
Fieller's confidence intervals for the ratio of two means in the assessment of average bioequivalence from crossover data
Authors: Vuorinen Jouni , Tuominen Juhani 
Published: April 2007

AbstractThe two‐period crossover design is the most commonly used study design for bioequivalence of one test formulation to be assessed in comparison to one reference formulation. Consequently, in this paper, all derivation is based on this particular design. It is assumed that for the underlying statistical model the usual assumptions of normality and additivity are satisfied on the original scale of measurement and that it is wanted to base the assessment of average bioavailability on the ratio of the unknown population means for the test and reference formulation. The purpose of this paper is to illustrate that it is reasonable to assume a uniform covariance structure for the two‐period crossover design, because the demand of equal variability in bioavailabilities, in addition to equal average bioavailabilities, for the reference and test formulation makes the assumption of uniform covariance structure very realistic, and also because the properties of a decision rule based upon a Fieller's confidence interval under a uniform covariance structure are competitive with those of the corresponding rule based on a general covariance structure.
Some practical improvements in the continual reassessment method for phase I studies
Authors: Goodman Steven N. , Zahurak Marianna L. , Piantadosi Steven 
Published: April 2007

AbstractThe Continual Reassessment Method (CRM) is a Bayesian phase I design whose purpose is to estimate the maximum tolerated dose of a drug that will be used in subsequent phase II and III studies. Its acceptance has been hindered by the greater duration of CRM designs compared to standard methods, as well as by concerns with excessive experimentation at high dosage levels, and with more frequent and severe toxicity. This paper presents the results of a simulation study in which one assigns more than one subject at a time to each dose level, and each dose increase is limited to one level. We show that these modifications address all of the most serious criticisms of the CRM, reducing the duration of the trial by 50–67 per cent, reducing toxicity incidence by 20–35 per cent, and lowering toxicity severity. These are achieved with minimal effects on accuracy. Most important, based on our experience at our institution, such modifications make the CRM acceptable to clinical investigators.
Multivariate tests for multiple endpoints in clinical trials
Authors: Follmann Dean 
Published: April 2007

AbstractClinical trials frequently lack a single definitive endpoint that completely describes treatment efficacy. When a treatment affects a disease in a multitude of ways, several endpoints are necessary to describe efficacy. There is a variety of statistical procedures to provide a single p‐value when a treatment affects several endpoints. This paper reviews several procedures including Hotelling's T2 test, an approximate likelihood ratio test (Tang et al.), the weighted version of O'Brien's test, tests involving the maximum of several test statistics, and a test based on the average of the maximum of several endpoints (Wittes). I propose a risk score test whose rejection boundary corresponds to a contour of constant risk. Calculations and simulation studies help to compare the different tests with an emphasis on the effect of non‐standard alternatives, and on identifying settings where some tests may lack clinical relevance.
A regression method for analysing ordinal data from intervention trials
Authors: Schnell Daniel J. , Magee Elvin , Sheridan John R. 
Published: April 2007

AbstractWe consider the case of a community intervention trial evaluated with a series of cross‐sectional surveys and having outcomes measured on an ordinal scale. We propose a modelling procedure that combines ridit analysis and linear regression methods. We use the multinomial distribution as the basis for variance estimation of the mean ridits and then use simple regression models to estimate differences (for example, between intervention and comparison areas) among the ridits. We illustrate this procedure with data from a community intervention trial promoting condom use, with the adoption of consistent condom use measured on a 5‐point ordinal scale.
Inference for smooth curves in longitudinal data with application to an aids clinical trial
Authors: Wang Yongxiao , Taylor Jeremy M. G. 
Published: April 2007

AbstractWe discuss a longitudinal study where data for many subjects are collected at irregular intervals. The study is a randomized trial of HIV infected subjects and the response variable of interest is serum neopterin. The mean of the outcome variable, taken over patients in each treatment group, is assumed to follow a smooth curve. Piecewise cubic polynomials with a moderate number of knots are used to model the curves. A general parametric form is assumed for the covariance structure. Maximum penalized likelihood estimation is used to smooth the over‐parameterized curves. Statistical inference for the mean curves, including confidence bands and hypothesis tests, is discussed. Two approaches, one using a Bayesian interpretation of the penalized likelihood and the other based on the asymptotic distribution of the maximum penalized likelihood estimates, are discussed and contrasted. The properties of the confidence bands obtained from these two approaches are evaluated by examining their coverage rates in a simulation study.
Variations in Pelvic Dimensions Do Not Predict the Risk of Circumferential Resection Margin (CRM) Involvement in Rectal Cancer
Authors: Salerno G. , Daniels I. R. , Brown G. , Norman A. R. , Moran B. J. , Heald R. J. 
Published: April 2007

AbstractBackgroundThe objective of this study was to assess the value of preoperative pelvimetry, using magnetic resonance imaging (MRI), in predicting the risk of an involved circumferential resection margin (CRM) in a group of patients with operable rectal cancer.MethodsA cohort of 186 patients from the MERCURY study was selected. These patients’ histological CRM status was compared against 14 pelvimetry parameters measured from the preoperative MRI. These measurements were taken by one of the investigators (G.S.), who was blinded to the final CRM status.ResultsThere was no correlation between the pelvimetry and the CRM status. However, there was a difference in the height of the rectal cancer and the positive CRM rate (p = 0.011). Of 61 patients with low rectal cancer, 10 had positive CRM at histology (16.4% with CI 8.2%–22.1%) compared with 5 of 110 patients with mid/upper rectal cancers (4.5% with CI 0.7%–8.4%).ConclusionsMagnetic resonance imaging can predict clear margins in most cases of rectal cancer. Circumferential resection margin positivity cannot be predicted from pelvimetry in patients with rectal cancer selected for curative surgery. The only predictive factor for a positive CRM in the patients studied was tumor height.
Epidemiologic Associations of Carpal Tunnel Syndrome and Sleep Position: Is there a Case for Causation?
Authors: McCabe Steven J. , Uebele Anna L. , Pihur Vasyl , Rosales Roberto S. , Atroshi Isam 
Published: May 2007

Introduction Carpal tunnel syndrome (CTS) is thought to be due to compression of the median nerve in the carpal tunnel. It is known that carpal tunnel pressures are elevated in wrist postures of flexion and extension and in those patients with CTS. Classic symptoms of CTS include night waking with pain, tingling, and numbness. These classic symptoms stimulated our interest in the relationship of sleep to the development of CTS. Method We reviewed the literature surrounding the epidemiology of CTS and the literature regarding sleep disturbances. Through careful distillation of these studies and a process of reasoning, we have developed a hypothesis for a causal mechanism of CTS. Results Epidemiologically, it has been shown that CTS is associated with age, gender, increased body mass index (BMI), diabetes, pregnancy, and is more common in some populations. The same associations noted above for CTS are strongly associated with sleep disturbances. Sleep disturbances due to age, gender, BMI, pregnancy, and population variations are all associated with sleeping in the lateral position supporting the hypothesis that a common causative mechanism of CTS is sleeping in a lateral position. Discussion We believe that the epidemiologic associations with CTS act through a common causative mechanism, increased sleeping in the lateral position which puts the wrist at increased risk of flexion or extension, compressing the median nerve in the carpal tunnel. This hypothesis is simple and explains the connection between a previously unconnected group of epidemiologic associations. This realization has real clinical significance in that it focuses our attention on the early disorder when it is completely reversible. It clarifies previously confused clinical circumstances, creates research questions that can be tested, and it invites us to change our clinical perspective in this most common form of nerve compression.
Altered melusin expression in the hearts of aortic stenosis patients
Authors: Brokat Sebastian , Thomas Jenny , Herda Lars R. , Knosalla Christoph , Pregla Reinhard , Brancaccio Mara , Accornero Federica , Tarone Guido , Hetzer Roland , Regitz‐Zagrosek Vera 
Published: May 2007

AbstractBackground:The role of melusin, a necessary component in pressure‐induced left‐ventricular hypertrophy (LVH) in mice, has not yet been determined in human cardiac hypertrophy. We analyzed for the first time the expression and regional distribution of melusin in human LVH due to aortic stenosis (AS) and determined AKT phosphorylation as a potential downstream effector of melusin signalling.Methods:Regional distribution of melusin was evaluated in four normal hearts. Melusin staining, gene expression and protein content were assessed in biopsies from normal and diseased hearts and melusin gene expression was correlated with LV functional changes. The pAKT/AKT ratio was determined in parallel and correlated with melusin protein content.Results:In normal hearts, melusin was found in the myocytes with a uniform regional distribution. Melusin staining, mRNA and protein were significantly decreased in human AS hearts. The reduction in melusin mRNA was significantly correlated with LVEF, LVEDD and LVESD. pAKT/AKT ratio was significantly decreased in human AS and was correlated with melusin content.Conclusion:Reduction in melusin expression parallels the functional cardiac impairment in human AS. The simultaneous decrease of melusin and AKT phosphorylation suggests a connection between the loss of melusin and the decrease in systolic function.
The Effect of Bacillus Calmette‐Guerin in a Mouse Model of Allergic Rhinitis
Authors: Kim Soo Whan , Yeo Sang Won 
Published: May 2007

OBJECTIVETo develop an allergic rhinitis model via local sensitization of mice with Dermatophagoides pteronyssinus and to use the model to investigate the antiallergic effect of Bacillus Calmette‐Guerin (BCG).METHODSBALB/c mice were randomized to the allergic rhinitis group, the BCG group sensitized with D pteronyssinus via local sensitization for 7 weeks, or the control group. The BCG group received 1 × 105 colony‐forming unit/mL of BCG seven times. We evaluated symptoms, nasal mucosa eosinophilia, serum total IgE, cytokines, and eosinophilia in bronchoalveolar lavage fluid.RESULTSIn the allergic rhinitis group, allergy symptoms (P < 0.001), eosinophil count (P < 0.001), total IgE (P < 0.001), inflammatory cells (P < 0.01), and IL‐13 (P = 0.046) increased and interferon γ (IFN‐γ) (P < 0.001) decreased compared with the control group. In the BCG group, allergy symptoms (P < 0.001), eosinophil count (P < 0.001), and inflammatory cells (P < 0.01) decreased and IFN‐γ (P = 0.031) increased compared with the allergic rhinitis group.CONCLUSIONIn an allergic rhinitis animal model developed via local sensitization of mice with D pteronyssinus, BCG was shown to exhibit an antiallergic effect.
Malignant Parotid Tumor and Facial Palsy
Authors: Tseng Fen‐Yu , Chen Zeng‐Chang , Hsu Chuan‐Jen , Ko Jeng‐Yuh , Lou Pei‐Jen , Chen Yuh‐Shyang 
Published: May 2007

OBJECTIVETo evaluate risk factors for postoperative facial palsy in patients with parotid carcinoma.STUDY DESIGN AND SETTINGWe conducted a retrospective chart review of patients with parotid carcinoma who underwent parotidectomy at National Taiwan University Hospital from 1980 to 2000.RESULTSEighty‐eight patients with a mean age of 53 ± 17 y were recruited. Sixty patients (68.2%) experienced postoperative facial palsy. Tumor size of larger than 4 cm was associated with an increased incidence of facial palsy (P = 0.0422). Facial palsy was noted in 95.5 percent of patients with facial nerve involvement and 51.3 percent of patients without facial nerve involvement (P = 0.0004). Of 42 patients with tumor over the deep lobe, 37 (88.1%) had facial palsy but only 50 percent (23 of 46) of those with tumor over the superficial lobe had facial palsy (P = 0.0001).CONCLUSIONThere were no significant associations between histopathology and facial palsy. Increasing tumor size, deep lobe tumor location, and tumor invasion of facial nerve increased the incidence of postparotidectomy facial palsy.SIGNIFICANCEBy paying attention to these risk factors a reduction of postoperative facial nerve palsy my be achieved.
Phase‐Shift Treatment for Predominant Tone Tinnitus
Authors: Lipman Ruthann I. , Lipman Sidney P. 
Published: May 2007

OBJECTIVESTo independently evaluate phase‐shift treatment for predominant tone tinnitus.STUDY DESIGNProspective, single‐blinded crossover study.METHODS61 subjects with predominant tone tinnitus participated in 2 weeks of control and 2 weeks of phase‐shift treatment. Frequency and intensity matching, pre‐ and post‐treatment tinnitus handicap inventory (THI) scores, and patient diaries were outcome measures.RESULTSInitial volume comparisons show a strong relationship between treatment and decrease in tinnitus intensity, with 57% of patients achieving successful treatment. Thirty‐seven percent decreased by one THI grade, 5% by two. Utilizing patient diaries, 42% of patients reported periods of complete residual inhibition (CRI) ranging from 1 hour to 7 days (average 2 days). No periods of CRI were reported in control weeks.CONCLUSIONPhase‐shift treatment significantly benefited the majority of our patients. These outcomes suggest that this device may be a valuable tool. Further long‐term studies with home therapy are warranted.
Pediatric Microvascular Reconstruction: A Report from the Microvascular Committee
Authors: Arnold David J. , Wax Mark K. 
Published: May 2007

BACKGROUNDFree tissue transfer is an integral part of modern head and neck surgery in the adult population. Its use in the pediatric population has not been well described. Recently, there has been an increase in the application of these techniques in the pediatric population. The morbidity of free tissue transfer in small pediatric patients and its effect on growth has not been well described.OBJECTIVETo evaluate the utility of microvascular reconstruction techniques in the pediatric population.STUDY DESIGNA consensus study was performed by the microvascular committee of the American Academy of Otolaryngology‐Head and Neck Surgery. Thirty active microvascular surgeons reviewed their databases to find patients less than 21 years of age who underwent free tissue transfer.RESULTS49 free tissue transfers performed between 1999 and 2005. The mean age was 12.1 years (age range, 3–21). The types of flaps transferred were radial forearm (10), fibula (21), rectus abdominus (7), scapula (1), latissimus dorsi (3), groin (1), gracillus (4), and jejunum (2). Morbidity at the donor site was relatively minimal. Five patients developed wound breakdown. One of these required return to the operating room. Morbidity at the reconstructed site was also rare. Patients were followed for an average of 49 months (range, 1–131 months), and no problems were noted with growth at the donor or recipient sites.CONCLUSIONSFree flaps in the pediatric population have morbidity and survival similar to those in the adult population.SIGNIFICANCEWhile indications differ from those in the adult population, these techniques are viable and valuable and should be considered in the pediatric reconstructive paradigm.
Head and Neck Manifestations and Quality of Life of Patients with Ectodermal Dysplasia
Authors: Mehta Umang , Brunworth Joseph , Fete Timothy J. , Sindwani Raj 
Published: May 2007

OBJECTIVESEctodermal dysplasias (EDs) are a group of genetic disorders characterized by deficient ectodermal and mesodermal development. Studies examining resultant otolaryngologic issues are few. The objectives of this study were to delineate the head and neck manifestations and quality of life in EDs.STUDY DESIGN AND SETTINGFor 75 individuals, comprehensive histories were taken and otolaryngologic examinations were performed, and subjects rated their otolaryngologic symptom severity. A validated quality of life instrument (SF‐8) was administered.RESULTSThe majority of subjects had a diagnosis of hypohidrotic ED (72%). Otolaryngologic conditions included otitis media (28%), cerumen impaction (48%), nasal obstruction/crusting (51%), heat intolerance (76%), and eczema (39%). Physical findings included peg teeth/hypodontia (76%), alopecia (41%), nasal crusting (41%), and saddle nose deformity (44%). Quality of life scores were generally high. Overall, health was rated “good to excellent” by 87 percent.CONCLUSIONPatients with ED frequently experience significant otolaryngologic symptoms, although most patients report a good quality of life.SIGNIFICANCEA greater understanding of the otolaryngologic issues in ED should help facilitate diagnosis and improve management.
Diazotrophic bacterioplankton in a coral reef lagoon: phylogeny, diel nitrogenase expression and response to phosphate enrichment
Authors: Hewson Ian , Moisander Pia H , Morrison Amanda E , Zehr Jonathan P 
Published: May 2007

Abstract
We investigated diazotrophic bacterioplankton assemblage composition in the Heron Reef lagoon (Great Barrier Reef, Australia) using culture-independent techniques targeting the nifH fragment of the nitrogenase gene. Seawater was collected at 3 h intervals over a period of 72 h (i.e. over diel as well as tidal cycles). An incubation experiment was also conducted to assess the impact of phosphate (PO43−) availability on nifH expression patterns. DNA-based nifH libraries contained primarily sequences that were most similar to nifH from sediment, microbial mat and surface-associated microorganisms, with a few sequences that clustered with typical open ocean phylotypes. In contrast to genomic DNA sequences, libraries prepared from gene transcripts (mRNA amplified by reverse transcription-polymerase chain reaction) were entirely cyanobacterial and contained phylotypes similar to those observed in open ocean plankton. The abundance of Trichodesmium and two uncultured cyanobacterial phylotypes from previous studies (group A and group B) were studied by quantitative-polymerase chain reaction in the lagoon samples. These were detected as transcripts, but were not detected in genomic DNA. The gene transcript abundance of these phylotypes demonstrated variability over several diel cycles. The PO43− enrichment experiment had a clearer pattern of gene expression over diel cycles than the lagoon sampling, however PO43− additions did not result in enhanced transcript abundance relative to control incubations. The results suggest that a number of diazotrophs in bacterioplankton of the reef lagoon may originate from sediment, coral or beachrock surfaces, sloughing into plankton with the flooding tide. The presence of typical open ocean phylotype transcripts in lagoon bacterioplankton may indicate that they are an important component of the N cycle of the coral reef.
New processes and players in the nitrogen cycle: the microbial ecology of anaerobic and archaeal ammonia oxidation
Authors: Francis Christopher A , Beman J Michael , Kuypers Marcel M M 
Published: May 2007

Abstract
Microbial activities drive the global nitrogen cycle, and in the past few years, our understanding of nitrogen cycling processes and the micro-organisms that mediate them has changed dramatically. During this time, the processes of anaerobic ammonium oxidation (anammox), and ammonia oxidation within the domain Archaea, have been recognized as two new links in the global nitrogen cycle. All available evidence indicates that these processes and organisms are critically important in the environment, and particularly in the ocean. Here we review what is currently known about the microbial ecology of anaerobic and archaeal ammonia oxidation, highlight relevant unknowns and discuss the implications of these discoveries for the global nitrogen and carbon cycles.
GAzer: gene set analyzer
Authors: Kim Sang-Bae , Yang Sungjin , Kim Seon-Kyu , Kim Sang Cheol , Woo Hyun Goo , Volsky David J. , Kim Seon-Young , Chu In-Sun 
Published: April 2007

Abstract
Summary: Gene Set Analyzer (GAzer) is a web-based integrated gene set analysis tool covering previously reported parametric and non-parametric models. Based on a simulation test for the reported algorithms, we classified and implemented three main statistical methods consisting of the z-statistic, gene permutation and sample permutation for ten gene set categories including Gene Ontology (GO) for human, mouse, rat and yeast. This tool identifies significantly altered gene sets scored by z-statistics and P-values from the z-test or permutation test and provides q-values and Bonferroni P-values to correct multiple hypothesis testing. GAzer allows users to observe changes in expression of each gene in a gene set or to see the significance of the gene sets containing a gene(s) of interest, thus allowing interactive data analysis both at the gene and gene set level. Moreover, GAzer offers extensive annotation for each gene.
Availability: The GAzer gene set analyzer is freely available at http://integromics.kobic.re.kr/GAzer/
Contact: kimsy@kribb.re.kr and chu@kribb.re.kr
Supplementary information: This can be found on the web page (http://integromics.kobic.re.kr/GAzer/supplement.jsp)