FIRMA: a method for detection of alternative splicing from exon array data.

MOTIVATION: Analyses of EST data show that alternative splicing is much more widespread than once thought. The advent of exon and tiling microarrays means that researchers now have the capacity to experimentally measure alternative splicing on a genome wide level. New methods are needed to analyze the data from these arrays. RESULTS: We present a method, finding isoforms using robust multichip analysis (FIRMA), for detecting differential alternative splicing in exon array data. FIRMA has been developed for Affymetrix exon arrays, but could in principle be extended to other exon arrays, tiling arrays or splice junction arrays. We have evaluated the method using simulated data, and have also applied it to two datasets: a panel of 11 human tissues and a set of 10 pairs of matched normal and tumor colon tissue. FIRMA is able to detect exons in several genes confirmed by reverse transcriptase PCR. AVAILABILITY: R code implementing our methods is contributed to the package aroma.affymetrix.

ESHRE PGD Consortium 'Best practice guidelines for clinical preimplantation genetic diagnosis (PGD) and preimplantation genetic screening (PGS)'.

Among the many educational materials produced by the European Society of Human Reproduction and Embryology (ESHRE) are guidelines. ESHRE guidelines may be developed for many reasons but their intent is always to promote best quality practices in reproductive medicine. In an era in which preimplantation genetic diagnosis (PGD) has become a reality, we must strive to maintain its efficacy and credibility by offering the safest and most effective treatment available. The dominant motivators for the development of current comprehensive guidelines for best PGD practice were (i) the absence of guidelines and/or regulation for PGD in many countries and (ii) the observation that no consensus exists on many of the clinical and technical aspects of PGD. As a consequence, the ESHRE PGD Consortium undertook to draw up guidelines aimed at giving information, support and guidance to potential, fledgling and established PGD centres. The success of a PGD treatment cycle is the result of great attention to detail. We have strived to provide a similar level of detail in this document and hope that it will assist staff in achieving the best clinical outcome for their patients.

Process versus content in eyewitness metamemory monitoring.

Three studies (Ns = 200, 135, and 187 college undergraduates) contrasted process versus content accounts of eyewitness metamemory monitoring. Subjective vividness, a cue related to memory content, was a better predictor of confidence and accuracy than were cues related to the retrieval process. Participants who were asked to recall, rather than recognize, event details displayed greater insight into accuracy, primarily because vividness was a more valid accuracy cue under recall conditions. Results reinforce the value of recall-based protocols for eliciting eyewitness testimony and suggest some specific conditions (e.g., yes-no recognition) under which investigators should be especially cautious in relying on confidence to infer accuracy. In addition, results point to a general framework for understanding moderating effects on eyewitness metamemory accuracy.

Exon deletions and duplications in BRCA1 detected by semiquantitative PCR.

rearrangements have recently been identified in the BRCA1 gene. Inclusion of a method for identifying such rearrangements should now be a prerequisite for providing a comprehensive mutation detection strategy. We have developed a semiquantitative PCR-based fluorescent assay for the detection of previously identified deletions. This method avoids the need for long PCR or Southern blotting and is suitable for large-scale epidemiological studies. The assay was used to screen 44 high-risk families within the U.K. Yorkshire Health Region. No deletions were detected, but five cases (11%) with an apparent duplication of exon 13 in BRCA1 were identified. The presence of this mutation was confirmed by long PCR. Further developments include extending the assay to include all exons of BRCA1.

Advances in non-nicotine pharmacotherapy for smoking cessation.

Progress in understanding the pharmacological nature of tobacco addiction, along with the modest success rates achieved by the nicotine replacement therapies, has provided the major impetus for the development of non-nicotine drugs as smoking cessation aids. This article reviews evidence from controlled trials of several non-nicotine medications for the treatment of nicotine dependence. Clonidine was the first non-nicotine medication to show efficacy for smoking cessation in multiple studies, but its effect was found to be limited at best. Positive results across several trials have been consistently demonstrated for amfebutamone (bupropion). Encouraging results have also been observed for nortriptyline and moclobemide. Studies of combined treatments using non-nicotine medications (amfebutamone, mecamylamine, oral dextrose) with nicotine replacement therapy suggest increased efficacy relative to treatments using one or the other treatment strategy alone. Thus, available evidence indicates that non-nicotine drug treatments offer a promising panoply of therapeutic strategies for the addicted smoker.

The educational attainment of young women: role model effects of female high school faculty.

To test for the presence of role model effects of female high school faculty and professional staff on young women in high school, we estimate several models of educational attainment for young women using data from the National Longitudinal Survey of Youth. Exposure to female high school faculty and professional staff has a positive impact on the educational attainment of young women. This result, combined with our finding that female faculty and professional staff have no significant impact on the educational attainment of young men, supports a female role model hypothesis.

Chemical modification of bovine tissues by dye-mediated photooxidation.

BACKGROUND AND AIMS OF THE STUDY: Photooxidation of pericardium has been shown chemically to alter and stabilize tissue. The characterization of photooxidatively induced, chemical modifications of bovine pericardial and arterial tissue is reported here. METHODS: Tissues were prepared by various methods of photooxidation and analyzed for thermal denaturation temperature, protein extraction, amino acid content and crosslink content. RESULTS: Photooxidation of tissue resulted in no significant time-dependent changes in thermal denaturation temperature, but did result in a time-dependent alteration and reduction in extracted proteins. This reduction is consistent with chemical alteration and stabilization of the tissue. Photooxidation also resulted in a time-dependent reduction of histidine content in treated tissues by histidine being converted to a non-detectable form. No other amino acid alteration was detected by amino acid analysis. Crosslink analysis of tissue hydrolyzates showed a time-dependent alteration in crosslink content of photooxidized tissue and an apparent addition of several types of new crosslinks. CONCLUSIONS: These chemical modifications are consistent with oxidative modification of amino acids in the tissues, resulting in an alteration of existing crosslinks and possible addition of new crosslinks in the tissues. This treatment process leads to in vivo and in vitro stability of pericardial and arterial tissues with potential use as bioprosthetic materials.

Reaction time and assessments of cognitive effort as predictors of eyewitness memory accuracy and confidence.

The authors investigate reaction time, subjective assessments of memory processing, and confidence as predictors of memory for the details of a crime. The authors also examine the mediation of a previously identified difference between recognition tasks and recall tasks in the correlation between confidence and accuracy. College undergraduates (n = 111) answered either recognition or recall questions. Reaction time and subjective assessments of cognitive effort were both negatively related to confidence and accuracy. Subjective assessments, however, were superior predictors of confidence, whereas reaction time was a unique predictor of accuracy. The reaction time-confidence and reaction time-accuracy correlations were stronger under recall conditions than under recognition conditions. Multiple regression results suggested a possible explanation for the superior insight of recall participants into memory accuracy.

Comparison of enzyme mismatch cleavage and chemical cleavage of mismatch on a defined set of heteroduplexes.

Two mutation detection methods based on the cleavage of mismatched heteroduplexes were compared and evaluated. These techniques, chemical cleavage of mismatch (CCM) and enzyme mismatch cleavage (EMC), have the advantages over other available methods of being able to detect and localize mutations in relatively large fragments of DNA (> or = 1 kb). We have constructed clones that enable us to create heteroduplexes of 500 bp, 1 kb, and 1.5 kb and have assessed each of the methods over a range of criteria. Both were able to detect and localize all four types of single-base mismatch and insertion/deletions of 1-5 bp. Whereas EMC was efficient at detection of insertion/deletions in a broad size range of fragments and has the advantage over CCM of using no hazardous chemicals, in our hands it has not been sufficiently robust that we felt confident to consider it for diagnostic use in its present form. CCM using hydroxylamine was efficient over the entire range of fragment sizes tested and using potassium permanganate with tetraethylammonium chloride was efficient up to 1 kb.

Teaching smoking cessation to family practice residents: an experiential approach.

BACKGROUND AND OBJECTIVES: Smoking cessation is a complex process influenced by the smoker's motivation to quit and the effective use of external support measures. Understanding the complexities of smoking cessation can be difficult for physicians, many of whom have never smoked. This paper describes an experiential educational approach that exposes family practice residents to the process of smoking cessation through active participation in an American Lung Association (ALA) Freedom From Smoking group. METHODS: We designed and observed a 1-month educational program in which residents co-led a modified ALA group. Ethnography, a qualitative research technique, was used to discover what residents learned. RESULTS: We identified five themes that describe what residents learned through their experience in the ALA Group: 1) the power of nicotine addiction, 2) the power of the smoking cessation group, 3) skills, tips, tools, and tricks to help the smoker quit, 4) the process of redefining success, and 5) the ability to understand the smoker. Residents' recall of their experience remained vivid, even 9 months after the training concluded. CONCLUSIONS: This experiential approach provided a rich, lasting learning experience for the residents we studied.

Molecular analysis of HLA-DQB1 alleles in childhood common acute lymphoblastic leukaemia.

Epidemiological studies suggest that childhood common acute lymphoblastic leukaemia (c-ALL) may be the rare outcome of early post-natal infection with a common infectious agent. One of the factors that may determine whether a child succumbs to c-ALL is how it responds to the candidate infection. Since immune responses to infection are under the partial control of (human leucocyte antigen) HLA genes, an association between an HLA allele and c-ALL could provide support for an infectious aetiology. To define the limit of c-ALL susceptibility within the HLA region, we have compared HLA-DQB1 allele frequencies in a cohort of 62 children with c-ALL with 76 newborn controls, using group-specific polymerase chain reaction (PCR) amplification, and single-strand conformation polymorphism (SSCP) analysis. We find that a significant excess of children with c-ALL type for DQB1*05 [relative risk (RR): 2.54, uncorrected P=0.038], and a marginal excess with DQB1*0501 (RR: 2.18; P=0.095). Only 3 of the 62 children with c-ALL have the other susceptibility allele, DPB1*0201 as well as DQB1*0501, whereas 15 had one or the other allele. This suggests that HLA-associated susceptibility may be determined independently by at least two loci, and is not due to linkage disequilibrium. The combined relative risk of the two groups of children with DPB1*0201 and/or DQB1*0501 is 2.76 (P=0.0076). Analysis of amino acids encoded by exon 2 of DQB1 reveal additional complexity, with significant (P<0.05) or borderline-significant increases in Gly26, His30, Val57, Glu66-Val67 encoding motifs in c-ALL compared with controls. Since these amino acids are not restricted to DQB1*0501, our results suggest that, as with DPB1, the increased risk of c-ALL associated with DQB1 is determined by specific amino acid encoding motifs rather than by an individual allele. These results also suggest that HLA-associated susceptibility to c-ALL may not be restricted to the region bounded by DPB1 and DQB1.

Ritalin for nicotine withdrawal: Nesbitt's paradox revisited.

This was a unblinded clinical trial of the stimulant methylphenidate (Ritalin) for nicotine withdrawal. Nineteen nicotine-dependent smokers received oral methylphenidate (30 mg target daily dosage) for 5 days following abrupt cessation. Tobacco withdrawal, Spielberger state anxiety, blood pressure, and pulse were measured at baseline, then serially for 7 days. Tobacco withdrawal and state anxiety increased significantly, but 12 (71%) of the 17 smokers who completed the study rated withdrawal relief "very define" and 13 (76%) rated this quit attempt "much easier than other times." Methylphenidate neither increased blood pressure nor blocked cessation-related pulse decrease and appears safe for this indication. Twelve (63%) of the enrolled smokers were confirmed abstinent at day 5. Methylphenidate effect on nicotine withdrawal should be studied in a placebo-controlled clinical trial.

Including smoking status as a new vital sign: it works!

BACKGROUND: Despite the adverse health consequences of smoking, many physicians still neglect to counsel smokers to quit. This study evaluated the effect of including smoking status as a vital sign on the frequency of physician discussions with patients about smoking and physician advice to quit smoking. METHODS: A consecutive sample of adult ambulatory patients in our metropolitan family practice residency program completed exit surveys on physician and nurse counseling about smoking. Control group data were collected for 1 month before the change was made to include smoking status as a vital sign on patient charts. Charts were then marked with a stamp as a chart prompt in the vital signs section. Data were collected for 2 months after smoking status was added to the stamp. RESULTS: There were 637 individuals surveyed, of whom 179 were current smokers; 95 in the "prestamp" group and 84 in the "poststamp" group. The percentage of patient-physician encounters during which smoking was discussed increased from 47% to 86% (P < .001). Physician advice to quit increased from 50% to 80% (P < .001). Physician discussion of smoking with patients increased across all of the five stages of change but most dramatically (53% to 95%) in the "preparation" stage. Physicians were much less likely to counsel patients in the "precontemplation" stage to quit smoking. CONCLUSIONS: Including smoking as a new vital sign significantly increased the likelihood of smoking-related discussions between patients and their physicians. The stamp is inexpensive and easy to use, and because it is a one-time office system change, it is more likely to be implemented and maintained in busy practices.

Preliminary evidence of an association between HLA-DPB1*0201 and childhood common acute lymphoblastic leukaemia supports an infectious aetiology.

It has been suggested that childhood leukaemia may be the abnormal outcome of a common infection. Rare events caused by common environmental events such as infections are likely to be influenced by host genetic susceptibility. We have therefore investigated whether immunogenetic susceptibility contributes to the risk of childhood common ALL (c-ALL). In this preliminary study, we report that children with c-ALL (n = 63) carry the HLA-DPB1 locus allele *0201 twice and nearly three times more frequently than adult (n = 92; relative risk (RR) = 2.9, P < 0.05) or infant controls (n = 82; RR = 2.1). Moreover, children with c-ALL are 3-4 times more likely than controls to be heterozygous for DPB1*0201/*0301, /*0401 and /*0402 (RRadult controls = 3.9; RRinfant controls = 2.8). These results suggest that HLA-DPB1*0201 either alone or with other DPB1 alleles contributes to the risk of childhood c-ALL, possibly by increasing susceptibility to an infectious agent.

Impact of compliance and side effects on the clinical outcome of patients treated with oral erythromycin.

STUDY OBJECTIVE: To determine the relationship among compliance, side effects, and self-reported outcome for patients in an erythromycin trial. DESIGN: A retrospective analysis of data from a multicenter, prospective, single-blind, randomized trial. SETTING: Five metropolitan ambulatory care offices. PATIENTS: The 252 adults (> 18 yrs) were prescribed oral erythromycin 1.0 g/day (base equivalent) for infectious disorders. INTERVENTION: Subjects received erythromycin for 10 days and reported compliance, drug efficacy, and side effects in a daily diary. Compliance was measured by tablet count. RESULTS: A negative correlation was found between gastrointestinal symptom severity score and percentage of tablets taken (p < 0.001). A significant positive correlation was seen between compliance and outcome (p < 0.001). Subjects who took greater than 80% of the drug achieved the treatment goal more frequently than those taking 80% or less (94% vs 59%, p < 0.001). CONCLUSIONS: Side effects of erythromycin adversely affected compliance. Compliance had a positive effect on self-reported outcome.

Surgical decompression of impingement in the weightbearing shoulder.

Shoulder pain is a common affliction, posing particular limitations on the spinal cord injured person. Abnormalities of the rotator cuff mechanism are a common cause of shoulder injury in the general population and it has recently been observed that a large percentage of persons with paraplegia suffer from chronic shoulder pain. This report describes six cases of impingement syndrome in four spinal cord injured persons who depend on upper extremity function for the execution of activities of daily living and mobility. All had failed prolonged trials of conservative therapy and subsequently underwent anterior acromioplasty and when indicated, repair of the supraspinatus tendon. In each case, functional capacity that approached or equalled premorbid levels was achieved. Pain complaints also markedly decreased from preoperative levels. It is suggested that surgical decompression of shoulder impingement and rotator cuff repair may be beneficial in spinal cord injured persons who have failed conservative therapy. Further study is required to determine the long-term efficacy of surgical intervention in this population.

Anxiety disorders in the general practice.

The author reviews the concept of anxiety and the diagnosis and treatment of panic disorder, generalized anxiety disorder, obsessive-compulsive disorder, social phobia, and post-traumatic stress disorder. The psychiatrist and primary care practitioner can collaborate for the patient's benefit.

A comparison of the gastrointestinal side effects of two forms of erythromycin.

BACKGROUND: The gastrointestinal (GI) side effects of erythromycin frequently limit therapy and compliance. PCE Dispertab, a more expensive brand of erythromycin, has been promoted as a well-tolerated new dosage form; however, no studies compare its GI side effects with those of other forms of erythromycin. We compared erythromycin PCE (particles-in-tablet) with E.E.S. (erythromycin ethylsuccinate) to determine whether there is a difference in the incidence and severity of GI side effects. METHODS: This was a multicenter, prospective, single-blind, randomized trial. Observers, but not participants, were blinded to the brand of erythromycin taken until after data analysis. We enrolled ambulatory patients who were at least 18 years old and weighed at least 90 lb for whom erythromycin had been prescribed at a dosage of 1.0 g/d. Subjects were given either the particles-in-tablet form, 333 mg three times daily, or the ethylsuccinate form, 400 mg four times daily, for 10 days and asked to report efficacy, compliance, and the frequency and severity of four GI symptoms (abdominal pain, nausea, vomiting, and diarrhea) in a daily diary. RESULTS: There were no significant differences between the particles-in-tablet and ethylsuccinate forms in incidence of GI side effects (63% and 61%, respectively), average daily GI symptom severity score (0.62 and 0.68, respectively), and GI-related discontinuations (8.5% and 8.2%, respectively). The incidence of moderate or severe nausea was 5% for the particles-in-tablet form and 25% for the ethylsuccinate form (P < .001). CONCLUSIONS: Although ethylsuccinate caused a higher incidence of moderate to severe nausea, there were no differences in the three main outcome measures: incidence of GI side effects, average daily GI-symptom severity score, and GI-related discontinuations. Therefore, we support prescribing erythromycin ethylsuccinate as a first line of treatment because it costs less.

Buspirone effect on tobacco withdrawal symptoms: a randomized placebo-controlled trial.

BACKGROUND: Withdrawal symptoms hinder smoking cessation in nicotine-dependent smokers. This prospective, double-blind, placebo-controlled clinical trial was conducted to evaluate buspirone for nicotine withdrawal symptoms. METHODS: Fifty-four heavy smokers (mean 33.1 cigarettes per day for 24 years) were randomly prescribed 30 mg/d of buspirone or placebo beginning 3 weeks before abrupt smoking cessation. Validated nicotine withdrawal and anxiety scales were administered at baseline and serially for 2 weeks after cessation. RESULTS: Baseline demographic and nicotine-dependence measures were similar for each group. Three smokers (1 on buspirone, 2 on placebo) dropped out of the protocol prior to the quit date. Both groups had significant withdrawal effects over time (analysis of variance [ANOVA] P = 0.0001). There was a significant buspirone effect on any nicotine withdrawal symptoms (ANOVA, alpha = 0.05). Smokers who relapsed, regardless of group, reported significantly worse craving, irritability, anxiety, and difficulty concentrating than abstainers (P less than 0.05). Relapse rates at follow-up visits were not significantly different between groups. Two-week abstinence rates were 52 percent for placebo and 62 percent for buspirone (chi-square, P = 0.760). CONCLUSIONS: In these heavy smokers, buspirone offered no relief from nicotine withdrawal symptoms. Regardless of treatment, relapsing smokers experienced more intense nicotine withdrawal.