The overlap between randomised evaluations of recruitment and retention interventions: An updated review of recruitment (Online Resource for Recruitment in Clinical triAls) and retention (Online Resource for Retention in Clinical triAls) literature

BACKGROUND

The Online Resource for Recruitment in Clinical triAls (ORRCA) and the Online Resource for Retention in Clinical triAls (ORRCA2) were established to organise and map the literature addressing participant recruitment and retention within clinical research. The two databases are updated on an ongoing basis using separate but parallel systematic reviews. However, recruitment and retention of research participants is widely acknowledged to be interconnected. While interventions aimed at addressing recruitment challenges can impact retention and vice versa, it is not clear how well they are simultaneously considered within methodological research. This study aims to report the recent update of ORRCA and ORRCA2 with a special emphasis on assessing crossover of the databases and how frequently randomised studies of methodological interventions measure the impact on both recruitment and retention outcomes.

METHODS

Two parallel systematic reviews were conducted in line with previously reported methods updating ORRCA (recruitment) and ORRCA2 (retention) with publications from 2018 and 2019. Articles were categorised according to their evidence type (randomised evaluation, non-randomised evaluation, application and observation) and against the recruitment and retention domain frameworks. Articles categorised as randomised evaluations were compared to identify studies appearing in both databases. For randomised studies that were only in one database, domain categories were used to assess whether the methodological intervention was likely to impact on the alternate construct. For example, whether a recruitment intervention might also impact retention.

RESULTS

In total, 806 of 17,767 articles screened for the recruitment database and 175 of 18,656 articles screened for the retention database were added as result of the update. Of these, 89 articles were classified as 'randomised evaluation', of which 6 were systematic reviews and 83 were randomised evaluations of methodological interventions. Ten of the randomised studies assessed recruitment and retention and were included in both databases. Of the randomised studies only in the recruitment database, 48/55 (87%) assessed the content or format of participant information which could have an impact on retention. Of the randomised studies only in the retention database, 6/18 (33%) assessed monetary incentives, 4/18 (22%) assessed data collection location and methods and 3/18 (17%) assessed non-monetary incentives, all of which could have an impact on recruitment.

CONCLUSION

Only a small proportion of randomised studies of methodological interventions assessed the impact on both recruitment and retention despite having a potential impact on both outcomes. Where possible, an integrated approach analysing both constructs should be the new standard for these types of evaluations to ensure that improvements to recruitment are not at the expense of retention and vice versa.

CWHM-974 is a fluphenazine derivative with improved antifungal activity against Candida albicans due to reduced susceptibility to multidrug transporter-mediated resistance mechanisms

Multidrug resistance (MDR) transporters such as ATP-Binding Cassette (ABC) and Major Facilitator Superfamily proteins are important mediators of antifungal drug resistance, particularly with respect to azole class drugs. Consequently, identifying molecules that are not susceptible to this mechanism of resistance is an important goal for new antifungal drug discovery. As part of a project to optimize the antifungal activity of clinically used phenothiazines, we synthesized a fluphenazine derivative (CWHM-974) with 8-fold higher activity against Candida spp. compared to the fluphenazine and with activity against Candida spp. with reduced fluconazole susceptibility due to increased MDR transporters. Here, we show that the improved C. albicans activity is because fluphenazine induces its own resistance by triggering expression of Candida drug resistance (CDR) transporters while CWHM-974 induces expression but does not appear to be a substrate for the transporters or is insensitive to their effects through other mechanisms. We also found that fluphenazine and CWHM-974 are antagonistic with fluconazole in C. albicans but not in C. glabrata, despite inducing CDR1 expression to high levels. Overall, CWHM-974 is one of the few examples of a molecule in which relatively small structural modifications significantly reduced susceptibility to multidrug transporter-mediated resistance.

Integrated multi-omics for rapid rare disease diagnosis on a national scale

Critically ill infants and children with rare diseases need equitable access to rapid and accurate diagnosis to direct clinical management. Over 2 years, the Acute Care Genomics program provided whole-genome sequencing to 290 families whose critically ill infants and children were admitted to hospitals throughout Australia with suspected genetic conditions. The average time to result was 2.9 d and diagnostic yield was 47%. We performed additional bioinformatic analyses and transcriptome sequencing in all patients who remained undiagnosed. Long-read sequencing and functional assays, ranging from clinically accredited enzyme analysis to bespoke quantitative proteomics, were deployed in selected cases. This resulted in an additional 19 diagnoses and an overall diagnostic yield of 54%. Diagnostic variants ranged from structural chromosomal abnormalities through to an intronic retrotransposon, disrupting splicing. Critical care management changed in 120 diagnosed patients (77%). This included major impacts, such as informing precision treatments, surgical and transplant decisions and palliation, in 94 patients (60%). Our results provide preliminary evidence of the clinical utility of integrating multi-omic approaches into mainstream diagnostic practice to fully realize the potential of rare disease genomic testing in a timely manner.

CWHM-974 is a fluphenazine derivative with improved antifungal activity against Candida albicans due to reduced susceptibility to multidrug transporter-mediated resistance mechanisms

Multidrug resistance (MDR) transporters such as ATP Binding Cassette (ABC) and Major Facilitator Superfamily (MFS) proteins are important mediators of antifungal drug resistance, particularly with respect to azole class drugs. Consequently, identifying molecules that are not susceptible to this mechanism of resistance is an important goal for new antifungal drug discovery. As part of a project to optimize the antifungal activity of clinically used phenothiazines, we synthesized a fluphenazine derivative (CWHM-974) with 8-fold higher activity against Candida spp. compared to the fluphenazine and with activity against Candida spp. with reduced fluconazole susceptibility due to increased multidrug resistance transporters. Here, we show that the improved C. albicans activity is because fluphenazine induces its own resistance by triggering expression of CDR transporters while CWHM-974 induces expression but does not appear to be a substrate for the transporters or is insensitive to their effects through other mechanisms. We also found that fluphenazine and CWHM-974 are antagonistic with fluconazole in C. albicans but not in C. glabrata , despite inducing CDR1 expression to high levels. Overall, CWHM-974 represents a unique example of a medicinal chemistry-based conversion of chemical scaffold from MDR-sensitive to MDR-resistant and, hence, active against fungi that have developed resistance to clinically used antifungals such as the azoles.

Findings from precision oncology in the clinic: rare, novel variants are a significant contributor to scaling molecular diagnostics

Background

Next generation sequencing for oncology patient management is now routine in clinical pathology laboratories. Although wet lab, sequencing and pipeline tasks are largely automated, the analysis of variants for clinical reporting remains largely a manual task. The increasing volume of sequencing data and the limited availability of genetic experts to analyse and report on variants in the data is a key scalability limit for molecular diagnostics.

Method

To determine the impact and size of the issue, we examined the longitudinally compiled genetic variants from 48,036 cancer patients over a six year period in a large cancer hospital from ten targeted cancer panel tests in germline, solid tumour and haematology contexts using hybridization capture and amplicon assays. This testing generated 24,168,398 sequenced variants of which 23,255 (8214 unique) were clinically reported.

Results

Of the reported variants, 17,240 (74.1%) were identified in more than one assay which allowed curated variant data to be reused in later reports. The remainder, 6015 (25.9%) were not subsequently seen in later assays and did not provide any reuse benefit. The number of new variants requiring curation has significantly increased over time from 1.72 to 3.73 variants per sample (292 curated variants per month). Analysis of the 23,255 variants reported, showed 28.6% (n = 2356) were not present in common public variant resources and therefore required de novo curation. These in-house only variants were enriched for indels, tumour suppressor genes and from solid tumour assays.

Conclusion

This analysis highlights the significant percentage of variants not present within common public variant resources and the level of non-recurrent variants that consequently require greater curation effort. Many of these variants are unique to a single patient and unlikely to appear in other patients reflecting the personalised nature of cancer genomics. This study depicts the real-world situation for pathology laboratories faced with curating increasing numbers of low-recurrence variants while needing to expedite the process of manual variant curation. In the absence of suitably accurate automated methods, new approaches are needed to scale oncology diagnostics for future genetic testing volumes.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12920-022-01214-y.

Developing an online, searchable database to systematically map and organise current literature on retention research (ORRCA2)

BACKGROUND

Addressing recruitment and retention challenges in trials is a key priority for methods research, but navigating the literature is difficult and time-consuming. In 2016, ORRCA (www.orrca.org.uk) launched a free, searchable database of recruitment research that has been widely accessed and used to support the update of systematic reviews and the selection of recruitment strategies for clinical trials. ORRCA2 aims to create a similar database to map the growing volume and importance of retention research.

METHODS

Searches of Medline (Ovid), CINAHL, PsycINFO, Scopus, Web of Science Core Collection and the Cochrane Library, restricted to English language and publications up to the end of 2017. Hand searches of key systematic reviews were undertaken and randomised evaluations of recruitment interventions within the ORRCA database on 1 October 2020 were also reviewed for any secondary retention outcomes. Records were screened by title and abstract before obtaining the full text of potentially relevant articles. Studies reporting or evaluating strategies, methods and study designs to improve retention within healthcare research were eligible. Case reports describing retention challenges or successes and studies evaluating participant reported reasons for withdrawal or losses were also included. Studies assessing adherence to treatments, attendance at appointments outside of research and statistical analysis methods for missing data were excluded. Eligible articles were categorised into one of the following evidence types: randomised evaluations, non-randomised evaluations, application of retention strategies without evaluation and observations of factors affecting retention. Articles were also mapped against a retention domain framework. Additional data were extracted on research outcomes, methods and host study context.

RESULTS

Of the 72,904 abstracts screened, 4,364 full texts were obtained, and 1,167 articles were eligible. Of these, 165 (14%) were randomised evaluations, 99 (8%) non-randomised evaluations, 319 (27%) strategies without evaluation and 584 (50%) observations of factors affecting retention. Eighty-four percent (n = 979) of studies assessed the numbers of participants retained, 27% (n = 317) assessed demographic differences between retained and lost participants, while only 4% (n = 44) assessed the cost of retention strategies. The most frequently reported domains within the 165 studies categorised as 'randomised evaluations of retention strategies' were participant monetary incentives (32%), participant reminders and prompts (30%), questionnaire design (30%) and data collection location and method (26%).

CONCLUSION

ORRCA2 builds on the success of ORRCA extending the database to organise the growing volume of retention research. Less than 15% of articles were randomised evaluations of retention strategies. Mapping of the literature highlights several areas for future research such as the role of research sites, clinical staff and study design in enhancing retention. Future studies should also include cost-benefit analysis of retention strategies.

Strategies to improve retention in randomised trials

BACKGROUND

Poor retention of participants in randomised trials can lead to missing outcome data which can introduce bias and reduce study power, affecting the generalisability, validity and reliability of results. Many strategies are used to improve retention but few have been formally evaluated.

OBJECTIVES

To quantify the effect of strategies to improve retention of participants in randomised trials and to investigate if the effect varied by trial setting.

SEARCH METHODS

We searched the Cochrane Central Register of Controlled Trials (CENTRAL), MEDLINE, Scopus, PsycINFO, CINAHL, Web of Science Core Collection (SCI-expanded, SSCI, CPSI-S, CPCI-SSH and ESCI) either directly with a specified search strategy or indirectly through the ORRCA database. We also searched the SWAT repository to identify ongoing or recently completed retention trials. We did our most recent searches in January 2020.

SELECTION CRITERIA

We included eligible randomised or quasi-randomised trials of evaluations of strategies to increase retention that were embedded in 'host' randomised trials from all disease areas and healthcare settings. We excluded studies aiming to increase treatment compliance.

DATA COLLECTION AND ANALYSIS

We extracted data on: the retention strategy being evaluated; location of study; host trial setting; method of randomisation; numbers and proportions in each intervention and comparator group. We used a risk difference (RD) and 95% confidence interval (CI) to estimate the effectiveness of the strategies to improve retention. We assessed heterogeneity between trials. We applied GRADE to determine the certainty of the evidence within each comparison.

MAIN RESULTS

We identified 70 eligible papers that reported data from 81 retention trials. We included 69 studies with more than 100,000 participants in the final meta-analyses, of which 67 studies evaluated interventions aimed at trial participants and two evaluated interventions aimed at trial staff involved in retention. All studies were in health care and most aimed to improve postal questionnaire response. Interventions were categorised into broad comparison groups: Data collection; Participants; Sites and site staff; Central study management; and Study design. These intervention groups consisted of 52 comparisons, none of which were supported by high-certainty evidence as determined by GRADE assessment. There were four comparisons presenting moderate-certainty evidence, three supporting retention (self-sampling kits, monetary reward together with reminder or prenotification and giving a pen at recruitment) and one reducing retention (inclusion of a diary with usual follow-up compared to usual follow-up alone). Of the remaining studies, 20 presented GRADE low-certainty evidence and 28 presented very low-certainty evidence. Our findings do provide a priority list for future replication studies, especially with regard to comparisons that currently rely on a single study.

AUTHORS' CONCLUSIONS

Most of the interventions we identified aimed to improve retention in the form of postal questionnaire response. There were few evaluations of ways to improve participants returning to trial sites for trial follow-up. None of the comparisons are supported by high-certainty evidence. Comparisons in the review where the evidence certainty could be improved with the addition of well-done studies should be the focus for future evaluations.

Battling the COVID-19 infodemic in an Irish context: the role of iHealthFacts

On the 11 ^th of March 2020, the World Health Organisation (WHO) declared a global pandemic due to the SARS-CoV-2 virus, which causes coronavirus disease 2019 (COVID-19). This was one month after Dr. Tedros Adhanom Ghebreyesus, Director-General of the WHO declared that we are also fighting an ‘infodemic’. The WHO has described an infodemic as an “over-abundance of information – some accurate and some not – that makes it hard for people to find trustworthy sources and reliable guidance when they need it”. iHealthFacts.ie is an Irish resource where the public can quickly and easily check the credibility and reliability of health claims circulating on social media. Unreliable claims can lead to poorly informed health choices. iHealthFacts is an initiative that supports the public to think critically about health claims and make well-informed choices. Here, we describe the role iHealthFacts plays in providing reliable information to the public and offer reflections from those involved in launching this initiative during a pandemic.

SUN-LB087 Successful Prevention of Common Complications of Severe Hypercalcemia Secondary to Subcutaneous Fat Necrosis of the Newborn Following Whole Body Therapeutic Hypothermia

Background: Subcutaneous fat necrosis (SCFN) is a rare form of panniculitis mostly seen in neonates with a history of significant perinatal stress and may be associated with life-threatening hypercalcemia. Clinical Case: An infant boy born by emergent C-section at 39 4/7 weeks to a 32 y/o G2P0 mother due to pre-eclampsia, emerged limp, cyanotic and apneic with heart rate<100 bpm and thick meconium-stained amniotic fluid. Following positive pressure ventilation, his heart rate improved, but, his poor respiratory effort and poor muscle tone persisted. Apgar scores were 2, 5, 6 and 8 at 1, 5, 10 and 15 minutes, respectively. The infant was transferred to the NICU on continuous positive airway pressure. Whole body therapeutic hypothermia (WBTH) was initiated based on the presence of neurologic dysfunction and markers of hypoxic-ischemic injury: metabolic acidosis (cord blood pH 6.89, incalculable bicarbonate), elevated lactate (4.1 mmol/L, n 0.5 - 2 mmol/L), abnormal liver function tests (AST 811 IU/L, n 13 - 39; ALT 1175 IU/L, n 4 - 36 IU/L; LDH >4000 IU/L, n 100 - 250 IU/L), abnormal coagulation panel (PT 75.4 sec, n 9.7 - 12.4 sec; PTT 58.7 sec, n 25 - 37 sec; INR 6.85, n 0.9 - 1.2) and thrombocytopenia (platelet count 90 K/uL, n 150 - 450 K/uL). IV fluids, platelet transfusions and antibiotics were given for presumed sepsis. WBTH was completed on day of life (DOL) 3 and infant was re-warmed overnight. SCFN presented on DOL 4 as erythematous, tender, nodular indurations throughout the skin over the dorsum. Supportive therapy was given: repositioning, morphine for pain during feeding and handling and bacitracin ointment to areas of skin desquamation. Labs were consistent with SCFN. On DOL 18, total serum calcium (TSC) increased to 11.8 mg/dL (n 8.8 - 11.2 mg/dL), intact parathyroid hormone (1 pg/mL, n 14 - 72 pg/mL), PTH related peptide (<2.0 pmol/L, n <2.0 pmol/L), 25 hydroxyvitamin D3 (22.8 ng/mL, n 20 - 50 ng/mL) and 1,25 dihydroxyvitamin D3 (80.7 pg/mL, n 19 - 79.3 pg/mL). Mother discontinued all vitamin supplementation and breastmilk was supplemented with low-calcium infant formula. TSC peaked on DOL 28 to 13.2 mg/dL, and oral furosemide (2 mg/kg/dose, BID) was started. On DOL 30, oral prednisolone (2mg/kg/day) and polycitrate for urine alkalization and prevention of nephrocalcinosis were initiated. Furosemide was discontinued on DOL 32. IV fluids and polycitrate were discontinued on DOL 42. Oral prednisolone was continued following a taper schedule. Urine calcium to urine creatinine ratios initially showed a marked elevation with peak of 1.67 (n <0.86) but eventually began to decline throughout the course of therapy. Head and repeat renal ultrasounds were normal. The infant was discharged home on DOL 50 with down-trending TSC levels and completed a slow oral prednisolone taper on DOL 130. Conclusion: Early recognition and treatment of SCFN and associated hypercalcemia is crucial to prevent morbidity and mortality. Unless otherwise noted, all abstracts presented at ENDO are embargoed until the date and time of presentation. For oral presentations, the abstracts are embargoed until the session begins. Abstracts presented at a news conference are embargoed until the date and time of the news conference. The Endocrine Society reserves the right to lift the embargo on specific abstracts that are selected for promotion prior to or during ENDO.

Late diagnosis, delayed presentation and late presentation among persons enrolled in a clinical HIV cohort in Ontario, Canada (1999-2013)

OBJECTIVES

Timely HIV diagnosis and presentation to medical care are important for treatment and prevention. Our objective was to measure late diagnosis, delayed presentation and late presentation among individuals in the Ontario HIV Treatment Network Cohort Study (OCS) who were newly diagnosed in Ontario.

METHODS

The OCS is a multi-site clinical cohort study of people living with HIV in Ontario, Canada. We measured prevalence of late diagnosis [CD4 count < 350 cells/μL or an AIDS-defining condition (ADC) within 3 months of HIV diagnosis], delayed presentation (≥ 3 months from HIV diagnosis to presentation to care), and late presentation (CD4 count < 350 cells/μL or ADC within 3 months of presentation). We identified characteristics associated with these outcomes and explored their overlap.

RESULTS

A total of 1819 OCS participants were newly diagnosed in Ontario from 1999 to 2013. Late diagnosis (53.0%) and presentation (54.0%) were common, and a quarter (23.1%) of participants were delayed presenters. In multivariable models, the participants of delayed presentation decreased over calendar time, but that of late diagnosis/presentation did not. Late diagnosis contributed to the majority (> 87%) of late presentation, and the prevalence of delayed presentation was similar among those diagnosed late versus early (13.4 versus 13.4%, respectively; P = 0.99). Characteristics associated with higher odds of late diagnosis/presentation in multivariable analyses included older age at diagnosis/presentation; African, Caribbean and Black race/ethnicity; Indigenous race/ethnicity; female sex; and being a male who did not report sex with men. There were lower odds of late diagnosis/presentation among participants who had ever injected drugs. In contrast, delayed presentation risk factors included younger age at diagnosis and having ever injected drugs.

CONCLUSIONS

Late presentation is common in Ontario, as it is in other high-income countries. Our findings suggest that efforts to reduce late presentation should focus on facilitating earlier diagnosis for the populations identified in this analysis.

PathOS: a decision support system for reporting high throughput sequencing of cancers in clinical diagnostic laboratories

Background

The increasing affordability of DNA sequencing has allowed it to be widely deployed in pathology laboratories. However, this has exposed many issues with the analysis and reporting of variants for clinical diagnostic use. Implementing a high-throughput sequencing (NGS) clinical reporting system requires a diverse combination of capabilities, statistical methods to identify variants, global variant databases, a validated bioinformatics pipeline, an auditable laboratory workflow, reproducible clinical assays and quality control monitoring throughout. These capabilities must be packaged in software that integrates the disparate components into a useable system.

Results

To meet these needs, we developed a web-based application, PathOS, which takes variant data from a patient sample through to a clinical report. PathOS has been used operationally in the Peter MacCallum Cancer Centre for two years for the analysis, curation and reporting of genetic tests for cancer patients, as well as the curation of large-scale research studies. PathOS has also been deployed in cloud environments allowing multiple institutions to use separate, secure and customisable instances of the system. Increasingly, the bottleneck of variant curation is limiting the adoption of clinical sequencing for molecular diagnostics. PathOS is focused on providing clinical variant curators and pathology laboratories with a decision support system needed for personalised medicine. While the genesis of PathOS has been within cancer molecular diagnostics, the system is applicable to NGS clinical reporting generally.

Conclusions

The widespread availability of genomic sequencers has highlighted the limited availability of software to support clinical decision-making in molecular pathology. PathOS is a system that has been developed and refined in a hospital laboratory context to meet the needs of clinical diagnostics. The software is available as a set of Docker images and source code at https://github.com/PapenfussLab/PathOS.

Electronic supplementary material

The online version of this article (doi:10.1186/s13073-017-0427-z) contains supplementary material, which is available to authorized users.

An Objective Measure of Noseband Tightness and Its Measurement Using a Novel Digital Tightness Gauge

Noseband tightness is difficult to assess in horses participating in equestrian sports such as dressage, show jumping and three-day-eventing. There is growing concern that nosebands are commonly tightened to such an extent as to restrict normal equine behaviour and possibly cause injury. In the absence of a clear agreed definition of noseband tightness, a simple model of the equine nose-noseband interface environment was developed in order to guide further studies in this area. The normal force component of the noseband tensile force was identified as the key contributor to sub-noseband tissue compression. The model was used to inform the design of a digital tightness gauge which could reliably measure the normal force component of the noseband tensile force. A digital tightness gauge was developed to measure this parameter under nosebands fitted to bridled horses. Results are presented for field tests using two prototype designs. Prototype version three was used in field trial 1 (n = 15, frontal nasal plane sub-noseband site). Results of this trial were used to develop an ergonomically designed prototype, version 4, which was tested in a second field trial (n = 12, frontal nasal plane and lateral sub-noseband site). Nosebands were set to three tightness settings in each trial as judged by a single rater using an International Society for Equitation Science (ISES) taper gauge. Normal forces in the range 7-95 N were recorded at the frontal nasal plane while a lower range 1-28 N was found at the lateral site for the taper gauge range used in the trials. The digital tightness gauge was found to be simple to use, reliable, and safe and its use did not agitate the animals in any discernable way. A simple six point tightness scale is suggested to aid regulation implementation and the control of noseband tightness using normal force measurement as the objective tightness discriminant.

Xenome--a tool for classifying reads from xenograft samples

Motivation: Shotgun sequence read data derived from xenograft material contains a mixture of reads arising from the host and reads arising from the graft. Classifying the read mixture to separate the two allows for more precise analysis to be performed.

Results: We present a technique, with an associated tool Xenome, which performs fast, accurate and specific classification of xenograft-derived sequence read data. We have evaluated it on RNA-Seq data from human, mouse and human-in-mouse xenograft datasets.

Availability:Xenome is available for non-commercial use from http://www.nicta.com.au/bioinformatics

Contact:tom.conway@nicta.com.au

Gossamer--a resource-efficient de novo assembler

MOTIVATION

The de novo assembly of short read high-throughput sequencing data poses significant computational challenges. The volume of data is huge; the reads are tiny compared to the underlying sequence, and there are significant numbers of sequencing errors. There are numerous software packages that allow users to assemble short reads, but most are either limited to relatively small genomes (e.g. bacteria) or require large computing infrastructure or employ greedy algorithms and thus often do not yield high-quality results.

RESULTS

We have developed Gossamer, an implementation of the de Bruijn approach to assembly that requires close to the theoretical minimum of memory, but still allows efficient processing. Our results show that it is space efficient and produces high-quality assemblies.

AVAILABILITY

Gossamer is available for non-commercial use from http://www.genomics.csse.unimelb.edu.au/product-gossamer.php.

Iterative dictionary construction for compression of large DNA data sets

Genomic repositories increasingly include individual as well as reference sequences, which tend to share long identical and near-identical strings of nucleotides. However, the sequential processing used by most compression algorithms, and the volumes of data involved, mean that these long-range repetitions are not detected. An order-insensitive, disk-based dictionary construction method can detect this repeated content and use it to compress collections of sequences. We explore a dictionary construction method that improves repeat identification in large DNA data sets. Our adaptation, COMRAD, of an existing disk-based method identifies exact repeated content in collections of sequences with similarities within and across the set of input sequences. COMRAD compresses the data over multiple passes, which is an expensive process, but allows COMRAD to compress large data sets within reasonable time and space. COMRAD allows for random access to individual sequences and subsequences without decompressing the whole data set. COMRAD has no competitor in terms of the size of data sets that it can compress (extending to many hundreds of gigabytes) and, even for smaller data sets, the results are competitive compared to alternatives; as an example, 39 S. cerevisiae genomes compressed to 0.25 bits per base.

The poisson margin test for normalization-free significance analysis of NGS data

The current methods for the determination of the statistical significance of peaks and regions in next generation sequencing (NGS) data require an explicit normalization step to compensate for (global or local) imbalances in the sizes of sequenced and mapped libraries. There are no canonical methods for performing such compensations; hence, a number of different procedures serving this goal in different ways can be found in the literature. Unfortunately, the normalization has a significant impact on the final results. Different methods yield very different numbers of detected "significant peaks" even in the simplest scenario of ChIP-Seq experiments that compare the enrichment in a single sample relative to a matching control. This becomes an even more acute issue in the more general case of the comparison of multiple samples, where a number of arbitrary design choices will be required in the data analysis stage, each option resulting in possibly (significantly) different outcomes. In this article, we investigate a principled statistical procedure that eliminates the need for a normalization step. We outline its basic properties, in particular the scaling upon depth of sequencing. For the sake of illustration and comparison, we report the results of re-analyzing a ChIP-Seq experiment for transcription factor binding site detection. In order to quantify the differences between outcomes, we use a novel method based on the accuracy of in silico prediction by support vector machine (SVM) models trained on part of the genome and tested on the remainder. See Kowalczyk et al. ( 2009 ) for supplementary material.

Epigenetic regulation of cell type-specific expression patterns in the human mammary epithelium

Differentiation is an epigenetic program that involves the gradual loss of pluripotency and acquisition of cell type–specific features. Understanding these processes requires genome-wide analysis of epigenetic and gene expression profiles, which have been challenging in primary tissue samples due to limited numbers of cells available. Here we describe the application of high-throughput sequencing technology for profiling histone and DNA methylation, as well as gene expression patterns of normal human mammary progenitor-enriched and luminal lineage-committed cells. We observed significant differences in histone H3 lysine 27 tri-methylation (H3K27me3) enrichment and DNA methylation of genes expressed in a cell type–specific manner, suggesting their regulation by epigenetic mechanisms and a dynamic interplay between the two processes that together define developmental potential. The technologies we developed and the epigenetically regulated genes we identified will accelerate the characterization of primary cell epigenomes and the dissection of human mammary epithelial lineage-commitment and luminal differentiation.

Cellular differentiation is a precisely controlled and largely irreversible process orchestrated by cell type–specific epigenetic programs. Abnormalities in these programs lead to developmental disorders and play a key role in tumorigenesis. To better understand the regulation of human mammary epithelial cell type specification, we analyzed the gene expression, DNA methylation, and histone H3 K4 and K27 trimethylation profiles of progenitor-enriched and more differentiated luminal epithelial cell populations from multiple individuals. Network analysis of these profiles and their comparison to that of human embryonic stem cells identified key regulators of mammary epithelial and luminal lineage commitment. The list of genes epigenetically regulated in a cell type–specific manner provides a rich resource for the further analysis of human breast development and the role of epigenetic mechanisms in breast tumorigenesis.

Reference-free validation of short read data

Background

High-throughput DNA sequencing techniques offer the ability to rapidly and cheaply sequence material such as whole genomes. However, the short-read data produced by these techniques can be biased or compromised at several stages in the sequencing process; the sources and properties of some of these biases are not always known. Accurate assessment of bias is required for experimental quality control, genome assembly, and interpretation of coverage results. An additional challenge is that, for new genomes or material from an unidentified source, there may be no reference available against which the reads can be checked.

Results

We propose analytical methods for identifying biases in a collection of short reads, without recourse to a reference. These, in conjunction with existing approaches, comprise a methodology that can be used to quantify the quality of a set of reads. Our methods involve use of three different measures: analysis of base calls; analysis of k-mers; and analysis of distributions of k-mers. We apply our methodology to wide range of short read data and show that, surprisingly, strong biases appear to be present. These include gross overrepresentation of some poly-base sequences, per-position biases towards some bases, and apparent preferences for some starting positions over others.

Conclusions

The existence of biases in short read data is known, but they appear to be greater and more diverse than identified in previous literature. Statistical analysis of a set of short reads can help identify issues prior to assembly or resequencing, and should help guide chemical or statistical methods for bias rectification.

Expression Vector for Zymomonas mobilis

This study describes the construction of several useful cloning vectors which can be conjugated from Escherichia coli into Zymomonas mobilis at high frequency, approaching 10 per donor or recipient. These vectors contain a broad-host-range replicon and mob site from RSF1010, a chloramphenicol acyltransferase gene under the control of an enteric consensus promoter, and a second mob site (originally derived from RP4). The addition of this second mob site appears to be responsible for a 2-order-of-magnitude increase in the efficiency of transfer into Z. mobilis. Such vectors may be useful for other gram-negative bacteria in which conjugation efficiencies are low. These vectors are stably maintained in Z. mobilis with no detectable loss of plasmid after 50 generations in the absence of selective pressure. One of these, pLOI193, contains the tetracycline gene from pBR322 and associated cloning sites for insertional inactivation. Another, pLOI204, contains a Z. mobilis promoter immediately upstream from a BamHI site which can be used for cloning. This promoter has been shown to efficiently drive the expression of beta-galactosidase in both Z. mobilis and E. coli. This promoter fragment from Z. mobilis has been sequenced, and the site for transcriptional initiation in E. coli and Z. mobilis has been identified.

Control of glycolytic flux in Zymomonas mobilis by glucose 6-phosphate dehydrogenase activity

Glycolytic genes in Zymomonas mobilis are highly expressed and constitute half of the cytoplasmic protein. The first four genes (glf, zwf, edd, glk) in this pathway form an operon encoding a glucose permease, glucose 6-phosphate dehydrogenase (G6-P dehydrogenase), 6-phosphogluconate dehydratase, and glucokinase, respectively. Each gene was overexpressed from a tac promoter to investigate the control of glycolysis during the early stages of batch fermentation when flux (qCO(2)) is highest. Almost half of flux control appears to reside with G6-P dehydrogenase (C(J) (G6-P dehydrogenase) = 0.4). Although Z. mobilis exhibits one of the highest rates of glycolysis known, recombinants with elevated G6-P dehydrogenase had a 10% to 13% higher glycolytic flux than the native organism. A small increase in flux was also observed for recombinants expressing glf. Results obtained did not allow a critical evaluation of glucokinase and this enzyme may also represent an important control point. 6-Phosphogluconate dehydratase appears to be saturating at native levels. With constructs containing the full operon, growth rate and flux were both reduced, complicating interpretations. However, results obtained were also consistent with G6-P dehydrogenase as a primary site of control. Flux was 17% higher in operon constructs which exhibited a 17% increase in G6-P dehydrogenase specific activity, relative to the average of other operon constructs which contain a frameshift mutation in zwf. It is unlikely that all flux control residues solely in G6-P dehydrogenase (calculated C(J) (G6-P dehydrogenase) = 1.0) although these results further support the importance of this enzyme. As reported in previous studies, changes in flux were not accompanied by changes in growth rate providing further evidence that ATP production does not limit biosynthesis in rich complex medium.

A genome-wide linkage scan for bone mineral density in an extended sample: evidence for linkage on 11q23 and Xq27

BACKGROUND

Osteoporosis is a major public health problem, mainly quantified by low bone mineral density (BMD). The majority of BMD variation is determined by genetic effects. A pilot whole genome linkage scan (WGS) was previously reported in 53 white pedigrees with 630 subjects. Several genomic regions were suggested to be linked to BMD variation.

OBJECTIVE

To substantiate these previous findings and detect new genomic regions.

METHODS

A WGS was conducted on an extended sample where the size was almost tripled (1816 subjects from 79 pedigrees). All the subjects were genotyped with 451 microsatellite markers spaced approximately 8.1 cM apart across the human genome. Two point and multipoint linkage analyses were carried out using the variance component method.

RESULTS

The strongest linkage signal was obtained on Xq27 with two point LOD scores of 4.30 for wrist BMD, and 2.57 for hip BMD, respectively. Another important region was 11q23, which achieved a maximum LOD score of 3.13 for spine BMD in multipoint analyses, confirming the results on this region in two earlier independent studies. Suggestive linkage evidence was also found on 7p14 and 20p12.

CONCLUSIONS

Together with the findings from other studies, the current study has further delineated the genetic basis of bone mass and highlights the importance of increasing sample size to confirm linkage findings and to identify new regions of linkage.

A second-stage genome scan for QTLs influencing BMD variation

Low bone mineral density (BMD) is a major risk factor for osteoporotic fracture. To identify genomic regions harboring quantitative trait loci (QTLs) contributing to BMD variation, we performed a two-stage genome screen. The first stage involved genotyping of a sample of 53 pedigrees with 630 individuals using 400 microsatellite markers spaced at approximately 10-cM intervals throughout the genome. Ten genomic regions with multi- and/or two-point LOD scores greater than 1.5 were observed. In the present second-stage study, 60 microsatellite markers, with a mean spacing of about 5 cM, were genotyped in these regions in an expanded sample of 79 pedigrees that contained 1816 subjects. Each pedigree was ascertained through a proband with extreme BMD at the hip or spine. BMD at the spine (L1-4), hip (the femoral neck, trochanter, and intertrochanteric region), and wrist (the ultradistal region) was measured by dual-energy X-ray absorptiometry (DXA) and was adjusted for age, sex, height, and weight. Two-point and multipoint linkage analyses were performed for each BMD site using statistical genetic methods that are implemented in the computer package SOLAR. Several regions (7q11, 10q26, 12q13, and 12q24) achieved LOD scores in excess of 1 in the second-stage followup study. The current results replicate some of our previous linkage findings and also highlight some of the difficulties facing microsatellite linkage mapping for complex human diseases.

Evidence for a major gene for bone mineral density/content in human pedigrees identified via probands with extreme bone mineral density

Bone mineral content (BMC) and/or bone mineral density (BMD, i.e. BMC scaled by bone size) are major determinants for osteoporosis, which is a serious health problem. The major determinant of variation in BMD/BMC is genetic. The few studies now available are inconsistent in the identification and/or even in the existence of major gene(s) for BMD/BMC. In 51 human pedigrees with 941 individuals (526 measured for phenotypes) identified via probands with extreme BMD values, we performed complex segregation analyses to test the existence of a genetic locus with a major effect on BMD/BMC variation. We analyzed BMD and BMC at the spine, hip and wrist jointly by employing, as the study phenotype, factor scores (FS) of the principle component that explains approximately 75% of the total BMD/BMC variation at the three sites. The results indicate that a major gene exists with a codominant effect that is responsible for approximately 16% of the FS variation when adjusted for significant effects of sex, body weight and age. A significant genotype-x-sex-x-age interaction was found, which may explain approximately 14% of the FS variation after adjusting for body weight. Testing of various models did not provide support for shared familial environmental effects but suggested the existence of residual polygenic effects, which may explain approximately 50% of the FS variation when adjusting for sex, body weight and age. This study indicates a promising aspect of studies to identify a major gene for BMD/BMC variation in our pedigrees identified via extreme probands.

DNA array analysis in a Microsoft Windows environment

Microsoft Windows-based computers have evolved to the point that they provide sufficient computational and visualization power for robust analysis of DNA array data. In fact, smaller laboratories might prefer to carry out some or all of their analyses and visualization in a Windows environment, rather than alternative platforms such as UNIX. We have developed a series of manually executed macros written in Visual Basic for Microsoft Excel spreadsheets, that allows for rapid and comprehensive gene expression data analysis. The first macro assigns gene names to spots on the DNA array and normalizes individual hybridizations by expressing the signal intensity for each gene as a percentage of the sum of all gene intensities. The second macro streamlines statistical consideration of the confidence in individual gene measurements for sets of experimental replicates by calculating probability values with the Student's t test. The third macro introduces a threshold value, calculates expression ratios between experimental conditions, and calculates the standard deviation of the mean of the log ratio values. Selected columns of data are copied by a fourth macro to create a processed data set suitable for entry into a Microsoft Access database. An Access database structure is described that allows simple queries across multiple experiments and export of data into third-party data visualization software packages. These analysis tools can be used in their present form by others working with commercial E. coli membrane arrays, or they may be adapted for use with other systems. The Excel spreadsheets with embedded Visual Basic macros and detailed instructions for their use are available at http://www.ou.edu/microarray.

Is population bone mineral density variation linked to the marker D11S987 on chromosome 11q12-13?

Our purpose is to test linkage of human chromosome 11q12-13 to BMD variation. Chromosome 11q12-13 has been linked to three BMD-related phenotypes that are inherited as Mendelian traits in human pedigrees: an autosomal dominant high bone mass trait, autosomal recessive osteoporosis pseudoglioma, and autosomal recessive osteopetrosis. A sibling pair study with 374 sibships showed significant linkage of D11S987 to normal BMD variation, with a maximum logarithm of odds score of 3.5. However, a subsequent linkage study with a total of 595 sibling pairs demonstrated reduced significance for linkage of D11S987 to bone mineral density variation, with a logarithm of odds score less than 2.2. We genotyped five markers in a genomic region of approximately 27 cM centering on D11S987 and measured bone mineral density and other traits (weight, etc.) for 635 individuals from 53 human pedigrees. Each of these pedigrees was ascertained through a proband with bone mineral density Z-scores less than -1.28 at the hip or spine. Adjusting for age, sex, and weight as covariates, we performed two-point and multipoint linkage analyses using the variance component linkage analysis method implemented in Sequential Oligogenic Linkage Analysis Routines. We found little evidence of linkage of these five markers to bone mineral density at the spine, hip, wrist and total body bone mineral content. The maximum logarithm of odds score at these five markers was 0.25, and the maximum logarithm of odds score at D11S987 was 0.15. Therefore, although we cannot exclude the linkage of D11S987 region to bone mineral density variation, there is no evidence for linkage of the marker D11S987 on human chromosome 11q12-13 to bone mineral density variation in our study population.

Characterization of genetic and lifestyle factors for determining variation in body mass index, fat mass, percentage of fat mass, and lean mass

In this study, we simultaneously characterized genetic and lifestyle factors (exercise, smoking, and alcohol consumption) in determining variation in body mass index (BMI), fat mass, percentage of fat mass (PFM), and lean mass while adjusting for the effects of age and sex. Six hundred fifty-eight Caucasian individuals from 48 pedigrees were studied for BMI. Among these individuals, 289 from 38 pedigrees were studied for fat mass, PFM, and lean mass measured by dual X-ray absorptiometry (DXA). After adjusting for age, sex, and lifestyle factors, the heritabilities (h(2)) of BMI, fat mass, PFM, and lean mass ranged from 0.52 to 0.57 with associated standard errors ranging from 0.09 to 0.14. After accounting for significant sex and age effects, exercise had significant effects for all the phenotypes studied, and the effects of smoking and alcohol consumption were not significant. Therefore, significant proportions of variation in BMI, fat mass, PFM, and lean mass were under genetic control, and exercise had a significant effect in reducing BMI, fat mass, and PFM and in increasing lean mass. This study warrants further genetic linkage analyses to search for genes for the obesity-related phenotypes measured by DXA in our population.

Intensive remedial instruction for children with severe reading disabilities: immediate and long-term outcomes from two instructional approaches

Sixty children with severe reading disabilities were randomly assigned to two instructional programs that incorporated principles of effective instruction but differed in depth and extent of instruction in phonemic awareness and phonemic decoding skills. All children received 67.5 hours of one-to-one instruction in two 50-minute sessions per day for 8 weeks. Both instructional programs produced very large improvements in generalized reading skills that were stable over a 2-year follow-up period. When compared to the growth in broad reading ability that the participants made during their previous 16 months in learning disabilities resource rooms, their growth during the intervention produced effect sizes of 4.4 for one of the interventions and 3.9 for the other. Although the children's average scores on reading accuracy and comprehension were in the average range at the end of the follow-up period, measures of reading rate showed continued severe impairment for most of the children. Within 1 year following the intervention, 40% of the children were found to be no longer in need of special education services. The two methods of instruction were not differentially effective for children who entered the study with different levels of phonological ability, and the best overall predictors of long-term growth were resource room teacher ratings of attention/behavior, general verbal ability, and prior levels of component reading skills.

Determination of bone mineral density of the hip and spine in human pedigrees by genetic and life-style factors

In 40 human pedigrees with 563 subjects, we evaluated the contribution of genetic and life-style factors (exercise, smoking, and alcohol consumption) and the interactions between non-genetic factors in determining bone mineral density (BMD) of the hip and spine. In our analysis, we adjusted for age, weight, height, menopausal status in females, life-style factors, and the significant interactions among these factors. For the spine and hip BMD, heritabilities (h(2)) (+/- SE) were, respectively, 0.68 (0.21) and 0.86 (0.28) in males and 0.64 (0.13) and 0.67 (0.14) in females. Exercise had significant beneficial effects for male spine BMD and female hip BMD. Alcohol consumption experienced in our sample had significant beneficial effects on hip BMD in both sexes. Although the main effect of smoking was not significant, there were significant interaction effects between smoking and other important factors (e.g., exercise, weight, alcohol consumption). For example, for female spine BMD, exercise had significant beneficial effects in smokers; however, its effect in non-smokers was non-significant. This result indicates that exercise may reduce deleterious effects of smoking (if any) on BMD, but may have minor effects in increasing BMD in non-smokers. The various interaction effects among risk factors explicitly revealed here for the first time indicate that the detailed effects and direction of individual risk factors may depend on the presence and magnitude of other factors. Weight invariably affected BMD of the hip and spine in both sexes. Age effects were significant for hip BMD, but not for male spine BMD.

Global carbon sinks and their variability inferred from atmospheric O2 and delta13C

Recent time-series measurements of atmospheric O2 show that the land biosphere and world oceans annually sequestered 1.4 +/- 0.8 and 2.0 +/- 0.6 gigatons of carbon, respectively, between mid-1991 and mid-1997. The rapid storage of carbon by the land biosphere from 1991 to 1997 contrasts with the 1980s, when the land biosphere was approximately neutral. Comparison with measurements of delta13CO2 implies an isotopic flux of 89 +/- 21 gigatons of carbon per mil per year, in agreement with model- and inventory-based estimates of this flux. Both the delta13C and the O2 data show significant interannual variability in carbon storage over the period of record. The general agreement of the independent estimates from O2 and delta13C is a robust signal of variable carbon uptake by both the land biosphere and the oceans.

Functional genomics: expression analysis of Escherichia coli growing on minimal and rich media

DNA arrays of the entire set of Escherichia coli genes were used to measure the genomic expression patterns of cells growing in late logarithmic phase on minimal glucose medium and on Luria broth containing glucose. Ratios of the transcript levels for all 4,290 E. coli protein-encoding genes (cds) were obtained, and analysis of the expression ratio data indicated that the physiological state of the cells under the two growth conditions could be ascertained. The cells in the rich medium grew faster, and expression of the majority of the translation apparatus genes was significantly elevated under this growth condition, consistent with known patterns of growth rate-dependent regulation and increased rate of protein synthesis in rapidly growing cells. The cells grown on minimal medium showed significantly elevated expression of many genes involved in biosynthesis of building blocks, most notably the amino acid biosynthetic pathways. Nearly half of the known RpoS-dependent genes were expressed at significantly higher levels in minimal medium than in rich medium, and rpoS expression was similarly elevated. The role of RpoS regulation in these logarithmic phase cells was suggested by the functions of the RpoS dependent genes that were induced. The hallmark features of E. coli cells growing on glucose minimal medium appeared to be the formation and excretion of acetate, metabolism of the acetate, and protection of the cells from acid stress. A hypothesis invoking RpoS and UspA (universal stress protein, also significantly elevated in minimal glucose medium) as playing a role in coordinating these various aspects and consequences of glucose and acetate metabolism was generated. This experiment demonstrates that genomic expression assays can be applied in a meaningful way to the study of whole-bacterial-cell physiology for the generation of hypotheses and as a guide for more detailed studies of particular genes of interest.

A pilot study describing local residents' perceptions of asthma and knowledge of asthma care in selected Chicago communities

STUDY OBJECTIVES

To understand inner-city Chicago residents' perception of the prevalence and severity of asthma as well as their knowledge of asthma control and management.

DESIGN

Cross-sectional survey using a random digital telephone dialing method.

SETTINGS

Five inner-city Chicago communities where a high prevalence and mortality of asthma have been recognized.

PARTICIPANTS

All the residents in the selected communities with a residential telephone had an equal opportunity to be surveyed.

MEASUREMENTS AND RESULTS

The unit of measurement was the household. Only one adult member (age 18 or older) in any randomly selected household was interviewed. The survey included questions modified from the Chicago Asthma Surveillance Initiative study. A total of 2,322 phone calls with 527 successful contacts were made over 1,938 distinct phone lines, resulting in a response rate of 175 of 527 calls (33.2%). Seventy-nine of the participants (45.1%) reported that at least one of their family members (including themselves) has asthma. Eight persons (4.6%) reported asthma as one of the top three health concerns in their community. Of the top three health reasons mentioned for children's being absent from school, only seven persons (4%) mentioned asthma. Participants were unlikely to perceive that the problems with access to asthma care and environmental triggers for asthma in their communities were any worse compared with other communities. Participants having family members with diagnosed asthma scored no better when asked general-knowledge questions about asthma or its signs and triggers than those without a family member having asthma.

CONCLUSIONS

The participants' knowledge and beliefs about the seriousness of asthma revealed in this study appeared unlikely to enhance or support compliance with the challenging requirements of the National Asthma Education and Prevention Panel guidelines. The study was conducted with a small sample, and the results should be carefully interpreted.

Metabolic imbalance and sporulation in an isocitrate dehydrogenase mutant of Bacillus subtilis

A Bacillus subtilis mutant with a deletion in the citC gene, encoding isocitrate dehydrogenase, the third enzyme of the tricarboxylic acid branch of the Krebs cycle, exhibited reduced growth yield in broth medium and had greatly reduced ability to sporulate compared to the wild type due to a block at stage I, i.e., a failure to form the polar division septum. In early stationary phase, mutant cells accumulated intracellular and extracellular concentrations of citrate and isocitrate that were at least 15-fold higher than in wild-type cells. The growth and sporulation defects of the mutant could be partially bypassed by deletion of the major citrate synthase gene (citZ), by raising the pH of the medium, or by supplementation of the medium with certain divalent cations, suggesting that abnormal accumulation of citrate affects survival of stationary-phase cells and sporulation by lowering extracellular pH and chelating metal ions. While these genetic and environmental alterations were not sufficient to allow the majority of the mutant cell population to pass the stage I block (lack of asymmetric septum formation), introduction of the sof-1 mutant form of the Spo0A transcription factor, when coupled with a reduction in citrate synthesis, restored sporulation gene expression and spore formation nearly to wild-type levels. Thus, the primary factor inhibiting sporulation in a citC mutant is abnormally high accumulation of citrate, but relief of this metabolic defect is not by itself sufficient to restore competence for sporulation.

Genetic determination of variation and covariation of peak bone mass at the hip and spine

The likelihood of low trauma fracture in the elderly is highly predictable by peak bone mass (PBM) at age approximately 25-50 yr. We estimated the magnitude of genetic determination of the variation and covariation of PBM of the spine and hip (adjusted by age, gender, and ethnicity) in 47 independent healthy full-sib pairs and 27 healthy mother-offspring pairs. For the spine and hip, the narrow-sense heritabilities (h(2)) (mean +/- SE) were 0.76 +/- 0.34 and 0.84 +/- 0.36, respectively, when estimated from full sibs, and 0.86 +/- 0.38 and 0.84 +/- 0.39, respectively, when estimated from parent-offspring. Some genetic loci underlying PBM variation at the hip and spine are the same or closely linked, as is reflected by the high genetic correlation of 0.95 +/- 0.05 between them when estimated from full sibs, and 0.57 +/- 0.27 when estimated from parent-offspring, respectively. Generally, common familial environmental effects shared by relatives may bias these estimates. However, these effects may be small, since our results reported herein and those in other earlier studies indicate that common familial environmental effects are probably negligible in causing similarity of bone mass among family members. The correlation of bone mass among randomly sampled couples living in the same household is small and nonsignificant as measured either by densitometry at the radius and ulna or by quantitative ultrasound at the patella. The problem of shared environmental effects notwithstanding, we conclude that much of the PBM variation and covariation at the hip and spine is determined genetically.

Physicians' perceptions of managed care: a structural equation model assessment of key dimensions

OBJECTIVES

To assess the interrelationship of physicians' own interest with that of the methods and the anticipated benefits of managed care, the authors developed a new instrument to assess physician's perception of job satisfaction, risk, need to adapt their practice behavior, quality of care, cost of care, and access under managed care.

METHODS

One hundred sixty-one attending physicians of an urban public hospital in a metropolitan area with low to moderate managed care penetration participated. A 24-item questionnaire with good psychometric properties was developed based on literature reviews, qualitative interviews with the key informants, and focus group discussion among a group of selected physician representatives. Confirmatory factory analysis and structural equation models were applied.

RESULTS

The study reveals that when physicians perceived that high job satisfaction would ensue, they also perceived that quality and access to care would improve under managed care. Physician's perception of the need to modify their practice behavior was associated with a perception of increasing the cost of care. Risk sharing, from the physician's perspective, did not translate to cost savings as expected by managed care organizations, and only resulted in a fractional improvement on a perception of quality and access of care.

CONCLUSIONS

Although this study reports the perceptions of a small group of physicians from a single hospital, the data suggest that increasing quality and decreasing cost may be included in the same equation, if physician job satisfaction also is included through organizational support and user-friendly work environment.

Sequence analysis of the GntII (subsidiary) system for gluconate metabolism reveals a novel pathway for L-idonic acid catabolism in Escherichia coli

The presence of two systems in Escherichia coli for gluconate transport and phosphorylation is puzzling. The main system, GntI, is well characterized, while the subsidiary system, GntII, is poorly understood. Genomic sequence analysis of the region known to contain genes of the GntII system led to a hypothesis which was tested biochemically and confirmed: the GntII system encodes a pathway for catabolism of L-idonic acid in which D-gluconate is an intermediate. The genes have been named accordingly: the idnK gene, encoding a thermosensitive gluconate kinase, is monocistronic and transcribed divergently from the idnD-idnO-idnT-idnR operon, which encodes L-idonate 5-dehydrogenase, 5-keto-D-gluconate 5-reductase, an L-idonate transporter, and an L-idonate regulatory protein, respectively. The metabolic sequence is as follows: IdnT allows uptake of L-idonate; IdnD catalyzes a reversible oxidation of L-idonate to form 5-ketogluconate; IdnO catalyzes a reversible reduction of 5-ketogluconate to form D-gluconate; IdnK catalyzes an ATP-dependent phosphorylation of D-gluconate to form 6-phosphogluconate, which is metabolized further via the Entner-Doudoroff pathway; and IdnR appears to act as a positive regulator of the IdnR regulon, with L-idonate or 5-ketogluconate serving as the true inducer of the pathway. The L-idonate 5-dehydrogenase and 5-keto-D-gluconate 5-reductase reactions were characterized both chemically and biochemically by using crude cell extracts, and it was firmly established that these two enzymes allow for the redox-coupled interconversion of L-idonate and D-gluconate via the intermediate 5-ketogluconate. E. coli K-12 strains are able to utilize L-idonate as the sole carbon and energy source, and as predicted, the ability of idnD, idnK, idnR, and edd mutants to grow on L-idonate is altered.

Primary care for the medically underserved: challenges and opportunities

The medically underserved present unique challenges to primary care practitioners. Sociocultural and financial barriers of the underserved impede access to necessary care; the prevalence and severity of diseases in the underserved population vary from those of the general population; the institution of preventive-care measures can be especially problematic; and the doctor-patient relationship is uncommonly complex. This article reviews current thinking about the causes of unequal health, the effects of unequal health care, and the special opportunities for disease prevention among the socioeconomically disadvantaged people in the US. Sensitivity to these and other issues can enhance primary care practitioners' efforts to improve care of the underserved now, pending future political consensus about universal health insurance.

Positive and negative transcriptional regulation of the Escherichia coli gluconate regulon gene gntT by GntR and the cyclic AMP (cAMP)-cAMP receptor protein complex

The gntT gene of Escherichia coli is specifically induced by gluconate and repressed via catabolite repression. Thus, gluconate is both an inducer and a repressor of gntT expression since gluconate is a catabolite-repressing sugar. In a gntR deletion mutant, the expression of a chromosomal gntT::lacZ fusion is both high and constitutive, confirming that GntR is the negative regulator of gntT. Indeed, GntR binds to two consensus gnt operator sites; one overlaps the -10 region of the gntT promoter, and the other is centered at +120 with respect to the transcriptional start site. The binding of GntR to these sites was proven in vitro by gel redardation assays and in vivo by site-directed mutagenesis of the binding sites. Binding of GntR to the operators is eliminated by gluconate and also by 6-phosphogluconate at a 10-fold-higher concentration. Interestingly, when gntR deletion strains are grown in the presence of gluconate, there is a twofold decrease in gntT expression which is independent of catabolite repression and binding of GntR to the operator sites. This novel response of gntR mutants to the inducer is termed ultrarepression. Transcription of gntT is activated by binding of the cyclic AMP (cAMP)-cAMP receptor protein (CRP) complex to a CRP binding site positioned at -71 upstream of the gntT transcription start site.

Rapid accumulation of intracellular 2-keto-3-deoxy-6-phosphogluconate in an Entner-Doudoroff aldolase mutant results in bacteriostasis

The accumulation of 2-keto-3-deoxy-6-phosphogluconate, the key intermediate of the Entner-Doudoroff pathway, has long been thought to inhibit growth of bacteria, but careful measurements of 2-keto-3-deoxy-6-phosphogluconate accumulation by growing cells and the correlation of intracellular 2-keto-3-deoxy-6-phosphogluconate levels to growth inhibition had not been made. A system designed for this purpose was developed in Escherichia coli strains, allowing 2-keto-3-deoxy-6-phosphogluconate accumulation to be experimentally induced and measured by extraction of the cell pool. Addition of gluconate to a strain which lacked 2-keto-3-deoxy-6-phosphogluconate aldolase and overproduced 6-phosphogluconate dehydratase resulted in an increase in the intracellular concentration of 2-keto-3-deoxy-6-phosphogluconate from undetectable levels to 2.0 mM within 15 s, as measured by anion-exchange HPLC. The accumulation of 2-keto-3-deoxy-6-phosphogluconate was correlated with an immediate and significant decrease in growth; this inhibition was determined to be bacteriostatic and not bactericidal. It had been proposed that the mechanism of 2-keto-3-deoxy-6-phosphogluconate toxicity involves competitive inhibition of 6-phosphogluconate dehydrogenase and the consequent block of the pentose phosphate pathway. An experiment addressing this hypothesis failed to provide any supporting data.

Strategic marketing and clinical management in health care: a possible way forward

This article examines and comments on the role of clinical directors in the NHS (UK), with specific reference to the relevance of a strategic marketing emphasis. It utilises qualitative methodologies to collect data from stakeholders--in particular, clinical directors and other managers--from two NHS trust hospitals. It examines the extent to which a marketing approach is applicable to clinical managers working in these two hospitals. It utilises a conceptual framework devised by Kottler and Andreason, to highlight whether a marketing approach is, in fact, utilised by these managers. It suggests that a strategic marketing approach (based upon relationships), remains relevant to clinical management, notwithstanding recent changes in government policy.

Kinetics of Sugar Transport and Phosphorylation Influence Glucose and Fructose Cometabolism by Zymomonas mobilis

The competitive inhibition of fructokinase by glucose has been proposed as the mechanism by which Zymomonas mobilis preferentially consumes glucose from mixtures of glucose and fructose and accumulates fructose when growing on sucrose. In this study, incorporation of radioactive fructose into biomass was used as a measure of fructose catabolism. It was determined that the rate of fructose incorporation by Z. mobilis CP4 was somewhat lower in the presence of an equimolar concentration of glucose but that the inhibition of fructokinase by glucose was not nearly as severe in vivo as was predicted from in vitro studies. Interestingly, addition of glucose to a culture of Z. mobilis CP4-M2, a glucokinaseless mutant, resulted in an immediate and nearly complete inhibition of fructose incorporation. Furthermore, addition of nonmetabolizeable glucose analogs had a similar effect on fructose catabolism by the wild-type Z. mobilis CP4, and fructose uptake by Z. mobilis CP4-M2 was shown to be severely inhibited by equimolar amounts of glucose. These results suggest that competition for fructose transport plays an important role in preferential catabolism of glucose from sugar mixtures. Indeed, the apparent K(infm) values for sugar uptake by Z. mobilis CP4 were approximately 200 mM for fructose and 13 mM for glucose. Other experiments supported the conclusion that a single facilitated diffusion transport system, encoded by the glf gene, is solely responsible for the uptake of both glucose and fructose. The results are discussed with regard to the hypothesis that the kinetics of sugar transport and phosphorylation allow the preferential consumption of glucose and accumulation of fructose, making the fructose available for the enzyme glucose-fructose oxidoreductase, which forms sorbitol, an important osmoprotectant for Z. mobilis when growing in the presence of high sugar concentrations.