Identification of functional elements and regulatory circuits by Drosophila modENCODE

To gain insight into how genomic information is translated into cellular and developmental programs, the Drosophila model organism Encyclopedia of DNA Elements (modENCODE) project is comprehensively mapping transcripts, histone modifications, chromosomal proteins, transcription factors, replication proteins and intermediates, and nucleosome properties across a developmental time course and in multiple cell lines. We have generated more than 700 data sets and discovered protein-coding, noncoding, RNA regulatory, replication, and chromatin elements, more than tripling the annotated portion of the Drosophila genome. Correlated activity patterns of these elements reveal a functional regulatory network, which predicts putative new functions for genes, reveals stage- and tissue-specific regulators, and enables gene-expression prediction. Our results provide a foundation for directed experimental and computational studies in Drosophila and related species and also a model for systematic data integration toward comprehensive genomic and functional annotation.

Integrative analysis of the Caenorhabditis elegans genome by the modENCODE project

We systematically generated large-scale data sets to improve genome annotation for the nematode Caenorhabditis elegans, a key model organism. These data sets include transcriptome profiling across a developmental time course, genome-wide identification of transcription factor-binding sites, and maps of chromatin organization. From this, we created more complete and accurate gene models, including alternative splice forms and candidate noncoding RNAs. We constructed hierarchical networks of transcription factor-binding and microRNA interactions and discovered chromosomal locations bound by an unusually large number of transcription factors. Different patterns of chromatin composition and histone modification were revealed between chromosome arms and centers, with similarly prominent differences between autosomes and the X chromosome. Integrating data types, we built statistical models relating chromatin, transcription factor binding, and gene expression. Overall, our analyses ascribed putative functions to most of the conserved genome.

Failure of conventional retrograde cystography to detect bladder ruptures in pelvic trauma

Conventional retrograde cystography is often used to investigate patients with suspected bladder ruptures in pelvic trauma. Clinical indicators suggestive of a rupture include haematuria and suprapubic tenderness and should increase the suspicion of bladder and urinary tract injury and prompt the clinician to undertake further investigations. Two patients with high-energy pelvic fractures had bladder ruptures detected intraoperatively despite normal preoperative retrograde cystogram. Both patients had significant clinical indicators suggestive of underlying bladder and urinary tract injury. In both cases, a routine conventional retrograde cystogram was performed but failed to identify the full extent of the bladder injury. A possible reason for misdiagnosis in these cases is the delay between injury and investigation due to tertiary referral of care.

Automated sampling and data processing derived from biomimetic membranes

Recent advances in biomimetic membrane systems have resulted in an increase in membrane lifetimes from hours to days and months. Long-lived membrane systems demand the development of both new automated monitoring equipment capable of measuring electrophysiological membrane characteristics and new data processing software to analyze and organize the large amounts of data generated. In this work, we developed an automated instrumental voltage clamp solution based on a custom-designed software controller application (the WaveManager), which enables automated on-line voltage clamp data acquisition applicable to long-time series experiments. We designed another software program for off-line data processing. The automation of the on-line voltage clamp data acquisition and off-line processing was furthermore integrated with a searchable database (DiscoverySheet) for efficient data management. The combined solution provides a cost efficient and fast way to acquire, process and administrate large amounts of voltage clamp data that may be too laborious and time consuming to handle manually.

The role of the sports and exercise medicine physician in the National Health Service: a questionnaire-based survey

OBJECTIVES

To investigate the opinions of general practitioners, orthopaedic surgeons, rheumatologists, sport and exercise medicine (SEM) registrars and public health consultants on training, caseload, the most appropriate setting and the position of SEM within the National Health Service (NHS) in the UK.

METHOD

A cross-sectional questionnaire-based survey investigated the opinions of the above professionals from three primary care trusts and associated hospitals in London and Birmingham.

RESULTS

With a 50% response rate (n = 226), 93% (208/224) of participants felt that there was a role for SEM in the NHS. 56% (124/223) agreed that this role should be in both primary and secondary care. 64% (136/212) of participants felt that their practice would benefit from the input of a SEM physician and 95% (191/202) would consider referring patients to SEM services. 74% (165/222) agreed that SEM should have a public health role, and 63% (140/222) believed that these responsibilities should be evenly balanced with the treatment of sports injuries. Despite the emphasis on public health work from SEM policy makers, none of the SEM registrars selected public health as an important training area. 31% (44/140) of participants felt that a lack of education in the medical profession regarding SEM represented the greatest hindrance to its development in the NHS.

CONCLUSION

Several areas of agreement were demonstrated across the specialties, many of which matched the views of policy makers. This study involved participants from a range of cognate disciplines and was the first to investigate this issue since SEM was recognised as a specialty in 2005.

Lactobacillus reuteri prevents colitis by reducing P-selectin-associated leukocyte- and platelet-endothelial cell interactions

Recent findings indicate that dextran sodium sulfate (DSS)-induced colitis is associated with a prothrombogenic phenotype, with P-selectin playing a major role in platelet recruitment. It has been suggested that probiotics may ameliorate colonic inflammation. We therefore investigated how treatment with Lactobacillus reuteri influenced P-selectin expression, leukocyte and platelet endothelial cell interactions, and colitis severity in DSS-treated rats. Rats were divided into the following four groups: nontreated, DSS treated (5% in drinking water for 9 days), L. reuteri, and L. reuteri and DSS treated. The rats were anesthetized with Inactin (120 mg/kg ip), and the dual radiolabeled monoclonal antibody technique was used to quantify P-selectin expression. Leukocyte-endothelial and platelet-endothelial cell interactions were studied in colonic venules with intravital microscopy. Colitis severity was assessed using a disease activity index. Disease activity index increased, as did the expression of P-selectin in the entire colon after DSS treatment, but both were reduced to control levels with L. reuteri pretreatment. The increased platelet- and leukocyte-endothelial cell interactions after DSS treatment were abolished by pretreatment with L. reuteri. L. reuteri protects against DSS-induced colitis in rats. The protection is associated with reduced P-selectin expression and a decrease in leukocyte- and platelet-endothelial cell interactions.

An in-home geriatric programme for vulnerable community-dwelling older people improves the detection of dementia in primary care

BACKGROUND/OBJECTIVE

Dementia is under-diagnosed in primary care. This study investigated whether an in-home geriatric assessment and management programme could improve the identification of patients with dementia in primary care.

METHODS

A secondary analysis was performed, using data of a randomised controlled trial that studied the effects of an in-home geriatric evaluation and management programme compared with usual care. In this trial, 151 vulnerable community-dwelling patients, aged 70 years and older, participated: 86 in the intervention group and 66 in de control group. The effect of the programme on the dementia detection rate was determined by comparing the number of new dementia diagnoses in both study arms at 6 months follow-up.

RESULTS

Of all 151 participants, 38 (25%) had a registered dementia diagnosis at baseline. During follow-up, 23 of 113 patients without a registered dementia diagnosis at baseline were identified as suffering from dementia. The difference between the numbers of new dementia diagnoses in the intervention group (19 of 66 patients) and the control group (4 of 47 patients) was significant. (p = 0.02)

CONCLUSION

An in-home geriatric assessment and management programme for vulnerable older patients improves the detection of dementia and can therefore contribute to overcoming of under-diagnosis of dementia.

Intruder configurations in the A=33 isobars: 33Mg and 33Al

The beta decay of 33Mg (N=21) presented in this Letter reveals intruder configurations in both the parent and the daughter nucleus. The lowest excited states in the N=20 daughter nucleus, 33Al, are found to have nearly 2p-2h intruder configuration, thus extending the "island of inversion" beyond Mg. The allowed direct beta-decay branch to the 5/2{+} ground state of the daughter nucleus 33Al implies positive parity for the ground state of the parent 33Mg, contrary to an earlier suggestion of negative parity from a g-factor measurement. An admixture of 1p-1h and 3p-3h configurations is proposed for the ground state of 33Mg to explain all of the experimental observables.

Can an EASYcare based dementia training programme improve diagnostic assessment and management of dementia by general practitioners and primary care nurses? The design of a randomised controlled trial

Background

Early diagnosis of dementia benefits both patient and caregiver. Nevertheless, dementia in primary care is currently under-diagnosed. Some educational interventions developed to improve dementia diagnosis and management were successful in increasing the number of dementia diagnoses and in changing attitudes and knowledge of health care staff. However, none of these interventions focussed on collaboration between GPs and nurses in dementia care. We developed an EASYcare-based Dementia Training Program (DTP) aimed at stimulating collaboration in dementia primary care. We expect this program to increase the number of cognitive assessments and dementia diagnoses and to improve attitudes and knowledge of GPs and nurses.

Methods

The DTP is a complex educational intervention that consists of two workshops, a coaching program, access to an internet forum, and a Computerized Clinical Decision Support System on dementia diagnostics. One hundred duos of GPs and nurses will be recruited, from which 2/3 will be allocated to the intervention group and 1/3 to the control group. The effects of implementation of the DTP will be studied in a cluster-randomised controlled trial. Primary outcomes will be the number of cognitive assessments and dementia diagnoses in a period of 9 months following workshop participation. Secondary outcomes are measured on GP and nurse level: adherence to national guidelines for dementia, attitude, confidence and knowledge regarding dementia diagnosis and management; on patient level: number of emergency calls, visits and consultations and patient satisfaction; and on caregiver level: informal caregiver burden and satisfaction. Data will be collected from GPs' electronic medical records, self-registration forms and questionnaires. Statistical analysis will be performed using the MANOVA-method. Also, exploratory analyses will be performed, in order to gain insight into barriers and facilitators for implementation and the possible causal relations between the rate of success of the intervention components and the outcomes.

Discussion

We developed multifaceted dementia training programme. Novelties in this programme are the training in fixed collaborative duos and the inclusion of an individual coaching program. The intervention is designed according to international guidelines and educational standards. Exploratory analysis will reveal its successful elements. Selection bias and contamination may be threats to the reliability of future results of this trial. Nevertheless, the results of this trial may provide useful information for policy makers and developers of continuing medical education.

Trial registration

ClinicalTrials.gov ID NCT00459784

Advanced Trauma Life Support (ATLS) and facial trauma: can one size fit all? Part 3: Hypovolaemia and facial injuries in the multiply injured patient

Hypovolaemic shock is a common cause of morbidity and mortality following trauma, accounting for approximately 30% to 40% of trauma deaths. Life-threatening blood loss from the maxillofacial region is uncommon, but represents one of a number of possible sites which must be rapidly identified and controlled. Bleeding from the face may not be obvious especially in awake, supine patients and it poses an obvious threat to the unprotected airway. Identification requires careful assessment. Control of bleeding in the maxillofacial region requires a number of correctly sequenced techniques. Computerized tomographic imaging is now playing an increasingly important role in identifying blood loss, especially in the chest, abdomen and pelvis. This need may potentially result in the transfer of patients, with unrecognised facial injuries, outside the relative safety of the emergency department. The concepts of the 'lethal triad' and 'biologic first hit' have resulted in new strategies in managing the profoundly shocked patient, although some of these remain controversial. Debate continues over the optimal blood pressure, fluid administration and role of surgical intervention in the actively bleeding patient. These may have an impact on the timing and extent of any proposed maxillofacial repairs, and are discussed.

Comparative proteomics profiling of a phospholamban mutant mouse model of dilated cardiomyopathy reveals progressive intracellular stress responses

Defective mobilization of Ca2+ by cardiomyocytes can lead to cardiac insufficiency, but the causative mechanisms leading to congestive heart failure (HF) remain unclear. In the present study we performed exhaustive global proteomics surveys of cardiac ventricle isolated from a mouse model of cardiomyopathy overexpressing a phospholamban mutant, R9C (PLN-R9C), and exhibiting impaired Ca2+ handling and death at 24 weeks and compared them with normal control littermates. The relative expression patterns of 6190 high confidence proteins were monitored by shotgun tandem mass spectrometry at 8, 16, and 24 weeks of disease progression. Significant differential abundance of 593 proteins was detected. These proteins mapped to select biological pathways such as endoplasmic reticulum stress response, cytoskeletal remodeling, and apoptosis and included known biomarkers of HF (e.g. brain natriuretic peptide/atrial natriuretic factor and angiotensin-converting enzyme) and other indicators of presymptomatic functional impairment. These altered proteomic profiles were concordant with cognate mRNA patterns recorded in parallel using high density mRNA microarrays, and top candidates were validated by RT-PCR and Western blotting. Mapping of our highest ranked proteins against a human diseased explant and to available data sets indicated that many of these proteins could serve as markers of disease. Indeed we showed that several of these proteins are detectable in mouse and human plasma and display differential abundance in the plasma of diseased mice and affected patients. These results offer a systems-wide perspective of the dynamic maladaptions associated with impaired Ca2+ homeostasis that perturb myocyte function and ultimately converge to cause HF.

The impact of induction chemotherapy on the outcome of second-line therapy with pemetrexed or docetaxel in patients with advanced non-small-cell lung cancer

BACKGROUND

Using data from a large phase III study of previously treated advanced non-small-cell lung cancer (NSCLC) that showed similar efficacy for pemetrexed and docetaxel, this retrospective analysis evaluates the impact of first-line chemotherapy on the outcome of second-line chemotherapy.

PATIENTS AND METHODS

In all, 571 patients with advanced NSCLC were randomly assigned to receive pemetrexed 500 mg/m(2) or docetaxel 75 mg/m(2) on day 1 of a 21-day cycle. Comparisons were made based on type of first-line therapy [gemcitabine + platinum (GP), taxane + platinum (TP), or other therapies (OT)], response to initial therapy, time since initial therapy, and clinical characteristics. The two second-line treatment groups were pooled for this analysis due to similar efficacy and were assumed to have no interaction with the first-line therapies.

RESULTS

Baseline characteristics were generally balanced. By multivariate analysis, gender, stage at diagnosis, performance status (PS), and best response to first-line therapy significantly influenced overall survival (OS). Additional factors by univariate analysis, histology, and time elapsed from first- to second-line therapy significantly influenced OS.

CONCLUSIONS

Future trials in the second-line setting should stratify patients by gender, stage at diagnosis, PS, and best response to first-line therapy.