Data management challenges in analysis and synthesis in the ecosystem sciences

Open-data has created an unprecedented opportunity with new challenges for ecosystem scientists. Skills in data management are essential to acquire, manage, publish, access and re-use data. These skills span many disciplines and require trans-disciplinary collaboration. Science synthesis centres support analysis and synthesis through collaborative 'Working Groups' where domain specialists work together to synthesise existing information to provide insight into critical problems. The Australian Centre for Ecological Analysis and Synthesis (ACEAS) served a wide range of stakeholders, from scientists to policy-makers to managers. This paper investigates the level of sophistication in data management in the ecosystem science community through the lens of the ACEAS experience, and identifies the important factors required to enable us to benefit from this new data-world and produce innovative science. ACEAS promoted the analysis and synthesis of data to solve transdisciplinary questions, and promoted the publication of the synthesised data. To do so, it provided support in many of the key skillsets required. Analysis and synthesis in multi-disciplinary and multi-organisational teams, and publishing data were new for most. Data were difficult to discover and access, and to make ready for analysis, largely due to lack of metadata. Data use and publication were hampered by concerns about data ownership and a desire for data citation. A web portal was created to visualise geospatial datasets to maximise data interpretation. By the end of the experience there was a significant increase in appreciation of the importance of a Data Management Plan. It is extremely doubtful that the work would have occurred or data delivered without the support of the Synthesis centre, as few of the participants had the necessary networks or skills. It is argued that participation in the Centre provided an important learning opportunity, and has resulted in improved knowledge and understanding of good data management practices.

Guidelines on the irritable bowel syndrome: mechanisms and practical management

BACKGROUND

IBS affects 5-11% of the population of most countries. Prevalence peaks in the third and fourth decades, with a female predominance.

AIM

To provide a guide for the assessment and management of adult patients with irritable bowel syndrome.

METHODS

Members of the Clinical Services Committee of The British Society of Gastroenterology were allocated particular areas to produce review documents. Literature searching included systematic searches using electronic databases such as Pubmed, EMBASE, MEDLINE, Web of Science, and Cochrane databases and extensive personal reference databases.

RESULTS

Patients can usefully be classified by predominant bowel habit. Few investigations are needed except when diarrhoea is a prominent feature. Alarm features may warrant further investigation. Adverse psychological features and somatisation are often present. Ascertaining the patients' concerns and explaining symptoms in simple terms improves outcome. IBS is a heterogeneous condition with a range of treatments, each of which benefits a small proportion of patients. Treatment of associated anxiety and depression often improves bowel and other symptoms. Randomised placebo controlled trials show benefit as follows: cognitive behavioural therapy and psychodynamic interpersonal therapy improve coping; hypnotherapy benefits global symptoms in otherwise refractory patients; antispasmodics and tricyclic antidepressants improve pain; ispaghula improves pain and bowel habit; 5-HT(3) antagonists improve global symptoms, diarrhoea, and pain but may rarely cause unexplained colitis; 5-HT(4) agonists improve global symptoms, constipation, and bloating; selective serotonin reuptake inhibitors improve global symptoms.

CONCLUSIONS

Better ways of identifying which patients will respond to specific treatments are urgently needed.

Guidelines on the irritable bowel syndrome: mechanisms and practical management

BACKGROUND

IBS affects 5-11% of the population of most countries. Prevalence peaks in the third and fourth decades, with a female predominance.

AIM

To provide a guide for the assessment and management of adult patients with irritable bowel syndrome.

METHODS

Members of the Clinical Services Committee of The British Society of Gastroenterology were allocated particular areas to produce review documents. Literature searching included systematic searches using electronic databases such as Pubmed, EMBASE, MEDLINE, Web of Science, and Cochrane databases and extensive personal reference databases.

RESULTS

Patients can usefully be classified by predominant bowel habit. Few investigations are needed except when diarrhoea is a prominent feature. Alarm features may warrant further investigation. Adverse psychological features and somatisation are often present. Ascertaining the patients' concerns and explaining symptoms in simple terms improves outcome. IBS is a heterogeneous condition with a range of treatments, each of which benefits a small proportion of patients. Treatment of associated anxiety and depression often improves bowel and other symptoms. Randomised placebo controlled trials show benefit as follows: cognitive behavioural therapy and psychodynamic interpersonal therapy improve coping; hypnotherapy benefits global symptoms in otherwise refractory patients; antispasmodics and tricyclic antidepressants improve pain; ispaghula improves pain and bowel habit; 5-HT(3) antagonists improve global symptoms, diarrhoea, and pain but may rarely cause unexplained colitis; 5-HT(4) agonists improve global symptoms, constipation, and bloating; selective serotonin reuptake inhibitors improve global symptoms.

CONCLUSIONS

Better ways of identifying which patients will respond to specific treatments are urgently needed.

Localized Igf-1 transgene expression sustains hypertrophy and regeneration in senescent skeletal muscle

Aging skeletal muscles suffer a steady decline in mass and functional performance, and compromised muscle integrity as fibrotic invasions replace contractile tissue, accompanied by a characteristic loss in the fastest, most powerful muscle fibers. The same programmed deficits in muscle structure and function are found in numerous neurodegenerative syndromes and disease-related cachexia. We have generated a model of persistent, functional myocyte hypertrophy using a tissue-restricted transgene encoding a locally acting isoform of insulin-like growth factor-1 that is expressed in skeletal muscle (mIgf-1). Transgenic embryos developed normally, and postnatal increases in muscle mass and strength were not accompanied by the additional pathological changes seen in other Igf-1 transgenic models. Expression of GATA-2, a transcription factor normally undetected in skeletal muscle, marked hypertrophic myocytes that escaped age-related muscle atrophy and retained the proliferative response to muscle injury characteristic of younger animals. The preservation of muscle architecture and age-independent regenerative capacity through localized mIgf-1 transgene expression suggests clinical strategies for the treatment of age or disease-related muscle frailty.

Sequential programs of retinoic acid synthesis in the myocardial and epicardial layers of the developing avian heart

Endogenous patterns of retinoic acid (RA) signaling in avian cardiac morphogenesis were characterized by localized expression of a key RA-synthetic enzyme, RALDH2, which displayed a biphasic pattern during heart development. RALDH2 immunoreactivity was initially apparent posterior to Hensen's node of stage 5-6 embryos and subsequently in somites and unsegmented paraxial and lateral plate mesoderm overlapping atrial precursors in the cardiogenic plate of stage 9- embryos. Initial RALDH2 synthesis in the posterior myocardium coincided with activation of the AMHC1 gene, a RA-responsive marker of inflow heart segments. A wave of RALDH2 synthesis then swept the myocardium in a posterior-to-anterior direction, reaching the outflow tract by stage 13, then fading from the myocardial layer. The second phase of RALDH2 expression, initiated at stage 18 in the proepicardial organ, persisted in migratory epicardial cells that completely enveloped the heart by stage 24. Early restriction of RALDH2 expression to the posterior cardiogenic plate, overlapping RA-inducible gene activation, provides evidence for commitment of posterior avian heart segments by localized production of RA, whereas subsequent RALDH2 expression exclusively in the migratory epicardium suggests a role for the morphogen in ventricular expansion and morphogenesis of underlying myocardial tissues.

Regulation of a muscle-specific transgene by persistent expression of Hox genes in postnatal murine limb muscle

Homeobox genes are necessary for the generation of the embryonic body plan in both invertebrate and vertebrate organisms. To investigate the potential function of homeodomain proteins in normal and regenerating skeletal muscle, we analyzed patterns of clustered homeobox gene expression in neonatal and adult muscle tissue. Transcripts encoding 5' genes in the HoxA cluster were detected in muscles from both the fore- and hindlimbs of neonatal and adult mice, whereas expression of HoxC gene transcripts was generally restricted to the muscles of the hindlimb. In contrast, transcripts encoding genes of the HoxB or HoxD clusters were not detected in muscles from either fore- or hindlimbs. Although ectopic expression of select HOX proteins in muscle cell cultures had modest effects upon the activity of a co-transfected myosin light chain (MLC) enhancer, mutation of a Hox binding site in this enhancer elicited increased linked reporter gene expression. Induction of muscle damage and regeneration was accompanied by the down-regulation of at least one Hox gene, concurrent with the activation of the regenerative program. Moreover, targeted ablation of the Hoxc-8 gene, normally expressed in mature fore- and hindlimb muscles, resulted in reduced expression of an MLC enhancer-driven transgene only in specific leg muscles. These results indicate that members of the HoxA and C clusters may, in combination, mediate various aspects of differentiation and patterning in adult musculature.

Is surveillance for stage 1 germ cell tumours of the testis appropriate outside a specialist centre?

OBJECTIVE

To assess the results of treatment for stage 1 germ cell tumours of the testis, outside a specialist centre.

PATIENTS AND METHODS

From May 1984 until March 1996, 123 patients with stage 1 disease were treated at our institution. Sixty patients with seminoma and 31 with teratoma were treated with orchidectomy only and surveillance; 32 patients with stage 1 seminoma elected for orchidectomy and adjuvant radiotherapy. The mean ages were 40, 31 and 35 years, and the median follow-up 52, 47 and 49 months, respectively.

RESULTS

There were no disease- or treatment-related deaths. However, 18 (30%) patients with seminoma treated by orchidectomy only relapsed (median time 8 months, range 3-19); 14 of these responded to radiotherapy, three to radiotherapy and chemotherapy for second relapses outside the irradiated fields, and one to chemotherapy initially, for large-volume relapse. Fifteen (48%) patients with teratoma relapsed (median time 3 months, range 1-12); all responded to 4-6 courses of bleomycin/etoposide/cisplatin chemotherapy. One patient had a second relapse and is currently disease-free 3 years after surgical excision of a lung metastasis.

CONCLUSION

These results show that stage 1 testis tumours can be managed successfully in a district general hospital. However, we are concerned about the high relapse rates and are now attempting to identify patients at greater risk of recurrence, to consider adjuvant therapy in this group.

A retinoic acid-inducible transgenic marker of sino-atrial development in the mouse heart

To study the specification of inflow structures in the heart we generated transgenic animals harboring the human alkaline phosphatase (HAP) gene driven by the proximal 840 bp of a quail SMyHC3 promoter. In transgenic mice, the SMyHC3-HAP reporter was expressed in posterior heart precursors at 8.25 dpc, in sinus venosa and in the atrium at 8.5 and 9.0 dpc, and in the atria from 10.5 dpc onwards. SMyHC3-HAP transgene expression overlapped synthesis and endogenous response to retinoic acid (RA) in the heart, as determined by antibodies directed against a key RA synthetic enzyme and by staining of RAREhsplacZ transgenic animals. A single pulse of all-trans RA administered to pregnant mice at 7.5, but not after 8.5, dpc induced cardiac dismorphology, ranging from complete absence of outflow tract and ventricles to hearts with reduced ventricles expressing both SMyHC3-HAP and ventricular markers. Blockade of RA synthesis with disulfiram inhibited RA-induced transcription and produced hearts lacking the atrial chamber. This study defines a novel marker for atrial-restricted transcription in the developing mouse heart. It also suggests that atrial-specific gene expression is controlled by localized synthesis of RA, and that exclusion of RA from ventricular precursors is essential for correct specification of the ventricles.

Modular elements of the MLC 1f/3f locus confer fiber-specific transcription regulation in transgenic mice

The two proteins encoded by the fast alkali myosin light chain (MLC) 1f/3f locus are developmentally regulated, muscle specific, and expressed exclusively in fast-twitch fibers. Their expression is independently regulated by two separate promoters and a downstream enhancer. Previous studies showed a reporter gene directed by the rat MLC If promoter and MLC enhancer to exhibit correct skeletal muscle-specific expression in transgenic mice during development and to be preferentially expressed in fast-twitch Type IIB fibers [Donoghue et al., (1991) J. Cell B.ol. 115:423-434]. The MLC 3f promoter also directed muscle-specific expression of a CAT reporter gene in adult transgenic mice and showed little dependence upon the enhancer. Here, we show that the MLC 3f promoter also directs transgene expression in the fast-twitch fibers of adult skeletal muscle, but almost exclusively to fiber Types IIA and IIX. MLC 3f transgene expression occurs in only a subset of the fiber types that express the endogenous locus, indicating modular elements included in the transgene confer fiber-specific transcription regulation. MyoD protein was also found to be restricted to fiber Types IIA and IIX, providing evidence for its possible role in mediating fiber-specific gene expression.

Unusual organization of the human T-cell receptor beta-chain gene complex is linked to recombination hotspots

Two rare Sfi I polymorphisms of 360 kb and 280 kb present within the human T-cell antigen receptor beta-chain gene complex were revealed by pulsed-field gel electrophoresis. They represent allelic variants of the polymorphic 330- and 300-kb Sfi I fragments previously described. The 360-kb polymorphism results from duplication of the 30-kb DNA fragment responsible for the 330/300-kb insertion/deletion-related polymorphism. The 280-kb polymorphism results from a 20-kb deletion from the 300-kb SfiI allele. The rare polymorphisms also map on either side of a Sal I site located near a recombination hotspot, suggesting that germline duplications and deletions arose from nonhomologous crossover events.

Effects of breast cancer treatments on plasma nutrient levels: implications for epidemiological studies

The interpretation of case-control studies in which blood nutrient levels are examined as etiological factors in cancer is complicated by the possibility that either the disease or its treatment may alter these levels. Circulating levels of selected nutrients were examined prior to diagnostic biopsy and compared with levels 3 to 4 months after diagnosis among 71 women with breast cancer and 95 women with benign breast disease. Among women with benign breast disease or women with breast cancer who were not given postsurgical adjuvant drug therapy, levels of alpha-carotene, lycopene, alpha-tocopherol, cholesterol, and triglycerides did not change over time. In contrast, women who received chemotherapy had increased levels of cholesterol, retinol, and alpha- and gamma-tocopherol, and women on antiestrogen therapy showed increased levels of triglycerides and alpha-tocopherol. Overall, the concentrations of carotenoids (lycopene, alpha-carotene, and beta-carotene) did not change in breast cancer cases, although subgroup analyses showed increased levels of beta-carotene among cases not receiving drug treatment and decreased levels among those receiving antiestrogens. In summary, blood levels of some nutrients did not appear to be affected by breast cancer or its treatments, but changes were noted for levels of plasma lipids, tocopherols, retinol, and beta-carotene. Those investigating the etiological relationship between breast cancer and circulating nutrients need to consider these effects in designing and interpreting epidemiological studies.

Associations between breast cancer, plasma triglycerides, and cholesterol

A case-control study investigating the association between plasma lipids and breast cancer was conducted among women aged 30-80 in Buffalo, NY. All eligible women from a large breast clinic and two area physicians' offices were requested to participate over a one-year period. Subjects completed a health questionnaire and donated a fasting blood sample prior to diagnostic breast biopsies. The 83 women found to have breast cancer (cases) had significantly higher plasma triglyceride values than did the 113 women found not to have breast cancer (controls). Lower plasma beta-carotene values were associated with breast cancer, but only in those women with elevated triglyceride or cholesterol. Plasma cholesterol values were lower in those breast cancer cases presenting with more advanced stages of cancer, suggesting that metabolic effects of clinical and preclinical breast cancer may lower cholesterol levels. Although the limitations of case-control studies are well-recognized, these data suggest an etiologic role for plasma triglycerides and beta-carotene or for related dietary factors.

Subcapsular orchidectomy for carcinoma of the prostate

Our results suggest that subcapsular orchidectomy is at least as effective as oestrogen therapy in producing long-lasting suppression of plasma testosterone. It has many advantages over oestrogen therapy, so that, like Huggins, we believe it to be the hormonal treatment of choice for patients who develop symptoms from carcinoma of the prostate.