Two for the price of one

This case is about an HIV seropositive young woman referred for the treatment of severe menorrhagia causing anaemia due to adenomyosis where the levonorgestrel-releasing intrauterine system (Mirena) proved useful in treating her heavy periods and also provided effective contraception without interference from the liver enzyme-inducing effects of antiretroviral medications.

How Cooper pairs vanish approaching the Mott insulator in Bi2Sr2CaCu2O8+delta

The antiferromagnetic ground state of copper oxide Mott insulators is achieved by localizing an electron at each copper atom in real space (r-space). Removing a small fraction of these electrons (hole doping) transforms this system into a superconducting fluid of delocalized Cooper pairs in momentum space (k-space). During this transformation, two distinctive classes of electronic excitations appear. At high energies, the mysterious 'pseudogap' excitations are found, whereas, at lower energies, Bogoliubov quasi-particles-the excitations resulting from the breaking of Cooper pairs-should exist. To explore this transformation, and to identify the two excitation types, we have imaged the electronic structure of Bi(2)Sr(2)CaCu(2)O(8+delta) in r-space and k-space simultaneously. We find that although the low-energy excitations are indeed Bogoliubov quasi-particles, they occupy only a restricted region of k-space that shrinks rapidly with diminishing hole density. Concomitantly, spectral weight is transferred to higher energy r-space states that lack the characteristics of excitations from delocalized Cooper pairs. Instead, these states break translational and rotational symmetries locally at the atomic scale in an energy-independent way. We demonstrate that these unusual r-space excitations are, in fact, the pseudogap states. Thus, as the Mott insulating state is approached by decreasing the hole density, the delocalized Cooper pairs vanish from k-space, to be replaced by locally translational- and rotational-symmetry-breaking pseudogap states in r-space.

The first RSBI (ISA-TAB) workshop: "can a simple format work for complex studies?"

This article summarizes the motivation for, and the proceedings of, the first ISA-TAB workshop held December 6-8, 2007, at the EBI, Cambridge, UK. This exploratory workshop, organized by members of the Microarray Gene Expression Data (MGED) Society's Reporting Structure for Biological Investigations (RSBI) working group, brought together a group of developers of a range of collaborative systems to discuss the use of a common format to address the pressing need of reporting and communicating data and metadata from biological, biomedical, and environmental studies employing combinations of genomics, transcriptomics, proteomics, and metabolomics technologies along with more conventional methodologies. The expertise of the participants comprised database development, data management, and hands-on experience in the development of data communication standards. The workshop's outcomes are set to help formalize the proposed Investigation, Study, Assay (ISA)-TAB tab-delimited format for representing and communicating experimental metadata. This article is part of the special issue of OMICS on the activities of the Genomics Standards Consortium (GSC).

Contraception and medical gynaecology for HIV-positive women in a one-stop clinic

HIV-positive women may be reluctant to attend gynaecology or family planning clinics for fear of divulging their condition. Therefore, a referral clinic was opened within the HIV clinic. Retrospective case-note reviews of 197 new patients revealed 109 with a variety of medical gynaecology conditions (menorrhagia being the commonest) and 88 sought contraception. The full range of contraceptives was used, including Mirena for the treatment of menorrhagia as well as contraception and the combined pill adjusted for interaction with liver enzyme-inducing antiretroviral drugs. The acceptance of contraceptive advice and gynaecological evaluation by the patients has resulted in improved reproductive health services for these HIV-positive women. In centres with large cohorts of HIV-positive women, this type of one-stop specialist clinic will be very effective in providing high-quality reproductive health care and hence, this type of clinic is recommended for such centres.

The minimum information about a genome sequence (MIGS) specification

With the quantity of genomic data increasing at an exponential rate, it is imperative that these data be captured electronically, in a standard format. Standardization activities must proceed within the auspices of open-access and international working bodies. To tackle the issues surrounding the development of better descriptions of genomic investigations, we have formed the Genomic Standards Consortium (GSC). Here, we introduce the minimum information about a genome sequence (MIGS) specification with the intent of promoting participation in its development and discussing the resources that will be required to develop improved mechanisms of metadata capture and exchange. As part of its wider goals, the GSC also supports improving the 'transparency' of the information contained in existing genomic databases.

Volumetric MRI vs clinical predictors of Alzheimer disease in mild cognitive impairment

OBJECTIVE

To compare volumetric MRI of whole brain and medial temporal lobe structures to clinical measures for predicting progression from amnestic mild cognitive impairment (MCI) to Alzheimer disease (AD).

METHODS

Baseline MRI scans from 129 subjects with amnestic MCI were obtained from participants in the Alzheimer's Disease Cooperative Study group's randomized, placebo-controlled clinical drug trial of donepezil, vitamin E, or placebo. Measures of whole brain, ventricular, hippocampal, and entorhinal cortex volumes were acquired. Participants were followed with clinical and cognitive evaluations until formal criteria for AD were met, or completion of 36 months of follow-up. Logistic regression modeling was done to assess the predictive value of all MRI measures, risk factors such as APOE genotype, age, family history of AD, education, sex, and cognitive test scores for progression to AD. Least angle regression modeling was used to determine which variables would produce an optimal predictive model, and whether adding MRI measures to a model with only clinical measures would improve predictive accuracy.

RESULTS

Of the four MRI measures evaluated, only ventricular volumes and hippocampal volumes were predictive of progression to AD. Maximal predictive accuracy using only MRI measures was obtained by hippocampal volumes by themselves (60.4%). When clinical variables were added to the model, the predictive accuracy increased to 78.8%. Use of MRI measures did not improve predictive accuracy beyond that obtained by cognitive measures alone. APOE status, MRI, or demographic variables were not necessary for the optimal predictive model. This optimal model included the Delayed 10-word list recall, New York University Delayed Paragraph Recall, and the Alzheimer's Disease Assessment Scale-Cognitive Subscale total score.

CONCLUSION

In moderate stages of amnestic mild cognitive impairment, common cognitive tests provide better predictive accuracy than measures of whole brain, ventricular, entorhinal cortex, or hippocampal volumes for assessing progression to Alzheimer disease.

Awareness of HIV post-exposure prophylaxis after sexual exposure and emergency hormonal contraception in HIV-positive women

Women attending a dedicated medical gynaecology and family planning referral clinic for women with HIV were surveyed using a standard questionnaire about their knowledge and attitudes to post-exposure prophylaxis after sexual exposure (PEPSE) and emergency hormonal contraception (EHC). Eighty percent of them had not heard of PEPSE, but once informed about it, 86% said they would inform a partner about it. Less than 10% had any idea of the duration of effectiveness. Seventy-three percent of the women knew about EC and 45% of them had used it previously. Ninety-eight percent of them would use it in the future if necessary. Eighty percent of them knew its period of effectiveness. There is a clear need for information about PEPSE, which needs to be delivered around the time of HIV diagnosis and reinforced later. Some women will need help in discussing it with HIV-negative partners.

Laparoscopic distal pancreatectomy: the Brisbane experience of forty-six cases

BACKGROUND AND AIMS

Laparoscopic distal pancreatectomy (LDP) is a safe alternative to conventional open distal pancreatectomy, with advantages that include smaller incisions, less pain, and shorter postoperative recovery. Despite these apparent advantages, however, uptake of the procedure has been slow, with only a handful of series published.

MATERIAL AND METHODS

All LDPs performed in Brisbane, Australia, over a 10-year period (May 1996 to June 2006) were retrospectively reviewed.

RESULTS

Forty-six consecutive LDPs were performed. A variety of lesions were resected, including nine cancers. Twelve patients were converted for oncological (6) or technical reasons (6). The spleen was retained in 14/29 patients, either by main splenic vessel preservation (9) or solely supported by the short gastric vessels (5), resulting in inferior pole infarction in 2 patients. Overall morbidity was 39%, including 15% pancreatic fistula. All fistulas resolved after a median of 6 weeks without re-operation. A non-significant trend toward fewer fistulas with stapled rather than sutured stump closure was observed (13% vs 19%; p=0.43). Median operative duration and hospital stay were 157 min and 7 days, respectively. There was no mortality.

CONCLUSION

LDP is a safe alternative to conventional resection for a wide range of lesions. As with open resection, pancreatic fistula is the dominant morbidity, but is generally indolent. While spleen preservation is often possible, care must be taken to avoid infarction of the inferior pole if the Warshaw technique is utilized.

Establishing reporting standards for metabolomic and metabonomic studies: a call for participation

Metabolite concentrations in cellular systems are very much dependent on the physiological, environmental, and genetic status of an organism and are regarded as the ultimate result of cellular regulation, resulting in the visible phenotypes. Therefore, the comprehensive analysis of metabolite levels and fluxes renders a suitable tool for assessing the degree of perturbation in biological systems. Lessons derived from development of other OMICS areas (genomics, proteomics, and transcriptomics) have shown that large-scale comparisons and interpretations will require the re-use of data over long periods of time and by multiple laboratories with different expertise and backgrounds. Reaching this goal will require standardization of reporting structures of metabolomic studies for journal publication purposes, for regulatory deposition, and for database dissemination. An initiative by the Metabolomics Society is presented that aims to define important aspects of metabolomic workflows. These include biological study designs, chemical analysis, and data processing, as well as the ontologies that are necessary in this framework.

Survival of arteriovenous fistula for dialysis at different centers in the North of England

BACKGROUND

Renal failure patients rely on their vascular access for hemodialysis. Surgery for construction of arteriovenous fistulae is provided by a range of specialists. The aim of this review was to assess the survival of arteriovenous fistulae for hemodialysis patients in different centers of Northern England.

METHODS

Data was collected on 473 hemodialysis patients in the North of England. Risk factors for failure were determined for each patient (age, sex, diabetes), together with their current mode of dialysis and history of surgical access procedures. This was expressed against their duration of dialysis. The dialysis units were then compared for fistula survival using the Kaplan Meier method.

RESULTS

68.3% (323) patients were dialysed through via arteriovenous fistulae and 31.7% (150) via neck line. Overall fistula survival rates were 85.1% at 1 year, 82.5% at 2 years and 72.7% at 3 years. The best 1 year survival was 91.6% and worst 76.1%. These were 74.4% and 53.1% at 5 years and 74.4% and 29.5% at 10 years; these differences were highly statistically significant (p = 0.0033).

CONCLUSION

Though graft survival is affected by many things, surgical training in access surgery is not mandatory and a review of surgical practice is urgently needed.

Two rare severe and fulminant presentations of Q fever in patients with minimal risk factors for this disease

We described two rare severe and fulminant clinical presentations of acute Q fever. The first patient had severe multiorgan failure. The second patient had fever and severe cholera-like diarrhoea. Coxiella burnetii polymerase chain reaction on blood or serum can be clinically useful in the diagnosis of acute Q fever before seroconversion.

Non-parametric surface-based regularisation for building statistical shape models

Determining groupwise correspondence across a set of unlabelled examples of either shapes or images, by the use of an optimisation procedure, is a well-established technique that has been shown to produce quantitatively better models than other approaches. However, the computational cost of the optimisation is high, leading to long convergence times. In this paper, we show how topologically non-trivial shapes can be mapped to regular grids (called shape images). This leads to an initial reduction in computational complexity. By also considering the question of regularisation, we show that a non-parametric fluid regulariser can be applied in a principled manner, the fluid flowing on the shape surface itself, whilst not loosing the computational gain made by the use of shape images. We show that this non-parametric regularisation leads to a further considerable gain, when compared to previous parametric regularisation methods. Quantitative evaluation is performed on biological datasets, and shown to yield a substantial decrease in convergence time, with no loss of model quality.

In dementia with Lewy bodies, Braak stage determines phenotype, not Lewy body distribution

We used an autopsy series to determine whether the newest dementia with Lewy bodies (DLB) consensus pathologic classification correlates with premortem diagnosis of DLB. Neocortical sections from a total of 95 cases with Lewy bodies were stained with alpha-synuclein antibodies. We assigned cases according to the DLB consensus' categories and found a significant association with the premortem clinical diagnosis of DLB. Clinical diagnosis of DLB, however, depended on the presence of low Alzheimer disease pathology (by Braak staging) rather than on Lewy body distribution.

Proteomic data exchange and storage: the need for common standards and public repositories

The ever increasing volumes of proteomic data now being produced by laboratories across the world have resulted in major issues in data storage and accessibility. The further demands of multilaboratory initiatives has highlighted issues when collaborators cannot import data generated within the same project but generated by different hardware types and processed by laboratory-specific work flows and analyses packages. There is an increasing need for common data standards that will allow the interchange of data between different instrumentation, search engines, and between laboratory databases. This could then lead to the establishment of data repositories from where benchmark datasets could be accessed and reanalyzed. The Human Proteome Organization is currently supporting efforts to establish such standards. The work of the Proteomics Standards Initiative has lead to the development of the mzData XML interchange standard and is now broadening its scope to produce a spectral analysis output format, mzIdent. Accompanying controlled vocabularies allow the accurate, while systematic, representation of metadata throughout both schema.

Chromosome 9p21 gene copy number and prognostic significance of p16 in ESFT

Chromosome 9p21 gene copy number in Ewing's sarcoma family of tumour (ESFT) cell lines and primary ESFT has been evaluated using Multiplex Ligation-dependent probe amplification, and the clinical significance of CDKN2A loss and p16/p14^ARF expression investigated. Homozygous deletion of CDKN2A was identified in 4/9 (44%) of ESFT cell lines and 4/42 (10%) primary ESFT; loss of one copy of CDKN2A was identified in a further 2/9 (22%) cell lines and 2/42 (5%) tumours. CDKN2B was co-deleted in three (33%) cell lines and two (5%) tumours. Co-deletion of the MTAP gene was observed in 1/9 (11%) cell lines and 3/42 (7%) tumours. No correlation was observed between CDKN2A deletion and clinical parameters. However, co-expression of high levels of p16/p14^ARF mRNA predicted a poor event-free survival (P=0.046, log-rank test). High levels of p16/p14^ARF mRNA did not correlate with high expression of p16 protein. Furthermore, p16 protein expression did not predict event-free or overall survival. Methylation is not a common mechanism of p16 gene silencing in ESFT. These studies demonstrate that loss (homozygous deletion or single copy) of CDKN2A was not prognostically significant in primary ESFT. However, high levels of p16/p14^ARF mRNA expression were predictive of a poor event-free survival and should be investigated further.