Minimum information about a microarray experiment (MIAME)-toward standards for microarray data

Microarray analysis has become a widely used tool for the generation of gene expression data on a genomic scale. Although many significant results have been derived from microarray studies, one limitation has been the lack of standards for presenting and exchanging such data. Here we present a proposal, the Minimum Information About a Microarray Experiment (MIAME), that describes the minimum information required to ensure that microarray data can be easily interpreted and that results derived from its analysis can be independently verified. The ultimate goal of this work is to establish a standard for recording and reporting microarray-based gene expression data, which will in turn facilitate the establishment of databases and public repositories and enable the development of data analysis tools. With respect to MIAME, we concentrate on defining the content and structure of the necessary information rather than the technical format for capturing it.

ArrayExpress--a public database of microarray experiments and gene expression profiles

ArrayExpress is a public database for high throughput functional genomics data. ArrayExpress consists of two parts—the ArrayExpress Repository, which is a MIAME supportive public archive of microarray data, and the ArrayExpress Data Warehouse, which is a database of gene expression profiles selected from the repository and consistently re-annotated. Archived experiments can be queried by experiment attributes, such as keywords, species, array platform, authors, journals or accession numbers. Gene expression profiles can be queried by gene names and properties, such as Gene Ontology terms and gene expression profiles can be visualized. ArrayExpress is a rapidly growing database, currently it contains data from >50 000 hybridizations and >1 500 000 individual expression profiles. ArrayExpress supports community standards, including MIAME, MAGE-ML and more recently the proposal for a spreadsheet based data exchange format: MAGE-TAB. Availability: .

Natural variation in a Drosophila clock gene and temperature compensation

The threonine-glycine (Thr-Gly) encoding repeat within the clock gene period of Drosophila melanogaster is polymorphic in length. The two major variants (Thr-Gly)17 and (Thr-Gly)20 are distributed as a highly significant latitudinal cline in Europe and North Africa. Thr-Gly length variation from both wild-caught and transgenic individuals is related to the flies' ability to maintain a circadian period at different temperatures. This phenomenon provides a selective explanation for the geographical distribution of Thr-Gly lengths and gives a rare glimpse of the interplay between molecular polymorphism, behavior, population biology, and natural selection.

ArrayExpress--a public repository for microarray gene expression data at the EBI

ArrayExpress is a public repository for microarray data that supports the MIAME (Minimum Information About a Microarray Experiment) requirements and stores well-annotated raw and normalized data. As of November 2004, ArrayExpress contains data from approximately 12,000 hybridizations covering 35 species. Data can be submitted online or directly from local databases or LIMS in a standard format, and password-protected access to prepublication data is provided for reviewers and authors. The data can be retrieved by accession number or queried by various parameters such as species, author and array platform. A facility to query experiments by gene and sample properties is provided for a growing subset of curated data that is loaded in to the ArrayExpress data warehouse. Data can be visualized and analysed using Expression Profiler, the integrated data analysis tool. ArrayExpress is available at http://www.ebi.ac.uk/arrayexpress.

Double gloving to reduce surgical cross-infection

BACKGROUND

The invasive nature of surgery, with its increased exposure to blood, means that during surgery there is a high risk of transfer of pathogens. Pathogens can be transferred through contact between surgical patients and the surgical team, resulting in post-operative or blood borne infections in patients or blood borne infections in the surgical team. Both patients and the surgical team need to be protected from this risk. This risk can be reduced by implementing protective barriers such as wearing surgical gloves. Wearing two pairs of surgical gloves, triple gloves, glove liners or cloth outer gloves, as opposed to one pair, is considered to provide an additional barrier and further reduce the risk of contamination.

OBJECTIVES

The primary objective of this review was to determine if additional glove protection reduces the number of surgical site or blood borne infections in patients or the surgical team. The secondary objective was to determine if additional glove protection reduces the number of perforations to the innermost pair of surgical gloves. The innermost gloves (next to skin) compared with the outermost gloves are considered to be the last barrier between the patient and the surgical team.

SEARCH STRATEGY

We searched the Cochrane Wounds Group Specialised Register (January 2006), and the Cochrane Central Register of Controlled Trials (CENTRAL)(The Cochrane Library Issue 4, 2005). We also contacted glove manufacturing companies and professional organisations.

SELECTION CRITERIA

Randomised controlled trials involving: single gloving, double gloving, triple gloving, glove liners, knitted outer gloves, steel weave outer gloves and perforation indicator systems.

DATA COLLECTION AND ANALYSIS

Both authors independently assessed the relevance and quality of each trial. Data was extracted by one author and cross checked for accuracy by the second author.

MAIN RESULTS

Two trials were found which addressed the primary outcome, namely, surgical site infections in patients. Both trials reported no infections. Thirty one randomised controlled trials measuring glove perforations were identified and included in the review. Fourteen trials of double gloving (wearing two pairs of surgical latex gloves) were pooled and showed that there were significantly more perforations to the single glove than the innermost of the double gloves (OR 4.10, 95% CI 3.30 to 5.09). Eight trials of indicator gloves (coloured latex gloves worn underneath latex gloves to more rapidly alert the team to perforations) showed that significantly fewer perforations were detected with single gloves compared with indicator gloves (OR 0.10, 95% CI 0.06 to 0.16) or with standard double glove compared with indicator gloves (OR 0.08, 95% CI 0.04 to 0.17). Two trials of glove liners (a glove knitted with cloth or polymers worn between two pairs of latex gloves)(OR 26.36, 95% CI 7.91 to 87.82), three trials of knitted gloves (knitted glove worn on top of latex surgical gloves)(OR 5.76, 95% CI 3.25 to 10.20) and one trial of triple gloving (three pairs of latex surgical gloves)(OR 69.41, 95% CI 3.89 to 1239.18) all compared with standard double gloves, showed there were significantly more perforations to the innermost glove of a standard double glove in all comparisons.

AUTHORS' CONCLUSIONS

There is no direct evidence that additional glove protection worn by the surgical team reduces surgical site infections in patients, however the review has insufficient power for this outcome. The addition of a second pair of surgical gloves significantly reduces perforations to innermost gloves. Triple gloving, knitted outer gloves and glove liners also significantly reduce perforations to the innermost glove. Perforation indicator systems results in significantly more innermost glove perforations being detected during surgery.

The EMBL nucleotide sequence database

The EMBL Nucleotide Sequence Database (http://www.ebi.ac.uk/embl/) is maintained at the European Bioinformatics Institute (EBI) in an international collaboration with the DNA Data Bank of Japan (DDBJ) and GenBank at the NCBI (USA). Data is exchanged amongst the collaborating databases on a daily basis. The major contributors to the EMBL database are individual authors and genome project groups. Webin is the preferred web-based submission system for individual submitters, whilst automatic procedures allow incorporation of sequence data from large-scale genome sequencing centres and from the European Patent Office (EPO). Database releases are produced quarterly. Network services allow free access to the most up-to-date data collection via ftp, email and World Wide Web interfaces. EBI's Sequence Retrieval System (SRS), a network browser for databanks in molecular biology, integrates and links the main nucleotide and protein databases plus many specialized databases. For sequence similarity searching a variety of tools (e.g. Blitz, Fasta, BLAST) are available which allow external users to compare their own sequences against the latest data in the EMBL Nucleotide Sequence Database and SWISS-PROT.

Double gloving to reduce surgical cross-infection

BACKGROUND

The invasive nature of surgery, with its increased exposure to blood, means that during surgery there is a high risk of transfer of pathogens. Pathogens can be transferred through contact between surgical patients and the surgical team, resulting in post-operative or blood borne infections in patients or blood borne infections in the surgical team. Both patients and the surgical team need to be protected from this risk. This risk can be reduced by implementing protective barriers such as wearing surgical gloves. Wearing two pairs of surgical gloves, as opposed to one pair, is considered to provide an additional barrier and further reduce the risk of contamination.

OBJECTIVES

The primary objective of this review was to determine if double gloving (wearing two pairs of gloves), rather than single gloving, reduces the number of post-operative or blood borne infections in surgical patients or blood borne infections in the surgical team. The secondary objective of this review was to determine if double gloving, rather than single gloving, reduces the number of perforations to the innermost pair of surgical gloves. The innermost gloves (next to skin) compared with the outermost gloves are considered to be the last barrier between the patient and the surgical team.

SEARCH STRATEGY

The reviewers searched the Cochrane Wounds Group Specialised Trials Register, MEDLINE, CINAHL, EMBASE and the Cochrane Controlled Trials Register. Glove manufacturing companies and professional organisations were also contacted.

SELECTION CRITERIA

Randomised controlled trials involving: single gloving, double gloving, glove liners or coloured puncture indicator systems.

DATA COLLECTION AND ANALYSIS

Both reviewers independently assessed the relevance and quality of each trial. Trials to be included were cross checked and authenticated by both reviewers. Data was extracted by one reviewer and cross checked for accuracy by the second reviewer.

MAIN RESULTS

Two trials were found which addressed the primary outcome. A total of 18 randomised controlled trials which measured glove perforations were identified and included in the review. DOUBLE GLOVING (wearing two pairs of latex gloves). Nine trials compared single latex gloves versus double latex gloves. These found no difference in the number of perforations between the single latex gloves and the outermost pair of the double latex gloves, but the number of perforations to the double latex-innermost glove was significantly reduced when two pairs of latex gloves were worn. ORTHOPAEDIC GLOVES (thicker than standard latex gloves). One trial compared single latex orthopaedic gloves with double latex gloves. This showed there was no difference in the number of perforations to the innermost gloves when wearing double latex gloves compared with a single pair of latex orthopaedic gloves. INDICATOR GLOVES (coloured latex gloves worn underneath latex gloves). Three trials compared double latex gloves versus double latex indicator gloves. These trials showed similar numbers of perforations to both the innermost and the outermost gloves for both gloving groups. Perforations to the outermost gloves were detected more easily when double latex indicator gloves were worn. Wearing double latex indicator gloves did not increase the detection of perforations to the innermost gloves. GLOVE LINERS (an insert worn between two pairs of latex gloves). Two trials compared double latex gloves versus double latex gloves with liners. These trials showed a significant reduction in the number of perforations to the innermost glove when a glove liner was worn between two pairs of latex gloves. CLOTH GLOVES (cloth gloves worn on top of latex gloves). Two trials compared double latex gloves versus latex inner with cloth outer gloves. These trials showed that wearing a cloth outer glove significantly reduced the number of perforations to the innermost latex glove. STEEL WEAVE GLOVES (steel weave gloves worn on top of latex gloves). One trial compared double latex gloves versus latex inner with steel weave outer gloves. This trial showed no reduction in the number of perforations to the innermost glove when wearing a steel weave outer glove.

REVIEWER'S CONCLUSIONS

Wearing two pairs of latex gloves significantly reduces the number of perforations to the innermost glove. This evidence comes from trials undertaken in 'low risk' surgical specialties, that is specialties which did not include orthopaedic joint surgery. Wearing two pairs of latex gloves does not cause the glove wearer to sustain more perforations to their outermost glove. Wearing double latex indicator gloves enables the glove wearer to detect perforations to the outermost glove more easily than when wearing double latex gloves. However wearing a double latex indicator system will not assist with the detection of perforations to the innermost glove, nor reduce the number of perforations to either the outermost or the innermost glove. Wearing a glove liner between two pairs of latex gloves to undertake joint replacement surgery significantly reduces the number of perforations to the innermost glove compared with double latex gloves only. Wearing cloth outer gloves to undertake joint replacement surgery significantly reduces the number of perforations to the innermost glove compared with wearing double latex gloves. Wearing steel weave outer gloves to undertake joint replacement surgery does not reduce the number of perforations to innermost gloves compared with double latex gloves.

The financial cost of optimising blood pressure control

We have investigated the financial costs of attempts to optimise blood pressure control in patients referred to our blood pressure clinic. At first referral, the average blood pressure in the 262 patients studied were 167/97 mmHg and the monthly costs of the antihypertensive drugs was 23.44 pounds. After 1 year of clinic attendance, the blood pressure was reduced to 149/87 mmHg, and the average drug costs had risen to 30.68 pounds. For drug expenditure alone, the cost of reducing systolic blood pressure by 1 mmHg was 0.36p pounds (Euro 0.55, USD 0.55) and for diastolic blood pressure the cost-was 0.72p pounds (Euro 1.12, USD 1.13).

Polytetrafluoroethylene femorodistal grafts: can the use of a vein collar offer patients a reasonable chance of success?

The growing number of patients with critical ischemia who lack a suitable autogenous vein for grafting pose a particular problem for the vascular team. In such patients the use of a polytetrafluoroethylene graft with a distal anastomotic vein cuff or patch has been advocated as an alternative to primary amputation. The use of such adjunctive techniques is reviewed through a 3-year retrospective study of 50 patients under the care of one surgeon. Data analyzed include patient demographics, risk factors, and presenting symptoms. All patients were included in a Duplex graft surveillance program. The cumulative patency rates at 1 and 2 years were 56% and 55%, respectively, with limb salvage rates of 85% and 80%. The data support a reconstructive approach to maintain the quality of the patient's life.

PAM trial protocol: a randomised feasibility study of psychedelic microdosing-assisted meaning-centred psychotherapy in advanced stage cancer patients

BACKGROUND

An advanced cancer diagnosis can be associated with a significant profile of distress. Psychedelic compounds have shown clinically significant effects in the treatment of psychological distress in patients with advanced-stage cancer. Given the challenges of delivering timely and effective intervention in the advanced cancer context, it is possible that an alternative, more pragmatic, approach lies in psychedelic 'microdosing'. Microdosing refers to repeated administration of psychedelics in sub-hallucinogenic doses. The purpose of this study is to evaluate the feasibility of conducting a full-scale randomised controlled trial comparing psychedelic microdose-assisted-meaning-centred psychotherapy (PA-MCP) to standard meaning-centred psychotherapy (MCP) in New Zealand indigenous (Māori) and non-indigenous people with advanced cancer and symptoms of anxiety and/or depression. Although MCP is a well-established psychotherapeutic treatment in advanced cancer populations, the potential efficacy and effectiveness of this therapy when delivered alongside a standardised microdose regimen of a psychedelic compound have not been investigated.

METHODS

Participants with advanced-stage cancer and symptoms of anxiety and/or depression (N = 40; 20 Māori, 20 non-Māori) will be randomised under double-blind conditions to receive 7 sessions of MCP alongside 13 doses of either an LSD microdose (4-20 µg) (PA-MCP) or inactive placebo (placebo-MCP). The feasibility, acceptability, and safety of this intervention and physiological and psychological measures will be recorded at baseline, at each session of MCP, and at a 1-month and 6-month follow-up.

DISCUSSION

Our findings will evaluate the feasibility, acceptability, and safety of a larger randomised controlled trial and provide an initial indication of the potential benefits of psychedelic microdosing for psychological distress in advanced-stage indigenous and non-indigenous cancer patients.

TRIAL REGISTRATION

NZCTR, ACTRN12623000478617. Registered 11 May 2023.  https://www.anzctr.org.au/Trial/Registration/TrialReview.aspx?id=385810&isReview=true .