A strategy for selecting data mining techniques in metabolomics.

There is a general agreement that the development of metabolomics depends not only on advances in chemical analysis techniques but also on advances in computing and data analysis methods. Metabolomics data usually requires intensive pre-processing, analysis, and mining procedures. Selecting and applying such procedures requires attention to issues including justification, traceability, and reproducibility.

Practical applications of metabolomics in plant biology.

The technologies being developed for the large-scale, essentially unbiased analysis of the small molecules present in organic extracts made from plant materials are greatly changing our way of thinking about what is possible in plant biology. A range of different separation and detection techniques are being refined and expanded and their combination with advanced data management and data analysis approaches is already giving plant scientists far deeper insights into the complexity of plant metabolism and plant metabolic composition than was imaginable just a few years ago. This field of "metabolomics", while still in its infancy, has nevertheless already been welcomed with open arms by the plant science community, partly because of these said advantages but also because of the broad potential applicability of the approaches in both fundamental and applied science.

Costimulated tumor-infiltrating lymphocytes are a feasible and safe alternative donor cell therapy for relapse after allogeneic stem cell transplantation.

Donor lymphocyte infusion (DLI), a standard relapse treatment after allogeneic stem cell transplantation (AlloSCT), has limited efficacy and often triggers GVHD. We hypothesized that after AlloSCT tumor-infiltrating donor lymphocytes could be costimulated ex vivo to preferentially activate/expand antitumor effectors. We tested the feasibility and safety of costimulated, tumor-derived donor lymphocyte (TDL) infusion in a phase 1 trial.

Revision of Poliaspis (Hemiptera, Coccoidea, Diaspididae), with descriptions of 8 new species from Australia.

Eight new Australian species of Poliaspis are described and illustrated: Poliaspis alluviasp. n., Poliaspis araucariaesp.

Phase I trial of adoptive cell transfer with mixed-profile type-I/type-II allogeneic T cells for metastatic breast cancer.

Purpose: Metastatic breast cancer (MBC) response to allogeneic lymphocytes requires donor T-cell engraftment and is limited by graft-versus-host disease (GVHD). In mice, type-II-polarized T cells promote engraftment and modulate GVHD, whereas type-I-polarized T cells mediate more potent graft-versus-tumor (GVT) effects. This phase I translational study evaluated adoptive transfer of ex vivo costimulated type-I/type-II (T1/T2) donor T cells with T-cell-depleted (TCD) allogeneic stem cell transplantation (AlloSCT) for MBC.

Classical far-field phase-sensitive ghost imaging.

We report the first (to our knowledge) far-field ghost images formed with phase-sensitive classical-state light and compare them with ghost images of the same object formed with conventional phase-insensitive classical-state light. To generate signal and reference beams with phase-sensitive cross correlation, we used a pair of synchronized spatial light modulators that imposed random, spatially varying, anticorrelated phase modulation on the outputs from 50-50 beam splitting of a laser beam. In agreement with theory, we found the phase-sensitive image to be inverted, whereas the phase-insensitive image is erect, with both having comparable spatial resolutions and signal-to-noise ratios.

Meeting Report from the Second "Minimum Information for Biological and Biomedical Investigations" (MIBBI) workshop.

This report summarizes the proceedings of the second workshop of the 'Minimum Information for Biological and Biomedical Investigations' (MIBBI) consortium held on Dec 1-2, 2010 in Rüdesheim, Germany through the sponsorship of the Beilstein-Institute. MIBBI is an umbrella organization uniting communities developing Minimum Information (MI) checklists to standardize the description of data sets, the workflows by which they were generated and the scientific context for the work. This workshop brought together representatives of more than twenty communities to present the status of their MI checklists and plans for future development.

Insights into genotype-phenotype correlations in spinal muscular atrophy: a retrospective study of 103 patients.

Spinal muscular atrophy (SMA) is an autosomal recessive disorder associated with homozygous deletion of the survival motor neuron 1 gene (SMN1). Its centromeric copy gene, SMN2, is the major modifying factor. However, the genotype-phenotype correlation is incomplete and is therefore not useful in clinical practice.

Developing a simplified consent form for biobanking.

Background: Consent forms have lengthened over time and become harder for participants to understand. We sought to demonstrate the feasibility of creating a simplified consent form for biobanking that comprises the minimum information necessary to meet ethical and regulatory requirements. We then gathered preliminary data concerning its content from hypothetical biobank participants.

Evolutionary relationships among primary endosymbionts of the mealybug subfamily phenacoccinae (hemiptera: Coccoidea: Pseudococcidae).

Mealybugs (Coccoidea: Pseudococcidae) are sap-sucking plant parasites that harbor bacterial endosymbionts within specialized organs. Previous studies have identified two subfamilies, Pseudococcinae and Phenacoccinae, within mealybugs and determined the primary endosymbionts (P-endosymbionts) of the Pseudococcinae to be Betaproteobacteria ("Candidatus Tremblaya princeps") containing Gammaproteobacteria secondary symbionts. Here, the P-endosymbionts of phenacoccine mealybugs are characterized based on 16S rRNA from the bacteria of 20 species of phenacoccine mealybugs and four outgroup Puto species (Coccoidea: Putoidae) and aligned to more than 100 published 16S rRNA sequences from symbiotic and free-living bacteria.

Gall-induction in insects: evolutionary dead-end or speciation driver?

Background: The tree of life is significantly asymmetrical - a result of differential speciation and extinction - but general causes of such asymmetry are unclear. Differences in niche partitioning are thought to be one possible general explanation. Ecological specialization might lead to increases in diversification rate or, alternatively, specialization might limit the evolutionary potential of specialist lineages and increase their extinction risk.

NCI First International Workshop on the Biology, Prevention, and Treatment of Relapse after Allogeneic Hematopoietic Stem Cell Transplantation: Report from the Committee on Treatment of Relapse after Allogeneic Hematopoietic Stem Cell Transplantation.

Relapse is a major cause of treatment failure after allogeneic hematopoietic stem cell transplantation (alloHSCT). Treatment options for relapse have been inadequate, and the majority of patients ultimately die of their disease. There is no standard approach to treating relapse after alloHSCT.

Simplifying informed consent for biorepositories: stakeholder perspectives.

Purpose: Complex and sometimes controversial information must be conveyed during the consent process for participation in biorepositories, and studies suggest that consent documents in general are growing in length and complexity. As a first step toward creating a simplified biorepository consent form, we gathered data from multiple stakeholders about what information was most important for prospective participants to know when making a decision about taking part in a biorepository.

Methods: We recruited 52 research participants, 12 researchers, and 20 institutional review board representatives from Durham and Kannapolis, NC.

Patient reactions to confidentiality, liability, and financial aspects of informed consent in cardiology research.

Background: Although the informed consent process is supposed to help potential research participants make informed and voluntary decisions about participating in research, little is known about how participants react to language in the informed consent document and whether their reactions are related to their willingness to enroll in clinical trials. We examined the relationship between patients' reactions to standard informed consent language and their willingness to participate in a hypothetical clinical trial.

Methods And Results: We simulated the consent process for a hypothetical cardiology clinical trial with 470 patients in an outpatient cardiovascular medicine clinic at a large academic medical center.

Oversight of financial conflicts of interest in commercially sponsored research in academic and nonacademic settings.

Background: Studies of conflicts of interest in clinical research have focused on academic centers, but most clinical research takes place in nonacademic settings.

Objective: To compare oversight and management of investigators' financial relationships in academic and nonacademic research settings.

Design, Setting, And Participants: Survey of officials at 199 sites that contributed participants to commercially sponsored phase 3 clinical trials published in JAMA or the New England Journal of Medicine in 2006 and 2007.

Australian gall-inducing scale insects on Eucalyptus: revision of Opisthoscelis Schrader (Coccoidea, Eriococcidae) and descriptions of a new genus and nine new species.

We revise the genus Opisthoscelis Schrader, and erect the genus Tanyscelisgen. n. with Opisthoscelis pisiformis Froggatt as its type species.

Sleep-wake functioning along the cancer continuum: focus group results from the Patient-Reported Outcomes Measurement Information System (PROMIS(®)).

Objective: Cancer and its treatments disturb sleep-wake functioning; however, there is little information available on the characteristics and consequences of sleep problems associated with cancer. As part of an effort to improve measurement of sleep-wake functioning, we explored the scope of difficulties with sleep in a diverse group of patients diagnosed with cancer.

Methods: We conducted 10 focus groups with patients recruited from the Duke University tumor registry and oncology/hematology clinics.

Strategies to improve long-term outcome in stage IIIB inflammatory breast cancer: multimodality treatment including dose-intensive induction and high-dose chemotherapy.

Inflammatory breast cancer (IBC) is a rare clinicopathologic entity with a poor prognosis, lagging far behind any other form of nonmetastatic breast cancer. Since the advent of systemic chemotherapy over 35 years ago, only minimal progress has been made in long-term outcome. Although multiple randomized trials of high-dose chemotherapy and autologous progenitor cell transplantation (ASCT) for the treatment of breast cancer have yielded disappointing results, these data are not necessarily relevant to IBC, a distinct clinical and pathologic entity.

Dietary behaviors and portion sizes of black women who enrolled in SisterTalk and variation by demographic characteristics.

Objective: To describe the dietary behaviors of black women who enrolled in the SisterTalk weight control study.

Design: Baseline data collected via telephone survey and in-person screening.

Setting: Boston, Massachusetts and surrounding areas.

Promoting coherent minimum reporting guidelines for biological and biomedical investigations: the MIBBI project.

The Minimum Information for Biological and Biomedical Investigations (MIBBI) project provides a resource for those exploring the range of extant minimum information checklists and fosters coordinated development of such checklists.

Clinical evidence of a graft-versus-lymphoma effect against relapsed diffuse large B-cell lymphoma after allogeneic hematopoietic stem-cell transplantation.

Background: A graft-versus-lymphoma effect against diffuse large B-cell lymphoma (DLBCL) is inferred by sustained relapse-free survival after allogeneic stem-cell transplantation; however, there are limited data on a direct graft-versus-lymphoma effect against DLBCL following immunotherapeutic intervention by either withdrawal of immunosuppression or donor lymphocyte infusion (DLI).

Materials And Methods: An analysis was carried out to determine whether a direct graft-versus-lymphoma effect exists against DLBCL. The analysis was restricted to patients with DLBCL, who were either not in complete remission at day +100 after allogeneic stem-cell transplantation or subsequently relapsed beyond this time point.

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.

Bioethical considerations of monoclonal B-cell lymphocytosis: donor transfer after haematopoietic stem cell transplantation.

Monoclonal B-cell lymphocytosis (MBL) is a recently described laboratory finding in otherwise healthy individuals. In MBL, a light chain-restricted, clonal B-cell population, often with a chronic lymphocytic leukaemia (CLL) phenotype, is identified by flow cytometry. Although the prognostic significance remains unclear, there is an increased incidence in ageing populations and those with a family history of CLL.

Feasibility, cost, and cost-effectiveness of a telephone-based motivational intervention for underserved pregnant smokers.

This study reports on the evaluation of the feasibility, cost, and cost-effectiveness of a proactively provided telephone-based motivational smoking cessation intervention to an underserved population of pregnant smokers who may or may not receive ongoing prenatal care. As part of the New England SCRIPT randomized clinical trial comparing the efficacy of three types of smoking cessation interventions for pregnant smokers, one-third of the women (n = 358) received a motivational telephone counseling intervention (MI) delivered by trained counselors using a semistructured protocol. Although this population was very mobile, the MI counselors were able to reach 86% of the women with at least one call and 46% received all three calls.