Depression as a risk factor for breast cancer : investigating methodological limitations in the literature.

Purpose: A relationship between depression and the development of breast cancer has not been convincingly shown in the research conducted over the past three decades. Methods: In an effort to better understand the conflicting results, a review was conducted focusing on the methodological problems associated with this literature, including time frame between the assessment of depression and the diagnosis of breast cancer and the use of somatic items in measuring depression. Fifteen breast cancer prospective studies were reviewed. Results: While twelve of the studies found positive associations between depression and breast cancer development, three studies found negative associations. With regards to the predictive associations between depression and breast cancer incidence the findings revealed that (a) studies using a longer time frame found a stronger association than studies using a shorter time frame, and (b) studies utilizing depression measures that did not contain somatic items found a smaller association than studies utilizing depression measures that did contain these items. Conclusions: Future studies should ensure that sufficient periods of time between the measurement of depression and the assessment of cancer and avoid measuring depression using somatic items

Quasi-experimental study designs series –Paper 9: Collecting Data from Quasi-Experimental Studies

Objective: To identify variables that must be coded when synthesizing primary studies that use quasi-experimental designs.  Study Design and Setting: All quasi-experimental (QE) designs.  Results: When designing a systematic review of QE studies potential sources of heterogeneity – both theory-based and methodological – must be identified. We outline key components of inclusion criteria for syntheses of quasi-experimental studies. We provide recommendations for coding content-relevant and methodological variables, and outlined the distinction between bivariate effect sizes and partial (i.e., adjusted) effect sizes. Designs used and controls employed are viewed as of greatest importance. Potential sources of bias and confounding are also addressed.  Conclusion: Careful consideration must be given to inclusion criteria and the coding of theoretical and methodological variables during the design phase of a synthesis of quasi-experimental studies. The success of the meta-regression analysis relies on the data available to the meta-analyst. Omission of critical moderator variables (i.e., effect modifiers) will undermine the conclusions of a meta-analysis

Can Non-Randomised Studies of Interventions Provide Unbiased Effect Estimates? A Systematic Review of Internal Replication Studies.

Non-randomized studies of intervention effects (NRS), also called quasi-experiments, provide useful decision support about development impacts. However, the assumptions underpinning them are usually untestable, their verification resting on empirical replication. The internal replication study aims to do this by comparing results from a causal benchmark study, usually a randomized controlled trial (RCT), with those from an NRS conducted at the same time in the sampled population. We aimed to determine the credibility and generalizability of findings in internal replication studies in development economics, through a systematic review and meta-analysis. We systematically searched for internal replication studies of RCTs conducted on socioeconomic interventions in low- and middle-income countries. We critically appraised the benchmark randomized studies, using an adapted tool. We extracted and statistically synthesized empirical measures of bias. We included 600 estimates of correspondence between NRS and benchmark RCTs. All internal replication studies were found to have at least "some concerns" about bias and some had high risk of bias. We found that study designs with selection on unobservables, in particular regression discontinuity, on average produced absolute standardized bias estimates that were approximately zero, that is, equivalent to the estimates produced by RCTs. But study conduct also mattered. For example, matching using pre-tests and nearest neighbor algorithms corresponded more closely to the benchmarks. The findings from this systematic review confirm that NRS can produce unbiased estimates. Authors of internal replication studies should publish pre-analysis protocols to enhance their credibility

Quasi-experimental study designs series – Paper 10: Synthesizing evidence for effects collected from quasi-experimental studies presents surmountable challenges

Objective: To outline issues of importance to analytic approaches to the synthesis of quasi-experiments (QEs), and to provide a statistical model for use in analysis. Study Design and Setting: We drew on the literatures of statistics, epidemiology, and social-science methodology to outline methods for synthesis of QE studies. The design and conduct of quasi-experiments, effect sizes from QEs, and moderator variables for the analysis of those effect sizes were discussed. Results: Biases, confounding, design complexities and comparisons across designs offer serious challenges to syntheses of QEs. Key components of meta-analyses of QEs were identified, including the aspects of QE study design to be coded and analyzed. Of utmost importance are the design and statistical controls implemented in the QEs. Such controls and any potential sources of bias and confounding must be modeled in analyses, along with aspects of the interventions and populations studied. Because of such controls, effect sizes from QEs are more complex than those from randomized experiments. A statistical meta-regression model that incorporates important features of the QEs under review was presented. Conclusion: Meta-analyses of quasi-experiments provide particular challenges, but thorough coding of intervention characteristics and study methods, along with careful analysis, should allow for sound inferences

p27KIP1 Deletions in Childhood Acute Lymphoblastic Leukemia

AbstractThe p27KIP1 gene, which encodes a cyclin-dependent kinase (CDK) inhibitor, has been assigned to chromosome band 12p12, a region often affected by cytogenetically apparent deletions or translocations in childhood acute lymphoblastic leukemia (ALL). As described here, fluorescence in situ hybridization (FISH) analysis of 35 primary ALL samples with cytogenetic evidence of 12p abnormalities revealed hemizygous deletions of p27KIP1 in 29 cases. Further analysis of 19 of these cases with two additional gene-specific probes from the 12p region (hematopoietic cell phosphatase, HCP and cyclin D2, CCND2) showed that p27KIP1 is located more proximally on the short arm of chromosome 12 and is deleted more frequently than either HCP or CCND2. Of 16 of these cases with hemizygous deletion of p27KIP1, only eight showed loss of HCP or CCND2, whereas loss of either of the latter two loci was uniformly associated with loss of p27KIP1. Missense mutations or mutations leading to premature termination codons were not detected in the coding sequences of the retained p27KIP1 alleles in any of the 16 ALL cases examined, indicating a lack of homozygous inactivation. By Southern blot analysis, one case of primary T-cell ALL had hemizygous loss of a single p27KIP1 allele and a 34.5-kb deletion, including the second coding exon of the other allele. Despite homozygous inactivation of p27KIP1 in this case, our data suggest that haploinsufficiency for p27KIP1 is the primary consequence of 12p chromosomal deletions in childhood ALL. The oncogenic role of reduced, but not absent, levels of p27KIP1 is supported by recent studies in murine models and evidence that this protein not only inhibits the activity of complexes containing CDK2 and cyclin E, but also promotes the assembly and catalytic activity of CDK4 or CDK6 in complexes with cyclin D

Theorising age and generation in development: A relational approach

This introduction outlines the analytical approach informing the articles presented in this special issue. The project of ‘generationing’ development involves re-thinking development as distinctly generational in its dynamics. For this, we adopt a relational approach to the study of young people in development, which overcomes the limitations inherent to common categorising approaches. Concepts of age and generation are employed to conceptualise young people as social actors and life phases such as childhood and youth in relational terms. Acknowledging the centrality of young people in social reproduction puts them at the heart of development studies and leads the articles comprising this special issue to explore how young people’s agency shapes and is shaped by the changing terms of social reproduction brought about by development

ROBINS-I: a tool for assessing risk of bias in non-randomized studies of interventions

Non-randomised studies of the effects of interventions are critical to many areas of healthcare evaluation, but their results may be biased. It is therefore important to understand and appraise their strengths and weaknesses. We developed ROBINS-I ("Risk Of Bias In Non-randomised Studies-of Interventions"), a new tool for evaluating risk of bias in estimates of the comparative effectiveness (harm or benefit) of interventions from studies that did not use randomisation to allocate units (individuals or clusters of individuals) to comparison groups. The tool will be particularly useful to those undertaking systematic reviews that include non-randomised studies

Metagenomics reveals sediment microbial community response to Deepwater Horizon oil spill

The Deepwater Horizon (DWH) oil spill in the spring of 2010 resulted in an input of ∼4.1 million barrels of oil to the Gulf of Mexico; >22% of this oil is unaccounted for, with unknown environmental consequences. Here we investigated the impact of oil deposition on microbial communities in surface sediments collected at 64 sites by targeted sequencing of 16S rRNA genes, shotgun metagenomic sequencing of 14 of these samples and mineralization experiments using (14)C-labeled model substrates. The 16S rRNA gene data indicated that the most heavily oil-impacted sediments were enriched in an uncultured Gammaproteobacterium and a Colwellia species, both of which were highly similar to sequences in the DWH deep-sea hydrocarbon plume. The primary drivers in structuring the microbial community were nitrogen and hydrocarbons. Annotation of unassembled metagenomic data revealed the most abundant hydrocarbon degradation pathway encoded genes involved in degrading aliphatic and simple aromatics via butane monooxygenase. The activity of key hydrocarbon degradation pathways by sediment microbes was confirmed by determining the mineralization of (14)C-labeled model substrates in the following order: propylene glycol, dodecane, toluene and phenanthrene. Further, analysis of metagenomic sequence data revealed an increase in abundance of genes involved in denitrification pathways in samples that exceeded the Environmental Protection Agency (EPA)'s benchmarks for polycyclic aromatic hydrocarbons (PAHs) compared with those that did not. Importantly, these data demonstrate that the indigenous sediment microbiota contributed an important ecosystem service for remediation of oil in the Gulf. However, PAHs were more recalcitrant to degradation, and their persistence could have deleterious impacts on the sediment ecosystem

Wild-type and mutant SOD1 share an aberrant conformation and a common pathogenic pathway in ALS.

Many mutations confer one or more toxic function(s) on copper/zinc superoxide dismutase 1 (SOD1) that impair motor neuron viability and cause familial amyotrophic lateral sclerosis (FALS). Using a conformation-specific antibody that detects misfolded SOD1 (C4F6), we found that oxidized wild-type SOD1 and mutant SOD1 share a conformational epitope that is not present in normal wild-type SOD1. In a subset of human sporadic ALS (SALS) cases, motor neurons in the lumbosacral spinal cord were markedly C4F6 immunoreactive, indicating that an aberrant wild-type SOD1 species was present. Recombinant, oxidized wild-type SOD1 and wild-type SOD1 immunopurified from SALS tissues inhibited kinesin-based fast axonal transport in a manner similar to that of FALS-linked mutant SOD1. Our findings suggest that wild-type SOD1 can be pathogenic in SALS and identify an SOD1-dependent pathogenic mechanism common to FALS and SALS