Testing the reproducibility and robustness of the cancer biology literature by robot

Scientific results should not just be ‘repeatable’ (replicable in the same laboratory under identical conditions), but also ‘reproducible’ (replicable in other laboratories under similar conditions). Results should also, if possible, be ‘robust’ (replicable under a wide range of conditions). The reproducibility and robustness of only a small fraction of published biomedical results has been tested; furthermore, when reproducibility is tested, it is often not found. This situation is termed ‘the reproducibility crisis'', and it is one the most important issues facing biomedicine. This crisis would be solved if it were possible to automate reproducibility testing. Here, we describe the semi-automated testing for reproducibility and robustness of simple statements (propositions) about cancer cell biology automatically extracted from the literature. From 12 260 papers, we automatically extracted statements predicted to describe experimental results regarding a change of gene expression in response to drug treatment in breast cancer, from these we selected 74 statements of high biomedical interest. To test the reproducibility of these statements, two different teams used the laboratory automation system Eve and two breast cancer cell lines (MCF7 and MDA-MB-231). Statistically significant evidence for repeatability was found for 43 statements, and significant evidence for reproducibility/robustness in 22 statements. In two cases, the automation made serendipitous discoveries. The reproduced/robust knowledge provides significant insight into cancer. We conclude that semi-automated reproducibility testing is currently achievable, that it could be scaled up to generate a substantive source of reliable knowledge and that automation has the potential to mitigate the reproducibility crisis.     

ADAM8-Dependent Extracellular Signaling in the Tumor Microenvironment Involves Regulated Release of Lipocalin 2 and MMP-9

The metalloprotease-disintegrin ADAM8 is critically involved in the progression of pancreatic cancer. Under malignant conditions, ADAM8 is highly expressed and could play an important role in cell–cell communication as expression has been observed in tumor and immune cells of the tumor microenvironment (TME) such as macrophages. To analyze the potential role of ADAM8 in the TME, ADAM8 knockout PDAC tumor cells were generated, and their release of extracellular vesicles (EVs) was analyzed. In EVs, ADAM8 is present as an active protease and associated with lipocalin 2 (LCN2) and matrix metalloprotease 9 (MMP-9) in an ADAM8-dependent manner, as ADAM8 KO cells show a lower abundance of LCN2 and MMP-9. Sorting of ADAM8 occurs independent of TSG101, even though ADAM8 contains the recognition motif PTAP for the ESCRTI protein TSG101 within the cytoplasmic domain (CD). When tumor cells were co-cultured with macrophages (THP-1 cells), expression of LCN2 and MMP-9 in ADAM8 KO cells was induced, suggesting that macrophage signaling can overcome ADAM8-dependent intracellular signaling in PDAC cells. In co-culture with macrophages, regulation of MMP-9 is independent of the M1/M2 polarization state, whereas LCN2 expression is preferentially affected by M1-like macrophages. From these data, we conclude that ADAM8 has a systemic effect in the tumor microenvironment, and its expression in distinct cell types has to be considered for ADAM8 targeting in tumors.     

Parental affect and coping.

Parental affect and coping strategies have been identified as being important for the understanding of the processes involved in the socialization of children. In the present study, 24 fathers (mean age 35.21 yrs old) and 62 mothers (mean age 35.05 yrs) (unrelated) described a stressful incident with one of their children and completed questionnaires addressing their appraisal of the event, their affect, and consequent coping strategy. Both child characteristics (age, birth order, and gender) and parent characteristics (gender, affect intensity, and ego level) were examined in relation to parents' appraisal of the cause of the event, their affect, and their coping strategy. Feelings of being angry, afraid, sad, and guilty, and use of coping strategies are discussed in light of the need for further research on emotion in parenting situations. (PsycINFO Database Record (c) 2010 APA, all rights reserved)     

Hematological malignancies with t(9;11)(p21-22;q23)--a laboratory and clinical study of 125 cases. European 11q23 Workshop participants

This paper reports clinical and cytogenetic data from 125 cases with t(9;11)(p21-22;q32) which were accepted for a European Union Concerted Action Workshop on 11q23. This chromosome abnormality is known to occur predominantly in acute myeloid leukemia (AML) FAB type M5a and less often in AML M4; in this series it was also found to occur, uncommonly, in other AML FAB types, in childhood acute lymphoblastic leukemia (ALL) (nine cases), in relatively young patients with myelodysplastic syndrome (MDS) (five cases), acute biphenotypic leukemia (two cases), and acute undifferentiated leukemia (one case). All age groups were represented but 50% of the patients were aged less than 15 years. The t(9;11) was the sole abnormality in 57 cases with AML; trisomy 8 was the most common additional abnormality (23 cases, including seven with further abnormalities), and 28 cases had other additional abnormalities. Among the t(9;11)+ve patients with AML, the white cell count (WBC) and age group were significant predictors of event-free survival; central nervous system (CNS) involvement or karyotype class (sole, with trisomy 8, or with other), also contributed to prognosis although our data could not show these to be independent factors. The best outcome was for patients aged 1-9 years, with low WBC, and with absence of CNS disease or presence of trisomy 8. For patients aged less than 15 years, the event-free survival for ALL patients was not significantly worse than that of AML patients.     

E. coli SeqA protein binds oriC in two different methyl-modulated reactions appropriate to its roles in DNA replication initiation and origin sequestration

The seqA gene negatively modulates replication initiation at the E. coli origin, oriC. seqA is also essential for sequestration, which acts at oriC and the dnaA promoter to ensure that replication initiation occurs exactly once per chromosome per cell cycle. Initiation is promoted by full methylation of GATC sites clustered in oriC; sequestration is specific to the hemimethylated forms generated by replication. SeqA protein purification and DNA binding are described. SeqA interacts with fully methylated oriC strongly and specifically. This reaction requires multiple molecules of SeqA and determinants throughout oriC, including segments involved in open complex formation. SeqA interacts more strongly with hemimethylated DNA; in this case, oriC and non-oriC sequences are bound similarly. Also, binding of hemimethylated oriC by membrane fractions is due to SeqA. Direct interaction of SeqA protein with the replication origin is likely to be involved in both replication initiation and sequestration.     

Pneumotachograph for flow and volume measurement in normal and dense atmospheres

Measurement of ventilatory flow during pulmonary function maneuvers and in severe exercise by the pneumotachograph flow transducer in dense atmospheres is handicapped by the inverse relationship between the linear range of such transducers and gas density. This limitation in the usefulness of the pneumotachograph can be overcome by mounting such flow transducers in parallel and taking into account the reduction in peak ventilatory flow transducers in parallel and taking into account the reduction in peak ventilatory flow which occurs with increasing density. The design of such assemblies, their static performance characteristics, and a drift subtractor, constructed to stabilize the output of the pneumotachograph pressure transducer, are described.     

A reevaluation of the relation between estrogen and emotionality in female rats.

It has been hypothesized that the emotionality of the female rat is reduced at estrus. In confirmation of previous research, the present 5 experiments with 112 Ss show that administration of estradiol benzoate (20 mug/kg) to female rats of the Maudsley Reactive (MR) strain increased open-field activity and decreased open-field defecation. In addition, ovariectomy increased open-field defecation in MR females. Supporting the generality of these findings, hormone administration reduced open-field defecation and increased open-field activity in intact females of a genetically heterogeneous background. Additional studies suggest that the decrease in open-field defecation at estrus is dependent on estrogenic suppression of food intake. Hormone replacement decreased food intake in the period preceding the open-field test, and colonic contents were also lower in rats treated with estradiol benzoate plus progesterone immediately after the completion of the open-field test. These changes were seen in both MR and genetically heterogeneous females. It is concluded that the decrease in open-field defecation at estrus may be mediated by a reduction in food intake and a consequent decrease in colonic contents and that the validity of the defecation response as a measure of emotionality may be seriously questioned under these circumstances. (24 ref) (PsycINFO Database Record (c) 2010 APA, all rights reserved)     

Media Exposure and Attention as Mediating Variables Influencing Social Risk Judgments

This study examined the hypothesis that media exposure and attention partially mediate the effects of variables such as demographics and personal experience on risk judgments. Risk judgments, including perceived severity, prevalence, controllability, familiarity, and concern about alcohol-related injuries, comprised the outcome measures. Alcohol-related injuries included assaults, motor vehicle crashes, and other injury incidents such as falls, fire, and drowning. Results supported the hypotheses of partial mediation with respect to most risk judgment factors. In particular, effects of education, gender, sensation seeking, and prior firsthand or secondhand experience with alcohol-related mishaps on judgments of concern and/or severity were partially mediated by media variables. The authors concluded that media effects on risk judgments can be usefully understood as part of a larger social process in which media are selectively attended to due to exogenous influences; part of the effect of these exogenous influences on these social risk judgments was via these media influences. Media use variables also retain a degree of influence after controlling for these exogenous factors.