Expression a La Bimode

The recently published article by Wang, and commented on by Ertel in this journal, describes development of a method, named the Bimodality Index, to objectively identify and rank meaningful and reliable bimodal patterns from large-scale gene expression datasets. This is an important step because genes with a bimodal distribution may be prime candidates to develop as molecular diagnostic tests for distinguishing clinically important groups. In their introduction, they make the point that a bimodal expression pattern may be observed when two distinct subgroups of samples are measured as one group, with each mode representing the mean expression of a gene in one of the sub-groups. Recently, it was reported that bimodal gene expression may represent another important phenomenon. Specifically, two clinically important groups may be distinguished on the basis of a gene being unimodal in one group and bimodal in the other group. For example, certain key antioxidant, DNA repair, and transcription factor genes each display a unimodal pattern in non-lung cancer subjects but a bimodal pattern in lung cancer subjects. Importantly, when two groups are distinguished on the basis of unimodal vs bimodal distribution of an analyte (in this case gene expression value), biomarker development requires use of two cut-points, one on either side of the unimodal distribution. It is timely then that an improved method for separating groups on the basis of two cut-points was described recently. Thus, the analytical method to discover genes with bimodal expression distribution described by Wang and recent statistical methods that enable separation of groups on the basis of two-cut points are likely to accelerate both diagnostic test discovery, as well as mechanistic understanding of disease and disease risk. It is important to recognize that transcript abundance methods vary in their linear dynamic range, and that the ability to identify bimodal distribution of genes will depend to a significant degree on the linear dynamic range of the method used

Moral anarchy in Nostromo, The Secret Agent, and Under Western Eyes

I have utilized Human Solidarity and The Moral Law to show that the theme of moral anarchy is suggested primarily through the actions and motivations of many of Joseph Conrad\u27s characters. Most of the characters fail to adhere to the rules which preserve the human bond, but Conrad suggests confessing one\u27s offenses and submitting to their consequences to re-establish oneself in the human comminty. The result may not be complete happiness but at least inner peace for the guilty

Quality Control Methods for Optimal BCR-ABL1 Clinical Testing in Human Whole Blood Samples

Reliable breakpoint cluster region (BCR)–Abelson (ABL) 1 measurement is essential for optimal management of chronic myelogenous leukemia. There is a need to optimize quality control, sensitivity, and reliability of methods used to measure a major molecular response and/or treatment failure. The effects of room temperature storage time, different primers, and RNA input in the reverse transcription (RT) reaction on BCR-ABL1 and β-glucuronidase (GUSB) cDNA yield were assessed in whole blood samples mixed with K562 cells. BCR-ABL1 was measured relative to GUSB to control for sample loading, and each gene was measured relative to known numbers of respective internal standard molecules to control for variation in quality and quantity of reagents, thermal cycler conditions, and presence of PCR inhibitors. Clinical sample and reference material measurements with this test were concordant with results reported by other laboratories. BCR-ABL1 per 103 GUSB values were significantly reduced (P = 0.004) after 48-hour storage. Gene-specific primers yielded more BCR-ABL1 cDNA than random hexamers at each RNA input. In addition, increasing RNA inhibited the RT reaction with random hexamers but not with gene-specific primers. Consequently, the yield of BCR-ABL1 was higher with gene-specific RT primers at all RNA inputs tested, increasing to as much as 158-fold. We conclude that optimal measurement of BCR-ABL1 per 103 GUSB in whole blood is obtained when gene-specific primers are used in RT and samples are analyzed within 24 hours after blood collection

Stable low-level expression of p21(WAF1/CIP1 )in A549 human bronchogenic carcinoma cell line-derived clones down-regulates E2F1 mRNA and restores cell proliferation control

BACKGROUND: Deregulated cell cycle progression and loss of proliferation control are key properties of malignant cells. In previous studies, an interactive transcript abundance index (ITAI) comprising three cell cycle control genes, [MYC × E2F1]/p21 accurately distinguished normal from malignant bronchial epithelial cells (BEC), using a cut-off threshold of 7,000. This cut-off is represented by a line with a slope of 7,000 on a bivariate plot of p21 versus [MYC × E2F1], with malignant BEC above the line and normal BEC below the line. This study was an effort to better quantify, at the transcript abundance level, the difference between normal and malignant BEC. The hypothesis was tested that experimental elevation of p21 in a malignant BEC line would decrease the value of the [MYC × E2F1]/p21 ITAI to a level below this line, resulting in loss of immortality and limited cell population doubling capacity. In order to test the hypothesis, a p21 expression vector was transfected into the A549 human bronchogenic carcinoma cell line, which has low constitutive p21 TA expression relative to normal BEC. RESULTS: Following transfection of p21, four A549/p21 clones with stable two-fold up-regulated p21 expression were isolated and expanded. For each clone, the increase in p21 transcript abundance (TA) was associated with increased total p21 protein level, more than 5-fold reduction in E2F1 TA, and 10-fold reduction in the [MYC × E2F1]/p21 ITAI to a value below the cut-off threshold. These changes in regulation of cell cycle control genes were associated with restoration of cell proliferation control. Specifically, each transfectant was capable of only 15 population doublings compared with unlimited population doublings for parental A549. This change was associated with an approximate 2-fold increase in population doubling time to 38.4 hours (from 22.3 hrs), resumption of contact-inhibition, and reduced dividing cell fraction as measured by flow cytometric DNA analysis. CONCLUSION: These results, likely due to increased p21-mediated down-regulation of E2F1 TA at the G1/S phase transition, are consistent with our hypothesis. Specifically, they provide experimental confirmation that a line with slope of 7,000 on the p21 versus [MYC × E2F1] bivariate plot quantifies the difference between normal and malignant BEC at the level of transcript abundance

A material flow modelling tool for resource efficient production planning in multi-product manufacturing systems

Resource efficiency is recognized as one of the greatest sustainability challenges facing the manufacturing industry in the future. Materials are a resource of primary importance, making a significant contribution to the economic costs and environmental impacts of production. During the manufacturing phase the majority of resource efficiency initiatives and management methodologies have been concerned primarily with improvements measured on an economic basis. More recently, the need for even greater levels of resource efficiency has extended the scope of these initiatives to consider complete manufacturing and industrial systems at an economic and environmental level. The flow of materials at each system level relates directly to material efficiency, which in turn influences the consumption of other resources such as water and energy. Initial research by the authors in material efficiency focused on material flow, proposing a material flow assessment approach, comprising a systematic framework for the analysis of quantitative and qualitative flow in manufacturing systems. The framework was designed to provide greater understanding of material flow through identification of strengths, weaknesses, constraints and opportunities for improvement, facilitating the implementation of improvement measures for greater efficiency in both environmental and economic terms. This paper presents an extension of this work, applying the material flow assessment framework to a complex multi-product and multi-site manufacturing system scenario. It begins with a description of the Resource Efficient Scheduling (RES) tool that supports the implementation of this framework. The tool models the interactions of quantitative and qualitative material flow factors associated with production planning and the resulting impacts on resource efficiency. This provides a more detailed understanding of the economic and resource impacts of different production plans, enabling greater flexibility and the ability to make better informed decisions. Finally a case study is presented, highlighting the application of the tool and its potential benefits

Measuring implementation strength: lessons from the evaluation of public health strategies in low- and middle-income settings.

Evaluation of strategies to ensure evidence-based, low-cost interventions reach those in need is critical. One approach is to measure the strength, or intensity, with which packages of interventions are delivered, in order to explore the association between implementation strength and public health gains. A recent systematic review suggested methodological guidance was needed. We described the approaches used in three examples of measures of implementation strength in evaluation. These addressed important public health topics with a substantial disease burden in low-and middle-income countries; they involved large-scale implementation; and featured evaluation designs without comparison areas. Strengths and weaknesses of the approaches were discussed. In the evaluation of Ethiopia's Health Extension Programme, implementation strength scoring for each kebele (ward) was based on aggregated data from interviews with mothers of children aged 12-23 months, reflecting their reports of contact with four elements of the programme. An evaluation of the Avahan HIV prevention programme in India used the cumulative amount of Avahan funding per HIV-infected person spent each year in each district. In these cases, a single measure was developed and the association with hypothesised programme outcomes presented. In the evaluation of the Affordable Medicines Facility-malaria, several implementation strength measures were developed based on the duration of activity of the programme and the level of implementation of supporting interventions. Measuring the strength of programme implementation and assessing its association with outcomes is a promising approach to strengthen pragmatic impact evaluation. Five key aspects of developing an implementation strength measure are to: (a) develop a logic model; (b) identify aspects of implementation to be assessed; (c) design and implement data collection from a range of data sources; (d) decide whether and how to combine data into a single measure; and, (e) plan whether and how to use the measure(s) in outcome analysis

Rainfall Stimulation of Primary Production in Western Atlantic Ocean Waters: Roles of Different Nitrogen Sources and Co-Limiting Nutrients

Using shipboard bioassays, we examined the roles rainfall, individual and combined nutrients play in accelerating primary production in coastal, Gulf Stream and pelagic (Sargasso Sea) locations in the North Atlantic Ocean off North Carolina, USA, from 1993 to 1995. Photosynthetic CO2 fixation and net chlorophyll a (chl a) production were measured In replicated bioassays to assess individual and combined impacts of different constituents of atmospheric deposition, including natural rainfall, a synthetic rain mix, dissolved inorganic nitrogen (DIN; NH4+ ,NO3-), dissolved organic nitrogen (DON; urea),phosphorus (PO43-) and iron (as EDTA-chelated and unchelated FeCl3).Natural rainfall and DIN additions most often stimulated CO2 fixation and chl a production, but frequencies and magnitudes of biostimulation, relative to controls, varied between these indicators. Spatial differences in the types and magnitudes of stimulation were also observed. When added in equimolar amounts, NH4+ was, at times, more stimulatory than NO3-. The NO3- stimulation was significantly enhanced by Fe-EDTA. Urea was marginally stimulatory at the coastal location. PO43- was never stimulatory. Fe-EDTA and EDTA by themselves stimulated production only at the offshore locations, suggesting increased Fe limitation with increasing distance from land. Synthetic rain, which contained both sources of DIN, but not Fe, generally proved less stimulatory per unit N than natural rainfall. Results indicate a broad sensitivity of these waters to N additions, which in the case of NO3- are enhanced by Fe-EDTA. At all locations, the high level of stimulation of primary production attributable to natural rain may be due to the supply of both DIN and CO-limiting nutrients (e.g. Fe), contributing to the eutrophication potential of waters downwind of urban, industrial and agricultural emissions

ABCC5, ERCC2, XPA and XRCC1 transcript abundance levels correlate with cisplatin chemoresistance in non-small cell lung cancer cell lines

BACKGROUND: Although 40–50% of non-small cell lung cancer (NSCLC) tumors respond to cisplatin chemotherapy, there currently is no way to prospectively identify potential responders. The purpose of this study was to determine whether transcript abundance (TA) levels of twelve selected DNA repair or multi-drug resistance genes (LIG1, ERCC2, ERCC3, DDIT3, ABCC1, ABCC4, ABCC5, ABCC10, GTF2H2, XPA, XPC and XRCC1) were associated with cisplatin chemoresistance and could therefore contribute to the development of a predictive marker. Standardized RT (StaRT)-PCR, was employed to assess these genes in a set of NSCLC cell lines with a previously published range of sensitivity to cisplatin. Data were obtained in the form of target gene molecules relative to 10(6 )β-actin (ACTB) molecules. To cancel the effect of ACTB variation among the different cell lines individual gene expression values were incorporated into ratios of one gene to another. Each two-gene ratio was compared as a single variable to chemoresistance for each of eight NSCLC cell lines using multiple regression. In an effort to validate these results, six additional lines then were evaluated. RESULTS: Following validation, single variable models best correlated with chemoresistance (p < 0.001), were ERCC2/XPC, ABCC5/GTF2H2, ERCC2/GTF2H2, XPA/XPC and XRCC1/XPC. All single variable models were examined hierarchically to achieve two variable models. The two variable model with the highest correlation was (ABCC5/GTF2H2, ERCC2/GTF2H2) with an R(2 )value of 0.96 (p < 0.001). CONCLUSION: These results provide markers suitable for assessment of small fine needle aspirate biopsies in an effort to prospectively identify cisplatin resistant tumors

Optimized assembly design for resource efficient production in a multiproduct manufacturing system

Resource efficiency is one of the greatest challenges for sustainable manufacturing. Material flow in manufacturing systems directly influences resource efficiency, financial cost and environmental impact. A framework for material flow assessment in manufacturing systems (MFAM) was applied to a complex multi-product manufacturing case study. This supported the identification of options to alter material flow through changes to the product assembly design, to improve overall resource efficiency through eliminating resource intensive changeovers. Alternative assembly designs were examined using a combination of intelligent computation techniques: k-means clustering, genetic algorithm and ant colony algorithm. This provided recommendations balancing improvement potential with extent of process modification impact