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Extremely rare circulating tumor cell (CTC) clusters are both increasingly appreciated as highly metastatic precursors and virtually unexplored. Technologies are primarily designed to detect single CTCs and often fail to account for the fragility of clusters or to leverage cluster-specific markers for higher sensitivity. Meanwhile, the few technologies targeting CTC clusters lack scalability. Here, we introduce the Cluster-Wells, which combines the speed and practicality of membrane filtration with the sensitive and deterministic screening afforded by microfluidic chips. The >100,000 microwells in the Cluster-Wells physically arrest CTC clusters in unprocessed whole blood, gently isolating virtually all clusters at a throughput of >25 mL/h, and allow viable clusters to be retrieved from the device. Using the Cluster-Wells, we isolated CTC clusters ranging from 2 to 100+ cells from prostate and ovarian cancer patients and analyzed a subset using RNA sequencing. Routine isolation of CTC clusters will democratize research on their utility in managing cancer.

Recent evidence has implicated microRNAs (miRNAs) as potentially significant players in the acquisition of cancer-drug resistance in pancreatic and other cancers. To evaluate the potential contribution of miRNAs in acquired resistance to cisplatin in pancreatic cancer, we compared levels of more than 2000 human miRNAs in a cisplatin-resistant cell line (BxPC3-R) derived from parental (BxPC3) cells by step-wise exposure to increasing concentrations of the drug over more than 20 passages. The acquired drug resistance was accompanied by significant changes in the expression of 57 miRNAs, of which 23 were downregulated and 34 were upregulated. Employing a hidden Markov model (HMM) algorithm, we identified downregulation of miR-374b as likely being directly involved in acquisition of the drug-resistant phenotype. Consistent with this prediction, ectopic overexpression of miR-374b in the resistant BxPC3-R cells restored cisplatin sensitivity to levels approaching those displayed by the BxPC3 parental cells. The results are consistent with a growing body of evidence implicating miRNAs in acquired cancer-drug resistance and with the potential therapeutic value of these small regulatory RNAs in blocking and/or reversing the process.

Background Gene-fusion or chimeric transcripts have been implicated in the onset and progression of a variety of cancers. Massively parallel RNA sequencing (RNA-Seq) of the cellular transcriptome is a promising approach for the identification of chimeric transcripts of potential functional significance. We report here the development and use of an integrated computational pipeline for the de novo assembly and characterization of chimeric transcripts in 55 primary breast cancer and normal tissue samples. Methods An integrated computational pipeline was employed to screen the transcriptome of breast cancer and control tissues for high-quality RNA-sequencing reads. Reads were de novo assembled into contigs followed by reference genome mapping. Chimeric transcripts were detected, filtered and characterized using our R-SAP algorithm. The relative abundance of reads was used to estimate levels of gene expression. Results De novo assembly allowed for the accurate detection of 1959 chimeric transcripts to nucleotide level resolution and facilitated detailed molecular characterization and quantitative analysis. A number of the chimeric transcripts are of potential functional significance including 79 novel fusion-protein transcripts and many chimeric transcripts with alterations in their un-translated leader regions. A number of chimeric transcripts in the cancer samples mapped to genomic regions devoid of any known genes. Several ‘pro-neoplastic’ fusions comprised of genes previously implicated in cancer are expressed at low levels in normal tissues but at high levels in cancer tissues. Conclusions Collectively, our results underscore the utility of deep sequencing technologies and improved bioinformatics workflows to uncover novel and potentially significant chimeric transcripts in cancer and normal somatic tissues. Electronic supplementary material The online version of this article (doi:10.1186/s12920-017-0289-7) contains supplementary material, which is available to authorized users.

High performance mass spectrometry was employed to interrogate the serum metabolome of early-stage ovarian cancer (OC) patients and age-matched control women. The resulting spectral features were used to establish a linear support vector machine (SVM) model of sixteen diagnostic metabolites that are able to identify early-stage OC with 100% accuracy in our patient cohort. The results provide evidence for the importance of lipid and fatty acid metabolism in OC and serve as the foundation of a clinically significant diagnostic test.

The causes of the housing bubble are investigated using Granger causality analysis and VAR modeling methods. The study employs the S&P/Case-Shiller aggregate 10 city monthly housing price index, available in the period 1987–2010/8, the 20 city monthly housing price index for 2000–2010/8, and the federal funds rate data for the period 1987–2010/8. The findings are consistent with the view that the interest rate policy of the Federal Reserve in the period 2001–2004 that pushed down the federal funds rate and kept it artificially low was a cause of the housing price bubble.

This paper is an empirical study of the capitalization rates for 132 office building sales in downtown Chicago from 1996 to 2007. The capitalization rate is hypothesized to be a function of the classic capital asset pricing model variable and variables intended to capture the expectation that the real market value of the building will change. The results show that the capitalization rate for office buildings incorporates a very low value for “beta.” A lower capitalization rate was associated with a smaller risk-free rate, a lower borrowing rate, class A buildings, newer buildings, buildings that had been renovated, a reduction in the vacancy rate in the downtown Chicago office market, and an increase in employment in the financial sector of the metropolitan area.

Background Genomic rearrangements or structural variants (SVs) are one of the most common classes of mutations in cancer. Methods An integrated DNA sequencing and transcriptional profiling (RNA sequence and microarray gene expression data) analysis was performed on six ovarian cancer patient samples. Matched sets of control (whole blood) samples from these same patients were used to distinguish cancer SVs of germline origin from those arising somatically in the cancer cell lineage. Results We detected 10,034 ovarian cancer SVs (5518 germline derived; 4516 somatically derived) at base-pair level resolution. Only 11 % of these variants were shown to have the potential to form gene fusions and, of these, less than 20 % were detected at the transcriptional level. Conclusions Collectively our results are consistent with the view that gene fusions and other SVs can be significant factors in the onset and progression of ovarian cancer. The results further indicate that it may not only be the occurrence of these variants in cancer but their regulation that contributes to their biological and clinical significance. Electronic supplementary material The online version of this article (doi:10.1186/s12920-015-0118-9) contains supplementary material, which is available to authorized users.

Human endogenous retroviruses (HERVs) represent vestiges of ancient infections that resulted in stable integration of the viral genome. These insertional elements of viral origin are in fact molecular fossils and, as such, a source of evolutionary information. A family of HERV insertions designated HERV-K includes members that are still polymorphic for the original insertional event. The goal of this report is to describe a novel genetic marker system based on polymorphic retroviral insertions (PRVIs) and to assess its potential usefulness in human population genetic analyses. The allelic frequencies of four insertionally polymorphic HERV-K loci were analyzed in nine geographically targeted, worldwide populations. A polymerase chain reaction assay was employed to examine the frequencies of the provirus and/or solo long terminal repeat insertions at these four loci. Several statistical and phylogenetic analyses were performed based on the frequency data. The phylogenetic relationships observed among the nine populations based on the four retroviral HERV-K loci are consistent not only with prior genetic analyses with other traditional marker systems but also with reported historical and biogeographical data. These polymorphic endogenous retroviral sequences display features that make them excellent tools for forensic and population genetic studies.

The fluorine stability of two parylenes, aliphatic-fluorinated AF-4 (α, α, α′, α′ poly(p-tetrafluoroxylylene) and aromatic-fluorinated VT-4 (2, 3, 5, 6 poly(p-tetrafluoroxylylene), were investigated underneath Al, Al2O3, and TaNX overlayers with and without exposure to oxygen reactive-ion etching (RIE). No fluorine diffusion was observed for Al films deposited onto the as-received parylenes. However, after oxygen RIE, x-ray photoelectron spectroscopy (XPS) depth profiling detected fluorine diffusion throughout Al and to a lesser extent Al2O3 but in contrast to Ta2.67N. Metal-fluoride bonding was evident at the metal/parylene interface for all the overlayers after the parylene was exposed to oxygen RIE and annealed.

This article is a theoretical examination of optimal financial leverage for real estate investment in the presence of uncertainty. The main result shows that uncertainty creates the possibility that a borrower will default on a real estate loan and that this possibility is the underlying factor in optimal leverage calculations for both borrower and lender.

We report the results of an analysis of natu- rally occurring cis-regulatory variation within and be- tween two families of the copia Drosophila long termi- nal repeat (LTR) retrotransposon. The copia 58 LTR and adjacent untranslated leader region (ULR) consists of a number of well-characterized sequence motifs which play a role in regulating expression of the element. In order to understand the evolutionary forces which may be responsible for generating and maintaining copia regulatory sequence variation, we have quantified levels of naturally occurring copia LTR-ULR nucleotide varia- tion and subjected the data to a series of tests of neutral- ity. Our analysis indicates that the copia LTR-ULR has been subject to negative purifying selection within fami- lies and positive adaptive selection between families. We discuss these findings with respect to the regulatory evo- lution of retrotransposons and the phenomenon of inter- element selection.

This article examines whether the pattern of urban land use should have been regulated by local government in the 1920s, the decade in which many cities adopted their first zoning ordinances. The study is based on the assumption that land values are influenced by the mix of land use on the block. Conditions for land-value maximization are derived, and the circumstances under which land-use zoning can increase land values are discussed. Empirical land-value and land-use functions are estimated for Chicago in 1921, two years before the first Chicago zoning ordinance was adopted. The empirical results for land values imply that the land-use zoning system adopted in 1923 could not have brought about a general increase in land values. The empirical results for land use document the regularities in the use of land prior to the introduction of zoning.

Transposable elements are ubiquitous in all organisms and represent a dynamic component of their genomes, causing mutations and thereby genetic variation. Because of their independent and expansive replication strategy, these elements are called selfish and were thought to have no impact on the adaptive evolution of their host organisms. Although most TE-induced mutations seem to exert only negative effects on the fitness of their carrier, recent evidence indicates that in the course of evolution at least some TE-mediated changes have become established features of the host genome. For example, the insertion of TEs may provide novel cis-regulatory regions to preexisting host genes or TE-derived trans-acting factors may undergo a molecular transition into novel host genes through a process described as molecular domestication. The stationary P element related gene clusters of D. guanche, D. madeirensis and D. subobscura provide an excellent model system to study the evolutionary impact of TEs on genome evolution. Each cluster unit consists of a cis-regulating section composed of different insertion sequences followed by the first three exons of a P element that are coding for a 66 kDa ‘repressor-like’ protein.

Since LTR retrotransposons and retroviruses are especially prone to regional duplications and recombination events, these viral-like systems may be especially conducive to the evolution of closely spaced combinatorial regulatory motifs. Using the Drosophila copia LTR retrotransposon as a model, we show that a regulatory region contained within the element's untranslated leader region (ULR) consists of multiple copies of an 8 bp motif (TTGTGAAA) with similarity to the core sequence of the SV40 enhancer. Naturally occurring variation in the number of these motifs is correlated with the enhancer strength of the ULR. Our results indicate that inter-element selection may favor the evolution of more active enhancers within permissive genetic backgrounds. We propose that LTR retroelements and perhaps other retrotransposons constitute drive mechanisms for the evolution of eukaryotic enhancers which can be subsequently distributed throughout host genomes to play a role in regulatory evolution.

This article examines urban highway congestion pricing in the instance in which it is not possible to levy a congestion toll on a major portion of the urban road system. This case is pertinent because of technical and/or political constraints. The article uses economic theory and numerical examples to show that the optimum second-best toll can vary appreciably from the optimal tolls in a regime in which efficient tolls can be imposed on all routes.

Background Ovarian cancer stem cells are characterized by self-renewal capacity, ability to differentiate into distinct lineages, as well as higher invasiveness and resistance to many anticancer agents. Since they may be responsible for the recurrence of ovarian cancer after initial response to chemotherapy, development of new therapies targeting this special cellular subpopulation embedded within bulk ovarian cancers is warranted. Methods A high-throughput screening (HTS) campaign was performed with 825 compounds from the Mechanistic Set chemical library [Developmental Therapeutics Program (DTP)/National Cancer Institute (NCI)] against ovarian cancer stem-like cells (CSC) using a resazurin-based cell cytotoxicity assay. Identified sets of active compounds were projected onto self-organizing maps to identify their putative cellular response groups. Results From 793 screening compounds with evaluable data, 158 were found to have significant inhibitory effects on ovarian CSC. Computational analysis indicates that the majority of these compounds are associated with mitotic cellular responses. Conclusions Our HTS has uncovered a number of candidate compounds that may, after further testing, prove effective in targeting both ovarian CSC and their more differentiated progeny.

BackgroundAccumulating evidence suggests that somatic stem cells undergo mutagenic transformation into cancer initiating cells. The serous subtype of ovarian adenocarcinoma in humans has been hypothesized to arise from at least two possible classes of progenitor cells: the ovarian surface epithelia (OSE) and/or an as yet undefined class of progenitor cells residing in the distal end of the fallopian tube.MethodsComparative gene expression profiling analyses were carried out on OSE removed from the surface of normal human ovaries and ovarian cancer epithelial cells (CEPI) isolated by laser capture micro-dissection (LCM) from human serous papillary ovarian adenocarcinomas. The results of the gene expression analyses were randomly confirmed in paraffin embedded tissues from ovarian adenocarcinoma of serous subtype and non-neoplastic ovarian tissues using immunohistochemistry. Differentially expressed genes were analyzed using gene ontology, molecular pathway, and gene set enrichment analysis algorithms.ResultsConsistent with multipotent capacity, genes in pathways previously associated with adult stem cell maintenance are highly expressed in ovarian surface epithelia and are not expressed or expressed at very low levels in serous ovarian adenocarcinoma. Among the over 2000 genes that are significantly differentially expressed, a number of pathways and novel pathway interactions are identified that may contribute to ovarian adenocarcinoma development.ConclusionsOur results are consistent with the hypothesis that human ovarian surface epithelia are multipotent and capable of serving as the origin of ovarian adenocarcinoma. While our findings do not rule out the possibility that ovarian cancers may also arise from other sources, they areinconsistentwith claims that ovarian surface epithelia cannot serve as the origin of ovarian cancer initiating cells.

BackgroundThe majority of ovarian cancer biomarker discovery efforts focus on the identification of proteins that can improve the predictive power of presently available diagnostic tests. We here show that metabolomics, the study of metabolic changes in biological systems, can also provide characteristic small molecule fingerprints related to this disease.ResultsIn this work, new approaches to automatic classification of metabolomic data produced from sera of ovarian cancer patients and benign controls are investigated. The performance of support vector machines (SVM) for the classification of liquid chromatography/time-of-flight mass spectrometry (LC/TOF MS) metabolomic data focusing on recognizing combinations or "panels" of potential metabolic diagnostic biomarkers was evaluated. Utilizing LC/TOF MS, sera from 37 ovarian cancer patients and 35 benign controls were studied. Optimum panels of spectral features observed in positive or/and negative ion mode electrospray (ESI) MS with the ability to distinguish between control and ovarian cancer samples were selected using state-of-the-art feature selection methods such as recursive feature elimination and L1-norm SVM.ConclusionThree evaluation processes (leave-one-out-cross-validation, 12-fold-cross-validation, 52-20-split-validation) were used to examine the SVM models based on the selected panels in terms of their ability for differentiating control vs. disease serum samples. The statistical significance for these feature selection results were comprehensively investigated. Classification of the serum sample test set was over 90% accurate indicating promise that the above approach may lead to the development of an accurate and reliable metabolomic-based approach for detecting ovarian cancer.

The parylene family of polymeric insulating materials is of interest in electronics because of its low dielectric constant and good sticking properties. It is vapor depositable at low temperatures. Copper is a good conductor and a suitable metal for an interconnection system. Consequently, the Cu/parylene system is a promising combination for multilayer interconnections and thin film packaging. To investigate one aspect of the feasibility of using these two materials for an interconnection scheme, the diffusion of copper into parylene at elevated temperatures has been investigated using the Rutherford back scattering technique. The chief findings of this paper are: 1. Detectable (RBS) Cu diffusion starts at ≥573 K. Higher temperature causes more diffusion as expected. 2. The α → Β-phase change is not the main source of the diffusion. 3. The copper deposited on the α-parylene does not diffuse even after extended anneals of six hours at 573 K. Thus, the copper-α-parylene interconnect system can have thermal budget allowance of more than six hour 4. The starting phase of the PA-n affects its diffusion resistant properties. Furthermore a thermal processing window showing a safe half hour of vacuum annealing at soldering temperatures has been demonstrated.

Cu films with a thickness around 3.5 μm have been deposited on rough Al2O3 ceramic substrates by the partially ionized beam deposition technique. While the ion bombardment parameters are similar for all depositions, the substrate temperature during deposition is varied from 50 °C to 300 °C. Physical structure of the films is studied by SEM in cross-sectional and surface geometries. X-ray diffraction 2θ scan is performed to obtain information on the microstructure of the films, such as (111) fiber texture and average crystallite size. Resistivity of the films is also measured. It has been found that the physical structure of the films varies from a typical columnar structure at 50 °C to a completely noncolumnar structure at 300 °C. The XRD results show that the films are polycrystalline and have different degrees of 〈111〉 preferred orientation, depending on the substrate temperature. The average crystallite size increases with the increase of substrate temperature. No correlation between the physical structure and microstructure of the films is observed. The resistivity of the films was also seen to change as a function of the substrate temperature. This can be explained by quantitative models in which grain and columnar boundaries in the films are responsible for the decrease in electric conductivity of the films.

BackgroundA large percentage of patients with recurrent ovarian cancer develop resistance to the taxane class of chemotherapeutics. While mechanisms of resistance are being discovered, novel treatment options and a better understanding of disease resistance are sorely needed. The mitotic kinase Aurora-A directly regulates cellular processes targeted by the taxanes and is overexpressed in several malignancies, including ovarian cancer. Recent data has shown that overexpression of Aurora-A can confer resistance to the taxane paclitaxel.MethodsWe used expression profiling of ovarian tumor samples to determine the most significantly overexpressed genes. In this study we sought to determine if chemical inhibition of the Aurora kinase family using VE-465 could synergize with paclitaxel to induce apoptosis in paclitaxel-resistant and sensitive ovarian cancer cells.ResultsAurora-A kinase and TPX2, an activator of Aurora-A, are two of the most significantly overexpressed genes in ovarian carcinomas. We show that inhibition of the Aurora kinases prevents phosphorylation of a mitotic marker and demonstrate a dose-dependent increase of apoptosis in treated ovarian cancer cells. We demonstrate at low doses that are specific to Aurora-A, VE-465 synergizes with paclitaxel to induce 4.5-fold greater apoptosis than paclitaxel alone in 1A9 cells. Higher doses are needed to induce apoptosis in paclitaxel-resistant PTX10 cells.ConclusionOur results show that VE-465 is a potent killer of taxane resistant ovarian cancer cells and can synergize with paclitaxel at low doses. These data suggest patients whose tumors exhibit high Aurora-A expression may benefit from a combination therapy of taxanes and Aurora-A inhibition.

Background Previous findings have suggested that epigenetic-mediated HLA-G expression in tumor cells may be associated with resistance to host immunosurveillance. To explore the potential role of DNA methylation on HLA-G expression in ovarian cancer, we correlated differences in HLA-G expression with methylation changes within the HLA-G regulatory region in an ovarian cancer cell line treated with 5-aza-deoxycytidine (5-aza-dC) and in malignant and benign ovarian tumor samples and ovarian surface epithelial cells (OSE) isolated from patients with normal ovaries. Results A region containing an intact hypoxia response element (HRE) remained completely methylated in the cell line after treatment with 5-aza-dC and was completely methylated in all of the ovarian tumor (malignant and benign) samples examined, but only variably methylated in normal OSE samples. HLA-G expression was significantly increased in the 5-aza-dC treated cell line but no significant difference was detected between the tumor and OSE samples examined. Conclusion Since HRE is the binding site of a known repressor of HLA-G expression (HIF-1), we hypothesize that methylation of the region surrounding the HRE may help maintain the potential for expression of HLA-G in ovarian tumors. The fact that no correlation exists between methylation and HLA-G gene expression between ovarian tumor samples and OSE, suggests that changes in methylation may be necessary but not sufficient for HLA-G expression in ovarian cancer.

A key process in our approach to monolithic three-dimensional (3D) integration is the bonding of 200-mm wafers using dielectric polymer thin films as bonding glues. After discussing the desired properties of polymer thin films, we describe how bonding protocols are evaluated using silicon and glass wafers. After bonding, the fraction of bonded area was inspected optically and a razor blade method was used to indicate bonding strength. Thermal stability and bonding integrity were evaluated using thermal cycling and backside grinding and polishing. To date, we have studied benzocyclobutene (BCB), Flare™, and methylsilsesquioxane (MSSQ) and Parylene-N as bonding glues. Wafer pairs bonded using BCB showed a larger fraction of bonded area, and those using Flare indicated higher thermal stability. Both BCB and Flare glues provided good bonding integrity after backside grinding tests. Changes in the chemical structures of BCB and Flare glue during bonding were analyzed using FTIR in order to understand the bonding mechanism and to improve the bonding process.

Low dielectric constant insulators offer the potential of improved interconnection delay and conductor packing density in advanced ICs, both with current metallization schemes and with future technologies such as copper. While polymer materials are very promising in such applications, significant issues must be addressed before oxide-based materials are replaced in mainstream applications. This invited paper reviews the directions of our program, which has emphasized the use of vapor deposited polymers compatible with uniform deposition over large diameter wafers and copper metallization. Therefore, emphasis is placed on polymer material characteristics compatible with inlaid metal (ie. Dual Damascene) patterning.

The identification and characterization of 42 families of chimpanzee endogenous retroviruses and a comparison to their human orthologs is described., Background Retrotransposons, the most abundant and widespread class of eukaryotic transposable elements, are believed to play a significant role in mutation and disease and to have contributed significantly to the evolution of genome structure and function. The recent sequencing of the chimpanzee genome is providing an unprecedented opportunity to study the functional significance of these elements in two closely related primate species and to better evaluate their role in primate evolution. Results We report here that the chimpanzee genome contains at least 42 separate families of endogenous retroviruses, nine of which were not previously identified. All but two (CERV 1/PTERV1 and CERV 2) of the 42 families of chimpanzee endogenous retroviruses were found to have orthologs in humans. Molecular analysis (PCR and Southern hybridization) of CERV 2 elements demonstrates that this family is present in chimpanzee, bonobo, gorilla and old-world monkeys but absent in human, orangutan and new-world monkeys. A survey of endogenous retroviral positional variation between chimpanzees and humans determined that approximately 7% of all chimpanzee-human INDEL variation is associated with endogenous retroviral sequences. Conclusion Nine families of chimpanzee endogenous retroviruses have been transpositionally active since chimpanzees and humans diverged from a common ancestor. Seven of these transpositionally active families have orthologs in humans, one of which has also been transpositionally active in humans since the human-chimpanzee divergence about six million years ago. Comparative analyses of orthologous regions of the human and chimpanzee genomes have revealed that a significant portion of INDEL variation between chimpanzees and humans is attributable to endogenous retroviruses and may be of evolutionary significance.

Epithelial ovarian tumours exhibit a range of malignant potential, presenting distinct clinical phenotypes. Improved knowledge of gene expression changes and functional pathways associated with these clinical phenotypes may lead to new treatment targets, markers for early detection and a better understanding of disease progression. Gene expression profiling (Affymetrix, U95Av2) was carried out on 18 ovarian tumours including benign adenomas, borderline adenocarcinomas of low malignant potential and malignant adenocarcinomas. Clustering the expression profiles of samples from patients not treated with chemotherapy prior to surgery effectively classified 92% of samples into their proper histopathological group. Some cancer samples from patients treated with chemotherapy prior to surgery clustered with the benign adenomas. Chemotherapy patients whose tumours exhibited benign-like expression patterns remained disease free for the duration of this study as indicated by continued normal serum CA-125 levels. Statistical analysis identified 163 differentially expressed genes: 61 genes under-expressed in cancer and 102 genes over-expressed in cancer. Profiling the functional categories of co-ordinately expressed genes within this list revealed significant correlation between increased malignant potential and loss of both IGF binding proteins and cell adhesion molecules. Interestingly, in several instances co-ordinately expressed genes sharing biological function also shared chromosomal location. Our findings indicate that gene expression profiling can reliably distinguish between benign and malignant ovarian tumours. Expression profiles of samples from patients pre-treated with chemotherapy may be useful in predicting disease free survival and the likelihood of recurrence. Loss of expression of IGF binding proteins as well as specific cell adhesion molecules may be a significant mechanism of disease progression in ovarian cancer. Expression levels in borderline tumours were intermediate between benign adenomas and malignant adenocarcinomas for a significant portion of the differentially expressed genes, suggesting that borderline tumours are a transitional state between benign and malignant tumours. Finally, genes displaying coordinated changes in gene expression were often genetically linked, suggesting that changes in expression for these genes are the consequence of regional duplications, deletions or epigenetic events.

Long terminal repeat (LTR) retrotransposons make up a large fraction of the typical mammalian genome. They comprise about 8% of the human genome and approximately 10% of the mouse genome. On account of their abundance, LTR retrotransposons are believed to hold major significance for genome structure and function. Recent advances in genome sequencing of a variety of model organisms has provided an unprecedented opportunity to evaluate better the diversity of LTR retrotransposons resident in eukaryotic genomes. Using a new data-mining program, LTR_STRUC, in conjunction with conventional techniques, we have mined the GenBank mouse (Mus musculus) database and the more complete Ensembl mouse dataset for LTR retrotransposons. We report here that the M. musculus genome contains at least 21 separate families of LTR retrotransposons; 13 of these families are described here for the first time. All families of mouse LTR retrotransposons are members of the gypsy-like superfamily of retroviral-like elements. Several different families of unrelated non-autonomous elements were identified, suggesting that the evolution of non-autonomy may be a common event. High sequence similarity between several LTR retrotransposons identified in this study and those found in distantly-related species suggests that horizontal transfer has been a significant factor in the evolution of mouse LTR retrotransposons.

Wide-spread hypomethylation of CpG dinucleotides is characteristic of many cancers. Retrotransposons have been identified as potential targets of hypomethylation during cellular transformation. We report the results of an preliminary examination of the methylation status of CpG dinucleotides associated with the L1 and HERV-W retrotransposons in benign and malignant human ovarian tumors. We find a reduction in the methylation of CpG dinucleotides within the promoter regions of these retroelements in malignant relative to non-malignant ovarian tissues. Consistent with these results, we find that relative L1 and HERV-W expression levels are elevated in representative samples of malignant vs. non-malignant ovarian tissues.

Background: Long terminal repeat (LTR) retrotransposons constitute a major fraction of the genomes of higher plants. For example, retrotransposons comprise more than 50% of the maize genome and more than 90% of the wheat genome. LTR retrotransposons are believed to have contributed significantly to the evolution of genome structure and function. The genome sequencing of selected experimental and agriculturally important species is providing an unprecedented opportunity to view the patterns of variation existing among the entire complement of retrotransposons in complete genomes. Results: Using a new data-mining program, LTR_STRUC, (LTR retrotransposon structure program), we have mined the GenBank rice (Oryza sativa) database as well as the more extensive (259 Mb) Monsanto rice dataset for LTR retrotransposons. Almost two-thirds (37) of the 59 families identified consist of copia-like elements, but gypsy-like elements outnumber copia-like elements by a ratio of approximately 2:1. At least 17% of the rice genome consists of LTR retrotransposons. In addition to the ubiquitous gypsy- and copia-like classes of LTR retrotransposons, the rice genome contains at least two novel families of unusually small, noncoding (non-autonomous) LTR retrotransposons. Conclusions: Each of the major clades of rice LTR retrotransposons is more closely related to elements present in other species than to the other clades of rice elements, suggesting that horizontal transfer may have occurred over the evolutionary history of rice LTR retrotransposons. Like LTR retrotransposons in other species with relatively small genomes, many rice LTR retrotransposons are relatively young, indicating a high rate of turnover.

An intraspecific comparison of α-glycerophosphate (α-GPDH: E.C.1.1.1.8) and alcohol dehydrogenase (ADH: E.C.1.1.1.1) enzyme activity levels was carried out in Drosophila melanogaster. The results indicate that (1) α-GPDH is a relatively conservative and ADH a relatively variable enzyme system with regard to structurally determined activity variation but that (2) the conservative nature of α-GPDH activity variation does not extend to the intra-genotypic level. The results are consistent with the view that different kinds of selective pressures are being exerted on the enzyme's structural and modifier gene loci.

Previous studies carried out in mammalian systems indicated that an organism's NAD+/NADH balance is carefully regulated but can be destabilized by dietary stresses. Since Drosophila alcohol dehydrogenase (ADH) uses NAD+ to remove a hydrogen from ethanol in the first step of alcohol catabolism, it is possible that under alcohol stress conditions the in vivo NAD+ levels in Drosophila may decrease. In this study genetically homozygous flies were stressed with maximally sublethal concentrations of ethanol (10%) for periods of up to 24 hr. The results indicate that NAD+ levels do in fact drop by at least 20% in response to ethanol stress. Evidence is presented that suggests that this decrease is the direct result of ADH-mediated catabolism.

In this paper the standard theory of the derived demand for inputs for the firm has been used to examine the effect on employment of a subsidy to the capital input via an industrial revenue bond. While the effect theoretically is ambiguous in sign, an empirical examination of the industrial revenue bond program in Chicago suggests that, ceteris paribus, employment does increase in firms selected for the program. The estimates of the arc crosselasticity of demand for labor for the groups of firms that participated in the Chicago program range from −.27 to −1.07. Systematic variations in the cross elasticity of demand for labor are found.

Housing segregation directly affects the employment opportunities for blacks by reducing access to jobs. In addition, an indirect effect exists if, holding other factors constant, employers tend to hire workers who reflect the racial composition of the surrounding area. This tendency implies that a change in the distribution of black residences (with an offsetting change in the distribution in white residences) will have an impact on the spatial distribution of employment opportunities for blacks who donot move. Empirical evidence is presented for both the direct and indirect effects for the Chicago SMSA in 1970 using the Journey to Work data from the Census.

Three alcohol dehydrogenase genotypes, homozygous for either the electrophoretically fast, slow, or null allele at the Adh locus in D. melanogaster, were tested for relative larval alcohol preference behavior (APB) over a range of ethanol concentrations. Differences in behavior between genotypes were not significant at concentrations below 10%. At concentrations greater than 10%, avoidance behavior was negatively correlated with the relative ADH activity levels of the genotypes tested. A model based on the differential buildup of toxic acetaldehyde is proposed to explain the avoidance response.

Polyimides have been considered as interlayer dielectrics for wafer scale integration (WSI) and wafer scale hybrid packaging (WSHP). However, high temperature curing steps for polyimide lead to large stresses in polyimide films. This is due to differing thermal expansion coefficients of the metal conductor, insulator and substrate materials causing yield and reliability problems. Polyimides also require the use of solvents, and tend to outgas during subsequent processing. They tend to absorb moisture with resulting degradation of dielectric constants. Also, the spin on method used to apply and planarize polyimide layers exhibits nonuniformity of thickness on large wafers. In this paper we examine parylene (Poly-p-xylylene) and some of its derivatives as possible interlayer dielectrics due to some of their attractive features. Parylene has a low dielectric constant. It can be vapor deposited at low temperatures and in vacuum. It is also highly resistant to corrosion and is a clear, transparent material with possible use for optical interconnections. This paper studies the reactive ion etching properties for polyimides and parylenes in an oxygen containing plasma under identical conditions. The etching rates of the parylenes and polyimides have been compared. The surface properties of these polymers are examined. Further, the film growth properties of aluminum deposited on the etched surfaces using the ionized cluster beam are investigated.

The gene products of the two major alleles of alcohol dehydrogenase (ADH-F and ADH-S) have been subjected to kinetic and biochemical analyses over a range of temperatures. Although temperature was found to have a significant effect on both kinetic and biochemical properties of Drosophila ADH, no significant differential effect was observed between the major ADH allozymes. The results are discussed within the context of the selective maintenance of Adh polymorphism in natural populations.

Polymeric materials have traditionally enjoyed widespread use in the electronics industry. Recent advances in the identification and synthesis of polymers with unusual electrical and optical properties have opened new opportunities for technological applications. Some of these novel properties are summarized in this paper with an emphasis on how these properties may be usefully exploited in the area of multichip packaging.

Functionally significant biochemical properties of the naturally occurring electrophoretic variants at the Adh locus (ADHfast and ADHSlow) are correlated with the adult flies' ability to utilize and survive in an ethanol environment. The results are consistent with the idea that an environmentally dependent form of balancing selection is responsible, at least in part, for the maintenance of the polymorphism at this locus.