bluuebunny/crossref_metadata_2025 huggingface dataset:
Sequences responsible for transcription termination on a gene segment in Saccharomyces cerevisiae.
Authors: Henikoff S , Cohen E H
Published: September 2015

We have mapped a signal sequence for mRNA 3'-end formation in Saccharomyces cerevisiae by using a Drosophila melanogaster DNA segment that complements a yeast adenine-8 mutation. That the 3' end of the transcript in S. cerevisiae nearly coincides with that in D. melanogaster is consistent with the possibility that mRNA termini are similarly determined in both organisms. Deletion analysis reveals that the complete signal is no more than 21 base pairs long. Part of the signal is the sequence TTTTTATA, which is seen in the termination region of several yeast genes. TTTTTATA appears to be able to act autonomously as a partial termination signal. The efficiency of the complete signal is affected by substitution of sequences downstream from it. This modulation of the effect of a signal is consistent with termination in S. cerevisiae, resembling rho-dependent termination in bacteria.
Disruption of regulatory gene GAL80 in Saccharomyces cerevisiae: effects on carbon-controlled regulation of the galactose/melibiose pathway genes.
Authors: Torchia T E , Hamilton R W , Cano C L , Hopper J E
Published: September 2015

In Saccharomyces cerevisiae, the transcriptional expression of the galactose-melibiose catabolic pathway genes is under the control of at least three regulatory genes, GAL4, GAL80, and GAL3. We have isolated the GAL80 gene and have studied the effect of a null mutation on the carbon-controlled regulation of the MEL1 and GAL cluster genes. The null mutation was achieved in vivo by replacing the chromosomal wild-type GAL80 allele with an in vitro-created GAL80 deletion-disruption mutation. Enzyme activities and RNA levels for the GAL cluster and MEL1 genes were constitutively expressed in the null mutant strain grown on glycerol-lactate and were higher than in the isogenic wild-type yeast strain when compared after growth on galactose. Carbon catabolite repression of the GAL cluster and MEL1 genes, which occurs at the level of transcription, is retained in the null mutant. Deletion of the GAL80 gene in a gal4 cell does not restore GAL cluster and MEL1 gene expression. The data demonstrate that (i) the GAL80 protein is a purely negative regulator, (ii) the GAL80 protein does not mediate carbon catabolite repression, and (iii) the GAL4 protein is not simply an antagonizer of GAL80-mediated repression.
Membrane interactions of simian virus 40 large T-antigen: influence of protein sequences and fatty acid acylation.
Authors: Klockmann U , Staufenbiel M , Deppert W
Published: September 2015

To sort out possible influences of protein sequences and fatty acid acylation on the plasma membrane association of simian virus 40 large T-antigen, we have analyzed the membrane interactions of carboxy-terminal fragments of large T-antigen, encoded by the adenovirus type 2 (Ad2+)-simian virus 40 hybrid viruses Ad2+ND1 and Ad2+ND2. The 28,000 (28K)-molecular-weight protein of Ad2+ND1 as well as the 42K and 56K proteins of Ad2+ND2 associate preferentially with membranous structures and were found in association with the membrane system of the endoplasmic reticulum and with plasma membranes. Neither the endoplasmic reticulum membrane- nor the plasma membrane-associated 28K protein of Ad2+ND1 is fatty acid acylated. We, therefore, conclude that fatty acid acylation is not necessary for membrane association of this protein and suggest that an amino acid sequence in this protein is responsible for its membrane interaction. In contrast, the 42K and 56K proteins of Ad2+ND2 in plasma membrane fractions contain fatty acid. However, the interaction of these proteins with the plasma membrane differs from that of the 28K protein of Ad2+ND1: whereas the 28K protein of Ad2+ND1 interacts stably with Nonidet P-40-soluble constituents of the plasma membrane, the 42K and 56K proteins of Ad2+ND2 are tightly bound to the Nonidet P-40-insoluble plasma membrane lamina. Thus, an amino acid sequence in the amino-terminal region of the 28K protein confers membrane affinity to these proteins, whereas a region between the amino-terminal end of the 42K protein of Ad2+ND2 and the amino-terminal end of the 28K protein of Ad2+ND1 contains a reactive site for fatty acid acylation. This posttranslational modification correlates with the stable association of the 42K and 56K proteins with the plasma membrane lamina. We suggest that the same sequences also mediate the proper plasma membrane association of large T-antigen in simian virus 40-transformed cells.
Human colon carcinoma Ki-ras2 oncogene and its corresponding proto-oncogene.
Authors: McCoy M S , Bargmann C I , Weinberg R A
Published: September 2015

We isolated cDNA clones corresponding to the normal human Ki-ras2 gene and to the transforming allele of the Ki-ras2 gene present in the human colon carcinoma cell line SW480. These two cDNAs encode p21 proteins which differ only at the amino acid at position 12. The normal cDNA encodes a glycine at this position, and the transforming allele encodes a valine. Expression of these cDNAs indicates that this amino acid 12 alteration confers oncogenic activity on the mutated gene. Analysis of the relationship of the cDNAs and Kirsten sarcoma virus ras gene to a genomic clone allowed us to identify two alternative 3' coding exons for the Ki-ras2 gene, suggesting that the Ki-ras2 gene encodes two p21 proteins which differ at their carboxy termini. Our data also show that only one of the p21s is necessary to convert cells to a tumorigenic phenotype.
Mendelian and non-mendelian mutations affecting surface antigen expression in Paramecium tetraurelia.
Authors: Epstein L M , Forney J D
Published: September 2015

A screening procedure was devised for the isolation of X-ray-induced mutations affecting the expression of the A immobilization antigen (i-antigen) in Paramecium tetraurelia. Two of the mutations isolated by this procedure proved to be in modifier genes. The two genes are unlinked to each other and unlinked to the structural A i-antigen gene. These are the first modifier genes identified in a Paramecium sp. that affect surface antigen expression. Another mutation was found to be a deletion of sequences just downstream from the A i-antigen gene. In cells carrying this mutation, the A i-antigen gene lies in close proximity to the end of a macronuclear chromosome. The expression of the A i-antigen is not affected in these cells, demonstrating that downstream sequences are not important for the regulation and expression of the A i-antigen gene. A stable cell line was also recovered which shows non-Mendelian inheritance of a macronuclear deletion of the A i-antigen gene. This mutant does not contain the gene in its macronucleus, but contains a complete copy of the gene in its micronucleus. In the cytoplasm of wild-type animals, the micronuclear gene is included in the developing macronucleus; in the cytoplasm of the mutant, the incorporation of the A i-antigen gene into the macronucleus is inhibited. This is the first evidence that a mechanism is available in ciliates to control the expression of a gene by regulating its incorporation into developing macronuclei.
Discontinuous DNA replication of Drosophila melanogaster is primed by octaribonucleotide primer.
Authors: Kitani T , Yoda K , Okazaki T
Published: September 2015

To investigate the precise structure of eucaryotic primer RNA made in vivo, short DNA chains isolated from nuclei of Drosophila melanogaster embryos were analyzed. Post-labeling of 5' ends of short DNA chains with polynucleotide kinase and [gamma-32P]ATP revealed that 7% of the DNA fragments were covalently linked with mono- to octaribonucleotide primers at their 5' ends. Octaribonucleotides, the major component (ca. 30%), formed the cap structure in the reaction with vaccinia guanylyltransferase and [alpha-32P]GTP, indicating that they were the intact primer RNA with tri- (or di-) phosphate termini, and the shorter ribooligomers were degradation intermediates. The intact primers started with purine (A/G ratio, 4:1), and the starting few ribonucleotide residues were rich in A.
Isolation and characterization of revertants from four different classes of aryl hydrocarbon hydroxylase-deficient hepa-1 mutants.
Authors: Van Gurp J R , Hankinson O
Published: September 2015

Revertants were selected from aryl hydrocarbon hydroxylase (AHH)-deficient recessive mutants belonging to three complementation groups and from a dominant mutant of the Hepa-1 cell line. The recessive mutants had low spontaneous reversion frequencies (less than 4 X 10(-7] that were increased by mutagenesis. The majority of these revertants also had reacquired only partial AHH activity. Revertants of group A mutants were identical to the wild type with respect to both in vivo and in vitro enzyme stability and the Km for the substrate, benzo [alpha]pyrene, and therefore failed to provide evidence that gene A is the AHH structural gene. Group B and group C mutants are defective in the functioning of the Ah receptor required for AHH induction. Revertants of these groups were normal with respect to in vivo temperature sensitivity for AHH induction and for the 50% effective dose for the inducer, 2,3,7,8-tetrachlorodibenzo-p-dioxin, and thus provided no evidence that the B and C genes code for components of the receptor. Two rare group C revertants possessed AHH activity in the absence of induction. The phenotype of one of these was shown to be recessive to the wild type. Spontaneous revertants of the dominant mutant occurred at a frequency 300-fold greater than those of the recessive mutants, and this frequency was not increased by mutagenesis. These revertants all displayed complete restoration of AHH activity to wild type levels. These observations and the results from cell hybridization studies suggest that the dominant revertants arose by a high frequency event leading to functional elimination of the dominant mutation.
Highly efficient RNA-synthesizing system that uses isolated human mitochondria: new initiation events and in vivo-like processing patterns.
Authors: Gaines G , Attardi G
Published: September 2015

A highly efficient RNA-synthesizing system with isolated HeLa cell mitochondria has been developed and characterized regarding its requirements and its products. In this system, transcription is initiated and the transcripts are processed in a way which closely reproduces the in vivo patterns. Total RNA labeling in isolated mitochondria proceeds at a constant rate for about 30 min at 37 degrees C; the estimated rate of synthesis is at least 10 to 15% of the in vivo rate. Polyadenylation of the mRNAs is less extensive in this system than in vivo. Furthermore, compared with the in vivo situation, rRNA synthesis in vitro is less efficient than mRNA synthesis. This is apparently due to a decreased rate of transcription initiation at the rRNA promoter and probably a tendency also for premature termination of the nascent rRNA chains. The 5'-end processing of rRNA also appears to be slowed down, and it is very sensitive to the incubation conditions, in contrast to mRNA processing. It is suggested that the lower efficiency and the lability of rRNA synthesis and processing in isolated mitochondria may be due to cessation of import from the cytoplasm of ribosomal proteins that play a crucial role in these processes. The formation of the light-strand-coded RNA 18 (7S RNA) is affected by high pH or high ATP concentration differently from the overall light-strand transcription. The dissociation of the two processes may have important implications for the mechanism of formation and the functional role of this unusual RNA species. The high efficiency, initiation capacity, and processing fidelity of the in vitro RNA-synthesizing system described here make it a valuable tool for the analysis of the role of nucleocytoplasmic-mitochondrial interactions in organelle gene expression.
Cellular oncogenes (c-erb-A and c-erb-B) located on different chicken chromosomes can be transduced into the same retroviral genome.
Authors: Symonds G , Stubblefield E , Guyaux M , Bishop J M
Published: September 2015

Avian erythroblastosis virus has transduced two cellular genes, c-erb-A and c-erb-B. Using fractionated chicken chromosomes, we found that the two genes are located on different chromosomes in the chicken genome: c-erb-A is on a microchromosome, and c-erb-B is on a large chromosome. The locations of two other cellular oncogenes (c-fps and c-myb) were also determined: c-fps is on a microchromosome, and c-myb is on chromosome of an intermediate size. Our results suggest that avian erythroblastosis virus had transduced the two cellular genes independently, conforming to previous indications that cellular oncogenes are dispersed among multiple chromosomes in every species that has been examined.
Metabolic turnover of human c-rasH p21 protein of EJ bladder carcinoma and its normal cellular and viral homologs.
Authors: Ulsh L S , Shih T Y
Published: September 2015

The EJ bladder carcinoma oncogene is activated by a point mutation in the c-rasH proto-oncogene at the 12th amino acid codon. In an attempt to understand the mechanism of oncogenic activation, a comparative study was undertaken to examine the metabolic turnover and subcellular localization of the p21 protein encoded by the EJ oncogene, the viral oncogene, and its normal cellular homolog. Pulse-labeling experiments indicated that both c-ras p21 proteins were synthesized by a very similar pathway, as was observed for the viral p21 protein of Harvey murine sarcoma virus. The pro-p21 proteins were detected in free cytosol, and the processed products were associated with plasma membrane. The intracellular half-life of p21 proteins was determined by pulse-labeling and chasing in the presence of excess unlabeled methionine. Although both p21 proteins of EJ and the normal c-ras genes which are not phosphorylated have a half-life of 20 h, the viral p21 protein of Harvey murine sarcoma virus which includes a phosphorylated form is much more stable in cells, having a half-life of 42 h, apparently due to phosphorylation.
High levels of intron-containing RNAs are associated with expression of the Drosophila DOPA decarboxylase gene.
Authors: Beall C J , Hirsh J
Published: September 2015

We have examined the structure and expression during embryonic development of the Drosophila DOPA decarboxylase gene, Ddc. The Ddc gene is transcribed to make at least five different size classes of RNA. These RNA species first appear late in embryogenesis, coincident with induction of Ddc enzyme activity. The most abundant and smallest RNA appears to be Ddc mRNA. The sequences encoding this RNA are split by two intervening sequences. Each of the larger RNA species contains some or all of the intervening sequences. We have noted two unusual features of Ddc expression during embryogenesis. First, the intervening-sequence-containing RNAs are present as 20% or more of the polyadenylated Ddc RNA molecules, an exceptionally high proportion. Second, these RNAs do not disappear as rapidly as Ddc mRNA after Ddc enzyme activity reaches fully induced levels. These observations indicate slow rates of RNA processing relative to mRNA half-life and suggest that post-transcriptional steps participate in regulating Ddc expression. Although four of the five RNA species were detected at multiple developmental stages during which Ddc is expressed, one was found uniquely during embryogenesis. This RNA differs from Ddc mRNA in length and in time of expression during embryogenesis but is transcribed in the same orientation and from the same genomic sequences as the Ddc primary transcript.
New human transforming genes detected by a tumorigenicity assay.
Authors: Fasano O , Birnbaum D , Edlund L , Fogh J , Wigler M
Published: September 2015

We have developed a sensitive bioassay for transforming genes based on the tumorigenicity of cotransfected NIH3T3 cells in nude mice. The assay differs substantially from the NIH3T3 focus assay. Using it, we have detected the transfer of three transforming genes from the DNA of MCF-7, a human mammary carcinoma cell line. One of these is N-ras, which is amplified in MCF-7 DNA. The other two, which we have called mcf2 and mcf3, do not appear to be related to known oncogenes. We cannot detect their transfer by using the NIH3T3 focus assay. We do not yet know whether either mcf2 or mcf3 is associated with genetic abnormalities in MCF-7 cells.
Effects of epidermal growth factor and 12-O-tetradecanoylphorbol-13-acetate on metabolism of the epidermal growth factor receptor in normal human fibroblasts.
Authors: Decker S J
Published: September 2015

The biosynthesis, phosphorylation, and degradation of the epidermal growth factor (EGF) receptor were examined in normal human fibroblasts. The receptor was initially synthesized as an Mr = 160,000 immature form which matured to an Mr = 170,000 form in a monensin-sensitive manner. Tunicamycin treatment led to the accumulation of an Mr = 130,000 protein. The receptor was phosphorylated on serine and threonine residues in normally growing and quiescent cells, and treatment with EGF or the tumor promoter 12-O-tetradecanoylphorbol-13-acetate (TPA) resulted in a two- to threefold increase in receptor-bound phosphate. EGF increased the amount of phosphoserine and phosphothreonine and caused the appearance of a minor amount of phosphotyrosine. TPA increased the levels of phosphoserine and phosphothreonine exclusively. Prior treatment with TPA inhibited the EGF-dependent appearance of phosphotyrosine in the receptor. Analysis of tryptic phosphopeptides revealed that six of the seven major peptides were common to the receptor from cells treated with EGF or TPA. EGF strongly stimulated [3H]thymidine incorporation in confluent cells, increased final saturation density three to fourfold, and increased whole-cell levels of phosphotyrosine about threefold. Treatment of cells with TPA before addition of EGF inhibited all three of these EGF-dependent responses. EGF also decreased the receptor half-life from 15 h to 1 h, but this was not inhibited by TPA. TPA alone had no detectable effect on the receptor half-life.
Genetic and physical analysis of the chicken tk gene.
Authors: Merrill G F , Harland R M , Groudine M , McKnight S L
Published: September 2015

Several aspects of the structure of the chicken thymidine kinase gene (tk) have been resolved as a result of genetic experiments and nucleotide sequencing. Deletion mapping established the locations of two functional boundaries in a region thought to correspond to the 5' terminus of the gene. One such boundary coincides with a transcriptional promoter, and the other coincides with the translation start codon of the chicken tk polypeptide. Similar deletion mapping assays identified a functional boundary at the 3' terminus of the gene. DNA sequence analysis confirms the prediction that this 3' region encodes the carboxyl terminus of the tk polypeptide. A recombinant cDNA clone complementary to genomic tk sequences was isolated. A comparison between genomic and cDNA sequences reveals the locations of six intervening sequences and allows prediction of the complete amino acid sequence of the chicken tk polypeptide.
Characterization of a ts mutant of BALB/3T3 cells and correction of the defect by in vitro addition of extracts from wild-type cells.
Authors: Zeng G C , Donegan J , Ozer H L , Hand R
Published: September 2015

ts20 is a temperature-sensitive mutant cell line derived from BALB/3T3 cells. DNA synthesis in the mutant decreased progressively after an initial increase during the first 3 h at the restrictive temperature. RNA and protein synthesis increased for 20 h and remained at a high level for 40 h. Cells were arrested in S phase as determined by flow microfluorimetry, and DNA chain elongation was retarded as measured by fiber autoradiography. Infection with polyomavirus did not bypass the defect in cell DNA synthesis, and the mutant did not support virus DNA replication at the restrictive temperature. After shift down to the permissive temperature, cell DNA synthesis was restored whereas virus DNA synthesis was not. Analysis of virus DNA synthesized at the restrictive temperature showed that the synthesis of form I and replicative intermediate DNA decreased concurrently and that the rate of completion of virus DNA molecules remained constant with increasing time at the restrictive temperature. These studies indicated that the mutation inhibited ongoing DNA synthesis at a step early in elongation of nascent chains. The defect in virus and cell DNA synthesis was expressed in vitro. [3H]dTTP incorporation was reduced, consistent with the in vivo data. The addition of a high-salt extract prepared from wild-type 3T3 cells preferentially stimulated the incorporation of [3H]dTTP into the DNA of mutant cells at the restrictive temperature. A similar extract prepared from mutant cells was less effective and was more heat labile as incubation of it at the restrictive temperature for 1 h destroyed its ability to stimulate DNA synthesis in vitro, whereas wild-type extract was not inactivated until incubated at that temperature for 3 h.
A short sequence in the p60src N terminus is required for p60src myristylation and membrane association and for cell transformation.
Authors: Cross F R , Garber E A , Pellman D , Hanafusa H
Published: September 2015

We have constructed mutants by using linker insertion followed by deletion in the region of cloned Rous sarcoma virus DNA coding for the N-terminal 9 kilodaltons of the src protein. Previous work implicated this region in the membrane association of the protein. The mutations had little effect on src tyrosine kinase activity. Substitution of a tri- or tetrapeptide for amino acids 15 to 27, 15 to 49, or 15 to 81 had little effect on the in vitro transforming capacity of the virus. Like wild-type p60src, the src proteins of these mutants associated with plasma membranes and were labeled with [3H]myristic acid. In contrast, a mutant whose src protein had the dipeptide Asp-Leu substituted for amino acids 2 to 81 and a mutant with the tripeptide Asp-Leu-Gly substituted for amino acids 2 to 15 were transformation defective, and the mutant proteins did not associate with membranes and were not labeled with [3H]myristic acid. These results suggest that amino acids 2 to 15 serve as an attachment site for myristic acid and as a membrane anchor. Since deletions including this region prevent transformation, and since tyrosine kinase activity is not diminished by the deletions, these results imply that target recognition is impaired by mutations altering the very N terminus, perhaps through their effect on membrane association.
Complex regulation of simian virus 40 early-region transcription from different overlapping promoters.
Authors: Buchman A R , Fromm M , Berg P
Published: September 2015

During simian virus 40 lytic infection there is a shift in initiation sites used to transcribe the early region, which encodes large T and small t antigens. Early in infection, transcription is initiated almost exclusively from sites that are downstream of the origin of DNA replication, whereas transcripts produced later are initiated mainly from sites on the upstream side. We have used mutant virus and specially constructed plasmid DNAs to investigate the factors regulating this transcriptional shift. In our studies simian virus 40 large T antigen appears to mediate the shift in transcription in two ways: first, T antigen represses transcription at the downstream sites late in infection by binding to the region where these RNAs are initiated; second, T antigen promotes transcription from sites on the upstream side by its ability to initiate replication or amplification, or both, of the template DNA. In addition, transcription from the downstream sites is heavily dependent on enhancer sequences located in the 72-base-pair repeat region, whereas transcription from the upstream sites late in infection does not require enhancer sequences. Thus, different overlapping promoters regulate simian virus 40 early-region expression in a manner that apparently coordinates the production of large T antigen with the increase in viral DNA.
Posttranscriptional modulation of gene expression in cultured rat hepatocytes.
Authors: Jefferson D M , Clayton D F , Darnell J E , Reid L M
Published: September 2015

The maintenance of high levels of two liver-specific mRNAs in cultured hepatocytes was achieved in a serum-free hormonally defined cell culture medium. However, this maintenance of liver-specific mRNA levels did not correlate with the level of transcription of the genes but was apparently due to increased stabilization of the tissue-specific mRNAs. The mRNA stabilization did not occur in serum-supplemented medium. In both defined and serum-supplemented medium, actin and tubulin mRNAs were also greatly increased, in both cases predominantly if not entirely due to increased mRNA stability.
Associations of pregnancy-associated plasma protein-A level with essential hypertension and hypertensive disorders in pregnancy in Chinese population: a meta-analysis of 20 research studies involving 3332 individuals
Authors: Cai Gaojun , Zhang Bifeng , Weng Weijin , Yang Liping , Shi Ganwei , Xue Sheliang , Fu Xingli
Published: September 2015

Objective

To explore the associations between serum pregnancy-associated plasma protein-A (PAPP-A) level, and essential hypertension (EH) and hypertensive disorders in pregnancy (HDP) in Chinese population.

Methods

Pertinent studies were independently searched in PubMed, Embase, Cochrane Library, Chinese Biomedical Database (CBM), Wanfang databases and China National Knowledge Infrastructure (CNKI). The standardised mean difference (SMD) with 95% CIs was used to estimate the size of the effect. The subgroup analyses and meta-regression analysis were performed to identify the sources of heterogeneity among studies. Sensitivity analysis was conducted to assess the stability of the results. The publication bias between studies was examined by using Begg's funnel plots and Egger's test.

Results

A total of 20 studies involving 1493 patients and 1839 controls were included in the current meta-analysis. The PAPP-A level was significantly higher in EH patients than in controls (SMD=1.960, 95% CI 1.305 to 2.615, p<0.001), and significant associations were observed in all subgroups. The PAPP-A level was also significantly higher in HDP patients than in healthy pregnant women (SMD=2.249; 95% CI 1.324 to 3.173, p<0.001). The positive association between PAPP-A level and the risk of HDP was consistently observed in all subgroups except the subgroup with low NOS score.

Conclusions

The present meta-analysis suggests that an elevated PAPP-A level may be associated with susceptibilities to EH and HDP.
Understanding hikers who approached a hazardous river in Yosemite National Park
Authors: Girasek Deborah C , Marschall Joy S , Pope Dov
Published: September 2015

Objectives

To understand the perceptions and motivations of hikers who approached a swift river at locations that have been associated with drowning in the past.

Methods

A survey was completed by 399 adults who had been observed getting ‘too close’ to the Merced River. The questionnaire covered trail familiarity, information sources, timing and motivation of their decision, perceived safety, knowledge and opinion of park rules.

Results

Sixty-eight per cent of invited hikers agreed to participate. Almost all had received advance information about their hike, but most often that did not include a river warning. Most respondents were observed in the risk zone by the footbridge, and their most frequent motivation was to ‘cool off’. Ninety-two per cent of hikers reported feeling very or somewhat safe by the river. Their risk perceptions did not correlate with expert ratings of danger. Males, younger subjects and those who had hiked the trail before were more likely to enter the most hazardous parts of the risk zone. Eleven per cent of people at the footbridge and 43% at the top of the waterfall thought that the park should not allow visitors to go where they had been. The most common reason they gave for this view was that the location was unsafe.

Conclusions

While this needs assessment identified channels for informing hikers of drowning risk, there are indications that they might not personalise such warnings. Another option would be to explore cooling alternatives that could compete with the swift water that runs along many hiking trails.
Design-based regression estimation of net change for forest inventories
Authors: Massey Alexander , Mandallaz Daniel
Published: September 2015

A simple design-based approach to estimating net change of a forest attribute such as timber volume is to observe the change directly on the plot level and then make that the response variable of interest using established estimation techniques such as multiphase regression estimators. This direct approach is only possible for inventories with permanent plots and is constrained to estimating net change over time periods matching the duration of the remeasurement cycle. Indirect estimation involves applying one of the aforementioned techniques to estimate the state at two time points and taking their difference. Indirect methods, although less common, are not necessarily constrained to permanent plots and can estimate net change over any desired time span for annual designs. This article compares design-based direct and indirect regression estimators under the Monte Carlo approach and illustrates their performances with data from the Swiss National Forest Inventory. The major finding is that direct estimation should be preferred whenever change is observable directly on the plot level but that multiphase indirect estimation can still improve precision when direct estimation is not possible such as for inventories employing only temporary plots.
Adaptations of enchytraeids to single and combined effects of physical and chemical stressors
Authors: Patrício Silva A.L. , Amorim M.J.B. , Holmstrup M.
Published: September 2015

Climate changes are expected to be greatest in the polar and temperate areas, where predictions point to an increase in freeze–thaw events and changes in precipitation, evaporation, and salinity patterns. These events will therefore affect biological activity of the soil compartment that may result in large impacts in ecosystem functioning and dynamics therein. This concern becomes even more important when considering the presence of contaminants due to intense anthropogenic activity, which may lead to synergistic or antagonistic effects and increase or decrease the impact on natural ecosystems. This paper reviews the effect of physical and chemical stressors on enchytraeids, with special emphasis on Enchytraeus albidus because most relevant studies have involved this species. E. albidus is a freeze-tolerant and euryhaline organism and several studies suggest that the absence of salinity may have important (negative) consequences not only for their freeze tolerance ability but also for their reproduction and capacity to deal with the presence of contaminants, such as metals and fungicides. Single and joint effects of constant freezing or freeze–thaw cycles and surfactants, such as 4-nonylphenol, affected negatively E. albidus freeze tolerance by decreasing the levels of cryoprotectants, membrane fluidity and interfering with cellular energy allocation. Because enchytraeids are of ecological significance in many important habitats along the Artic and cold-temperate environments, a reduction in abundance may result in disturbances of the decomposition processes in soils. The knowledge of the biological, physiological, and biochemical limits of enchytraeids to combined effect of physical and chemical stressors are crucial to provide a scientific basis for improving the setting of safety factors when extrapolating from controlled (and optimal) laboratory conditions to natural soil ecosystems. Therefore, there is a need to expand and evolve experiments that more realistically mimic the situation in the field, where interactions between factors are highly relevant. The synergistic or antagonistic interactions identified in the present review may also represent a stepping stone in the evaluation and possible inclusion of natural factors, like cold and salinity, in standardized enchytraeid test guidelines and consequently in risk assessment of chemicals.
Min-Max Regret Version of the Linear Time–Cost Tradeoff Problem with Multiple Milestones and Completely Ordered Jobs
Authors: Choi Byung-Cheon , Park Myoung-Ju
Published: September 2015

We consider a linear time–cost tradeoff problem with multiple milestones and uncertain processing times such that all jobs are completely ordered. The performance measure is expressed as the sum of total weighted number of tardy jobs and total crashing cost. The processing times uncertainty is described through two types of scenarios: discrete and interval scenarios. The objective is to minimize maximum deviation from optimality over all scenarios. For the discrete scenario case, we prove its NP-hardness, develop a pseudo-polynomial time approach, and present a polynomially solvable case. Finally, we show that the interval scenario case is also NP-hard.
Einstein–Born–Infeld black holes with a scalar hair in three dimensions
Authors: Mazharimousavi S. Habib , Halilsoy M.
Published: September 2015

We present black hole solutions in (2+1)-dimensional Einstein’s theory of gravity coupled with Born–Infeld (BI) nonlinear electrodynamic and a massless self-interacting scalar field. The model has five free parameters: mass [Formula: see text], cosmological constant [Formula: see text], electric [Formula: see text] and scalar [Formula: see text] charges and BI parameter [Formula: see text]. To attain exact solution for such a highly nonlinear system we adjust, i.e. finely tune, the parameters of the theory with the integration constants. In the limit [Formula: see text], we recover the results of Einstein–Maxwell–Scalar theory, obtained before. The self-interacting potential admits finite minima apt for the vacuum contribution. Hawking temperature of the model is investigated versus properly tuned parameters. By employing this tuned-solution as basis, we obtain also a dynamic solution which in the proper limit admits the known solution in Einstein gravity coupled with self-interacting scalar field. Finally, we establish the equations of a general scalar–tensor field coupled to nonlinear electrodynamics (NED) field in 2+1 dimensions without searching for exact solutions.
Thoughts on the vacuum energy in the quantum N-portrait
Authors: Kühnel Florian
Published: September 2015

An application of the quantum N-portrait to the Universe is discussed, wherein the spacetime geometry is understood as a Bose–Einstein condensate of N soft gravitons. If near or at the critical point of a quantum phase transition, indications are found that the vacuum energy is partly suppressed by 1/N, as being due to quanta not in the condensate state. Time evolution decreases this suppression, which might have implications for cosmic expansion.
Modeling and Analysis for Minimization of Mean Flow Time in FMS Simulation
Authors: Sreenivasulu A. , Venkatachalapathi N. , Prasanthi G.
Published: September 2015

The aim of this paper is to deal with a simulation study on effect of part launching, part sequencing at central buffer and tool selection rules on a flexible manufacturing system (FMS) involving tool movement along with part movement policy. A typical FMS is selected for a study of discrete event simulation model. Simulation experiments are conducted on various combinations of decision rules and it is found to be good in evaluated performance measures.
New experimental method to study the combined effect of temperature and salt weathering
Authors: Hamed Ayman , Aly Nevin , Gomez-Heras Miguel , Alvarez de Buergo Monica
Published: September 2015

This study presents a new experimental chamber, which builds upon previous methods of testing salt weathering. This method is based on capillary rising in samples, as this corresponds to the actual imbibition process in building stone. This set-up allows control in setting both a specific thermal regime and cycling temperatures. Some of the significant additions of this experimental set-up are: continuous flow of the saline solution, as the samples will be fed with a constant concentration throughout the experiments; and continuous monitoring of environmental temperature, relative humidity and sample weights. Recorded results in this research belong to limestone samples from Mokattam, Cairo. Results are also considered as a proof to the practical advantages of the experimental chamber in salt-weathering studies and its environmental controls.
Framing sustainability as a property of software quality
Authors: Lago Patricia , Koçak Sedef Akinli , Crnkovic Ivica , Penzenstadler Birgit
Published: September 2015

This framework addresses the environmental dimension of software performance, as applied here by a paper mill and a car-sharing service.
H
-Matrix-Based Finite-Element-Based Thermal Analysis for 3D ICs
Authors: Chen Hai-Bao , Li Ying-Chi , Tan Sheldon X.-D. , Huang Xin , Wang Hai , Wong Ngai
Published: September 2015

In this article, we propose an efficient finite-element-based (FE-based) method for both steady and transient thermal analyses of high-performance integrated circuits based on the hierarchical matrix (
H
-matrix) representation.
H
-matrix has been shown to provide a data-sparse way to approximate the matrices and their inverses with almost linear-space and time complexities. In this work, we apply the
H
-matrix concept for solving heating diffusion problems modeled by parabolic partial differential equations (PDEs) based on the finite element method. We show that the matrix from a FE-based steady and transient thermal analysis can be represented by
H
-matrix without any approximation, and its inverse and Cholesky factors can be evaluated by
H
-matrix with controlled accuracy. We then show and prove that the memory and time complexities of the solver are bounded by
O
(
k
1
N
log
N
) and
O
(
k
1
2
N
log
2
N
), respectively, where
k
1
is a small quantity determined by accuracy requirements and
N
is the number of unknowns in the system. The comparison with existing product-quality LU solvers, CSPARSE and UMFPACK, on a number of 3D IC thermal matrices, shows that the new method is much more memory efficient than these methods, which however prevents CPU time comparison with those methods on large examples. But the proposed method can solve all the given thermal circuits with decent scalabilities, which shows good agreement with the predicted theoretical results.
Memory-Model-Aware Testing
Authors: Furbach Florian , Meyer Roland , Schneider Klaus , Senftleben Maximilian
Published: September 2015

To improve the performance of the memory system, multiprocessors implement weak memory consistency models. Weak memory models admit different views of the processes on their load and store instructions, thus allowing for computations that are not sequentially consistent. Program analyses have to take into account the memory model of the targeted hardware. This is challenging because numerous memory models have been developed, and every memory model requires its own analysis.

In this article, we study a prominent approach to program analysis: testing. The testing problem takes as input sequences of operations, one for each process in the concurrent program. The task is to check whether these sequences can be interleaved to an execution of the entire program that respects the constraints of a memory model under consideration. We determine the complexity of the testing problem for most of the known memory models. Moreover, we study the impact on the complexity of parameters, such as the number of concurrent processes, the length of their executions, and the number of shared variables.

What differentiates our contribution from related results is a uniform approach that avoids considering each memory model on its own. We build upon work of Steinke and Nutt. They showed that the existing memory models form a hierarchy where one model is called weaker than another one if it includes the latter’s behavior. Using the Steinke-Nutt hierarchy, we develop three general concepts that allow us to quickly determine the complexity of a testing problem. First, we generalize the technique of problem reductions from complexity theory. So-called range reductions propagate hardness results between memory models, and we apply them to establish
NP
lower bounds for the stronger memory models. Second, for the weaker models, we present polynomial-time testing algorithms that are inspired by determinization algorithms for automata. Finally, we describe a single SAT encoding of the testing problem that works for all memory models in the Steinke-Nutt hierarchy to prove their membership in
NP
. Our results are general enough to carry over to future weak memory models. Moreover, they show that SAT solvers are adequate tools for testing.
Fast Simulation of Networks-on-Chip with Priority-Preemptive Arbitration
Authors: Indrusiak Leandro Soares , Harbin James , Dos Santos Osmar Marchi
Published: September 2015

An increasingly time-consuming part of the design flow of on-chip multiprocessors is the simulation of the interconnect architecture. The accurate simulation of state-of-the art network-on-chip interconnects can take hours, and this process is repeated for each design iteration because it provides valuable insights on communication latencies that can greatly affect the overall performance of the system. In this article, we identify a time-predictable network-on-chip architecture and show that its timing behaviour can be predicted using models which are far less complex than the architecture itself. We then explore such a feature to produce simplified and lightweight simulation models that can produce latency figures with more than 90% accuracy and simulate more than 1,000 times faster when compared to a cycle-accurate model of the same interconnect.
VSSD
Authors: Chang Da-Wei , Chen Hsin-Hung , Su Wei-Jian
Published: September 2015

Performance isolation is critical in shared storage systems, a popular storage solution. In a shared storage system, interference between requests from different users can affect the accuracy of I/O cost accounting, resulting in poor performance isolation. Recently, NAND flash-memory-based solid-state drives (SSDs) have been increasingly used in shared storage systems. However, interference in SSD-based shared storage systems has not been addressed. In this article, two types of interference, namely, queuing delay (QD) interference and garbage collection (GC) interference, are identified in a shared SSD. Additionally, a framework called VSSD is proposed to address these types of interference. VSSD is composed of two components: the FACO credit-based I/O scheduler designed to address QD interference and the ViSA flash translation layer designed to address GC interference. The VSSD framework aims to be implemented in the firmware running on an SSD controller. With VSSD, interference in an SSD can be eliminated and performance isolation can be ensured. Both synthetic and application workloads are used to evaluate the effectiveness of the proposed VSSD framework. The performance results show the following. First, QD and GC interference exists and can result in poor performance isolation between users on SSD-based shared storage systems. Second, VSSD is effective in eliminating the interference and achieving performance isolation between users. Third, the overhead of VSSD is insignificant.
Accurate Analysis and Prediction of Enterprise Service-Level Performance
Authors: Duan Qing , Koneru Abhishek , Zeng Jun , Chakrabarty Krishnendu , Dispoto Gary
Published: September 2015

An enterprise service-level performance time series is a sequence of data points that quantify demand, throughput, average order-delivery time, quality of service, or end-to-end cost. Analytical and predictive models of such time series can be embedded into an enterprise information system (EIS) in order to provide meaningful insights into potential business problems and generate guidance for appropriate solutions. Time-series analysis includes periodicity detection, decomposition, and correlation analysis. Time-series prediction can be modeled as a regression problem to forecast a sequence of future time-series datapoints based on the given time series. The state-of-the-art (baseline) methods employed in time-series prediction generally apply advanced machine-learning algorithms. In this article, we propose a new univariate method for dealing with midterm time-series prediction. The proposed method first analyzes the hierarchical periodic structure in one time series and decomposes it into trend, season, and noise components. By discarding the noise component, the proposed method only focuses on predicting repetitive season and smoothed trend components. As a result, this method significantly improves upon the performance of baseline methods in midterm time-series prediction. Moreover, we propose a new multivariate method for dealing with short-term time-series prediction. The proposed method utilizes cross-correlation information derived from multiple time series. The amount of data taken from each time series for training the regression model is determined by results from hierarchical cross-correlation analysis. Such a data-filtering strategy leads to improved algorithm efficiency and prediction accuracy. By combining statistical methods with advanced machine-learning algorithms, we have achieved a significantly superior performance in both short-term and midterm time-series predictions compared to state-of-the-art (baseline) methods.
Rise of concerns about AI
Authors: Dietterich Thomas G. , Horvitz Eric J.
Published: September 2015

Research, leadership, and communication about AI futures.
Dismantling the barriers to entry
Authors: Harris Rich
Published: September 2015

We have to choose to build a Web that is accessible to everyone.
A Review and Taxonomy of Interactive Optimization Methods in Operations Research
Authors: Meignan David , Knust Sigrid , Frayret Jean-Marc , Pesant Gilles , Gaud Nicolas
Published: September 2015

This article presents a review and a classification of interactive optimization methods. These interactive methods are used for solving optimization problems. The interaction with an end user or decision maker aims at improving the efficiency of the optimization procedure, enriching the optimization model, or informing the user regarding the solutions proposed by the optimization system. First, we present the challenges of using optimization methods as a tool for supporting decision making, and we justify the integration of the user in the optimization process. This integration is generally achieved via a dynamic interaction between the user and the system. Next, the different classes of interactive optimization approaches are presented. This detailed review includes trial and error, interactive reoptimization, interactive multiobjective optimization, interactive evolutionary algorithms, human-guided search, and other approaches that are less well covered in the research literature. On the basis of this review, we propose a classification that aims to better describe and compare interaction mechanisms. This classification offers two complementary views on interactive optimization methods. The first perspective focuses on the user’s contribution to the optimization process, and the second concerns the components of interactive optimization systems. Finally, on the basis of this review and classification, we identify some open issues and potential perspectives for interactive optimization methods.