Miracle-dz/UniFAR-FTUs huggingface dataset:
Evaluation of a plasmid-based transgenic mouse model for detecting in vivo mutations.

To study in vivo somatic mutations a C57BL/6 transgenic mouse model was constructed harboring multiple chromosomally integrated copies of the plasmid pUR288, which carried the lacZ reporter gene as the mutational target. We previously demonstrated that lacZ-containing plasmids could be rescued from their integrated state efficient enough to detect mutations in lacZ by positive selection. The smaller size of the plasmid vector, as compared with our earlier transgenic mouse model based on bacteriophage lambda vectors, should offer considerable advantages in terms of rescue efficiency and sensitivity to large size alterations in the lacZ gene. To evaluate the plasmid-based mouse model for its suitability to detect in vivo mutations, we determined mutant frequencies in different organs of untreated and ethyl nitrosourea (ENU)-treated animals using a new, improved protocol. The rescue efficiencies obtained were as high as 200,000/micrograms genomic DNA; millions of transformants could be obtained in one single experiment. The average spontaneous mutant frequency in four different organs of 4- to 8-week-old mice ranged from 4.41 to 6.82 x 10(-5), compared with a mutant frequency of the same plasmid grown in Escherichia coli of approximately 1 x 10(-5) or less. Single treatments with 100 and 250 mg ENU/kg body wt resulted in a 7- and 14-fold increase, respectively, in spleen mutant frequency at 14 days after i.p. administration of the alkylating agent. Restriction enzyme analysis showed that a considerable portion of spontaneous mutants were size changes varying from approximately 100 to 3000 bp. Some mutant plasmids contained mouse genomic sequences, which is indicative of large genetic rearrangement events involving the 3' flanking regions of the transgene cluster. Among the ENU-induced mutants, size changes comprised only a minor fraction of the total, which is in keeping with the known ENU mutation spectra in vitro and in vivo. The high rescue efficiency of this plasmid-based model, in combination with its sensitivity to a broad spectrum of mutations, including large deletions, makes it very suitable as a general in vivo mutagenicity test system.
Distributed Control for Identical Dynamically Coupled Systems: A Decomposition Approach

We consider the problem of designing distributed controllers for a class of systems which can be obtained from the interconnection of a number of identical subsystems. If the state space matrices of these systems satisfy a certain structural property, then it is possible to derive a procedure for designing a distributed controller which has the same interconnection pattern as the plant. This procedure is basically a multiobjective optimization under linear matrix inequality constraints, with system norms as performance indices. The explicit expressions for computing these controllers are given for both H infin or H 2 performance, and both for static state feedback and dynamic output feedback (in discrete time). At the end of the paper, two application examples illustrate the effectiveness of the approach.
MODELS and METHODS for LOT SIZING and SCHEDULING

The intent of this extended abstract is to briefly describe the work developed by the PhD student Carina Pimentel during her PhD studies, since 2007 until now. The core subject of this work is the development of models and methods for solving medium/short term production planning problems. Two different problems are studied. The first one is a classical lot sizing problem. For this problem several exact approaches were developed and compared. The second problem, motivated by a real situation, is a lot splitting and scheduling problem. For the latter, a new mixed integer programming model is developed, as well as several heuristic approaches that efficiently solve it.
A Comparative Study on the Child and Family Effects of Adding a Parent Involvement Program to an Existing Early Intervention Program.

AUTHOR Innocenti, Mark S. ; And Others TITLE A Comparative Study on the Child and Family Effects of Adding a Parent Involvement Program to an Existing Early Intervention Program. INSTITUTION Utah State Univ., Logan. Early Intervention Research Inst. SPONS AGENCY Department of Education, Washington, DC. PUB DATE 25 Mar 93 CONTRACT HS90010001 NOTE 16p. ; Paper presented at the Biennial Meeting of the Society for Research in Child Development (60th, New Orleans, LA, March 25-28, 1993). PUB TYPE Reports Research/Technical (143) Speeches /Conference Papers (150)
Intravaginal insertion in KwaZulu-Natal: sexual practices and preferences in the context of microbicide gel use

Intravaginal insertion is often associated with the concept of ‘dry’ sex. All HIV-prevention microbicides tested to date have been vaginally applied lubricant-based gels. In this paper, we examine whether the use of intravaginal insertions could be in conflict with the introduction of vaginal microbicide gels. The Africa Centre site was part of the Microbicides Development Programme evaluating PRO2000/5 microbicide gel. We conducted in-depth-interviews and focus-group discussions with women enrolled in the trial as well as women and men from the community. The analysis focused on people's knowledge of intravaginal insertion in the community and trial participants' experience of using trial gels. Intravaginal use of a variety of products was widely acknowledged. We found that the experience of using trial gels – which made sex ‘hot’, ‘tight’ and ‘dry’ – matched the desired outcomes of intravaginal insertion. We found that vaginal ‘dryness’ described the removal of excessive amounts of unusual discharge, rather than the removal of normal vaginal secretions and that intravaginal insertion is not exclusively associated with a desire for ‘dry’ sex. Study findings provide evidence that vaginal microbicide gels may be more acceptable in communities where intravaginal insertion is practiced than was previously thought.
Detection call algorithms for high-throughput gene expression microarray data

Extensive methodological research has been conducted to improve gene expression summary methods. However, in addition to quantitative gene expression summaries, most platforms, including all those examined in the MicroArray Quality Control project, provide a qualitative detection call result for each gene on the platform. These detection call algorithms are intended to render an assessment of whether or not each transcript is reliably measured. In this paper, we review uses of these qualitative detection call results in the analysis of microarray data. We also review the detection call algorithms for two widely used gene expression microarray platforms, Affymetrix GeneChips and Illumina BeadArrays, and more clearly formalize the mathematical notation for the Illumina BeadArray detection call algorithm. Both algorithms result in a P-value which is then used for determining the qualitative detection calls. We examined the performance of these detection call algorithms and default parameters by applying the methods to two spike-in datasets. We show that the default parameters for qualitative detection calls yield few absent calls for high spike-in concentrations. When genes of interest are expected to be present at very low concentrations, spike-in datasets can be useful for appropriately adjusting the tuning parameters for qualitative detection calls.
Cytopathicity of Chlamydia is largely reproduced by expression of a single chlamydial protease

Chlamydiae replicate in a vacuole within epithelial cells and commonly induce cell damage and a deleterious inflammatory response of unknown molecular pathogenesis. The chlamydial protease-like activity factor (CPAF) translocates from the vacuole to the cytosol, where it cleaves several cellular proteins. CPAF is synthesized as an inactive precursor that is processed and activated during infection. Here, we show that CPAF can be activated in uninfected cells by experimentally induced oligomerization, reminiscent of the activation mode of initiator caspases. CPAF activity induces proteolysis of cellular substrates including two novel targets, cyclin B1 and PARP, and indirectly results in the processing of pro-apoptotic BH3-only proteins. CPAF activation induces striking morphological changes in the cell and, later, cell death. Biochemical and ultrastructural analysis of the cell death pathway identify the mechanism of cell death as nonapoptotic. Active CPAF in uninfected human cells thus mimics many features of chlamydial infection, implicating CPAF as a major factor of chlamydial pathogenicity, Chlamydia-associated cell damage, and inflammation.
Cluster infall in the concordance ΛCDM model

We perform statistical analyses of the infall of dark matter on to clusters in numerical simulations within the concordance ACDM (cold dark matter) model. By studying the infall profile around clusters of different mass, we find a linear relation between the mass and maximum infall velocities which reach ∼900 km s -1 for the most massive groups. The maximum infall velocity and the group mass follow a suitable power-law fit of the form V max inf = (M/m 0 ) γ . By comparing the measured infall velocity to the linear infall model with an exponential cut-off introduced by Croft et al., we find that the best agreement is obtained for a critical overdensity δ c = 45. We study the dependence of the direction of infall with respect to the cluster centres, and find that in the case of massive groups, the maximum alignment occurs at scales r ∼ 6h -1 Mpc. We obtain a logarithmic power-law relation between the average infall angle and the group mass. We also study the dependence of the results on the local dark matter density, finding a remarkable difference in the dynamical behaviour of low- and high-density particles.
Cross-domain activity recognition

In activity recognition, one major challenge is huge manual effort in labeling when a new domain of activities is to be tested. In this paper, we ask an interesting question: can we transfer the available labeled data from a set of existing activities in one domain to help recognize the activities in another different but related domain? Our answer is "yes", provided that the sensor data from the two domains are related in some way. We develop a bridge between the activities in two domains by learning a similarity function via Web search, under the condition that the sensor data are from the same feature space. Based on the learned similarity measures, our algorithm interprets the data from the source domain as the data in the domain with different confidence levels, thus accomplishing the cross-domain knowledge transfer task. Our algorithm is evaluated on several real-world datasets to demonstrate its effectiveness.
Self-esteem modulates automatic attentional responses to self-relevant stimuli: evidence from event-related brain potentials

Previous studies have widely shown that self-esteem modulates the attention bias towards social rejection or emotion-related information. However, little is known about the influences of self-esteem on attention bias towards self-relevant stimuli. We aimed to investigate neural correlates that underlie the modulation effect of self-esteem on self-relevant processing. Event-related potentials were recorded for subjects’ own names and close others’ names (the names of their friends) while subjects performed a three-stimulus oddball task. The results showed larger P2 amplitudes for one’s own name than for close-other’s name in the low self-esteem group, whereas this P2 effect were not observed in the high self-esteem group. In addition, one’s own name elicited equivalent N250 amplitudes and larger P3 amplitudes compared with close-other’s name in both high and low self-esteem groups. However, no interaction effects were observed between self-esteem and self-relevant processing in the N250 and P3 components. Thus, we found that the modulation effects of self-esteem on self-relevant processing occurred at the early P2 stage, but not at the later N250 and P3 stages. These findings reflect that individuals with low self-esteem demonstrate automatic attention towards their own names.
A Longitudinal Study: Changes in Cortical Thickness and Surface Area during Pubertal Maturation

Sex hormones have been shown to contribute to the organization and function of the brain during puberty and adolescence. Moreover, it has been suggested that distinct hormone changes in girls versus boys may contribute to the emergence of sex differences in internalizing and externalizing behavior during adolescence. In the current longitudinal study, the influence of within-subject changes in puberty (physical and hormonal) on cortical thickness and surface area was examined across a 2-year span, while controlling for age. Greater increases in Tanner Stage predicted less superior frontal thinning and decreases in precuneus surface area in both sexes. Significant Tanner Stage and sex interactions were also seen, with less right superior temporal thinning in girls but not boys, as well as greater decreases in the right bank of the superior temporal sulcus surface area in boys compared to girls. In addition, within-subject changes in testosterone over the 2-year follow-up period were found to relate to decreases in middle superior frontal surface area in boys, but increases in surface area in girls. Lastly, larger increases in estradiol in girls predicted greater middle temporal lobe thinning. These results show that within-subject physical and hormonal markers of puberty relate to region and sex-specific changes in cortical development across adolescence.
A Chandra Archival Study of the Temperature and Metal Abundance Profiles in Hot Galaxy Clusters at 0.1 ≲ z ≲ 0.3

We present an analysis of the temperature and metallicity profiles of 12 galaxy clusters in the redshift range 0.1-0.3 selected from the Chandra archive with at least ~20,000 net ACIS counts and kT > 6 keV. We divide the sample between seven cooling-core (CC) and five non-cooling-core (NCC) clusters according to their central cooling time. We find that single power laws can properly describe both the temperature and metallicity profiles at radii larger than 0.1r180 in both CC and NCC systems, with NCC objects showing steeper profiles outward. A significant deviation is present only in the inner 0.1r180. We perform a comparison of our sample with the De Grandi & Molendi BeppoSAX sample of local CC and NCC clusters, finding a complete agreement in the CC cluster profile and a marginally higher value (at ~1 σ) in the inner regions of the NCC clusters. The slope of the power law describing kT(r) within 0.1r180 correlates strongly with the ratio between the cooling time and the age of the universe at the cluster redshift, with a slope >0 and τc/τage ≲ 0.6 in CC systems.
Efficient FFTs on IRAM

Computing Fast Fourier Transforms (FFTs) is notoriously difficult on conventional general-purpose architectures because FFTs require high memory bandwidth and strided memory accesses. Since FFTs are important in signal processing, several DSPs have hardware support for performing FFTs; moreover, some DSPs are designed solely for the purpose of computing FFTs and related transforms. In this paper, we show that the performance of the general-purpose VIRAM processor in computing floating-point FFTs is competitive with that of existing floating point DSPs and specialized fixed-point FFT chips. Furthermore, VIRAM is a complete “system on a chip,” and therefore has power, area, and cost advantages over multi-chip systems based on DSPs. VIRAM’s advantages result from a combination of hardware technology, instruction set design, and algorithmic techniques. In particular our FFT results are achieved by: an integrated processor-in-memory design that provides high memory bandwidth; vector processing, which provides simple and efficient utilization of the high memory bandwidth; a small amount of ISA support for in-register permutations; and an algorithm tuned to the VIRAM instruction set and implementation.
Is an Alternative Globalization Possible?

Building on Polanyi's concept of the “double-movement” through which society defends itself against domination by the self-regulating market, this article sets out some key organizational and ideological hurdles that the contemporary “movement of movements” must surmount to challenge the hegemony of neo-liberal globalization. After outlining neo-liberalism's failures, it makes an argument for the possibility of “counter-hegemonic globalization,” defined as a globally organized project of transformation aimed at replacing the dominant (hegemonic) global regime with one that maximizes democratic political control and makes the equitable development of human capabilities and environmental stewardship its priorities.
Free-Lunch Learning: Modeling Spontaneous Recovery of Memory

After a language has been learned and then forgotten, relearning some words appears to facilitate spontaneous recovery of other words. More generally, relearning partially forgotten associations induces recovery of other associations in humans, an effect we call free-lunch learning (FLL). Using neural network models, we prove that FLL is a necessary consequence of storing associations as distributed representations. Specifically, we prove that (1) FLL becomes increasingly likely as the number of synapses (connection weights) increases, suggesting that FLL contributes to memory in neurophysiological systems, and (2) the magnitude of FLL is greatest if inactive synapses are removed, suggesting a computational role for synaptic pruning in physiological systems. We also demonstrate that FLL is different from generalization effects conventionally associated with neural network models. As FLL is a generic property of distributed representations, it may constitute an important factor in human memory.
Self-test methodology for at-speed test of crosstalk in chip interconnects

The effect of crosstalk errors is most significant in high-performance circuits, mandating at-speed testing for crosstalk defects. This paper describes a self-test methodology that we have developed to enable on-chip at-speed testing of crosstalk defects in System-on-Chip interconnects. The self-test methodology is based on the Maximal Aggressor Fault Model [13], that enables testing of the interconnect with a linear number of test patterns. To enable self-testing of the interconnects, we have designed efficient on-chip test generators and error detectors to be embedded in necessary cores; while the test generators generate test vectors for crosstalk faults, the error detectors analyze the transmission of the test sequences received from the interconnects, and detect any transmission errors. We have also designed test controllers to initiate and manage test transactions by activating the appropriate test generators and error detectors, and having error diagnosis capability. We have developed, simulated, and synthesized parameterized HDL models of the self-test structures. We have applied the self-test methodology to test crosstalk defects in the buses of a DSP chip. Using a new high-level crosstalk simulation technique, we have validated the self-test methodology, including the self-test structures inserted in the DSP chip.
The bacteriocin lactococcin A specifically increases permeability of lactococcal cytoplasmic membranes in a voltage-independent, protein-mediated manner

Lactococcin A is a bacteriocin produced by Lactococcus lactis. Its structural gene has recently been cloned and sequenced (M. J. van Belkum, B. J. Hayema, R. E. Jeeninga, J. Kok, and G. Venema, Appl. Environ. Microbiol. 57:492-498, 1991). Purified lactococcin A increased the permeability of the cytoplasmic membrane of L. lactis and dissipated the membrane potential. A significantly higher concentration of lactococcin A was needed to dissipate the membrane potential in an immune strain of L. lactis. Lactococcin A at low concentrations (0.029 microgram/mg of protein) inhibited secondary and phosphate-bond driven transport of amino acids in sensitive cells and caused efflux of preaccumulated amino acids. Accumulation of amino acids by immune cells was not affected by this concentration of lactococcin A. Lactococcin A also inhibited proton motive force-driven leucine uptake and leucine counterflow in membrane vesicles of the sensitive strain but not in membrane vesicles of the immune strain. These observations indicate that lactococcin A makes the membrane permeable for leucine in the presence or absence of a proton motive force and that the immunity factor(s) is membrane linked. Membrane vesicles of Clostridium acetobutylicum, Bacillus subtilis, and Escherichia coli were not affected by lactococcin A, nor were liposomes derived from phospholipids of L. lactis. These results indicate that lactococcin A acts on the cytoplasmic membrane and is very specific towards lactococci. The combined results obtained with cells, vesicles, and liposomes suggest that the specificity of lactococcin A may be mediated by a receptor protein associated with the cytoplasmic membrane.
Collective Intelligence Based Computational Approach to Web Intelligence

The World Wide Web has undergone major transformation during last few years, primarily due to its newly discovered ability to harness collective intelligence of the millions of users across the world. Users are no longer only passive consumers; they are actively participating to create new and useful content and more rich & personalized web applications. Techniques to leverage user contributions are on one hand making the Web a collective knowledge system (applications like Wikipedia), and on the other hand provide a new approach to mine the unstructured web-content for useful inferences & new knowledge. In this paper, we have discussed how the collective intelligence phenomenon is bringing about the paradigm shift in the Web; and presented our experimental work on a social-inference oriented approach for opinion analysis on the Blogosphere.
Elevated Carbon Dioxide Increases Contents of Flavonoids and Phenolic Compounds, and Antioxidant Activities in Malaysian Young Ginger (Zingiber officinale Roscoe.) Varieties

Zingiber officinale Roscoe. (Family Zingiberaceae) is well known in Asia. The plant is widely cultivated in village gardens in the tropics for its medicinal properties and as a marketable spice in Malaysia. Ginger varieties are rich in physiologically active phenolics and flavonoids with a range of pharmacological activities. Experiments were conducted to determine the feasibility of increasing levels of flavonoids (quercetin, rutin, catechin, epicatechin, kaempferol, naringenin, fisetin and morin) and phenolic acid (gallic acid, vanillic acid, ferulic acid, tannic acid, cinnamic acid and salicylic acid), and antioxidant activities in different parts of Malaysian young ginger varieties (Halia Bentong and Halia Bara) with CO2 enrichment in a controlled environment system. Both varieties showed an increase in phenolic compounds and flavonoids in response to CO2 enrichment from 400 to 800 µmol mol-1 CO2. These increases were greater in rhizomes compared to leaves. High performance liquid chromatography (HPLC) results showed that quercetin and gallic acid were the most abundant flavonoid and phenolic acid in Malaysian young ginger varieties. Under elevated CO2 conditions, kaempferol and fisetin were among the flavonoid compounds, and gallic acid and vanillic acid were among the phenolic compounds whose levels increased in both varieties. As CO2 concentration was increased from 400 to 800 µmol mol-1, free radical scavenging power (DPPH) increased about 30% in Halia Bentong and 21.4% in Halia Bara; and the rhizomes exhibited more enhanced free radical scavenging power, with 44.9% in Halia Bentong and 46.2% in Halia Bara. Leaves of both varieties also displayed good levels of flavonoid compounds and antioxidant activities. These results indicate that the yield and pharmaceutical quality of Malaysian young ginger varieties can be enhanced by controlled environment production and CO2 enrichment.