Miracle-dz/UniFAR-FTUs huggingface dataset:
Robust Estimation of cDNA Microarray Intensities with Replicates

We consider robust estimation of gene intensities from cDNA microarray data with replicates. Several statistical methods for estimating gene intensities from microarrays have been proposed, but there has been little work on robust estimation of the intensities. This is particularly relevant for experiments with replicates, because even one outlying replicate can have a disastrous effect on the estimated intensity for the gene concerned. Because of the many steps involved in the experimental process from hybridization to image analysis, cDNA microarray data often contain outliers. For example, an outlying data value could occur because of scratches or dust on the surface, imperfections in the glass, or imperfections in the array production. We develop a Bayesian hierarchical model for robust estimation of cDNA microarray intensities. Outliers are modeled explicitly using a t-distribution, and our model also addresses classical issues such as design effects, normalization, transformation, and nonconstant variance. Parameter estimation is carried out using Markov Chain Monte Carlo. The method is illustrated using two publicly available gene expression data sets. The between-replicate variability of the intensity estimates is reduced by 64% in one case and by 83% in the other compared to raw log ratios. The method is also compared to the ANOVA normalized log ratio, the removal of outliers based on Dixon’s test, and the lowess normalized log ratio, and the between-replicate variation is reduced by more than 55% relative to the best of these methods for both data sets. We also address the issue of whether the image background should be removed when estimating intensities. It has been argued that one should not do so because it increases variability, while the arguments for doing so are that there is a physical basis for the image background, and that not doing so will bias the estimated log-ratios of differentially expressed genes downwards. We show that the arguments on both sides of this debate are correct for our data, but that by using our model one can have the best of both worlds: one can subtract the background without greatly increasing variability.
Spectrum of CHL dyons from genus-two partition function

We compute the genus-two chiral partition function of the left-moving heterotic string for a 2 CHL orbifold. The required twisted determinants can be evaluated explicitly in terms of the untwisted determinants and theta functions using orbifold techniques. The dependence on Prym periods cancels neatly once summation over odd charges is properly taken into account. The resulting partition function is a Siegel modular form of level two and precisely equals recently proposed dyon partition function for this model. This result provides an independent weak coupling derivation of the dyon partition function using the M-theory lift of string webs representing the dyons. We discuss generalization of this technique to general N orbifolds.
BTZ black hole with Chern-Simons and higher derivative terms

The entropy of a BTZ black hole in the presence of gravitational Chern-Simons terms has previously been analyzed using Euclidean action formalism. In this paper we treat the BTZ solution as a two dimensional black hole by regarding the angular coordinate as a compact direction, and use Wald's Noether charge method to calculate the entropy of this black hole in the presence of higher derivative and gravitational Chern-Simons terms. The parameters labelling the black hole solution can be determined by extremizing an entropy function whose value at the extremum gives the entropy of the black hole.
Wireless Sensor Networks for Activity Monitoring using Multi-sensor Multi-modal Node Architecture

A multi-sensor, multi-modal sensor node for human and vehicle activity monitoring is designed and developed. As a first step to achieve our objective, we have used a dual pyroelectric IR (PIR) sensor system for human activity monitoring. The sampled data from two PIR sensors, under laboratory conditions, is first processed individually to determine the event window size, which is then fed to simple algorithms to determine direction and potentially measure speed of passing humans. We also show that human count can be obtained for some special scenarios. Preliminary results of our experimentation show the effectiveness of the simple algorithms proposed.
Labor Mobility, Redistribution, and Pension Reform in Europe

In this Paper, we discuss the main characteristics of European mandatory pension systems and the implications for these systems of increasing factor mobility. In particular, we expect the extent of redistribution (both intra- and intergenerational) in national pension systems to decrease. The latter result should hold true even in the presence of mobility limited to some particular subgroups in the working population. The present Paper explores this issue by considering three types of mobility: not only mobility at the beginning of the working life, but also mobility during the working career and mobility at retirement. (This abstract was borrowed from another version of this item.)
The Currency of Ideas

A plastic container has a bottom wall; upstanding side walls; a snap acting top wall with a dispensing opening, said top capable of flexing in two concentric annular zones to assume two stable positions; and a diaphragm across the upper portion of said container just below said top wall, said diaphragm having at least one perforation around the periphery thereof. The top is snapped into a convex up position to dispense the contents through the perforations and thereafter through the dispensing opening, and is snapped into a concave down position to close the container. This container primarily comprises parts fabricated from sheet material by thermoforming and die cutting.
Technologies and Tensions: Designing Online Environments for Teaching Technical Communication

Introduction: Technology and Traditional Collides This chapter discusses how technical communication teachers and researchers (in particular, untenured teachers and researchers) who work in virtual spaces need to be aware of the traditional contexts that surround them; that is, we need to acknowledge the complex web of departmental, institutional, political, and extra-organizational factors that envelops our work in the areas of electronic interconnectivity, collaboration, and the virtual distribution of information. Specifically, I assert that as technical communication faculty motivated to integrate technology into our research and our classrooms, we often mistakenly believe that the problem we face is a technical, rather than contextual one.
Identifying the role that animals play in their social networks

Techniques recently developed for the analysis of human social networks are applied to the social network of bottlenose dolphins living in Doubtful Sound, New Zealand. We identify communities and subcommunities within the dolphin population and present evidence that sex– and age–related homophily play a role in the formation of clusters of preferred companionship. We also identify brokers who act as links between sub–communities and who appear to be crucial to the social cohesion of the population as a whole. The network is found to be similar to human social networks in some respects but different in some others, such as the level of assortative mixing by degree within the population. This difference elucidates some of the means by which the network forms and evolves.
An efficient implementation of uplink baseband signal generator in LTE UE transmitters

An efficient hardware-optimized uplink baseband signal generation algorithm and its ASIC implementation in the LTE user equipment (UE) transmitter are presented in this paper. Optimization covers top level as well as module level. A paralleled Turbo encoder and a Cooley-Tukey based DFT are proposed. The optimized algorithm achieves significantly lower computational complexity compared with the original algorithm in the LTE specification and better performance compared to the existing results. The ASIC architecture is designed to reduce the logic complexity and implemented in 55nm CMOS, which achieves short time latency and low hardware cost in terms of the cell area.
Use of the Strengths and Difficulties Questionnaire to identify treatment needs in looked-after children referred to CAMHS

Background: In England and Wales, the single-informant Strengths and Difficulties Questionnaire (SDQ) is used to assess and monitor looked-after children’s (LAC) mental health; and some targeted Child and Adolescent Mental Health Services (CAMHS) include a minimum SDQ score in their acceptance criteria. However, its ability to identify LAC who need mental health treatment is insufficiently understood. Methods: One hundred and forty four LAC referrals to a Targeted CAMHS Team were screened as part of a larger study. To establish how well the SDQ identified children who required treatment, Total Difficulties Scores from single-informant SDQs submitted at referral were compared to treatment recommendations following routine CAMHS assessment in a real-world setting. To explain the results, clinicians (n = 9) from the team were interviewed and key themes identified using thematic analysis. Results: AUROC analysis found that the single-informant SDQ discriminated between children who were assessed as needing a mental health intervention and those who did not with low accuracy when SDQs were completed by carers or young people themselves, and moderate accuracy for teacher-completed SDQs. Optimal cutoff scores are calculated and are lower than advised in scoring guidance. Key themes from clinician interviews identified possible gaps and limitations: Developmental trauma and attachment difficulties, A different kind of patient? , Seeing the “bad” but neglecting the sad, and The importance of clinical judgment. Conclusions: Contrary to current UK Government policy, this study suggests that the single-report SDQ should not be relied upon as a sole means of identifying mental health difficulties in this vulnerable, high-risk population.
An Evaluation Framework for Semantic Search in P2P Networks

We address the problem of evaluating peer-to-peer information retrieval (P2PIR) systems with semantic overlay structure. The P2PIR community lacks a commonly accepted testbed, such as TREC is for the classic IR community. The problem with using classic test collections in a P2P scenario is that they provide no realistic distribution of documents and queries over peers, which is, however, crucial for realistically simulating and evaluating semantic overlays. On the other hand, document collections that can be easily distributed (e.g. by exploiting categories or author information) lack both queries and relevance judgments. Therefore, we propose an evaluation framework, which provides a strategy for constructing a P2PIR testbed, consisting of a prescription for content distribution, query generation and measuring effectiveness without the need for human relevance judgments. It can be used with any document collection that contains author information and document relatedness (e.g. references in scientific literature). Author information is used for assigning documents to peers, relatedness is used for generating queries from related documents. The ranking produced by the P2PIR system is evaluated by comparing it to the ranking of a centralised IR system using a new evaluation measure related to mean average precision. The combination of these three things – realistic content distribution, realistic and automated query generation and distribution, and a meaningful and flexible evaluation measure for rankings – offers an improvement over existing P2PIR evaluation approaches.
A self-tuning page cleaner for DB2

The buffer pool in a DBMS is used to cache the disk pages of the database. Because typical database workloads are I/O-bound, the effectiveness of the buffer pool management algorithm is a crucial factor in the performance of the DBMS. In IBM's DB2 buffer pool, the page cleaning algorithm is used to write changed pages to disks before they are selected for replacement. We conducted a detailed study of page cleaning in DB2 version 7.1. 0 for Windows by both trace-driven simulation and measurements. Our results show that system throughput can be increased by 19% when the page cleaning algorithm is carefully tuned. In practice, however the manual tuning of this algorithm is difficult. A self-tuning algorithm for page cleaning is proposed posed in this paper to automate this tuning task. Simulation results show that the self-tuning algorithm can achieve performance comparable to the best manually tuned system.
An Empirically Efficient Analytical Cascade Calibration of the Libor Market Model Based Only on Directly Quoted Swaptions Data

This work focuses on the swaptions automatic cascade calibration algorithm (CCA) for the LIBOR Market Model (LMM) first appeared in Brigo and Mercurio (2001). This method induces a direct analytical correspondence between market swaption volatilities and LMM parameters, and allows for a perfect recovery of market quoted swaption volatilities if a common industry swaptions approximation is used. We present explicitly an extension of the CCA to calibrate the entire swaption matrix rather than its upper triangular part. Then, while previous tests on earlier data showed the appearance of numerical problems, we present here different calibration cases leading to acceptable results. We analyze the characteristics of the configurations used and concentrate on the effects of different exogenous instantaneous historical or parametric correlation matrices. We also investigate the influence of manipulations in input swaptions data for missing quotes, and devise a new algorithm maintaining all the positive characteristics of the CCA while relying only on directly quoted market data. Empirical results on a larger range of market situations and instantaneous covariance assumptions show this algorithm to be more robust and efficient than the previous version. Calibrated parameters are in general regular and financially satisfactory, as confirmed by the analysis of various diagnostics implied structures. Finally we Monte Carlo investigate the reliability of the underlying LMM swaption analytical approximation in the new context, and present some possibilities to include information coming from the semi-annual tenor cap market.
Model spectrum-progression with DTW and ANN for speech synthesis

In this paper, an ANN based spectrum-progression model (SPM) is proposed. This model is intended to improve the fluency level of synthetic Mandarin speech under the situation that only a small training corpus is available. In constructing this model, first each target syllable is matched with its reference syllable by using DTW. Then, each warped path, i.e. spectrum-progression path, is time normalized to fixed dimensions, and used to train an ANN based SPM. After training, the SPM is used together with other modules such as text analysis, prosody parameter generation, and signal sample generation to synthesize Mandarin speech. Then, the synthetic speech is used to conduct perception tests. The test results show that the SPM proposed here can indeed improve the fluency level noticeably.
Training topic classifiers for conversational speech with limited data

In this paper we demonstrate how automatically generated transcriptions can be used to develop an effective topic classification application. Two key contributions of our work are (a) investigating the impact of unsupervised transcriptions on topic classification where the transcription system has been trained with very limited amounts of data, and (b) demonstrating the use of mixture language models that significantly improve topic classification performance.
When the immune system goes on the attack

757 Bdellovibrio’s voracious appetite for bacteria has been known for more than 40 years, and it is puzzling to Schuster that the subject was not more vigorously pursued by researchers. He has already started cooperating with a biotechnology company to develop a treatment for external wounds infected by Pseudomonas. “So far we’re concentrating on external applications,” he said, but he is disappointed in the low level of interest from industry, which considers the discovery to be too far from application for investment. Meanwhile, the sequencing of another Bdellovibrio strain is allowing genomic comparisons, further increasing the understanding of the genes involved in predation. These number over 240. Not surprisingly, “genetic modification [of Bdellovibrio] is still a thing of the future; we need to understand the genetic traits first,” Schuster commented. But the basic research is already a perfect example of the confluence of many fields: microbiology, cell biology, molecular biology and immunology.
Evidence for a contribution of lateral inhibition to orientation tuning and direction selectivity in cat visual cortex: reversible inactivation of functionally characterized sites combined with neuroanatomical tracing techniques

We have previously reported that cells in cat areas 17 and 18 can show increases in response to non‐optimal orientations or directions, commensurate with a loss of inhibition, during inactivation of laterally remote, visuotopically corresponding sites by iontophoresis of γ‐aminobutyric acid (GABA). We now present anatomical evidence for inhibitory projections from inactivation sites to recording sites where ‘disinhibitory’ effects were elicited. We made microinjections of [3H]‐nipecotic acid, which selectively exploits the GABA re‐uptake mechanism, < 100 μm from recording sites where cells had shown either an increase in response to non‐optimal orientations during inactivation of a cross‐orientation site (n = 2) or an increase in response to the non‐preferred direction during inactivation of an iso‐orientation site with opposite direction preference (n = 5). Retrogradely labelled GABAergic neurons were detected autoradiographically and their distribution was reconstructed from series of horizontal sections. In every case, radiolabelled cells were found in the vicinity of the inactivation site (three to six within 150 μm). The injection and inactivation sites were located in layers II/III–IV and their horizontal separation ranged from 400 to 560 μm. In another experiment, iontophoresis of biocytin at an inactivation site in layer III labelled two large basket cells with terminals in close proximity to cross‐orientation recording sites in layers II/III where disinhibitory effects on orientation tuning had been elicited. We argue that the inactivation of inhibitory projections from inactivation to recording sites made a major contribution to the observed effects by reducing the strength of inhibition during non‐optimal stimulation in recurrently connected excitatory neurons presynaptic to a recorded cell. The results provide further evidence that cortical orientation tuning and direction selectivity are sharpened, respectively, by cross‐orientation inhibition and iso‐orientation inhibition between cells with opposite direction preferences.
The impact of group communication paradigms on groupware support

Group Communication Paradigms play an important role in the management of group activities, such as reliable information diffusion in support of replication and cooperation. They consequently provide an appropriate framework for groupware applications support. To meet the new challenges posed by large scale distributed settings like the Internet, a new generation of group communication systems has emerged, built on the lessons learnt from early prototypes. This paper presents new services/features proposed by this new generation of systems and shows their relevance in the context of groupware support. Experiments with a cooperative application demonstrate how the features of a group-based system like NAVTECH can be used to enhance the functionality of groupware applications. NAVTECH is a modem group communication and activity support system developed at INESC.
Involvement of AlgQ in Transcriptional Regulation of Pyoverdine Genes in Pseudomonas aeruginosa PAO1

ABSTRACT In response to iron limitation, Pseudomonas aeruginosa produces the fluorescent siderophore pyoverdine. Transcription of pyoverdine biosynthetic (pvd) genes is driven by the iron starvation sigma factor PvdS, which is negatively regulated by the Fur-Fe(II) holorepressor. We studied the effect of AlgQ, the Escherichia coli Rsd orthologue, on pyoverdine production by P. aeruginosa PAO1. AlgQ is a global regulatory protein which activates alginate, ppGpp, and inorganic polyphosphate synthesis through a cascade involving nucleoside diphosphate kinase (Ndk). AlgQ is also capable of interacting with region 4 of RpoD. In a reconstituted E. coli system, PvdS-dependent transcription from the pvdA promoter was doubled by the multicopy algQ gene. The P. aeruginosa ΔalgQ mutant exhibited a moderate but reproducible reduction in pyoverdine production compared with wild-type PAO1, as a result of a decline in transcription of pvd genes. PvdS expression was not affected by the algQ mutation. Single-copy algQ fully restored pyoverdine production and expression of pvd genes in the ΔalgQ mutant, while ndk did not. An increased intracellular concentration of RpoD mimicked the ΔalgQ phenotype, whereas PvdS overexpression suppressed the algQ mutation. E. coli rsd could partially substitute for algQ in transcriptional modulation of pvd genes. We propose that AlgQ acts as an anti-sigma factor for RpoD, eliciting core RNA polymerase recruitment by PvdS and transcription initiation at pvd promoters. AlgQ provides a link between the pyoverdine and alginate regulatory networks. These systems have similarities in responsiveness and physiological function: both depend on alternative sigma factors, respond to nutrient starvation, and act as virulence determinants for P. aeruginosa.
Parallel Implementation of the 2D Discrete Wavelet Transform on Graphics Processing Units: Filter Bank versus Lifting

The widespread usage of the discrete wavelet transform (DWT) has motivated the development of fast DWT algorithms and their tuning on all sorts of computer systems. Several studies have compared the performance of the most popular schemes, known as filter bank scheme (FBS) and lifting scheme (LS), and have always concluded that LS is the most efficient option. However, there is no such study on streaming processors such as modern Graphics Processing Units (GPUs). Current trends have transformed these devices into powerful stream processors with enough flexibility to perform intensive and complex floating-point calculations. The opportunities opened up by these platforms, as well as the growing popularity of the DWT within the computer graphics field, make a new performance comparison of great practical interest. Our study indicates that FBS outperforms LS in current-generation GPUs. In our experiments, the actual FBS gains range between 10 percent and 140 percent, depending on the problem size and the type and length of the wavelet filter. Moreover, design trends suggest higher gains in future-generation GPUs.