Miracle-dz/UniFAR-FTUs huggingface dataset:
Fast content-based visual mapping for interactive exploration of document collections.

This paper presents a fast technique for map generation of document collections that, besides being able to group (and separate) documents by their contents, runs at very manageable computational costs, generating maps of preprocessed text in a matter of seconds. Based on multi-dimensional projection techniques and an algorithm for projection improvement, it results in a surface map that allows the user to identify a number of important relationships between documents and groups of documents that are reflected as visual attributes such as height, color, isolines as well as aural attributes (such as pitch). The map is interactive, allowing further exploration and narrowing of focus on a search task. The technique, named IDMAP (Interactive Document Map), is fully described in this paper. The results are bound to support a large number of applications that rely on retrieval and examination of document collections.
A pseudo random postfix OFDM based modulator for multiple antennae systems

This contribution extends the recently proposed pseudo-random-postfix OFDM (PRP-OFDM) transceiver to the multiple transmit multiple receive (MTMR) antennae context. In this paper a new generic MTMR modulator is proposed that grants a low complexity semi-blind identification of all channels between any transmit and receive antenna based on order-one statistics. A new channel tracking strategy is detailed based on a moving average (MA) Doppler modeling that preserves the Jakes channel coefficients correlation properties. Moreover two transceiver architectures are presented with an Alamouti based apace-time (ST) block code: equalization schemes with or without postfix interference cancellation and related modulators. Performance is illustrated by simulations in the context of the 5.2 GHz OFDM WLAN IEEE 802.11a standard.
Unsupervised clustering of vibration signals for identifying anomalous conditions in a nuclear turbine

We consider a real industrial case concerning 148 shut-down multidimensional transients of a nuclear power plant NPP turbine. The objective is to identify groups of transients with similar functional behaviors, and distinguish transients with peculiar behaviors which can be representative of anomalous conditions in the turbine. This objective is pursued by analyzing 7 vibration signals referred to the turbine shaft. The novelty of the work consists in transforming the signals into the “turbine speed-domain” for aligning them according to the turbine speed, so as to easily recognize outlier transients and then performing a fuzzy similarity analysis based on pointwise differences. Spectral analysis and Fuzzy C-Means FMC clustering are applied to identify the turbine anomalous conditions.
CEPSTRUM-LIKE ICA REPRESENTATIONS FOR TEXT INDEPENDENT SPEAKER RECOGNITION

Automatic methods to determine voiceprints in speech samples predominantly use short-time spectra to yield specific features of a given speaker. Among these, the Mel Frequency Cepstrum Coefficient (MFCC) features are widely used today. The speaker recognition method presented here is based on short-time spectra, however the feature extraction process does not correspond to the MFCC process. The motivation was to avoid what we see as shortcomings of present approaches, particularly the blurring effect in the frequency domain, which confuses rather than helps in distinguishing speakers. We introduce a speech synthesis model that can be identified using Independent Component Analysis (ICA). The ICA representations of log spectral data result in cepstral-like, independent coefficients, which capture correlations among frequency bands specific to the given speaker. It also results in speaker specific basis functions. Coefficients determined from test data using a speaker’s true basis functions show a low degree of correlation, while those determined using other basis functions do not. This enables the system to reliably recognize speakers. The resulting speaker recognition method is text-independent, invariant over time, and robust to channel variability. Its effectiveness has been tested in representing and recognizing speakers from a set of 462 people from the TIMIT database.
Emotion Cause Detection with Linguistic Constructions

This paper proposes a multi-label approach to detect emotion causes. The multi-label model not only detects multi-clause causes, but also captures the long-distance information to facilitate emotion cause detection. In addition, based on the linguistic analysis, we create two sets of linguistic patterns during feature extraction. Both manually generalized patterns and automatically generalized patterns are designed to extract general cause expressions or specific constructions for emotion causes. Experiments show that our system achieves a performance much higher than a baseline model.
Standardizing biomass reactions and ensuring complete mass balance in genome‐scale metabolic models

Motivation In a genome‐scale metabolic model, the biomass produced is defined to have a molecular weight (MW) of 1 g mmol−1. This is critical for correctly predicting growth yields, contrasting multiple models and more importantly modeling microbial communities. However, the standard is rarely verified in the current practice and the chemical formulae of biomass components such as proteins, nucleic acids and lipids are often represented by undefined side groups (e.g. X, R). Results We introduced a systematic procedure for checking the biomass weight and ensuring complete mass balance of a model. We identified significant departures after examining 64 published models. The biomass weights of 34 models differed by 5‐50%, while 8 models have discrepancies >50%. In total 20 models were manually curated. By maximizing the original versus corrected biomass reactions, flux balance analysis revealed >10% differences in growth yields for 12 of the curated models. Biomass MW discrepancies are accentuated in microbial community simulations as they can cause significant and systematic errors in the community composition. Microbes with underestimated biomass MWs are overpredicted in the community whereas microbes with overestimated biomass weights are underpredicted. The observed departures in community composition are disproportionately larger than the discrepancies in the biomass weight estimate. We propose the presented procedure as a standard practice for metabolic reconstructions. Availability and implementation The MALTAB and Python scripts are available in the Supplementary Material. Contact costas@psu.edu or joshua.chan@connect.polyu. hk Supplementary information Supplementary data are available at Bioinformatics online.
Direct regulation of nucleosome density by the conserved AAA-ATPase Yta7

Yta7 is a highly conserved bromodomain-containing protein with AAA-ATPase homology originally implicated in heterochromatin boundary function in Saccharomyces cerevisiae. Although increased activity of the human ortholog has been implicated in malignant breast tumors, Yta7's precise mode of action is unknown. Transcriptional analysis in yeast cells revealed a role for Yta7 and its ATPase function in gene induction, including galactose- and sporulation-induced transcription. This requirement was direct and activating, because Yta7 associated with the GAL gene cluster only upon transcriptional induction. Suggestive of a role in transcriptional elongation, Yta7 localized to the ORFs of highly transcribed genes. Intriguingly, the yta7Δ mutant's transcriptional defects were partially suppressed by decreased dosage of histones H3 and H4. Consistent with this suppression, cells lacking Yta7 exhibited both increased levels of chromatin-incorporated histone H3 and decreased nucleosome spacing. Importantly, this modulation of H3 levels occurred independently of changes in H3 transcript level. Because Yta7 binds histone H3 in vitro, these results suggested a direct role for Yta7 in H3 eviction or degradation. Further, local loss of Yta7 activity at a long inducible gene resulted in accumulation of H3 at the 3′ end upon transcriptional activation, implying Yta7 may regulate H3 cotranscriptionally.
Complete Genome Sequence of Staphylococcus succinus 14BME20 Isolated from a Traditional Korean Fermented Soybean Food

ABSTRACT The complete genome sequence of Staphylococcus succinus 14BME20, isolated from a Korean fermented soybean food and selected as a possible starter culture candidate, was determined. Comparative genome analysis with S. succinus CSM-77 from a Triassic salt mine revealed the presence of strain-specific genes for lipid degradation in strain 14BME20.
Platelet-activating factor augments meningeal inflammation elicited by Haemophilus influenzae lipooligosaccharide in an animal model of meningitis

Research into the pathophysiology of bacterial meningitis has suggested a role for various endogenous inflammatory mediators, such as platelet-activating factor (PAF). In the present study, rats were inoculated intracisternally with various doses of PAF, with Haemophilus influenzae lipooligosaccharide (LOS) in high doses (20 ng) alone, and with a low dose of LOS (200 pg) with or without low doses of PAF (25 ng to 2.5 micrograms). Values for cerebrospinal fluid leukocytosis and percent blood-brain barrier permeability to systemically administered 125I-labeled albumin observed after inoculation of low-dose LOS with PAF were greater (P < 0.05) than those observed after inoculation of low-dose LOS alone and not statistically different from those observed after inoculation of high-dose LOS. PAF alone elicited an inflammatory response only at high doses (25 micrograms). These results support the hypothesis that low cerebrospinal fluid PAF concentrations, such as those observed in children with bacterial meningitis, may augment the inflammatory response to the presence of bacteria in the subarachnoid space.
On the Role of Access Charges Under Network Competition

We aim to clarify the role of access charges under two-way network competition, employing a reduced-form approach. Retaining the key features of specific network competition models but imposing less structure, we analyze the impact of changes in access charges on linear and non-linear retail prices. We derive su.cient conditions for usage fees to be increasing (and subscriber charges to be decreasing) in access charges. These conditions are shown to be satisfied only under rather restrictive assumptions on the demand for calls, suggesting that implementing collusion by inflating access charges is likely to be nonfeasible.
Embedding nonlinear optimization in RRT* for optimal kinodynamic planning

Some of the latest developments in motion planning methods have addressed the merging of optimal control with sampling-based approaches, to handle the problem of optimal kinodynamic motion planning for complex robot systems in cluttered environments. These include embedding the Linear Quadratic Regulator method in an RRT* context, or solving the kinematic problem with an RRT algorithm first and then feeding the solution to an NLP solver. An alternative approach is presented here, in which NLP is embedded in an RRT* context from the start. The resulting methodological features are illustrated with numerical examples. These include problems in which differential constraints play a fundamental role.
RhoC Expression and Head and Neck Cancer Metastasis

RhoC protein, a known marker of metastases in aggressive breast cancers and melanoma, has also been found to be overexpressed in certain head and neck cancers, thus we investigated the correlation between RhoC expression and the metastatic behavior of head and neck squamous cell carcinoma. Selective inhibition of RhoC expression was achieved using lentiviral small hairpin RNA (shRNA) transduced and tracked with green fluorescent protein to achieve 70% to 80% RhoC inhibition. Fluorescence microscopy of the RhoC knockdown stable clones showed strong green fluorescence in the majority of cells, signifying a high efficiency of transduction. Importantly, quantitative real-time PCR showed no significant decrease in the mRNA expression levels of other members of the Ras superfamily. Cell motility and invasion were markedly diminished in RhoC-depleted cell lines as compared with control transduced lines. H&E staining of lung tissue obtained from severe combined immunodeficiency mice, which had been implanted with RhoC knockdown cells, showed a marked decrease in lung metastasis and inflammation of the blood vessels. The cultured lung tissue showed a significant decrease in cell growth in mice implanted with RhoC-depleted cell lines as compared with shRNA-scrambled sequence control lines. Microscopic studies of CD31 expression revealed substantial quantitative and qualitative differences in the primary tumor microvessel density as compared with parental and shRNA-scrambled controls. This study is the first of its kind to establish the involvement of RhoC specifically in head and neck metastasis. These findings suggest that RhoC warrants further investigation to delineate its robustness as a novel potentially therapeutic target. (Mol Cancer Res 2009;7(11):1771–80)
Sentence level information patterns for novelty detection

The detection of new information in a document stream is an important component of many potential applications. In this thesis, a new novelty detection approach based on the identification of sentence level information patterns is proposed. Given a user's information need, some information patterns in sentences such as combinations of query words, sentence lengths, named entities and phrases, and other sentence patterns, may contain more important and relevant information than single words. The work of the thesis includes three parts. First, we redefine "what is novelty detection" in the lights of the proposed information patterns. Examples of several different types of information patterns are given corresponding to different types of uses' information need. Second, we analyze why the proposed information pattern concept has a significant impact in novelty detection. A thorough analysis of sentence level information patterns is elaborated on data from the TREC novelty tracks, including sentence lengths, named entities (NEs), and sentence level opinion patterns. Finally, we present how we perform novelty detection based on information patterns, which focuses on the identification of previously unseen query-related patterns in sentences. A unified pattern-based approach is presented to novelty detection for both specific NE topics and more general topics. Experiments on novelty detection were carried out on data from the TREC 2002, 2003 and 2004 novelty tracks. Experimental results show that the proposed approach significantly improves the performance of novelty detection for both specific and general topics, therefore the overall performance for all topics, in terms of precision at top ranks. Future research directions are suggested.
Microsatellite Analysis Reveals Genetic Monogamy Among Female Boreal Owls

ANALISIS DE MICROSATELITES REVELAN MONOGAMIA GENETICA EN HEMBRAS DE AEGOLIUS FUNEREUS Utilizando datos de siete loci microsatelitales, evaluamos la paternidad genetica de pichones de la especie Aegolius funereus en el oeste de los Estados Unidos, incluyendo a Alaska. No encontramos evidencia de fertilizaciones extra-pareja entre 109 pichones de 32 nidos. Estos nidos fueron muestreados en seis subpoblaciones diferentes, algunas de las cuales presentaban altas densidades de individuos nidificantes. Con base en nuestros resultados y en los de otros cuatro estudios, concluimos que las fertilizaciones extra-pareja son extremadamente raras en A. funereus, y que las hembras son social y geneticamente monogamas, con excepcion de eventos de poliandria secuencial. Los machos podrian aprovisionar varios nidos cuando los recursos son abundantes, pero las hembras no participan en fertilizaciones extra-pareja. Aunque la densidad y la sincronia de la nidificacion parecen influenciar la frecuencia de las fertilizaciones .
Clostridium difficile associated disease

Direct gas-liquid chromatography of faecal specimens with isocaproic acid as a marker was used for the rapid diagnosis of Clostridium difficile associated diarrhoeal diseases. Ninety stools were examined and results were compared with conventional culture on selective medium and cytotoxin assay in tissue culture. Using a combined analysis of isocaproic acid and butyric acid peak heights we defined three categories: positive, negative, and indeterminate. When the indeterminate group was excluded, the positive and negative predictive values of gas-liquid chromatography analysis were 86-9% and 85% respectively compared with culture and 71-4% and 95% respectively compared with cytotoxin assay.
Copyright 2009 by Human Factors and Ergonomics Society, Inc. All rights reserved. 10.1518/107118109X12524443345276

In video-based surveillance people monitor a wide spatial area through video sensors for anomalous events related to safety and security. The size of the area, the number of video sensors, and the camera’s narrow field-of-view make this a challenging cognitive task. Computer vision researchers have developed a wide range of algorithms to recognize patterns in the video stream (intelligent cameras). These advances create a challenge for human supervision of these intelligent surveillance camera networks. This paper presents a new visualization that has been developed and implemented to integrate video-based computer vision algorithms with control of pan-tilt-zoom cameras in a manner that supports the human supervisory role.
Efficient Parsing for Bilexical Context-Free Grammars and Head Automaton Grammars

Several recent stochastic parsers use bilexical grammars, where each word type idiosyncratically prefers particular complements with particular head words. We present O(n4) parsing algorithms for two bilexical formalisms, improving the prior upper bounds of O(n5). For a common special case that was known to allow O(n3) parsing (Eisner, 1997), we present an O(n3) algorithm with an improved grammar constant.
Agreement between Clinical History Method, Orbscan IIz, and Pentacam in Estimating Corneal Power after Myopic Excimer Laser Surgery

The purpose of this study was to investigate the agreement between the clinical history method (CHM), Orbscan IIz, and Pentacam in estimating corneal power after myopic excimer laser surgery. Fifty five patients who had myopic LASIK/PRK were recruited into this study. One eye of each patient was randomly selected by a computer-generated process. At 6 months after surgery, postoperative corneal power was calculated from the CHM, Orbscan IIz total optical power at the 3.0 and 4.0 mm zones, and Pentacam equivalent keratometric readings (EKRs) at 3.0, 4.0, and 4.5 mm. Statistical analyses included multilevel models, Pearson’s correlation test, and Bland-Altman plots. The Orbscan IIz 3.0-mm and 4.0 mm total optical power, and Pentacam 3.0-mm, 4.0-mm, and 4.5-mm EKR values had strong linear positive correlations with the CHM values (r = 0.90–0.94, P = <0.001, for all comparisons, Pearson’s correlation). However, only Pentacam 3.0-mm EKR was not statistically different from CHM (P = 0.17, multilevel models). The mean 3.0- and 4.0-mm total optical powers of the Orbscan IIz were significantly flatter than the values derived from CHM, while the average EKRs of the Pentacam at 4.0 and 4.5 mm were significantly steeper. The mean Orbscan IIz 3.0-mm total optical power was the lowest keratometric reading compared to the other 5 values. Large 95% LoA was observed between each of these values, particularly EKRs, and those obtained with the CHM. The width of the 95% LoA was narrowest for Orbscan IIz 3.0-mm total optical power. In conclusion, the keratometric values extracted from these 3 methods were disparate, either because of a statistically significant difference in the mean values or moderate agreement between them. Therefore, they are not considered equivalent and cannot be used interchangeably.
FReSET: an evaluation framework for folksonomy-based recommender systems

FReSET is a new recommender systems evaluation framework aiming to support research on folksonomy-based recommender systems. It provides interfaces for the implementation of folksonomy-based recommender systems and supports the consistent and reproducible offline evaluations on historical data. Unlike other recommender systems framework projects, the emphasis here is on providing a flexible framework allowing users to implement their own folksonomy-based recommender algorithms and pre-processing filtering methods rather than just providing a collection of collaborative filtering implementations. FReSET includes a graphical interface for result visualization and different cross-validation implementations to complement the basic functionality.
Reproducibility of two functional field exercise tests for children with cerebral palsy who self‐propel a manual wheelchair

The aim of this study was to examine the test–retest reproducibility (reliability and agreement) of the 6‐minute push test (6MPT) and the one‐stroke push test (1SPT), and construct validity of the 6MPT in children with cerebral palsy (CP) who self‐propel a manual wheelchair.
H++: a server for estimating pKas and adding missing hydrogens to macromolecules

The structure and function of macromolecules depend critically on the ionization (protonation) states of their acidic and basic groups. A number of existing practical methods predict protonation equilibrium pK constants of macromolecules based upon their atomic resolution Protein Data Bank (PDB) structures; the calculations are often performed within the framework of the continuum electrostatics model. Unfortunately, these methodologies are complex, involve multiple steps and require considerable investment of effort. Our web server provides access to a tool that automates this process, allowing both experts and novices to quickly obtain estimates of pKs as well as other related characteristics of biomolecules such as isoelectric points, titration curves and energies of protonation microstates. Protons are added to the input structure according to the calculated ionization states of its titratable groups at the user-specified pH; the output is in the PQR (PDB + charges + radii) format. In addition, corresponding coordinate and topology files are generated in the format supported by the molecular modeling package AMBER. The server is intended for a broad community of biochemists, molecular modelers, structural biologists and drug designers; it can also be used as an educational tool in biochemistry courses.
Adapting learned robotics behaviours through policy adjustment

We present an approach to learning control policies for physical robots that achieves high efficiency by adjusting existing policies that have been learned on similar source systems, such as a similar robot with different physical parameters, or an approximate dynamics model simulator. This can be viewed as calibrating a policy learned on a source system, to match a desired behaviour in similar target systems. Our approach assumes that the trajectories described by the source robot are feasible on the target robot. By making this assumption, we only need to learn a mapping from the source robot state and action spaces to the target robot action space, which we call a policy adjustment model. We demonstrate our approach in simulation in the cart-pole balancing task and a two link double pendulum. We also validate our approach with a physical cart-pole system, where we adjust a learned policy under changes to the weight of the pole.