Miracle-dz/UniFAR-FTUs huggingface dataset:
Independent Vector Analysis for Source Separation Using a Mixture of Gaussians Prior

Convolutive mixtures of signals, which are common in acoustic environments, can be difficult to separate into their component sources. Here we present a uniform probabilistic framework to separate convolutive mixtures of acoustic signals using independent vector analysis (IVA), which is based on a joint distribution for the frequency components originating from the same source and is capable of preventing permutation disorder. Different gaussian mixture models (GMM) served as source priors, in contrast to the original IVA model, where all sources were modeled by identical multivariate Laplacian distributions. This flexible source prior enabled the IVA model to separate different type of signals. Three classes of models were derived and tested: noiseless IVA, online IVA, and noisy IVA. In the IVA model without sensor noise, the unmixing matrices were efficiently estimated by the expectation maximization (EM) algorithm. An online EM algorithm was derived for the online IVA algorithm to track the movement of the sources and separate them under nonstationary conditions. The noisy IVA model included the sensor noise and combined denoising with separation. An EM algorithm was developed that found the model parameters and separated the sources simultaneously. These algorithms were applied to separate mixtures of speech and music. Performance as measured by the signal-to-interference ratio (SIR) was substantial for all three models.
Molecular analysis of the UV-inducible pili operon from Sulfolobus acidocaldarius

Upon ultraviolet (UV) stress, hyperthermophilic Sulfolobus species show a highly induced transcription of a gene cluster responsible for pili biogenesis: the UV‐inducible pili operon (ups operon). This operon is involved in UV‐induced pili assembly, cellular aggregation, and subsequent DNA exchange between cells. As the system increases the fitness of Sulfolobus cells after UV light exposure, we assume that transfer of DNA takes place in order to repair UV‐induced DNA damages via homologous recombination. Here, we studied all genes present in the ups cluster via gene deletion analysis with a focus on UpsX, a protein that shows no identifiable functional domains. UspX does not seem to be structurally essential for UV‐induced pili formation and cellular aggregation, but appears to be important for efficient DNA transfer. In addition, we could show that pilin subunits UpsA and UpsB probably both function as major pilin subunits in the ups pili.
Mammaglobin as a novel breast cancer biomarker: multigene reverse transcription-PCR assay and sandwich ELISA.

BACKGROUND The aim of this study was to examine the potential usefulness of a mammaglobin multigene reverse transcription-PCR (RT-PCR) assay and a mammaglobin sandwich ELISA as diagnostic tools in breast cancer. METHODS We studied peripheral blood samples from 147 untreated Senegalese women with biopsy-confirmed breast cancer and gathered patient information regarding demographic, and clinical staging of disease. The samples were tested for mammaglobin and three breast cancer-associated gene transcripts by a multigene real-time RT-PCR assay and for serum mammaglobin protein by a sandwich ELISA assay. RESULTS In 77% of the breast cancer blood samples, a positive signal was obtained in the multigene RT-PCR assay detecting mammaglobin and three complementary transcribed genes. Fifty samples from healthy female donors tested negative. Significant correlations were found between mammaglobin protein in serum, presence of mammaglobin mRNA-expressing cells in blood, stage of disease, and tumor size. Circulating mammaglobin protein was detected in 68% of the breast cancer sera, and was increased in 38% in comparison with a mixed control population. The RT-PCR assay and the ELISA for mammaglobin produced a combined sensitivity of 84% and specificity of 97%. CONCLUSION The ELISA and RT-PCR for mammaglobin and mammaglobin-producing cells could be valuable tools for diagnosis and prognosis of breast cancer.
Local or Global Minima: Flexible Dual-Front Active Contours

Most variational active contour models are designed to find local minima of data-dependent energy functionals with the hope that reasonable initial placement of the active contour will drive it toward a "desirable" local minimum as opposed to an undesirable configuration due to noise or complex image structure. As such, there has been much research into the design of complex region-based energy functionals that are less likely to yield undesirable local minima when compared to simpler edge-based energy functionals whose sensitivity to noise and texture is significantly worse. Unfortunately, most of these more "robust" region-based energy functionals are applicable to a much narrower class of imagery compared to typical edge-based energies due to stronger global assumptions about the underlying image data. Devising new implementation algorithms for active contours that attempt to capture more global minimizers of already proposed image-based energies would allow us to choose an energy that makes sense for a particular class of energy without concern over its sensitivity to local minima. Such implementations have been proposed for capturing global minima. However, sometimes the completely-global minimum is just as undesirable as a minimum that is too local. In this paper, we propose a novel, fast, and flexible dual front implementation of active contours, motivated by minimal path techniques and utilizing fast sweeping algorithms, which is easily manipulated to yield minima with variable "degrees" of localness and globalness. By simply adjusting the size of active regions, the ability to gracefully move from capturing minima that are more local (according to the initial placement of the active contour/surface) to minima that are more global allows this model to more easily obtain "desirable" minimizers (which often are neither the most local nor the most global). Experiments on various 2D and 3D images and comparisons with some active contour models and region-growing methods are also given to illustrate the properties of this model and its performance in a variety of segmentation applications
Prevalence of Yersinia enterocolitica in Pigs Slaughtered in Chinese Abattoirs

ABSTRACT The distribution of Yersinia enterocolitica in slaughtered pigs in China was studied. A total of 8,773 samples were collected and examined from different pig abattoirs in 11 provinces from 2009 to 2011. Of these, 4,495 were oral-pharyngeal swab (tonsils) samples from pigs, 1,239 were from intestinal contents, and 3,039 were feces samples from abattoirs or local pigpens. The data showed that 1,132 strains were obtained, from which the isolation rate for Yersinia enterocolitica was 19.53% (878/4,495) from the tonsil samples, 7.51% (93/1,239) from intestinal contents, and 5.30% (161/3,039) from feces. Of the 850 pathogenic Yersinia strains, except for three of bioserotype 2/O:9 and three of bioserotype 4/O:3, most (844/850) were of bioserotype 3/O:3. Interestingly, pathogenic Y. enterocolitica accounted for the majority of the isolated strains from most provinces (85.17% to 100%), whereas from Heilongjiang, 96.52% (111/115) were classified as nonpathogenic biotype 1A with various serotypes, and only 3.48% of the strains (4/115) were pathogenic 3/O:3. All of the pathogenic strains were analyzed using pulsed-field gel electrophoresis (PFGE), and 49 patterns were obtained for the O:3 pathogenic strains; most of them were K6GN11C30021 (53.13%: 450/847) and K6GN11C30012 (21.37%: 181/847). Several strains from diarrhea patient samples revealed PFGE patterns identical to that from samples of local pigs, suggesting a possible link between porcine isolates and human infection. The results above suggested that Yersinia enterocolitica in slaughtered pigs from Chinese abattoirs was characterized by region-specific PFGE patterns and confirmed that strains isolated from pigs are closely related to those from human infections.
Geoarchaeology of Holocene oasis formation, hydro-agricultural management and climate change in Masafi, southeast Arabia (UAE)

Abstract Oases are subject to decreasing resources and changing human activities. Fully aware of their rich heritage, the United Arab Emirates (UAE) have undertaken work to preserve and revitalize these oases. However, there is a clear lack of understanding of the dynamic links between climate change, hydraulic and agricultural management, and socioeconomic activities. To clarify these links, our team conducted a systematic geoarchaeological, geophysical, spatial, and chronological study of the Masafi oasis, UAE. Results indicate the existence of a natural humid area as early as the late Pleistocene (~18 cal ka BP). These conditions persist during the early-mid Holocene with drainage activation and soil development (~12–6.3 ka). During the late Holocene, after the emergence of the “artificial” oasis around ~3250 cal yr BP, cycles of intense management suggesting water availability (~3250–2380 cal yr BP; 550 cal yr BP) alternate with episodes of fluvial detritism (~2380–1870 cal yr BP; >550 cal yr BP) and scattered evidence of farming activities with complex hydroclimatic signatures (~2300–550 cal yr BP). These results, together with regional environmental data, indicate that water and soil resources were available and exploited strategically throughout the Holocene despite adverse climatic conditions, and the oasis of Masafi could have acted as a desert refugium.
Predictive regulatory models in Drosophila melanogaster by integrative inference of transcriptional networks

Gaining insights on gene regulation from large-scale functional data sets is a grand challenge in systems biology. In this article, we develop and apply methods for transcriptional regulatory network inference from diverse functional genomics data sets and demonstrate their value for gene function and gene expression prediction. We formulate the network inference problem in a machine-learning framework and use both supervised and unsupervised methods to predict regulatory edges by integrating transcription factor (TF) binding, evolutionarily conserved sequence motifs, gene expression, and chromatin modification data sets as input features. Applying these methods to Drosophila melanogaster, we predict ∼300,000 regulatory edges in a network of ∼600 TFs and 12,000 target genes. We validate our predictions using known regulatory interactions, gene functional annotations, tissue-specific expression, protein–protein interactions, and three-dimensional maps of chromosome conformation. We use the inferred network to identify putative functions for hundreds of previously uncharacterized genes, including many in nervous system development, which are independently confirmed based on their tissue-specific expression patterns. Last, we use the regulatory network to predict target gene expression levels as a function of TF expression, and find significantly higher predictive power for integrative networks than for motif or ChIP-based networks. Our work reveals the complementarity between physical evidence of regulatory interactions (TF binding, motif conservation) and functional evidence (coordinated expression or chromatin patterns) and demonstrates the power of data integration for network inference and studies of gene regulation at the systems level.
The monitoring and early detection of Internet worms

After many Internet-scale worm incidents in recent years, it is clear that a simple self-propagating worm can quickly spread across the Internet and cause severe damage to our society. Facing this great security threat, we need to build an early detection system that can detect the presence of a worm in the Internet as quickly as possible in order to give people accurate early warning information and possible reaction time for counteractions. This paper first presents an Internet worm monitoring system. Then, based on the idea of "detecting the trend, not the burst" of monitored illegitimate traffic, we present a "trend detection" methodology to detect a worm at its early propagation stage by using Kalman filter estimation, which is robust to background noise in the monitored data. In addition, for uniform-scan worms such as Code Red, we can effectively predict the overall vulnerable population size, and estimate accurately how many computers are really infected in the global Internet based on the biased monitored data. For monitoring a nonuniform scan worm, especially a sequential-scan worm such as Blaster, we show that it is crucial for the address space covered by the worm monitoring system to be as distributed as possible.
Title : Analysis and Design of Full-Order Flux Observers for Sensorless Induction Motors Year : 2004 Version : Post print

This paper deals with the flux estimation for sensorless induction motor drives. The linearized model of the speedadaptive full-order flux observer is applied to help choosing the observer gain and the speed-adaptation gains. It is shown that the linearized model reveals potential instability problems that are difficult to find by other means. An observer gain and a method to vary the speed-adaptation gains in the field-weakening region are proposed. Experimental results show stable operation in a very wide speed range.
Torsion in Milnor fiber homology

In a recent paper, Dimca and N emethi pose the problem of nding a homogeneous polynomial f such that the homology of the complement of the hypersurface dened by f is torsion-free, but the homology of the Milnor ber of f has torsion. We prove that this is indeed possible, and show by construction that for each prime p, there is a polynomial with p-torsion in the homology of the Milnor ber. The techniques make use of properties of characteristic varieties of hyperplane arrangements.
Software aging in the eucalyptus cloud computing infrastructure

The need for high reliability, availability and performance has significantly increased in modern applications, that handle rapidly growing demands while providing uninterruptible services. Cloud computing systems fundamentally provide access to large pools of data and computational resources. Eucalyptus is a software framework largely used to implement private clouds and hybrid-style Infrastructure as a Service. It implements the Amazon Web Service (AWS) API, allowing interoperability with other AWS-based services. This article investigates the software aging effects in the Eucalyptus framework, considering workloads composed of intensive requests for remote storage attachment and virtual machine instantiations. We found problems that may be harmful to system dependability and performance, specifically regarding to RAM memory and swap space exhaustion, besides highly excessive CPU utilization by the virtual machines. We also present an approach that applies time series analysis to schedule rejuvenation, so as to reduce the downtime by predicting the proper moment to perform the rejuvenation. We experimentally evaluate our approach using an Eucalyptus test bed. The results show that our approach achieves higher availability, when compared to a threshold-triggered rejuvenation method based on continuous monitoring of resources utilization.
Learning in Parkinson’s disease: eyeblink conditioning, declarative learning, and procedural learning

OBJECTIVE To assess the degree of learning ability in Parkinson’s disease. METHODS Three different learning tasks: eyeblink classical conditioning with delay and trace paradigms, the California verbal learning test (CVLT), and a serial reaction time task (SRTT) were studied in patients with Parkinson’s disease and normal (control) subjects. RESULTS In the eyeblink conditioning tasks, both patients and normal subjects showed significant learning effects without between group differences. In the CVLT, patients remembered significantly fewer words than normal subjects in both short term and long term cued recall tasks. In the SRTT, normal subjects had significantly reduced response time and error rates across blocks of repeated sequence trials, whereas patients had significantly reduced error, but not response time rates. CONCLUSION Impairment of nigrostriatal pathways selectively affects performance in complex learning tasks that are competitive and require alertness such as the SRTT, but not in simple learning procedures such as eyeblink conditioning.
Eye Tracking in Human-Computer Interaction and Usability Research : Current Status and Future Prospects

Eye-movement tracking is a method that is increasingly being employed to study usability issues in HCI contexts. The objectives of the present chapter are threefold. First, we introduce the reader to the basics of eye-movement technology, and also present key aspects of practical guidance to those who might be interested in using eye tracking in HCI research, whether in usability-evaluation studies, or for capturing people’s eye movements as an input mechanism to drive system interaction. Second, we examine various ways in which eye movements can be systematically measured to examine interface usability. We illustrate the advantages of a range of different eye-movement metrics with reference to state-of-the-art usability research. Third, we discuss the various opportunities for eye-movement studies in future HCI research, and detail some of the challenges that need to be overcome to enable effective application of the technique in studying the complexities of advanced interactive-system use.
Title: Ongoing Activity in the Optic Tectum Is Correlated on a Trial-by-trial Basis with the Pupil Dilation Response Running Title: Ongoing Activity in the Optic Tectum Introduction

24 The selection of the appropriate stimulus to induce an orienting response is a basic 25 task thought to be partly achieved by tectal circuitry. Here we addressed the relationship 26 between neural activity in the optic tectum (OT) and orienting behavioral responses. We 27 recorded multiunit activity in the intermediate/deep layers of the OT of the barn owl 28 simultaneously with pupil dilation responses (PDR, a well-known orienting response 29 common to birds and mammals). A trial-by-trial analysis of the responses revealed that 30 the PDR generally did not correlate with the evoked neural responses but significantly 31 correlated with the rate of ongoing neural activity measured shortly before the stimulus. 32 Following this finding, we characterized ongoing activity in the OT and showed that in 33 the intermediate/deep layers it tended to fluctuate spontaneously. It is characterized by 34 short periods of high ongoing activity during which the probability of a PDR to an 35 auditory stimulus inside the receptive field is increased. These high ongoing activity 36 periods were correlated with increase in the power of gamma band local field potential 37 oscillations. Through dual recordings, we showed that the correlation coefficients of 38 ongoing activity decreased as a function of distance between recording sites in the tectal 39 map. Significant correlations were also found between recording sites in the OT and the 40 forebrain entopallium. Our results suggest that an increase of ongoing activity in the OT 41 reflects an internal state during which coupling between sensory stimulation and 42 behavioral responses increases.
Amiodarone induced optic neuropathy

Aim: To determine the clinical features of amiodarone induced optic neuropathy, which may help distinguish it from non-arteritic anterior ischaemic optic neuropathy. Methods: Retrospective observational case series of patients diagnosed with amiodarone induced optic neuropathy at the neuro-ophthalmology service from March 1998 to February 2001. Amiodarone was discontinued after discussion with the patient's cardiologist. Visual acuity, colour vision, automated perimetry, and funduscopy were performed on initial and follow up examinations. Results: Three patients with amiodarone induced optic neuropathy presented with mildly decreased vision, visual field defects, and bilateral optic disc swelling. Upon discontinuing the medication, visual function and optic disc swelling slowly improved in all three patients. Conclusion: Amiodarone induced optic neuropathy can present with visual dysfunction, and is typically a bilateral process. Upon discontinuation of amiodarone, slow resolution of optic disc swelling occurs and visual function improves in some patients.
Gemcitabine‐based combination chemotherapy as salvage treatment for refractory or relapsing aggressive non‐Hodgkin's lymphoma

Although CHOP (cyclophosphamide, adriamycin, vincristine, and prednisolone) or more intensive chemotherapy regimens with or without rituximab can cure around 50% of advanced-stage aggressive non-Hodgkin's lymphoma (NHL), a substantial proportion of the patients develop refractory or relapsing diseases. However, high-dose chemotherapy followed by autologous stem cell transplantation usually rescues a limited number of patients. Historically, traditional chemotherapy regimens, including ESHAP (etoposide, methylprednisolone, high-dose Ara-C, and cisplatin), ICE (ifosfamide, carboplatin, and etoposide), DHAP (high-dose Ara-C, cisplatin, and dexamethasone), and EPOCH (etoposide, doxorubicin, vincristine, cyclophosphamide, and prednisone) are used for salvage treatment in refractory or relapsing NHL [1]; however, the use of these regimens is often limited by the relatively severe toxicities. For example, high-dose Ara-C-containing regimens (ESHAP and DHAP) have significant hematological, skin, conjunctival, and mucosal toxicities [2,3]. Accumulated cardiac toxicity would be a major problem of anthracycline-containing regimens (EPOCH) for patients after standard first-line CHOP-based regimens [4]. Previous studies using ICE for a salvage chemotherapy regimen usually enrolled transplant-eligible patients, and the hematological toxicity remained significant, although the aggressive prophylactic granulocyte colony stimulating factor (G-CSF) was used [5]. Therefore, a safe and effective salvage chemotherapy regimen is needed for the treatment of relapsing or refractory aggressive NHL, irrespective of the initial response to chemotherapy, patients' age, or patients' comorbidities.
Secondary Transmission of Toxic Baits in German Cockroach (Dictyoptera: Blattellidae)

Abstract The death rates of three toxic gel baits (fipronil bait, 0.05%; hydramethylnon, bait 2.15%; and abamectin B1 bait, 0.05%) were estimated in Blattella germanica (L.). After ingestion, all three baits killed similar proportions of cockroaches, but they died more rapidly after ingestion of fipronil bait than after ingestion of abamectin B1 bait or of hydramethylnon bait. Laboratory experiments evaluated the impact of secondary transmission of fipronil bait and hydramethylnon bait. Mortality rates caused by secondary transmission were higher for fipronil bait than for hydramethylnon bait. Under controlled laboratory conditions, secondary transmission occurred mainly through direct contact with, or ingestion of, traces of baits dispersed in the environment by contaminated cockroaches. These traces were either deposited by “trampling” in the environment or on dead contaminated cockroaches. Social interactions and cannibalism played a minor role in secondary transmission of these two baits.