Miracle-dz/UniFAR-FTUs huggingface dataset:
Integrative analysis reveals the direct and indirect interactions between DNA copy number aberrations and gene expression changes

MOTIVATION DNA copy number aberrations (CNAs) and gene expression (GE) changes provide valuable information for studying chromosomal instability and its consequences in cancer. While it is clear that the structural aberrations and the transcript levels are intertwined, their relationship is more complex and subtle than initially suspected. Most studies so far have focused on how a CNA affects the expression levels of those genes contained within that CNA. RESULTS To better understand the impact of CNAs on expression, we investigated the correlation of each CNA to all other genes in the genome. The correlations are computed over multiple patients that have both expression and copy number measurements in brain, bladder and breast cancer data sets. We find that a CNA has a direct impact on the gene amplified or deleted, but it also has a broad, indirect impact elsewhere. To identify a set of CNAs that is coordinately associated with the expression changes of a set of genes, we used a biclustering algorithm on the correlation matrix. For each of the three cancer types examined, the aberrations in several loci are associated with cancer-type specific biological pathways that have been described in the literature: CNAs of chromosome (chr) 7p13 were significantly correlated with epidermal growth factor receptor signaling pathway in glioblastoma multiforme, chr 13q with NF-kappaB cascades in bladder cancer, and chr 11p with Reck pathway in breast cancer. In all three data sets, gene sets related to cell cycle/division such as M phase, DNA replication and cell division were also associated with CNAs. Our results suggest that CNAs are both directly and indirectly correlated with changes in expression and that it is beneficial to examine the indirect effects of CNAs. AVAILABILITY The code is available upon request.
A probabilistic measure of air traffic complexity in three-dimensional airspace

In this paper, we propose a new method to evaluate air traffic complexity in 3-D airspace through a probabilistic measure of the airspace occupancy. The key novelty of the approach is that uncertainty in the future aircraft positions is explicitly accounted for when evaluating complexity. Analytic –though approximate– expressions of the complexity measure are derived. Prospective applications for the proposed complexity metric include the timely identification of those multi-aircraft conflict situations that would be difficult to solve because of limited maneuverability space, and the design of trajectories so as to avoid congested regions that would require many tactical maneuvers to pass them through. Numerical examples are provided to illustrate the approach. Copyright c © 2010 John Wiley & Sons, Ltd.
Phonetic subspace mixture model for speaker diarization

This paper presents an improved distance measure for speaker clustering in speaker diarization systems. The proposed phonetic subspace mixture (PSM) model introduces phonetic information to the ΔBIC distance measure. Therefore, the new PSM model-based ΔBIC distance measure can remove the effect of phonetic content on the diarization results. The typical ΔBIC distance measure can be seen as a special case of the new ΔBIC distance measure. Our experiment results show that the new distance measurement consistently improves the speaker diarization performance on three datasets.
Cooperative spatial multiplexing with distributed amplify-and-forward relays

We propose a MIMO spatial multiplexing system with distributed single-antenna relay stations which operate in the amplify-and-forward mode. A maximum likelihood detector is implemented at the receiver. We evaluate the system bit error rate (BER) performance by means of a semi-analytic bounding method which can closely bound BER at high signal to noise ratio (SNR), and hence determine diversity order. We consider the effect of fading on links between the source and relays on the achievable diversity order.
Magnetoencephalographic and electroencephalographic studies of spontaneous activity and evoked responses in the sensorimotor system

6 Introduction 7 Review of literature 8 Oscillatory brain activity 8 Alpha rhythm 8 Mu and beta rhythms 9 Self-organized criticality (SOC) 10 Synchrony in the brain 11 Somatosensory system and primary motor cortex 11 Receptors and spinal cord 11 Brain stem and thalamus 12 Primary somatosensory cortex (SI) 12 Secondary somatosensory cortex (SII) 13 Posterior parietal cortex (PPC) 14 Other areas related to somatosensory processing 14 Primary motor cortex (MI) 14 Somatosensory evoked responses 15 Somatosensory evoked potentials (SEP) 15 Somatosensory evoked fields (SEF) 16 Experimental techniques 17 Magnetoand Electroencephalography (MEG, EEG) 17 Transcranial magnetic stimulation (TMS) 17 Aims of study 19 Materials and methods 20 Stimulation 20 Recordings 20 Data analysis 21 Results and discussion 22 I. Suppression of mu rhythm by somatosensory stimulation 22 Results 22 Discussion 23
Adapting Reinforcement Learning for Trust: Effective Modeling in Dynamic Environments

In open multiagent systems, agents need to model their environments in order to identify trustworthy agents. Models of the environment should be accurate so that decisions about whom to interact with can be done soundly. Traditional trust models are based on modeling specific properties of agents, such as their expertise or reliability. Building those models requires too many prior interactions to be accurate. This paper proposes an approach that is based on keeping track of outcomes of agent's actions towards others rather than modeling other agents' performances explicitly. Contrary to existing modeling approaches that require domain knowledge to build models, our proposed approach can be effectively realized in multiagent systems when the agent's actions are clearly identified. Comparisons with other modeling approaches in various environments reveal that our proposed approach can create more precise models in short time and can adjust its behavior quickly when other agents' behaviors change.
A multi-region deep neural network model in speech recognition

This work proposes a new architecture for deep neural network training. Instead of having one cascade of fully connected hidden layers between the input features and the target output, the new architecture organizes hidden layers into several regions with each region having its own target. Regions communicate with each other during the training process by connections among intermediate hidden layers to share learned internal representations from their respective targets. They do not have to share the same input features. This paper presents the performance of acoustic models built using this architecture with speaker independent and dependent features. Experimental re-sults are compared with not only the baseline DNN model, but also the ensemble DNN, unfolded RNN and stacked DNN. Experiments on the IARPA sponsored Babel tasks demonstrate improvements ranging from 0.8% to 2.7 % absolute reduction in WER.
Sigma-delta modulator based control systems for MEMS gyroscopes

In this paper a review is presented about recent developments of using sigma-delta modulator (SDM) control systems for micromachined, capacitive vibratory rate MEMS gyroscopes. The design choices, their benefits and disadvantages are briefly discussed. As the most promising control system, a higher order, band-pass SDM is identified since it achieves high quantization noise shaping at a relatively low sampling frequency, in addition to the normal closed loop, force feedback control advantages such as improved bandwidth, linearity and dynamic range. Previous work applied this type of control system to gyroscopes with a relatively small proof mass. Here, results are presented applying the approach to a comparatively large, bulk-micromachined gyroscope sensing element, which has the potential to result in a high performance sensor. System level simulations are presented illustrating the benefits of the approach.
Efficient Testing of Bipartite Graphs for Forbidden Induced Subgraphs

Alon et. al. [N. Alon, E. Fischer, M. Krivelevich, and M. Szegedy, Combinatorica, 20 (2000), pp. 451-476] showed that every property that is characterized by a finite collection of forbidden induced subgraphs is $\epsilon$-testable. However, the complexity of the test is double-tower with respect to $1/\epsilon$, as the only tool known to construct such tests uses a variant of Szemeredi's regularity lemma. Here we show that any property of bipartite graphs that is characterized by a finite collection of forbidden induced subgraphs is $\epsilon$-testable, with a number of queries that is polynomial in $1/\epsilon$. Our main tool is a new “conditional” version of the regularity lemma for binary matrices, which may be interesting on its own.
Information-Theoretic Motor Skill Learning

While there has been recent successes in learning single control policies, there are several several open challenges in robot motor skill learning. Firstly, many motor tasks can be solved in multiple ways, and, hence, we need to be able to learn each of these solutions as separate options from which the agent can choose from. Furthermore, we need to learn how to adapt an option to the current situation. Finally, we need to be able to combine several options sequentially in order to solve an overall-task. As we want to use our method for real robots, a high data efficiency is a natural additional requirement for motor skill learning. In this paper we summarize our work on information-theoretic motor skill learning. We show how to adapt the relative entropy policy search (REPS) algorithm for learning parametrized options and extend the algorithm in a mathematical sound way such that it can meet all these requirements. Finally, we summarize our experiments conducted on real robots.
Chromosome Conformation Capture (3C) (PROT05)

A cardiac pacemaker having a pacing rate responsive to a control function of a physiological parameter indicative of activity levels. The coefficients of the function are automatically calculated and modified in response to the trend of the measured physiological parameter in order to correspond to the patient real needs. For monitoring the physiological parameter minute ventilation (VE), the basic value VE low and maximum value VE max are calculated in order to vary the slope and intercept of the straight line representative of the control relation of the pacing rate FC by the minute volume VE.
Towards Faster Rates and Oracle Property for Low-Rank Matrix Estimation

We present a unified framework for low-rank matrix estimation with nonconvex penalty. A proximal gradient homotopy algorithm is developed to solve the proposed optimization problem. Theoretically, we first prove that the proposed estimator attains a faster statistical rate than the traditional low-rank matrix estimator with nuclear norm penalty. Moreover, we rigorously show that under a certain condition on the magnitude of the nonzero singular values, the proposed estimator enjoys oracle property (i.e., exactly recovers the true rank of the matrix), besides attaining a faster rate. Extensive numerical experiments on both synthetic and real world datasets corroborate our theoretical findings.
Survey of the Superorder Dictyoptera Mantodea from Sanghar, Sindh, Pakistan

This paper deals with the fauna of different species of Mantodea from different localities of Sanghar (district). A total of 16 species from 12 genera including (Blepharopsis, Empusa, Humbertiella, Deiphobe, Archimantis, Hierodula, Mantis, Stalilia, Polyspilota, Iris, Rivetina and Eremphilia belong to 05 families Mantidae, Tarachodidae, Empusidae, liturgusidae and Eremiaphilidae) were identified and presented. A comparison of Pakistani Mantodea’s fauna at global level was also done and six new regional record species were also found and presented here. During this study significant numbers were captured. It was also noticed that its predatory behavior has very important for reorganization of it’s as bio-control agent.
Erosion and regional exhumation of an Early Cretaceous subduction/accretion complex in the Northern Andes

ABSTRACT A multi-technique provenance analysis, together with whole-rock geochemistry from arc related volcano-sedimentary rocks of the Albian-Aptian Quebradagrande Complex (Central Colombian Andes, Northern Andes), were conducted to reconstruct the tectono-stratigraphic relations with the adjacent Early Cretaceous subduction/accretion Arquía Complex, in order to understand the tectonic modification of the Andean margin before the onset of the Andean orogeny. The presence of olivine, spinel, serpentine, high-pressure garnets and glaucophane in the sandstones of the Quebradagrande Complex suggests that the subduction/accretion Arquía Complex was a major source area during basin filling. Carboniferous and older detrital zircons suggest that the pre-Cretaceous continental basement of the Colombian Central Cordillera, which limits the Quebradagrande Complex to the east, was also a major basin source. Whole-rock geochemistry from associated volcanic rocks, showing suprasubduction to NMORB signature, is characteristic of a magmatic arc formed in thinned continental crust. Integration of the results with the Early Cretaceous record of the Central Cordillera indicates that the continental margin experiences a major slab-roll back event that promotes extensional tectonics, affecting the arc and facilitating the exhumation of a subduction/accretion complex. During the Late Cretaceous, both complexes were deformed and a new magmatic arc was formed. The extensional tectonics reflects the complex plate kinematic readjustments that affected western South America during the Cretaceous. Graphic Abstract
Cardiovascular effects of endothelin in trout.

The cardiovascular effects of endothelin-1 (ET-1) in trout were examined in unanesthetized fish, perfused tissues, and isolated vascular rings. In vivo, a bolus of 500 ng/kg body wt ET-1 transiently lowered arterial (postgill) blood pressure (BP) by nearly 30%; 1,500 ng/kg body wt produced a triphasic, pressor-depressor-pressor, response. Continuous infusion of 0.1, 1, 10, and 30 ng.kg-1.min-1 progressively lowered BP but did not affect heart rate (HR), urine flow, or electrolyte excretion. In the in situ perfused heart ET-1 (10(-11) to 10(-8) M) had no effect on HR or power output. ET-1 produced dose-dependent increases in vascular resistance in the perfused gill, renal-skeletal muscle, and splanchnic circulations, and increased tension, independent of endothelium, in vascular rings from celiacomesenteric (CA) and coronary arteries and anterior cardinal veins (CV). Ventral aortas were refractory to ET-1. In vitro, ET-1 effects were slow in onset and long lasting. External calcium was required for maximal ET-1 responses in gill and CA. ET-1 effects on CA but not CV were partially inhibited by calcium channel blockers, diltiazem, and D 600, and by the guanylate cyclase activators, atrial natriuretic factor, and sodium nitroprusside. [3H]water flux across the perfused gill was stimulated by ET-1 through what appeared to be a vascular-independent mechanism. These experiments show that the trout vasculature is exquisitely sensitive to ET-1, and they suggest that the physiological expression of this peptide has been highly conserved during the course of vertebrate evolution.
Measuring and modeling the dissolution of nonideally shaped dense nonaqueous phase liquid pools in saturated porous media

A three‐dimensional physical aquifer model was used to study the dissolution of a dense nonaqueous phase liquid (DNAPL) pool. The model aquifer comprised a packing of homogeneous, medium‐sized sand and conveyed steady, unidirectional flow. Tetrachloroethene (PCE) pools were introduced within model aquifers atop glass‐ and clay‐lined aquifer bottoms. Transient breakthrough at an interstitial velocity of 7.2 cm/h, and three‐dimensional steady state concentration distributions at velocities ranging from 0.4 to 7.2 cm/h were monitored over periods of 59 and 71 days for the glass‐ and clay‐bottom experiments, respectively. Pool‐averaged mass transfer coefficients were obtained from the observations via a single‐parameter fit using an analytical model formulated with a second type boundary condition to describe pool dissolution [ Chrysikopoulos, 1995 ]. Other model parameters (interstitial velocity, longitudinal and transverse dispersion coefficients, and pool geometry) were estimated independently. Simulated and observed dissolution behavior agreed well, except for locations relatively close to the pool or the glass‐bottom plate. Estimated mass transfer coefficients ranged from 0.15 to 0.22 cm/h, increasing weakly with velocity toward a limiting value. Pool mass depletions of 31 and 43% for the glass‐ and clay‐bottom experiments failed to produce observable changes in the plumes and suggested that changes in pool interfacial area over the period of the experiment were negligible. Dimensionless mass transfer behavior was quantified using a modified Sherwood number (Sh*). Observed Sh* values were found to be about 2–3 times greater than values predicted by an existing theoretical mass transfer correlation, and 3–4 times greater than those estimated previously for an ideally configured trichloroethene (TCE) pool (circular and smooth). It appeared that the analytical model's failure to account for pore‐scale pool‐water interfacial characteristics and larger scale pool shape irregularities biased the Sh* estimates toward greater values.
The Corrected Normalized Correlation Coefficient: A Novel Way of Matching Score Calculation for LDA-Based Face Verification

The paper presents a novel way of matching score calculation for LDA-based face verification. Different from the classical matching schemes, where the decision regarding the identity of the user currently presented to the face verification system is made based on the similarity (or distance) between the "live" feature vector and the template of the claimed identity, we propose to employ a measure we named the corrected normalized correlation coefficient, which considers both the similarity with the template of the claimed identity as well as the similarity with all other templates stored in the database. The effectiveness of the proposed measure was assessed on the publicly available XM2VTS database where encouraging results were achieved.
Generalized window advertising for TCP congestion control

AbstracL Congestion in the Internet is a major cause of network performance degradation. The Generalized Window Advertising (GWA) scheme proposed in this paper is a new approach for enhancing the congestion control properties of TCP. GWA requires only minor modifications to the existing protocol stack and is completely backward compatible, allowing GWA-hosts to interact with non-GWA hosts without modifications. GWA exploits the notion of end-host-network cooperation, with the congestion level notified from the network to end hosts. It is based on solid control theory results that guarantee performance and stable network operation. GWA is able to avoid window oscillations and the related fluctuations in offered load and network performance. This makes it more robust to sustained network overload due to a large number of connections competing for the same bottleneck, a situation where traditional TCP implementations fail to provide satisfactory performance. GWA-TCP is compared with traditional TCP, TCP with RED and also ECN using the ns-2 simulator. Results show that in most cases GWA-TCP outperforms the traditional schemes. In particular, when compared with ECN, it provides smoother network operation and increased fairness.
Solar Flare Hard X-Ray Emission from the High Corona

One of the largest solar hard X-ray (HXR) flares and solar energetic particle (SEP) events recorded by the Mars Odyssey mission while orbiting Mars occurred on 2002 October 27 and is related to a very fast (~2300 km s-1) coronal mass ejection (CME). From the Earth, the flare site is 40.4° ± 3.5° behind the solar limb and only emissions from the high corona at least 1.5 × 105 km radially above the main flare site can be seen. Nevertheless, the Earth-orbiting Reuven Ramaty High Energy Solar Spectroscopic Imager (RHESSI) observed HXR emission up to 60 keV with a relatively flat, nonthermal spectrum (γ between 3 and 3.5) that has an onset simultaneous with the main HXR emission observed above 60 keV by the Gamma-Ray Spectrometer (GRS) orbiting Mars. While GRS records several smaller enhancements after the main peak, the high coronal source observed by RHESSI shows a long exponential decay (τ = 135 ± 5 s) with progressive spectral hardening. The emissions from the high corona originate from an extended source (~1.5 × 105 km in diameter) that expands (390 ± 70 km s-1) and moves upwards (750 ± 80 km s-1) in the same direction as the CME. These observations reveal the existence of energetic electrons in the high corona in closed magnetic structures related to the CME that are accelerated at the same time as the main energy release in the flare. Although the number of energetic electrons in the high corona is only a small fraction of the total accelerated electrons, about 10% of all electrons in the high coronal source are nonthermal (>10 keV).
Testing for Associations between Loci and Environmental Gradients Using Latent Factor Mixed Models

Adaptation to local environments often occurs through natural selection acting on a large number of loci, each having a weak phenotypic effect. One way to detect these loci is to identify genetic polymorphisms that exhibit high correlation with environmental variables used as proxies for ecological pressures. Here, we propose new algorithms based on population genetics, ecological modeling, and statistical learning techniques to screen genomes for signatures of local adaptation. Implemented in the computer program “latent factor mixed model” (LFMM), these algorithms employ an approach in which population structure is introduced using unobserved variables. These fast and computationally efficient algorithms detect correlations between environmental and genetic variation while simultaneously inferring background levels of population structure. Comparing these new algorithms with related methods provides evidence that LFMM can efficiently estimate random effects due to population history and isolation-by-distance patterns when computing gene-environment correlations, and decrease the number of false-positive associations in genome scans. We then apply these models to plant and human genetic data, identifying several genes with functions related to development that exhibit strong correlations with climatic gradients.
Soft-switching SiC interleaved boost converter

A DC-DC converter topology is presented combining the soft switching effects of the Snubber Assisted Zero Voltage and Zero Current Transition (SAZZ) topology and the increased inductor frequency of the dual interleaved boost converter with interphase transformer. The snubber capacitors and output capacitances of the main devices are discharged prior to turn on using a single auxiliary inductor, eliminating turn on losses. Furthermore, the turn off losses are significantly reduced since the energy stored in the device output capacitance at turn off is recovered at turn on. The effectiveness of the topology is demonstrated on a SiC prototype operating at 12.5 kW, 112 kHz, reducing the switching losses by 50%.