Miracle-dz/UniFAR-FTUs huggingface dataset:
Linking the signaling cascades and dynamic regulatory networks controlling stress responses

Accurate models of the cross-talk between signaling pathways and transcriptional regulatory networks within cells are essential to understand complex response programs. We present a new computational method that combines condition-specific time-series expression data with general protein interaction data to reconstruct dynamic and causal stress response networks. These networks characterize the pathways involved in the response, their time of activation, and the affected genes. The signaling and regulatory components of our networks are linked via a set of common transcription factors that serve as targets in the signaling network and as regulators of the transcriptional response network. Detailed case studies of stress responses in budding yeast demonstrate the predictive power of our method. Our method correctly identifies the core signaling proteins and transcription factors of the response programs. It further predicts the involvement of additional transcription factors and other proteins not previously implicated in the response pathways. We experimentally verify several of these predictions for the osmotic stress response network. Our approach requires little condition-specific data: only a partial set of upstream initiators and time-series gene expression data, which are readily available for many conditions and species. Consequently, our method is widely applicable and can be used to derive accurate, dynamic response models in several species.
Diffusion–Perfusion Mismatch: An Opportunity for Improvement in Cortical Function

Objective: There has been controversy over whether diffusion–perfusion mismatch provides a biomarker for the ischemic penumbra. In the context of clinical stroke trials, regions of the diffusion–perfusion mismatch that do not progress to infarct in the absence of reperfusion are considered to represent “benign oligemia. ” However, at least in some cases (particularly large vessel stenosis), some of this hypoperfused tissue may remain dysfunctional for a prolonged period without progressing to infarct and may recover function if eventually reperfused. We hypothesized that patients with persistent diffusion–perfusion mismatch using a hypoperfusion threshold of 4–5.9 s delay on time-to-peak (TTP) maps at least sometimes have persistent cognitive deficits relative to those who show some reperfusion of this hypoperfused tissue. Methods: We tested this hypothesis in 38 patients with acute ischemic stroke who had simple cognitive tests (naming or line cancelation) and MRI with diffusion and perfusion imaging within 24 h of onset and again within 10 days, most of whom had large vessel stenosis or occlusion. Results: A persistent perfusion deficit of 4–5.9 s delay in TTP on follow up MRI was associated with a persistent cognitive deficit at that time point (p < 0.001). When we evaluated only patients who did not have infarct growth (n = 14), persistent hypoperfusion (persistent mismatch) was associated with a lack of cognitive improvement compared with those who had reperfused. The initial volume of hypoperfusion did not correlate with the later infarct volume (progression to infarct), but change in volume of hypoperfusion correlated with change in cognitive performance (p = 0.0001). Moreover, multivariable regression showed that the change in volume of hypoperfused tissue of 4–5.9 s delay (p = 0.002), and change in volume of ischemic tissue on diffusion weighted imaging (p = 0.02) were independently associated with change in cognitive function. Conclusion: Our results provide additional evidence that non-infarcted tissue with a TTP delay of 4–5.9 s may be associated with persistent deficits, even if it does not always result in imminent progression to infarct. This tissue may represent the occasional opportunity to intervene to improve function even days after onset of symptoms.
Pearl Millet and Grain Sorghum Yield Response to Water Supply in Nebraska

Pearl millet [Pennisetum glaucum (L.) R. Br. ] is a drought-tolerant crop that may serve as an alternative summer crop in Nebraska. Field experiments were conducted in 2000 and 2001 near Sidney and Mead, NE, to determine the water use efficiency (WUE) and yield response to water supply at critical developmental stages of pearl millet and grain sorghum [Sorghum bicolor (L.) Moench]. Four water regimes were used: (i) no irrigation, (ii) single irrigation at boot stage, (iii) single irrigation at mid-grain fill, and (iv) multiple irrigations. Pearl millet grain yields were 60 to 80% that of grain sorghum. Average grain yields at Mead were 5.1 Mg ha -1 for pearl millet and 6.1 Mg ha -1 for grain sorghum. At Sidney, average pearl millet yields were 1.9 and 3.9 Mg ha -1 in 2000 and 2001, respectively, and average grain sorghum yields were 4.1 and 5.0 Mg ha -1 in 2000 and 2001, respectively. Both crops used a similar amount of water (336 and 330 mm in 2000 and 370 and 374 mm in 2001 for pearl millet and grain sorghum, respectively) and responded to irrigation with a linear increase in grain yield as water use increased. Grain sorghum had greater WUE than pearl millet (12.4-13.4 kg vs. 5.1-10.4 kg grain ha -1 mm -1 ). Pearl millet, with lower and less stable yields, does not currently have the potential to be a substitute crop for grain sorghum in Nebraska.
The Economic Impacts of Climate Change : Evidence from Agricultural Output and Random Fluctuations in Weather

This paper measures the economic impact of climate change on US agricultural land by estimating the effect of random year-to-year variation in temperature and precipitation on agricultural profits. The preferred estimates indicate that climate change will increase annual profits by $1.3 billion in 2002 dollars (2002$) or 4 percent. This estimate is robust to numerous specification checks and relatively precise, so large negative or positive effects are unlikely. We also find the hedonic approach—which is the standard in the previous literature—to be unreliable because it produces estimates that are extremely sensitive to seemingly minor choices about control variables, sample, and weighting. (JEL L25, Q12, Q51, Q54)
Factors Predictive of Type of Powered Mobility Received by Veterans with Disability

Background The goal of this observational study was to determine factors predictive of the type of powered mobility prescribed to veterans with disability. Material/Methods A retrospective chart review was conducted for all veterans (n=170) who received powered mobility from a designated power mobility clinic. Logistic regression analysis was used to determined factors predictive of the type of powered mobility provided. Results Sixty-four (38%) veterans were provided powered wheelchairs and 106 (62%) were provided powered scooters. Of the variables examined, only primary medical conditions for referral and disability severity (as measured by the 2-minute timed walk test; 2-MWT) were predictive of the types of powered mobility prescribed. Veterans who were able to walk longer distances were more likely to be prescribed powered scooters. Age, gender, race, level of education, marital and employment status, number of chronic medical conditions, and upper and lower limb muscle strength were not significant predictors. Conclusions This study suggests that the primary medical conditions for referral and 2-MWT can assist clinicians in the determination of the type of powered mobility to prescribe to veterans with disability.
Implementation of a traffic engineering technique that preserves IP Fast Reroute inCOMET

With Intradomain Routing Protocols, by optimizing the configuration (Trafic Engineering -TE) of link weights, operators can significantly improve the load of their links, which is known to be an NP-hard problem. Another emerging issue for ISP networks is the fast restoration of IP services in the case of failures. Recently, Fast Reroute techniques have been proposed for pure IP networks. The Loop Free Alternates (LFA) is one of the most promising technique. An LFA for a router A, for a destination d, is a neighbor C of A which does not use A to reach d, so that A can prepare itself to directly reroute the traffic destined to d along its link with C upon the failure of the link that A is using to reach d. Our objective is to provide a TE technique that takes the coverage of LFAs into account during the network resource usage optimization. Constraint Programming and Constraint-Based Local Search are well suited for solving such complex combinatorial problems. Especially in COMET, some classical problems can be modeled in only about a dozen lines of code. So, we have chosen a local search algorithm implemented in COMET for solving our traffic engineering problem.
Measuring performance of web image context extraction

Images on the Web appear with textual contents providing meaningful information to their semantics. Methods that automatically determine and extract the Web image context from an HTML document are widely used in different applications. However, the performance of the image context extraction has rather been evaluated on its own. Keeping this imperative in mind, we present a framework to objective evaluation and comparison of the performance of image context extraction methods. This is achieved by collecting a large ground truth dataset consisting of diverse Web documents from real Web servers and by defining performance measures adapted to fit the special properties of the context extraction task. To show the capabilities of the proposed framework, common extraction methods from the literature have been evaluated and the results are summarized in this paper.
Free boson representation of DYh(sl(2))(k) and the deformation of the Feigin-Fuchs

A realization of the Yangian double with center DY(h) over bar(sl(2))(k) of level-k(not equal 0, -2) in terms of free boson fields is constructed. The screening currents are also presented, which commute with DY(h) over bar(sl(2)) module, total difference. In the (h) over bar --> 0 limit, the currents of Yangian double DY(h) over bar(sl(2))(k) become the Feigin-Fuchs realization of affine Lie sl(2)(k), while the screening currents of Yangian double DY(h) over bar(sl(2))(k) become the screening currents of the affine Lie algebra sl(2)(k).
Instrument contact force estimation using endoscopic image sequence and 3D reconstruction model

This paper presents a method to estimate contact force for minimally invasive surgery (MIS) using endoscopic imagery. In order to provide surgeons the information of contact force as surgical instruments get contact to human tissue, we developed a method to calculate tissue deformation by reconstructing 3D model using real-time image processing. The force information will be fed back to a haptic device to allow the surgeon to feel contact force as well as to show the force value on monitor for the surgeon. We propose a 3D reconstruction method to model the tissue surface under deformation, and use the deformation data to obtain contact force near the instrument tip. Using image tracking, we locate a surgical instrument in the endoscopy scene, then determine the deformation area in the image scene. Several experiments validate the effectiveness of method of deformation calculation.
Person recognition using fingerprints and top-view finger images

Our multimodal biometric system combines fingerprinting with a top-view finger image captured by a CCD camera without user intervention. The greyscale image is preprocessed to enhance its edges, skin furrows, and the nail shape before being manipulated by a bank of oriented filters. A square tessellation is applied to the filtered image to create a feature map, called a NailCode, which is employed in Euclidean distance computations. The NailCode reduces system errors by 17.68% in the verification mode, and by 6.82% in the identification mode.
Hierarchical Oriented Predictions for Resolution Scalable Lossless and Near-lossless Compression of Ct and Mri Biomedical Images

CT or MRI Medical imaging produces digital form of human body pictures. There exists a need for compression of these images for storage and communication purposes. Current compression schemes provide a very high compression rate with a considerable loss of quality. In medicine, it is necessary to have high image quality in region of interest, i.e. diagnostically important regions. This paper discusses a hybrid model of lossless compression in region of interest with high compression rate lossy compression in other regions. The hybrid technique provides efficient and accurate coding of the medical images. We first survey a number of lossless and lossy compression schemes for the hybrid coder. An application to abdomen CT imaging with the special interest on human colon is presented.
Trends in online learning communities

In the past decade, there has been a trend toward using the Internet to support traditional classroom teaching and to substitute traditional teaching for online learning. In particular, online learning communities play an important role in distant education. This trend raises important questions about the nature of online learning, the types of learning promoted by online learning communities, the challenges inherent in online learning communities, and the ways in which online learning communities can be improved. Moreover, it is important to understand online learning communities in the context of people's everyday lives. This special issue brings together studies that examine how online learning communities have evolved, the types of online learning communities available, and what design features are useful for promoting vibrant online learning communities. These studies show online learning communities as a complex phenomenon and propose new frameworks and research methods. This introduction outlines the important questions asked in these papers about online learning communities as well as results from empirical studies. It concludes with a set of design considerations that emerge from the studies.
A Robust QRS Complex Detection Algorithm Using Dynamic Thresholds

Automatic QRS complex detection is important in ECG signal analysis. QRS detection methods are affected by the quality of the ECG recordings and the abnormalities in the ECG signals. In this paper, a generic algorithm is introduced to improve the detection of QRS complexes in arrhythmia ECG signals that suffer from: (1) non-stationary effects, (2) low signal-to-noise ratio, (3) negative QRS polarities, (4) low QRS amplitudes, and (5) ventricular ectopics. We compared the algorithm to the method described by Chouhan et al. [16] by applying both algorithms to 19 records of the MIT-BIH database. It was shown that the new algorithm achieves significantly better detection rates resulting in an overall 97.5% sensitivity and 99.9% positive predictivity.
A novel signal constellation set for communication system using APSK signals of DVB-S2 standard with high nonlinearity

Being robust to nonlinear distortion by owning a lower peak to average power ratio in comparision with QAM signal, APSK was recommended for using in the digital satellite video broadcasting, second generation (DVB-S2). However, the adverse effects of nonlinearity could still be reduced by redistributing signal points in the constellation. In this paper, we propose a new signal set and the mapping for the APSK signal conforming to the DVB-S2 standard at high nonlinearity level. Moreover, this new proposed APSK signal further improves the performance of HPA in terms of power efficiency.
Ensembles of data-reduction-based classifiers for distributed learning from very large data sets

An ensemble of classifiers is a set of classification models and a method to combine their predictions into a joint decision. They were primarily devised to improve classification accuracies over individual classifiers. However, the growing need for learning from very large data sets has opened new application areas for this strategy. According to this approach, new ensembles of classifiers have been addressed to partition a large data set into possible disjoint moderate-sized (sub)sets, which are then distributed along with a number of individual classifiers across multiple processors for parallel operation. A second benefit of reducing sizes is to make feasible the use of well-known learning methods which are not appropriate for handling huge amount of data. This paper presents such a distributed model as a solution to the problem of learning on very large data sets. As individual classifiers, data-reduction-based techniques are proposed due to their abilities to reduce complexities and, in much cases, error rates.
Artificial bandwidth extension of speech supported by watermark-transmitted side information

In recent years research in the area of artificial bandwidth extension (BWE) of speech signals has made significant progress. The intention of BWE is to produce wideband speech with a cut-off frequency of for instance 7 kHz from a narrowband version (e.g., with telephone bandwidth, i.e., 300 Hz − 3.4 kHz). The respective algorithms are based on the estimation of parameters of a source model for speech production given the knowledge of thenarrowband signal. Atheoretical performance bound on this estimation has been formulated in [1]. In order to overcome this boundary we propose the transmission of (compact) side information which can support the parameter estimation. Since a common additional channel would conflict with the requirement of backwards compatibility in narrowband communication systems, the side information is embedded as digital watermark into the narrowband speech.
Probing the origins of aromatase inhibitory activity of disubstituted coumarins via QSAR and molecular docking

This study investigated the quantitative structure-activity relationship (QSAR) of imidazole derivatives of 4,7-disubstituted coumarins as inhibitors of aromatase, a potential therapeutic protein target for the treatment of breast cancer. Herein, a series of 3,7- and 4,7-disubstituted coumarin derivatives (1-34) with R1 and R2 substituents bearing aromatase inhibitory activity were modeled as a function of molecular and quantum chemical descriptors derived from low-energy conformer geometrically optimized at B3LYP/6-31G(d) level of theory. Insights on origins of aromatase inhibitory activity was afforded by the computed set of 7 descriptors comprising of F10[N-O], Inflammat-50, Psychotic-80, H-047, BELe1, B10[C-O] and MAXDP. Such significant descriptors were used for QSAR model construction and results indicated that model 4 afforded the best statistical performance. Good predictive performance were achieved as verified from the internal (comprising the training and the leave-one-out cross-validation (LOO-CV) sets) and external sets affording the following statistical parameters: R2Tr = 0.9576 and RMSETr = 0.0958 for the training set; Q2CV = 0.9239 and RMSECV = 0.1304 for the LOO-CV set as well as Q2Ext = 0.7268 and RMSEExt = 0.2927 for the external set. Significant descriptors showed correlation with functional substituents, particularly, R1 in governing high potency as aromatase inhibitor. Molecular docking calculations suggest that key residues interacting with the coumarins were predominantly lipophilic or non-polar while a few were polar and positively-charged. Findings illuminated herein serve as the impetus that can be used to rationally guide the design of new aromatase inhibitors.
No-Reflow Phenomenon: A Major Issue Concerning Revascularization in Acute Coronary Syndromes

The no-reflow phenomenon (NRp), a dreaded complication of primary and also of any complex percutaneous coronary intervention (PCI), is characterized by insufficient myocardial perfusion in a territory of a coronary artery without evidence of mechanical obstruction. Microvascular injury is the underlying mechanism of NRp and its manifestation is not only impaired TIMI flow (<3), but also impaired TIMI myocardial perfusion grade (TMPG) which should be assessed in case of chest pain, persistent ST segment elevation or hemodynamic compromise despite the presence of TIMI III flow. The NRp mechanism is multifaceted, the evidence base for its treatment is inconsistent and limited, but its predictors are well known. The armamentarium against NRp consists of preventive and therapeutic strategies, both mechanical and pharmacological. A brief overview of all the above issues concerning NRp is attempted herein. Rhythmos 2019;14(2):27-30.
Practical experiences with pose space deformation

Pose Space Deformation (PSD) [Lewis et al. 2000] is a shape interpolation technique for animation. This method uses radial basis functions (RBFs) to perform per-vertex, multidimensional scattered-data interpolation. This formulation effectively interpolates a driven shape according to a set of targets, each at a particular driver value. In the case of correcting a pinched elbow, the skinned geometry is the driven, the targets are the sculpted adjustments, and the driver is the elbow joint. This paper presents some practical experience with PSD acquired while creating the film BOLT.
Design of mixed gates for leakage reduction

Leakage power dissipation is one of the most critical factors for the overall current dissipation and future designs. However, design techniques for the reduction of leakage power should not decrease design performance. Therefore, an enhanced Dual Vth/Dual Tox CMOS ap-proach is presented which applies mixed gates consisting of different transistor types. The paper introduces the new and fundamental idea of different gate types before the various possible configurations are analyzed. This is followed by extraction and exploration of design rules and recommendations. Simulations of modified ISCAS'85 designs show an average leakage reduction of 60% at constant performance compared to raw designs. This corresponds to an additional reduction of 20% compared to previous Dual Vth/Dual Tox CMOS approaches.
A region-based object tracking scheme using Adaboost-based feature selection

This paper presents an object extraction system for video surveillance applications that require pixel-wise extraction accuracy. The proposed mechanism is composed of two trackers. The first tracker extract video objects by using Adaboost on pixel-based global seed features, it can provide more detailed segmentation of target. The second tracker applies bidirectional labeling on regions as well as uses Adaboost on region-based local seed features to refine the object masks obtained from the first tracker. The system is featured with an interactive tool which allows users to deal with serious object occlusion situations. A confidence measure is proposed to minimize the effort of human interactions.
Forecasting for Products with Short Life Cycle Based on Improved BASS Model

The forecasting studies for short life cycle products were summarized in this paper.The characteristics of short life cycle products were analyzed.BASS model and its development were introduced.After feasibility analysis,BASS model was applied to forecast the demand of short life cycle products.The forecasting information was complemented with the similar product data and the model was revised with seasonal factor.The numerical illustration proved that the revised BASS model could generate good forecast for products with short life cycle.The forecasting error of MAD,RMSE and MAPE were better than other methods.
A TeXQuery-based XML full-text search engine

We demonstrate an XML full-text search engine that implements the TeXQuery language. TeXQuery is a powerful full-text search extension to XQuery that provides a rich set of fully composable full-text primitives, such as phrase matching, proximity distance, stemming and thesauri. TeXQuery enables users to seamlessly query over both structure data and text, by embedding full-text primitives in XQuery and vice versa. TeXQuery also supports a flexible scoring construct that scores query results based on full-text predicates and permits top-k queries. TeXQuery is the precursor of the full-text language extension to XPath 2.0 and XQuery 1.0 currently being developed by W3C.