Miracle-dz/UniFAR-FTUs huggingface dataset:
Growth/Differentiation Factor-5 (GDF-5) and Skeletal Development

Background: Growth/differentiation factor-5 (GDF-5) has been shown to be essential for normal appendicular skeletal and joint development in humans and mice. In brachypod , a Gdf-5 gene mouse mutant, the defect is first apparent during early chondrogenesis, with the cartilage blastema already reduced in size by E12.5. This defect is associated with changes in the expression of cell surface molecules. Methods: To understand further how GDF-5 controls cartilage formation, we first mapped the expression of the Gdf-5 gene during skeletal development (please note that the abbreviation for the gene is given in italics and the abbreviation for the protein expressed by the gene is given in capital letters). Subsequently, we over-expressed GDF-5 in the developing chick embryo using a replication competent retrovirus, RCAS(BP). We determined its effects on skeletal development by histological examination and its effects on early growth by autoradiography of proliferating cells. In addition, we examined the effect of GDF-5 on chondrogenic differentiation using micromass and single cell suspension cultures of limb mesenchymal cells. Results: These studies show that the Gdf-5 gene is expressed in the early cartilage condensation, the perichondrium, and the joint interzone. Over-expression of GDF-5 in chick limb buds, during the condensation stage or later when the skeletal elements have formed, increased the size of the affected elements. In both cases, the increase in size was associated with an increase in cell number and, at later stages, this was correlated with an increase in S-phase cells. In vitro studies showed that GDF-5 could increase cell adhesiveness, and this may be a mechanism through which GDF-5 initiates condensation formation. Conclusion: These studies show that GDF-5 acts at two stages of skeletal development and by two distinct mechanisms. First, GDF-5 promotes the initial stages of chondrogenesis by promoting cell adhesion, which is consistent with the expression of Gdf-5 in the cartilage condensation. Second, GDF-5 can increase the size of the skeletal elements by increasing proliferation within the epiphyseal cartilage adjacent to its expression within the joint interzone.
The complete genome sequence of Mycobacterium bovis

Mycobacterium bovis is the causative agent of tuberculosis in a range of animal species and man, with worldwide annual losses to agriculture of $3 billion. The human burden of tuberculosis caused by the bovine tubercle bacillus is still largely unknown. M. bovis was also the progenitor for the M. bovis bacillus Calmette–Guérin vaccine strain, the most widely used human vaccine. Here we describe the 4,345,492-bp genome sequence of M. bovis AF2122/97 and its comparison with the genomes of Mycobacterium tuberculosis and Mycobacterium leprae. Strikingly, the genome sequence of M. bovis is >99.95% identical to that of M. tuberculosis, but deletion of genetic information has led to a reduced genome size. Comparison with M. leprae reveals a number of common gene losses, suggesting the removal of functional redundancy. Cell wall components and secreted proteins show the greatest variation, indicating their potential role in host–bacillus interactions or immune evasion. Furthermore, there are no genes unique to M. bovis, implying that differential gene expression may be the key to the host tropisms of human and bovine bacilli. The genome sequence therefore offers major insight on the evolution, host preference, and pathobiology of M. bovis.
Genetic association of FTO/IRX region with obesity and overweight in the Polish population

Background/Objectives Genome-wide association studies (GWAS) have identified many loci associated with body mass index (BMI) in many different populations. Variants in the FTO locus are reported to be one of the strongest genetic predictors of obesity. Recent publications pointed also to a topologically associated domain (TAD) which is identified as a novel region affecting BMI. The TAD area encompasses the IRXB cluster (IRX3, IRX5, IRX6), FTO and RPGRIP1L genes. Subjects/Methods In this study, we investigated the relationship between variation of the FTO and IRX genes and obesity in Poles. We presented a case—control association analysis (normal versus overweight and/or obesity group) of Polish adult individuals (N = 5418). We determined whether or not the chromosomal region 16:53 500 000–55 500 000 contains polymorphic variants which are correlated with BMI in Polish population, including sex and age stratified analysis. Results The obtained results showed that the problem of weight-height abnormalities differently affects populations of Polish women and men (χ2 = 187.1; p<0.0001). From 353 SNPs enrolled to this study, 86 were statistically significant (highest χ2 = 15.72; p = 7.35E-05 observed for rs1558902). Linkage disequilibrium (LD) analysis revealed 61 blocks in the tested region of chromosome 16, with 24 SNPs located within the same block (block 8) of approximately 40 kb, in almost complete LD (|D’|>0.98, r2>0.80). We confirmed presence of the genetic susceptibility loci located in intron 1 of the FTO gene, which were correlated with BMI in our study group. For the first time, our analyses revealed strong association of FTO intronic variants (block 8) with overweight in group of men only. We have also identified association of the IRX region with overweight and/or obesity in Polish individuals. Conclusion Our study demonstrated how tested SNPs make differential contributions to obesity and overweight risk. We revealed sex dependent differences in the distribution of tested loci which are associated with BMI in the population of Poles.
Plasma Homocysteine Concentration, Statin Therapy, and the Risk of First Acute Coronary Events

Background—Elevated homocysteine levels are associated with increased coronary risk, and it has been suggested that homocysteine screening may provide a method to identify high-risk patients for aggressive primary prevention. Methods and Results—Homocysteine was measured at baseline and after 1 year among 5569 participants in the Air Force/Texas Coronary Atherosclerosis Prevention Study (AFCAPS/TexCAPS), a randomized trial of lovastatin in the primary prevention of acute coronary events. The effects of homocysteine, LDL cholesterol, and lovastatin on risk were assessed over 5.2 years of trial follow-up. Median baseline homocysteine levels were significantly higher among study participants who subsequently had acute coronary events compared with those who did not (12.1 versus 10.9 &mgr;mol/L, P <0.001). The relative risks of future events from lowest (referent) to highest quartile of homocysteine were 1.0, 1.6, 1.6, and 2.2 (P <0.001). These effects were similar among those allocated to lovastatin and those allocated to placebo and were modestly attenuated after adjustment for other traditional risk factors. As predicted, the subgroup of participants with elevated LDL cholesterol and elevated homocysteine levels were at high risk and benefited greatly from statin therapy (relative risk, 0.46; 95% CI, 0.29 to 0.75; number needed to treat=26). However, in contrast to findings in this trial for C-reactive protein, homocysteine evaluation did not help to define low LDL subgroups with different responses to lovastatin therapy. Conclusions—Although homocysteine predicted future coronary events in AFCAPS/TexCAPS, we found little evidence that homocysteine evaluation provided an improved method to target statin therapy among those with low-to-normal LDL cholesterol levels.
PubliyPrime : Exploiting Overlay Neighborhoods to Defeat Byzantine Publish / Subscribe Brokers

Publish/Subscribe (pub/sub) systems operating in hostile multi-domain environments face various types of internal and external threats. This paper focuses on internal threats manifested when pub/sub brokers misbehave by deviating from their prescribed protocol. Broker misbehavior may partially or fully compromise the pub/sub service integrity. In this paper, we exploit the notion of overlay neighborhoods and develop a solution to protect content-based pub/sub systems against misbehaving (a.k.a., byzantine) brokers. Our approach gives correct brokers the ability to oversee the actions of their neighbors, identify cases of deviation from the protocol and take steps to subvert the threat. As a result of this collective oversight, the system can preserve its service integrity despite presence of a configurable number of byzantine brokers. We have implemented our solution and report on our experimental evaluation results.
Personalized classifiers: evolving a classifier from a large reference knowledge graph

Identifying the right choice of categories for organizing and representing a large digital library of documents is a challenging task. A completely automated approach to category creation from the underlying collection could be prone to noise. On the other hand, an absolutely manual approach to the creation of categories could be cumbersome and expensive. Through this work, we propose an intermediate solution, in which, a global, collaboratively-developed Knowledge Graph of categories can be adapted to a local document categorization problem effectively. We model our classification problem as that of inferring structured labels in an Associative Markov Network meta-model over SVMs, where the label space is derived from a large global category graph. We propose a joint Active Learning model over the label and the document spaces in order to incorporate active labeling feedback from the users to train the model parameters.
An Exploration of Market Pricing Efficiency During the Dairy Options Pilot Program

Put options have been recommended as a substitute for price support programs (Gardner, 1977), and subsidized option purchases have received some support in lieu of subsidized insurance programs. Put options are an interesting alternative to price supports because their market-determined price levels allow for flexibility and adjustments to relevant current and expected market conditions. One difficulty with the use of put options as a substitute for commodity price supports is the relative thinness of these options markets for some commodities. Market thinness is defined here as the absence of traders willing to take the necessary opposite position in the market in lieu of a relatively large price premium, particularly for a large number of contracts. We explore empirically how a thin market responds when trading increases as a result of a subsidized put option program. USDA initiated the Dairy Options Pilot Program (DOPP) in 1999 in an effort to provide dairy producers with real-world experiences trading options (Vandeveer et al., 2003). Subsequently, additional rounds of DOPP occurred to give more producers a chance to participate. In total, over 1,300 producers bought 6,500 milk put option contracts through the DOPP program from 1999 to 2002. In contrast, over this four-year period total put options traded at the CME milk futures market totaled over 36,000 contracts. This, the volume from the DOPP program represented a fairly large share of total trading activity in the dairy put options market. An interesting feature of the subsidized milk options program is that dairy farmers may have made relatively little use of commodities markets due to the long-standing dairy price support programs. If this is the case, many of the dairy farmers making use of this subsidized options purchase program would have been relatively uniformed traders. Although DOPP may have increased trading volume, market performance may or may not have been enhanced due to the relative unfamiliarity with options trading by these dairy producers. We define a measure for observed options pricing efficiency using Black's formula in our study of the DOPP program, and statistically evaluate the size of the "error" in options pricing. We find that DOPP trades occurred at statistically significantly higher prices than did other trades, that DOPP volume had a price-reducing effect on other options trades, and that some brokers with large DOPP volume filled these orders at relatively large prices.
Multi-view hair capture using orientation fields

Reconstructing realistic 3D hair geometry is challenging due to omnipresent occlusions, complex discontinuities and specular appearance. To address these challenges, we propose a multi-view hair reconstruction algorithm based on orientation fields with structure-aware aggregation. Our key insight is that while hair's color appearance is view-dependent, the response to oriented filters that captures the local hair orientation is more stable. We apply the structure-aware aggregation to the MRF matching energy to enforce the structural continuities implied from the local hair orientations. Multiple depth maps from the MRF optimization are then fused into a globally consistent hair geometry with a template refinement procedure. Compared to the state-of-the-art color-based methods, our method faithfully reconstructs detailed hair structures. We demonstrate the results for a number of hair styles, ranging from straight to curly, and show that our framework is suitable for capturing hair in motion.
Facial Performance Transfer via Deformable Models and Parametric Correspondence

The issue of transferring facial performance from one person's face to another's has been an area of interest for the movie industry and the computer graphics community for quite some time. In recent years, deformable face models, such as the Active Appearance Model (AAM), have made it possible to track and synthesize faces in real time. Not surprisingly, deformable face model-based approaches for facial performance transfer have gained tremendous interest in the computer vision and graphics community. In this paper, we focus on the problem of real-time facial performance transfer using the AAM framework. We propose a novel approach of learning the mapping between the parameters of two completely independent AAMs, using them to facilitate the facial performance transfer in a more realistic manner than previous approaches. The main advantage of modeling this parametric correspondence is that it allows a "meaningful” transfer of both the nonrigid shape and texture across faces irrespective of the speakers' gender, shape, and size of the faces, and illumination conditions. We explore linear and nonlinear methods for modeling the parametric correspondence between the AAMs and show that the sparse linear regression method performs the best. Moreover, we show the utility of the proposed framework for a cross-language facial performance transfer that is an area of interest for the movie dubbing industry.
The Diadic Measure of Environmental Congruence

In the diadic method of measuring environmental congruence (or P-E Fit), the personality type of each individual in an environment is compared with that of each of the others in the same environment, using Holland's typology. Congruence score is defined as the mean of these comparisons, and the environmental homogeneity as the mean of the relevant congruence scores. In an effort to test the efficacy of this method, a study was conducted on 205 participants in 25 environments. Correlations of . 22 and . 46 were found between diadic congruence scores and satisfaction in individual and environmental analyses, respectively. These figures are similar to the correlations found between homogeneity and satisfaction (congruence and homogeneity correlated .81). A comprehensive interpretation of the findings, relating to environmental importance as well, is suggested.
Feature Selection : A Limited-Memory Substitution Algorithm and Its Asynchronous Parallel Variation

This paper considers the feature selection scenario where only a few features are accessible at any time point. For example, features are generated sequentially and visible one by one. Therefore, one has to make an online decision to identify key features after all features are only scanned once or twice. The optimization based approach is a powerful tool for the online feature selection. However, most existing optimization based algorithms explicitly or implicitly adopt L1 norm regularization to identify important features, and suffer two main disadvantages: 1) the penalty term for L1 norm term is hard to choose; and 2) the memory usage is hard to control or predict. To overcome these two drawbacks, this paper proposes a limited-memory and model parameter free online feature selection algorithm, namely online substitution (OS) algorithm. To improve the selection efficiency, an asynchronous parallel extension for OS (Asy-OS) is proposed. Convergence guarantees are provided for both algorithms. Empirical study suggests that the performance of OS and Asy-OS is comparable to the benchmark algorithm Grafting, but requires much less memory cost and can be easily extended to the parallel implementation.
An Adaptive Local Dependency Language Model: Relaxing the NaBayes' Assumption

We describe a new probabilistic approach in the language modeling framework that captures adaptively the local term dependencies in documents. The new model works by boosting scores of documents that contain topic-specific local dependencies and exhibits the behavior of the unigram model in the absence of such dependencies. Contributions of the current work include adapting van Rijsbergen’s [14] work in the classical probabilistic framework to the language modeling framework and adaptive modeling of withinsentence dependencies. We evaluated our model on two different tasks of the Topic Detection and Tracking (TDT) research program, namely Story Link Detection and Topic Tracking. Our results show that the Local dependency language model consistently outperforms the basic unigram model on both the tasks.
Socio-economic differentials in health: The role of nutrition

This paper examines the role of nutrition in generating inequalities in health. While the precise role is difficult to delineate, in several cases, nutritional deficiencies or excesses which will generate health problems are socially patterned in such a way to further disadvantage the poor. This paper discusses differentials in mortality and morbidity, and their origins; social class, central obesity, and metabolism; social patterning of diet and nutrition; and life-course influences on health inequalities.
The digital library as a community of information agents

sound decisions. Again, decision-theoretic agents will be able to apply economic and game-theoretic models for dealing with multiagent interactions. These tools include various mechanisms such as auctions, bidding schemes, and negotiation strategies. Finally, there will be the need and opportunity to conduct system-level analyses of the multiple agents, investigating the roles of system-wide constraints on behavior, whether these are imposed by the library administration (“artificial social laws”) or arrived at dynamically through gradual adaptation (“artificial social conventions”). In short, digital libraries offer an interesting intellectual playground, and within it, the notion of information agents presents an exciting new challenge. We believe that AI has the right set of tools to tackle this challenge, with contributions from multiple areas, including knowledge representation, reasoning about uncertainty, and multiagent systems. However, the new challenge will stretch and test these tools in novel ways, which will benefit the community as a whole.
A semi-automatic method for neuron centerline extraction in confocal microscopic image stack

An algorithm for extracting the centerlines of neurons from 3-D image stack collected from a laser scanning confocal microscope is presented. Recovery of neuronal structure from image stack is critical for quantitative analysis of neuron-morphology. Many methods have been proposed to extract the centerline from the tubular structure in medical images, such as vessels. But the same methods do not work well in processing of neurons. One of the reasons is that the physical limitations of the spatial resolution of the image stack collect by confocal microscopy in the z-direction is much worse than the resolution in x and y directions. In our studied cases the mean voxel size of the image stack is 0.17x0. 17x10 mum3 i.e., the resolution in z-direction cannot reflect the fact that the neuron has a tubular structure. In this paper, we propose an almost automatic neuron-tracing algorithm for a set of confocal microscopic images of neuron. The method is designed based on finding a minimal path in the volume to extract the centerlines of a neuron.
Fauccal : an Open Source Toolbox for Fully Automatic Camera Calibration

Recently, the authors presented a fully automatic camera calibration algorithm. The open-source software FAUCCAL (Fully Automatic Camera Calibration) is now freely available on the Internet. Input is simply different images of standard chess-board patterns; the software then proceeds automatically to produce calibration results and statistical data for camera parameters selected by the user. With this software, feature points are first extracted with a Harris operator, among which valid pattern nodes are separated and subsequently ordered in columns and rows in correspondence with pattern nodes. Initial values for all unknown parameters are estimated automatically. Based on the established point correspondences and initial values, a final bundle adjustment allows fully recovering – without use of any external information – the camera geometry parameters selected by the user. Besides camera constant, principal point location and radial-symmetric lens distortion polynomial, these may include decentering lens distortion, aspect ratio and skewness. Graphical output is also provided. The FAUCCAL site provides users with the source code in Matlab, detailed documentation of the software (including tips), links to bibliographical references and an image test dataset with results. It is believed that our software will prove useful to everyone, and particularly non-photogrammetrists, involved in the field of cultural heritage documentation. The authors welcome any questions but also suggestions, comments and criticism which will help improve this toolbox.
The Sobolev Regularity of Refinable Functions

Refinable functions underlie the theory and constructions of wavelet systems on the one hand and the theory and convergence analysis of uniform subdivision algorithms on the other. The regularity of such functions dictates, in the context of wavelets, the smoothness of the derived wavelet system and, in the subdivision context, the smoothness of the limiting surface of the iterative process. Since the refinable function is, in many circumstances, not known analytically, the analysis of its regularity must be based on the explicitly known mask. We establish in this paper a formula that computes, for isotropic dilation and in any number of variables, the sharp L"2-regularity of the refinable function @f in terms of the spectral radius of the restriction of the associated transfer operator to a specific invariant subspace. For a compactly supported refinable function @f, the relevant invariant space is proved to be finite dimensional and is completely characterized in terms of the dependence relations among the shifts of @f together with the polynomials that these shifts reproduce. The previously known formula for this compact support case requires the further assumptions that the mask is finitely supported and that the shifts of @f are stable. Adopting a stability assumption (but without assuming the finiteness of the mask), we derive that known formula from our general one. Moreover, we show that in the absence of stability, the lower bound provided by that previously known formula may be abysmal. Our characterization is further extended to the FSI (i.e., vector) case, to the unisotropic dilation matrix case, and to even snore general setups. We also establish corresponding results for refinable distributions.