Miracle-dz/UniFAR-FTUs huggingface dataset:
Gene function prediction using protein domain probability and hierarchical Gene Ontology information

The Gene Ontology (GO) is a controlled vocabulary of terms to describe protein functions. It also includes a hierarchical description of the relationships among the terms in the form of a directed acyclic graph (DAG). Several systems have been developed that employ pattern recognition to assign gene function, using a variety of features, including sequence similarity, presence of protein functional domains and gene expression patterns, but most of these approaches have not considered the hierarchical structure of the GO. The DAG represents the functional relationships between the GO terms, thus it should be an important component of an automated annotation system. We propose a Bayesian, multi-label classifier that incorporates the relationships among GO terms found in the GO DAG. A comparative analysis of our method to other previously described annotation systems shows that our method provides improved annotation accuracy when the performance of individual GO terms are compared. More importantly, our method enables the classification of significantly more GO terms to more proteins than were previously possible.
Intensity-modulated x-ray (IMXT) versus proton (IMPT) therapy for theragnostic hypoxia-based dose painting

In this work the abilities of intensity-modulated x-ray therapy (IMXT) and intensity-modulated proton therapy (IMPT) to deliver boosts based on theragnostic imaging were assessed. Theragnostic imaging is the use of functional or molecular imaging data for prescribing radiation dose distributions. Distal gradient tracking, an IMPT method designed for the delivery of non-uniform dose distributions, was assessed. Dose prescriptions for a hypoxic region in a head and neck squamous cell carcinoma patient were designed to either uniformly boost the region or redistribute the dose based on positron emission tomography (PET) images of the 61Cu(II)-diacetyl-bis(N4-methylthiosemicarbazone) (61Cu-ATSM) hypoxia surrogate. Treatment plans for the prescriptions were created for four different delivery methods: IMXT delivered with step-and-shoot and with helical tomotherapy, and IMPT delivered with spot scanning and distal gradient tracking. IMXT and IMPT delivered comparable dose distributions within the boost region for both uniform and redistributed theragnostic boosts. Normal tissue integral dose was lower by a factor of up to 3 for IMPT relative to the IMXT. For all delivery methods, the mean dose to the nearby organs at risk changed by less than 2 Gy for redistributed versus uniform boosts. The distal gradient tracking method resulted in comparable plans to the spot scanning method while reducing the number of proton beam spots by a factor of over 3.
Molecular Profiling of Stomatal Meristemoids Reveals New Component of Asymmetric Cell Division and Commonalities among Stem Cell Populations in Arabidopsis[C][W][OA]

This work presents the transcriptome profile of the meristemoid, a transient and low-density proliferating stomatal precursor cell with stem cell–like properties. The work identifies a new protein exhibiting polar localization during asymmetric division of stomatal cell lineages, reveals molecular characteristics of the meristemoid, and illuminates common themes in gene expression among plant stem cells. The balance between maintenance and differentiation of stem cells is a central question in developmental biology. Development of stomata in Arabidopsis thaliana begins with de novo asymmetric divisions producing meristemoids, proliferating precursor cells with stem cell–like properties. The transient and asynchronous nature of the meristemoid has made it difficult to study its molecular characteristics. Synthetic combination of stomatal differentiation mutants due to loss- or gain-of-function mutations in SPEECHLESS, MUTE, and SCREAM create seedlings with an epidermis overwhelmingly composed of pavement cells, meristemoids, or stomata, respectively. Through transcriptome analysis, we define and characterize the molecular signatures of meristemoids. The reporter localization studies of meristemoid-enriched proteins reveals pathways not previously associated with stomatal development. We identified a novel protein, POLAR, and demonstrate through time-lapse live imaging that it exhibits transient polar localization and segregates unevenly during meristemoid asymmetric divisions. The polar localization of POLAR requires BREAKING OF ASYMMETRY IN THE STOMATAL LINEAGE. Comparative bioinformatic analysis of the transcriptional profiles of a meristemoid with shoot and root apical meristems highlighted cytokinin signaling and the ERECTA family receptor-like kinases in the broad regulation of stem cell populations. Our work reveals molecular constituents of stomatal stem cells and illuminates a common theme among stem cell populations in plants.
Hierarchical Aggregation Based Deep Aging Feature for Age Prediction

We propose a new, hierarchical, aggregation-based deep neural network to learn aging features from facial images. Our deep-aging feature vector is designed to capture both local and global aging cues from facial images. A Convolutional Neural Network (CNN) is employed to extract region- specific features at the lowest level of our hierarchy. These features are then hierarchically aggregated to consecutive higher levels and the resultant aging feature vector, of dimensionality 110, achieves both good discriminative ability and efficiency. Experimental results of age prediction on the MORPH-II databases show that our method outperforms state-of-the-art aging features by a clear margin. Experimental trails of our method across race and gender provide further confidence in its performance and robustness.
Flickr-based semantic context to refine automatic photo annotation

Automatic photo annotation task aims to describe the semantic content by detecting high level concepts in order to further facilitate concept based video retrieval. Most of existing approaches are based on independent semantic concept detectors without considering the contextual correlation between concepts. This drawback has its impact over the efficiency of such systems. Recently, harnessing contextual information to improve the effectiveness of concepts detection becomes a promising direction in such field. In this paper, we propose a new contextbased annotation refinement process. For this purpose, we define a new semantic measure called “Second Order Co-occurence Flickr context similarity” (SOCFCS) which aims to extract the semantic context correlation between two concepts by exploring Flickr resources (Flickr related-tags). Our measure is an extension of FCS measure by taking into consideration the FCS values of common Flickr related-tags of the two target concepts. Our proposed measure is applied to build a concept network which models the semantic context inter-relationships among concepts. A Random Walk with Restart process is performed over this network to refine the annotation results by exploring the contextual correlation among concepts. Experimental studies are conducted on ImageCLEF 2011 Collection containing 10000 images and 99 concepts. The results demonstrate the effectiveness of our proposed approach.
Spherical Blend Skinning on GPU

Skeletal animation is commonly used for real-time animation of humans, animals, etc. There are several methods available for propagating a skeleton pose to a skin mesh, but unfortunately, one of the most commonly used methods, linear blend skinning, has inconvenient artifacts. It is, however, a simple and very fast method, and it can easily be implemented on a GPU. An improved skinning method, spherical blend skinning, has been proposed. This method requires a rotation center to be computed by solving a linear matrix system, and further, it requires interpolation of quaternions. Thus, this method is more complex and slower than linear blend skinning, but it requires and produces exactly the same input and output as linear blend skinning making it easy to interchange the two methods. In this paper, we propose a method that enables spherical blend skinning to run on a GPU with performance comparable to GPU implementations of linear blend skinning, making spherical blend skinning a possible choice for many real-time applications such as computer games. The proposed method is implemented in C++, OpenGL [Shreiner et al. 2005] and Cg [NVIDIA 2005] in the OpenTissue framework [OpenTissue 2007]. Shaders are shown in pseudo code general enough to make implementation in other language combinations quite easy.
Prehistoric genomes reveal the genetic foundation and cost of horse domestication

Significance The domestication of the horse revolutionized warfare, trade, and the exchange of people and ideas. This at least 5,500-y-long process, which ultimately transformed wild horses into the hundreds of breeds living today, is difficult to reconstruct from archeological data and modern genetics alone. We therefore sequenced two complete horse genomes, predating domestication by thousands of years, to characterize the genetic footprint of domestication. These ancient genomes reveal predomestic population structure and a significant fraction of genetic variation shared with the domestic breeds but absent from Przewalski’s horses. We find positive selection on genes involved in various aspects of locomotion, physiology, and cognition. Finally, we show that modern horse genomes contain an excess of deleterious mutations, likely representing the genetic cost of domestication. The domestication of the horse ∼5.5 kya and the emergence of mounted riding, chariotry, and cavalry dramatically transformed human civilization. However, the genetics underlying horse domestication are difficult to reconstruct, given the near extinction of wild horses. We therefore sequenced two ancient horse genomes from Taymyr, Russia (at 7.4- and 24.3-fold coverage), both predating the earliest archeological evidence of domestication. We compared these genomes with genomes of domesticated horses and the wild Przewalski’s horse and found genetic structure within Eurasia in the Late Pleistocene, with the ancient population contributing significantly to the genetic variation of domesticated breeds. We furthermore identified a conservative set of 125 potential domestication targets using four complementary scans for genes that have undergone positive selection. One group of genes is involved in muscular and limb development, articular junctions, and the cardiac system, and may represent physiological adaptations to human utilization. A second group consists of genes with cognitive functions, including social behavior, learning capabilities, fear response, and agreeableness, which may have been key for taming horses. We also found that domestication is associated with inbreeding and an excess of deleterious mutations. This genetic load is in line with the “cost of domestication” hypothesis also reported for rice, tomatoes, and dogs, and it is generally attributed to the relaxation of purifying selection resulting from the strong demographic bottlenecks accompanying domestication. Our work demonstrates the power of ancient genomes to reconstruct the complex genetic changes that transformed wild animals into their domesticated forms, and the population context in which this process took place.
Vision in Protection and Control Area - Meeting the Challenges of 21st Century

This paper addresses applications of modern technology, advanced feedback control schemes using wide area measurements, and wide-area visualization techniques to improve grid reliability in complex and multifaceted power system conditions. Reliability aspects of P&C systems such as methods to identify and correct hidden failures and methodologies for optimal testing are also described. As new technologies offer significant improvements, large numbers of legacy P&C systems are still in operation. Upgrading aging P&C systems with modern counterparts not only reduces possibilities for failure, but offers unprecedented capabilities for reliable and high quality data and flexibility in operations which are presently largely untapped. Possibility to monitor equipment performance and to identify failed parts or components helps with equipment life projections and replacement decisions. Integration of P&C systems into Enterprise Systems for improved Asset Management, including value of standardization, is also assessed. The goal of this paper is to provide a comprehensive and systematic approach to meeting the P&C challenges of the 21st century
Audio-visual intent-to-speak detection for human-computer interaction

Introduces a practical system that aims to detect a user's intent to speak to a computer, by considering both audio and visual cues. The whole system is designed to intuitively turn on the microphone for speech recognition without needing to click on a mouse, thus improving the human-like communication between users and computers. The first step is to detect a frontal face through a simple desktop video camera image, by using some well-known image processing techniques for face and facial feature detection on one image. The second step is an audio-visual speech event detection that combines both visual and audio indications of speech. In this paper, we consider visual measures of speech activity as well as audio energy to determine if the previously detected user is actually speaking or not.
The Australian Self‐report Delinquency Scale: A revision

Abstract Objectives The Australian Self‐Reported Delinquency Scale has been a widely adopted measure of delinquency, yet requires updating to ensure appropriate content coverage and consistency with contemporary language. The aim of this research was to revise the Australian Self‐Reported Delinquency Scale and derive a measure of contemporary delinquent behaviour among Australian adolescents with satisfactory psychometric properties. Method In Study 1, we conducted focus groups with 16 adolescents and 20 professionals (youth workers, police officers, school teachers/counsellors) in Canberra to update items included in the measure. Contents of the scale were revised accordingly, yielding a 56‐item checklist of contemporary delinquent activities. In Study 2, 312 students (57.7% male, aged 13–17) from government and independent schools in Canberra completed the 56‐item Delinquency Checklist. Results Subsequent item analysis and exploratory and confirmatory factor analyses resulted in a 30‐item Australian Self‐Reported Delinquency Scale‐Revised with eight subscales (Driving/Vehicle, Theft, Cheat, Disturb, Fight, Drugs) including two new subscales (Alcohol and Media), with evidence of reliability and validity. Conclusions The revision of the Australian Self‐Reported Delinquency Scale‐Revised, complemented by a 56‐item Delinquency Checklist, may prove useful in educational, rehabilitation, and research settings, and aid in evaluating clinical interventions with increased specificity.
Release profile and stability evaluation of optimized chitosan/alginate nanoparticles as EGFR antisense vector

Chitosan/alginate nanoparticles which had been optimized in our previous study using two different N/P ratios were chosen and their ability to release epidermal growth factor receptor (EGFR) antisense was investigated. In addition, the stability of these nanoparticles in aqueous medium and after freeze-drying was investigated. In the case of both N/P ratios (5, 25), nanoparticles started releasing EGFR antisense as soon as they were exposed to the medium and the release lasted for approximately 50 hours. Nanoparticle size, shape, zeta potential, and release profile did not show any significant change after the freeze-drying process (followed by reswelling). The nanoparticles were reswellable again after freeze-drying in phosphate buffer with a pH of 7.4 over a period of six hours. Agarose gel electrophoresis of the nanoparticles with the two different N/P ratios showed that these nanoparticles could protect EGFR antisense molecules for six hours.
Clinical Significances of Antibodies to Ro/SS-A Autoantigens and Its Subtypes in Primary Sjogren’s Syndrome

Objective To evaluate the patterns of Ro autoantigen recognition in Korean patients with primary Sjogren’s syndrome (SS) and to investigate its clinical significance in SS. Methods Sera from primary SS (n=51) and systemic lupus erythematosus (SLE) (n=132) were tested by double immunodiffusion test and immunoblotting for reactivity with 60kDa and 52kDa Ro/SS-A proteins. Clinical manifestations were evaluated on the basis of the presence of anti-Ro/SS-A antibodies and anti-60 kDa/52kDa proteins. Results The prevalence of anti-Ro/SS-A antibodies in Korean patients with primary SS was 64.7%. In immunoblotting analysis, the incidence of anti-60kDa without anti-52kDa was lower in patients with SS(3.0% vs. 11.6%, p>0.05), whereas anti-52kDa without anti-60kDa was more common in SS patients than in SLE patients(42.5% vs. 4.3%, p<0.001). Patients with anti-Ro/SS-A antibody were significantly associated with the presence of vasculitis, hyperglobulinemia and rheumatoid factor in primary SS (p<0.05). Conclusion The patterns of 52kDa and 60kDa Ro autoantigen recognition were quite different in the SLE and primary SS. Anti-52kDa without anti-60kDa antibody may be used as a diagnostic marker for primary SS. Although the presence of anti-Ro/SS-A antibody was closely associated with certain clinical features in SS, these clinical manifestations were not correlated with the presence of antibodies against each 52kDa and 60kDa proteins. Extended studies with a large population are required to determine the clinical correlation of autoantibodies against each peptides or epitopes of Ro/SS-A proteins.
A Two Step Process to Named Entity Recognition

Speech transcriptions are very complex to process by taggers for conventional written language due to the lack of capitalization and punctuation marks. We report in this paper our first attempt toward named entity recognition on speech transcriptions. In this work, we experimented on simulated speech transcriptions. Our experimental result s show that our method is robust and achieves high classification accuracies.
Explore Biological Pathways from Noisy Array Data by Directed Acyclic Boolean Networks

We consider the structure of directed acyclic Boolean (DAB) networks as a tool for exploring biological pathways. In a DAB network, the basic objects are binary elements and their Boolean duals. A DAB is characterized by two kinds of pairwise relations: similarity and prerequisite. The latter is a partial order relation, namely, the on-status of one element is necessary for the on-status of another element. A DAB network is uniquely determined by the state space of its elements. We arrange samples from the state space of a DAB network in a binary array and introduce a random mechanism of measurement error. Our inference strategy consists of two stages. First, we consider each pair of elements and try to identify their most likely relation. In the meantime, we assign a score, s-p-score, to this relation. Second, we rank the s-p-scores obtained from the first stage. We expect that relations with smaller s-p-scores are more likely to be true, and those with larger s-p-scores are more likely to be false. The key idea is the definition of s-scores (referring to similarity), p-scores (referring to prerequisite), and s-p-scores. As with classical statistical tests, control of false negatives and false positives are our primary concerns. We illustrate the method by a simulated example, the classical arginine biosynthetic pathway, and show some exploratory results on a published microarray expression dataset of yeast Saccharomyces cerevisiae obtained from experiments with activation and genetic perturbation of the pheromone response MAPK pathway.
Essays on Citizenship

The pre-history of the Citizenship Report 1997 the introduction of politics in schools (1969) on bias (1972) political literacy (with Ian Lister, 1978) basic concepts for political education (1978) citizenship and education (1992) a defence of the Citizenship Order, 1999 towards 2002 - the good and the active citizen for some special groups - values education, human rights, global citizenship governors the presuppositions of citizenship education the decline of political thinking in British public life a meditation on democracy, politics and inclusive citizenship.
Politically-Connected Firms: Can They Squeeze the State?

For a sample of 42 countries, I examine firms whose controlling shareholders and top managers are members of national parliaments or governments. I find that this overlap is quite widespread, especially in highly corrupted countries. Connected companies enjoy easier access to debt financing, lower taxation, and stronger market power. These benefits increase when companies are connected through their owner, with a minister, or a seasoned politician. Furthermore, these benefits are generally larger when the firm operates in a country with high corruption, low protection of property rights, a highly interventionist government, or a non-democratic government. Even though these connections provide significant benefits, connected firms under-perform their peers on an ex-ante basis. Therefore connections, by driving benefits to relatively poorly performing firms, distort the allocation of funds and investment decisions.
The Effect of Newspaper Entry and Exit on Electoral Politics

We use new data on entries and exits of US daily newspapers from 1869 to 2004 to estimate effects on political participation, party vote shares, and electoral competitiveness. Our identification strategy exploits the precise timing of these events and allows for the possibility of confounding trends. We find that newspapers have a robust positive effect on political participation, with one additional newspaper increasing both presidential and congressional turnout by approximately 0.3 percentage points. Newspaper competition is not a key driver of turnout: our effect is driven mainly by the first newspaper in a market, and the effect of a second or third paper is significantly smaller. The effect on presidential turnout diminishes after the introduction of radio and television, while the estimated effect on congressional turnout remains similar up to recent years. We find no evidence that partisan newspapers affect party vote shares, with confidence intervals that rule out even moderate-sized effects. We find no clear evidence that newspapers systematically help or hurt incumbents.
Statistical and process models for cognitive neuroscience and aging

Contents: M.J. Wenger, C. Schuster, Preface. S.D. Edland, R.C. Petersen, Longitudinal Study in Cognition and Aging. F.G. Ashby, V.V. Valentin, Computational Cognitive Neuroscience: Building and Testing Biologically Plausible Computational Models of Neuroscience, Neuroimaging, and Behavioral Data. M.E. Hasselmo, J. McGaughy, C. Linster, Modeling the Role of Acetylcholine and Hippocampal Theta Rhythm in Memory-Guided Behavior. J.M.J. Murre, M. Meeter, A.G. Chessa, Modeling Amnesia: Connectionist and Mathematical Approaches. A. Keinan, A. Kaufman, C.C. Hilgetag, I. Meilijson, E. Ruppin, Who Does What: Taking Measures. A. Cichocki, Generalized Component Analysis and Blind Source Separation Methods for Analyzing Multichannel Brain Signals. T.C. Ferree, M.A. Kramer, D.J. McGonigle, R.C. Hwa, Quantifying Scaling Properties in Neurophysiological Time Series. T. -P. Jung, T. -W. Lee, Applications of Independent Component Analysis to Electroencephalography.