Miracle-dz/UniFAR-FTUs huggingface dataset:
Unleashing the power of meta-threading for evolution/structure-based function inference of proteins

Protein threading is widely used in the prediction of protein structure and the subsequent functional annotation. Most threading approaches employ similar criteria for the template identification for use in both protein structure and function modeling. Using structure similarity alone might result in a high false positive rate in protein function inference, which suggests that selecting functional templates should be subject to a different set of constraints. In this study, we extend the functionality of eThread, a recently developed approach to meta-threading, focusing on the optimal selection of functional templates. We optimized the selection of template proteins to cover a broad spectrum of protein molecular function: ligand, metal, inorganic cluster, protein, and nucleic acid binding. In large-scale benchmarks, we demonstrate that the recognition rates in identifying templates that bind molecular partners in similar locations are very high, typically 70–80%, at the expense of a relatively low false positive rate. eThread also provides useful insights into the chemical properties of binding molecules and the structural features of binding. For instance, the sensitivity in recognizing similar protein-binding interfaces is 58% at only 18% false positive rate. Furthermore, in comparative analysis, we demonstrate that meta-threading supported by machine learning outperforms single-threading approaches in functional template selection. We show that meta-threading effectively detects many facets of protein molecular function, even in a low-sequence identity regime. The enhanced version of eThread is freely available as a webserver and stand-alone software at http://www.brylinski. org/ethread.
A genome-wide transcriptional analysis of morphology determination in Candida albicans

Morphology determination is critical for virulence of the human fungal pathogen Candida albicans. A genome-wide transcriptional analysis shows that genes associated with specifying the C. albicans pseudohyphal morphology represent a subset of hyphal genes and reveals fundamental differences between forward and reverse morphological transitions.
Automatic scene recognition for low-resource devices using evolving classifiers

In this paper an original approach is proposed which makes possible autonomous scenes recognition performed on-line by an evolving self-learning classifier. Existing approaches for scene recognition are off-line and used in intelligent albums for picture categorization/selection. The emergence of powerful mobile platforms with camera on board and sensor-based autonomous (robotic) systems is pushing forward the requirement for efficient self-learning and adaptive/evolving algorithms. Fast real-time and online algorithms for categorisation of the real world environment based on live video stream are essential for understanding and situation awareness as well as for localization and context awareness. In scene analysis the critical problem is feature extraction mechanism for a quick description of the scene. In this paper we apply a well known technique called spatial envelop or GIST. Visual scenes can be quite different but very often they can be grouped in similar types/categories. For example, pictures from different cities across the Globe, e.g. Tokyo, Vancouver, New York, Moscow, Dusseldorf, etc. bear the similar pattern of an urban scene — high rise buildings, despite the differences in the architectural style. Same applies for the beaches of Miami, Maldives, Varna, Costa del Sol, etc. One assumption based on which such automatic video classifiers can be build is to pre-train them using a large number of such images from different groups. Variety of possible scenes suggests the limitations of such an approach. Therefore, we use in this paper the recently propose evolving fuzzy rule-based classifier, simpl_eClass, which is self-learning and thus updates its rules and categories descriptions with each new image. In addition, it is fully recursive, computationally efficient and yet linguistically transparent.
At cancer diagnosis: a ‘window of opportunity’ for behavioural change towards physical activity. A randomised feasibility study in patients with colon and breast cancer

Introduction Challenges exist in identifying, recruiting and motivating sedentary patients with cancer to initiate physical activity towards recommended levels. We hypothesise that the onset period of adjuvant chemotherapy can be ‘the open window of opportunity’ to identify and motivate sedentary patients with breast and colon cancers, at risk for developing coronary heart disease, to initiate and sustain lifestyle changes. Aims To investigate the feasibility of oncologists/nurses screening for physical inactivity, in order to identify and recruit an at-risk population of sedentary patients with breast or colon cancer at the onset of adjuvant chemotherapy. Furthermore, the study will examine the adherence to one of two multimodal exercise interventions lasting 12 weeks; (1) hospital-based, high intensity, group exercise intervention (2) home-based, low intensity, individual, pedometer intervention. Both arms will be compared with a control group. Methods and analyses All newly referred patients will be screened for sedentary behaviour, using national recommendations. Testing at baseline, 6, 12 and 39 weeks will include; (1) physiological testing (VO2-peak, one repetition maximum muscle strength and lung function (2) fasting full body dual-energy X-ray absorptiometry scan (3) fasting blood glucose, insulin, lipids and cholesterols, (4) psychometric questionnaires (general well-being, quality of life, anxiety and depression, motivational readiness). The randomised controlled trial feasibility design is selected in order to examine barriers for recruitment, programme adherence, safety aspects and potential efficacy to the interventions during adjuvant chemotherapy. Ethics and dissemination The Scientific Committee of the Capital Region (case No. H-1-2011-131) and the Danish Data Protection Agency (j. No. 2011-41-6349) approved the study. Data will be entered and locked into a database hosted by the Copenhagen Trial Unit, Rigshosptialet. Data will be available for analyses to project members and the trial statistician after the 45 included patients have completed the 12-week test. Results will be published in peer-reviewed scientific journals. Trial registration Current Controlled Trials ISRCTN24901641.
Image compressibility assessment and the application of structure-preserving image retargeting

A number of algorithms have been proposed for intelligent image/video retargeting with important content retained as much as possible. In some cases, we can notice that they suffer from artifacts in the resized results, such as ridge or structure twist. In this paper, we suggest that the compressibility of an image should be estimated properly first by analyzing the image structure to determine the optimal scaling factors for the resizing algorithm. To cope with this problem, we propose a compressibility assessment scheme by combining the entropies of image gradient magnitude and orientation distributions. In order to further improve the result, we also present a structure-preserving media retargeting technique that preserves the content and image structure as best as possible. Since we focus on protecting the content structure, a block structure energy is introduced with a top-down strategy to constrain the image structure inside to scale uniformly in either x or y direction. Our experiments demonstrate that the proposed compressibility assessment scheme provides better preservation of content and structure in the resized images/videos than those by the previous methods.
Semiconductor Measurement Technology : The Dopant Density and Temperature Dependence of Electron Mobility and Resistivity 1 Jn N-Type Silicon-f

Traditional analysis of electron mobility in n-type silicon neglects the effects of electron-electron scattering and scattering anisotropy in the mobility calculations. As a result, theory fails to conform with experiment when dopant density exceeds 2 x 10^^ cm~^. In this work, an improved theoretical model for computing mobility and resistivity as functions of dopant density and temperature has been formulated for n-type silicon. The model has been applied to phosphorus-doped silicon for dopant densities from 10^^ to 10^^ cm~^, and temperatures between 100 and 500 K. The electron mobility was calculated analytically by appropriately combining lattice, ionized impurity, and neutral impurity scattering contributions. The effect of electron-electron scattering on both lattice and ionized impurity scattering mobilities was incorporated empirically for dopant densities greater than 2 X 10^^ cm~^. Additionally, the anisotropic scattering effect was also considered in the mobility calculations. Theoretical calculations of resistivity and ionized donor density were made for phosphorus-doped silicon for temperatures between 100 and 500 K. Resistivity measurements on seven phosphorus-doped silicon slices with dopant densities from 1.2 x lO-^'* to 2.5 x 10^^ cm~^ were carried out for temperatures between 100 and 500 K. Electron mobility at 300 K was deduced from resistivity and junction C-V measurements for dopant densities from 10^'* to 10^^ cm~^. Agreement between theory and experiment for both electron mobility and resistivity of phosphorus-doped silicon was within ±7 percent in the range of dopant densities and temperatures studied.
Advances in adenovirus-mediated p53 cancer gene therapy

Introduction: The tumor suppressor p53 gene regulates diverse cellular processes, such as cell-cycle arrest, senescence, apoptosis and autophagy, and it is frequently inactivated by genetic alterations in ∼ 50% of all types of human cancers. To restore wild-type p53 function in p53-inactivated tumors, adenovirus-mediated p53 gene therapy has been developed as a promising antitumor strategy in preclinical experiments and clinical studies. Areas covered: This review focuses on the clinical relevance of replication-deficient adenovirus vectors that carry the wild-type p53 gene (Ad-p53; Advexin, Gendicine and SCH-58500) in clinical studies of patients with various cancers and the future perspectives regarding conditionally replicating adenovirus vectors expressing the wild-type p53 gene (CRAd-p53; AdDelta24-p53, SG600-p53, OBP-702) in preclinical experiments. Moreover, the recent advances in our understanding of the molecular basis for the p53-mediated tumor suppression network induced by Ad-p53 and CRAd-p53 vectors and the combination therapies for promoting the therapeutic potential of adenovirus-mediated p53 gene therapy are discussed. Expert opinion: Exploration of the molecular mechanism underlying the p53-mediated tumor suppression network and the effective strategy for enhancing the p53-mediated cell death signaling pathway would provide novel insights into the improvement of clinical outcome in p53-based cancer gene therapy.
Expression of cell-adhesion molecules in embryonic induction. I. Morphogenesis of nestling feathers

The potential relationship of cell adhesion to embryonic induction during feather formation was examined by immunohistochemical analysis of the spatiotemporal distribution of three cell-adhesion molecules (CAMs), neural CAM (N-CAM), liver CAM (L-CAM), and neuron-glia CAM (Ng- CAM), and of substrate molecules (laminin and fibronectin) in embryonic chicken skin. The N-CAM found at sites of embryonic induction in the feather was found to be similar to brain N-CAM as judged by immuno- cross-reactivity, migratory position in PAGE, and the presence of embryonic to adult conversion. In contrast to the N-CAM found in the brain, however, only one polypeptide of Mr 140,000 was seen. N-CAM- positive dermal condensations were distributed periodically under L-CAM- positive feather placodes at those sites where basement membranes are known to be disrupted. After initiation of induction, L-CAM-positive placode cells became transiently N-CAM-positive. N-CAM was asymmetrically concentrated in the dorsal region of the feather bud, while fibronectin was concentrated in the ventral region. During feather follicle formation, N-CAM was expressed in the dermal papilla and was closely apposed to the L-CAM-positive papillar ectoderm, while the dermal papilla showed no evidence of laminin or fibronectin. The collar epithelium was both N-CAM- and L-CAM-positive. During the formation of the feather filament, N-CAM appeared periodically and asymmetrically on basilar cells located in the valleys between adjacent barb ridges. In contrast to the two primary CAMs, Ng-CAM was found only on nerves supplying the feather and the skin. These studies indicate that at each site of induction during feather morphogenesis, a general pattern is repeated in which an epithelial structure linked by L-CAM is confronted with periodically propagating condensations of cells linked by N-CAM.
Indoor localization without infrastructure using the acoustic background spectrum

We introduce a new technique for determining a mobile phone's indoor location even when Wi-Fi infrastructure is unavailable or sparse. Our technique is based on a new ambient sound fingerprint called the Acoustic Background Spectrum (ABS). An ABS serves well as a room fingerprint because it is compact, easily computed, robust to transient sounds, and surprisingly distinctive. As with other fingerprint-based localization techniques, location is determined by measuring the current fingerprint and then choosing the "closest" fingerprint from a database. An experiment involving 33 rooms yielded 69% correct fingerprint matches meaning that, in the majority of observations, the fingerprint was closer to a previous visit's fingerprint than to any fingerprints from the other 32 rooms. An implementation of ABS-localization called Batphone is publicly available for Apple iPhones. We used Batphone to show the benefit of using ABS-localization together with a commercial Wi-Fi-based localization method. In this second experiment, adding ABS improved room-level localization accuracy from 30% (Wi-Fi only) to 69% (Wi-Fi and ABS). While Wi-Fi-based localization has difficulty distinguishing nearby rooms, Batphone performs just as well with nearby rooms; it can distinguish pairs of adjacent rooms with 92% accuracy.
Sildenafil improves alveolar growth and pulmonary hypertension in hyperoxia-induced lung injury.

RATIONALE Bronchopulmonary dysplasia (BPD), the chronic lung disease of preterm infants, and pulmonary emphysema, both significant global health problems, are characterized by an arrest in alveolar growth/loss of alveoli structures. Mechanisms that inhibit distal lung growth are poorly understood, but recent studies suggest that impaired vascular endothelial growth factor signaling and reduced nitric oxide (NO) production decreases alveolar and vessel growth in the developing lung, features observed in experimental oxygen-induced BPD. NO exerts its biological activity by stimulating guanosine 3',5'-cyclic monophosphate (cGMP) production. OBJECTIVES Because cGMP is inactivated by phosphodiesterase (PDE) enzymes, we hypothesized that the cGMP-specific PDE5 inhibitor sildenafil would promote angiogenesis and attenuate oxygen-induced lung injury in newborn rats. METHODS, MEASUREMENTS, AND MAIN RESULTS: In vitro, sildenafil (10(-4) M) increased endothelial capillary network formation of human pulmonary endothelial cells exposed to hyperoxia. In vivo, rat pups were randomly exposed from birth to normoxia, hyperoxia (95% O(2), BPD model), and hyperoxia+sildenafil (100 mg/kg/day subcutaneously). Rat pups exposed to hyperoxia showed fewer and enlarged air spaces as well as decreased capillary density, mimicking pathologic features seen in human BPD. These structural anomalies were associated with echographic (decreased pulmonary acceleration time) and structural (right ventricular hypertrophy and increased medial wall thickness) signs of pulmonary hypertension. Sildenafil preserved alveolar growth and lung angiogenesis, and decreased pulmonary vascular resistance, right ventricular hypertrophy and medial wall thickness. CONCLUSIONS Our findings suggest a role for the NO/cGMP pathway during alveolar development. Sildenafil may have therapeutic potential in diseases associated with impaired alveolar structures.
Characteristics of TRK-130 (Naltalimide), a Novel Opioid Ligand, as a New Therapeutic Agent for Overactive Bladder

We characterized TRK-130 (N-[(5R,6R,14S)-17-(cyclopropylmethyl)-4,5-epoxy-3,14-dihydroxymorphinan-6-yl]phthalimide; naltalimide), an opioid ligand, to clarify the therapeutic potential for overactive bladder (OAB). In radioligand-binding assays with cells expressing human µ-opioid receptors (MORs), δ-opioid receptors (DORs), or κ-opioid receptors (KORs), TRK-130 showed high selectivity for MORs (Ki for MORs, DORs, and KORs = 0.268, 121, and 8.97 nM, respectively). In a functional assay (cAMP accumulation) with cells expressing each human opioid receptor subtype, TRK-130 showed potent but partial agonistic activity for MORs [EC50 (Emax) for MORs, DORs, and KORs = 2.39 nM (66.1%), 26.1 nM (71.0%), and 9.51 nM (62.6%), respectively]. In isovolumetric rhythmic bladder contractions (RBCs) in anesthetized guinea pigs, TRK-130 dose-dependently prolonged the shutdown time (the duration of complete cessation of the bladder contractions) (ED30 = 0.0034 mg/kg i.v.) without affecting amplitude of RBCs. Furthermore, TRK-130 ameliorated formalin-induced frequent urination at doses of higher than 0.01 mg/kg p.o. in guinea pigs under the freely moving condition. Meanwhile, TRK-130 showed only a negligible effect on the gastrointestinal transit at doses of up to 10 mg/kg s.c. in mice. These results indicate that TRK-130 is a potent and selective human MOR partial agonist without undesirable opioid adverse effects such as constipation and enhances the storage function by suppressing the afferent limb of the micturition reflex pathway, suggesting that TRK-130 would be a new therapeutic agent for OAB.
Functional characteristics and sites of gene expression of the alpha 1, beta 1, gamma 2-isoform of the rat GABAA receptor

GABAA receptors, the major synaptic targets for the neurotransmitter GABA, constitute gated chloride channels. By their allosteric, drug- induced modulation, they serve as control elements for the regulation of anxiety, vigilance, and epileptiform activity. The structural requirements of fully functional GABAA receptors in the mammalian brain have remained elusive so far. We report here on the cloning of the gamma 2-subunit cDNA of rat brain and its functional analysis by coexpression with the alpha 1- and beta 1-subunits in Xenopus oocytes, and on the sites of gene expression of the 3 subunits in the rat brain. The recombinant receptor displayed GABA-inducible currents (Imax = 6 microA; Ka = 75 microM) which were allosterically modulated by benzodiazepine receptor ligands (enhancement and inhibition by diazepam and methyl-6,7-dimethoxy-4-ethyl-beta-carboline-3-carboxylate, respectively). In the absence of GABA, pentobarbital elicited a maximal current amplitude similar to that of GABA. A minor population of channels is expressed which is open in the absence of GABA or pentobarbital. Mapping subunit gene expression by in situ hybridization histochemistry suggests that the alpha 1-, beta 1-, and gamma 2- subunits are likely receptor constituents in some neuronal populations, e.g., mitral cells of the olfactory bulb, pyramidal cells of the hippocampus, and granule cells of the dentate gyrus and cerebellum.
Modelling Evolvable Systems: A Temporal Logic View

There is a growing trend to develop and deploy computing systems that adapt or evolve themselves dynamically according to use and observed changes in their environment. Evolution may be triggered either from within the system or be forced by some external, and not necessarily human, agent. The traditional view of system specification being invariant for the duration of a run will no longer hold for such an evolvable system; it will be rare to be able to predict all possible ways in which a system may evolve. In this contribution, we consider one approach to how temporal logic, and specifications based on temporal logic, can be used to support formal reasoning about evolvable systems in a natural way. Our approach builds on our past work in temporal logic-based specification, the imperative view of temporal logic as in our work on executable temporal logic, MetateM, developed jointly with Dov Gabbay in the late 1980s [3], [2], and the more recent work on the Eagle logic for run-time verification [4], [1]. A rather crude view of formal systems development has basic steps comprising:
Attendance Allowance and Disability Living Allowance claimants in the older population: Is there a difference in their economic circumstances?

The UK Disability Living Allowance (DLA) is a non-means-tested cash benefit claimable initially only by people under 65, but receipt of which can be continued after that age. The similar Attendance Allowance (AA) can only be claimed after age 65. Recent proposals for benefit reform have suggested more favourable treatment for DLA recipients, on grounds that they have longer histories of disability and consequently lower financial security. We investigate this claim using detailed survey data on household incomes and find no evidence of higher levels of income deprivation among DLA than AA recipients in terms of equivalised pre-benefit family income.
Exactly Rao-Blackwellized unscented particle filters for SLAM

This paper addresses the limitation of the conventional Rao-Blackwellized unscented particle filters. The problem is on the usage of the overconfident optimal proposal distribution caused by perfect map assumption, so that predictive robot poses are sampled from the underestimated error covariance in the particle filtering process. The proposed solution computes more precise error covariance of the robot which contains uncertainties of the robot, map, and measurement noise. Experimental results using the benchmark dataset confirmed that the covariance of the proposed method is always larger than that of the conventional method while inducing slower increasing rate of the weight variance with less resamplings.
Semisupervised SVM batch mode active learning with applications to image retrieval

Support vector machine (SVM) active learning is one popular and successful technique for relevance feedback in content-based image retrieval (CBIR). Despite the success, conventional SVM active learning has two main drawbacks. First, the performance of SVM is usually limited by the number of labeled examples. It often suffers a poor performance for the small-sized labeled examples, which is the case in relevance feedback. Second, conventional approaches do not take into account the redundancy among examples, and could select multiple examples that are similar (or even identical). In this work, we propose a novel scheme for explicitly addressing the drawbacks. It first learns a kernel function from a mixture of labeled and unlabeled data, and therefore alleviates the problem of small-sized training data. The kernel will then be used for a batch mode active learning method to identify the most informative and diverse examples via a min-max framework. Two novel algorithms are proposed to solve the related combinatorial optimization: the first approach approximates the problem into a quadratic program, and the second solves the combinatorial optimization approximately by a greedy algorithm that exploits the merits of submodular functions. Extensive experiments with image retrieval using both natural photo images and medical images show that the proposed algorithms are significantly more effective than the state-of-the-art approaches. A demo is available at http://msm.cais. ntu.edu. sg/LSCBIR/.