Miracle-dz/UniFAR-FTUs huggingface dataset:
Mesh pose‐editing using examples

An easy‐to‐use mesh pose‐editing system is presented. We take advantage of both skeleton‐based and example‐based approaches in order to provide an intuitive way for artists to edit mesh poses. Our system automatically extracts the skeletons of the remaining example models once the skeleton of a reference mesh is constructed. In our editing system the desired skeleton can be easily and naturally posed using an inverse kinematics (IK) algorithm incorporated with searching the optimal weights in the defined skeleton space of examples meshes. Eventually, the desired shape with detailed deformation can be constructed by blending the example meshes. Experimental results show that the proposed system provides an easy and intuitive control on mesh pose‐editing. Copyright © 2007 John Wiley & Sons, Ltd.
Answering label-constraint reachability in large graphs

In this paper, we study a variant of reachability queries, called label-constraint reachability (LCR) queries, specifically,given a label set S and two vertices u1 and u2 in a large directed graph G, we verify whether there exists a path from u1 to u2 under label constraint S. Like traditional reachability queries, LCR queries are very useful, such as pathway finding in biological networks, inferring over RDF (resource description f ramework) graphs, relationship finding in social networks. However, LCR queries are much more complicated than their traditional counterpart.Several techniques are proposed in this paper to minimize the search space in computing path-label transitive closure. Furthermore, we demonstrate the superiority of our method by extensive experiments.
Two Chitotriose-Specific Lectins Show Anti-Angiogenesis, Induces Caspase-9-Mediated Apoptosis and Early Arrest of Pancreatic Tumor Cell Cycle

The antiproliferative activity of two chito- specific agglutinins purified from Benincasa hispida (BhL) and Datura innoxia (DiL9) of different plant family origin was investigated on various cancer cell lines. Both lectins showed chitotriose specificity, by inhibiting lectin hemagglutinating activity. On further studies, it was revealed that these agglutinins caused remarkable concentration-dependent antiproliferative effect on human pancreatic cancerous cells but not on the normal human umbilical vein endothelial cells even at higher doses determined using MTT assay. The GI50 values were approximately 8.4 μg ml-1 (0.247 μM) and 142 μg ml-1(14.8 μM) for BhL and DiL9, respectively, against PANC-1 cells. The growth inhibitory effect of these lectins on pancreatic cancer cells were shown to be a consequence of lectin cell surface binding and triggering G0/G1 arrest, mitochondrial membrane depolarization, sustained increase of the intracellular calcium release and the apoptotic signal is amplified by activation of caspases executing cell death. Interestingly, these lectins also showed anti-angiogenic activity by disrupting the endothelial tubulogenesis. Therefore, we report for the first time two chito-specific lectins specifically binding to tumor glycans; they can be considered to be a class of molecules with antitumor activity against pancreatic cancer cells mediated through caspase dependent mitochondrial apoptotic pathway.
Nondeterministic Lisp as a Substrate for Constraint Logic Programming

We have implemented a comprehensive constraint-based programming language as an extension to COMMON LISP. This constraint package provides a unified framework for solving both numeric and non-numeric systems of constraints using a combination of local propagation techniques including binding propagation, Boolean constraint propagation, generalized forward checking, propagation of bounds, and unification. The backtracking facility of the nondeterministic dialect of COMMON LISP used to implement this constraint package acts as a general fallback constraint solving method mitigating the incompleteness of local propagation.
Targeted TET oxidase activity through methyl‐CpG‐binding domain extensively suppresses cancer cell proliferation

DNA methyltransferase (DNMT) inhibitors are epigenetic drugs used to treat myelodysplastic syndrome. They not only induce DNA demethylation but also have significant cytostatic and cytotoxic effects; however, the relationships between these characteristics have not been established yet due to the lack of a method to induce only DNA demethylation. Herein, we show that a fusion protein comprised of the methyl‐CpG‐binding domain (MBD) and the catalytic domain of Ten‐eleven translocation protein 1 (TET1‐CD) globally demethylates and upregulates a number of methylated genes. These upregulated genes frequently contained CpG islands (CGIs) within ± 1000 bp of the transcription start site (TSS). Interestingly, 65% of the genes upregulated fivefold or more by MBD‐TET1‐CDwt were also reactivated after treatment with a DNMT inhibitor, 5‐azacytidine (Aza‐CR), suggesting that gene reactivation by both methods primarily shares the same mechanism, DNA demethylation. In order to examine whether DNA demethylation affects the growth of cancer cells, we have established a tetracycline inducible system that can regulate the expression of MBD‐TET1‐CDwt in a prostate cancer cell line, LNCaP. The induction of MBD‐TET1‐CDwt demethylated and upregulated glutathione S‐transferase pi 1 (GSTP1), one of the hypermethylated genes in prostate cancer. In accordance with the reactivation of methylated genes, induction of MBD‐TET1‐CDwt extensively suppressed the growth of LNCaP cells through G1/S arrest. These results clearly indicate that TET oxidase activity recruited at methyl‐CpG sites through MBD induces reactivation of hypermethylated genes by DNA demethylation and allows us to analyze the effect of only global DNA demethylation in a wide variety of cancer cells.
Counting People in the Crowd Using a Generic Head Detector

Crowd counting and density estimation is still one of the important task in video surveillance. Usually a regression based method is used to estimate the number of people from a sequence of images. In this paper we investigate to estimate the count of people in a crowded scene. We detect the head region since this is the most visible part of the body in a crowded scene. The head detector is based on state-of-art cascade of boosted integral features. To prune the search region we propose a novel interest point detector based on gradient orientation feature to locate regions similar to the top of head region from gray level images. Two different background subtraction methods are evaluated to further reduce the search region. We evaluate our approach on PETS 2012 and Turin metro station databases. Experiments on these databases show good performance of our method for crowd counting.
A Multi-level Study of Free-Loading in Dynamic Groups: The Importance of Initial Network Topology

Free-loading (to be distinguished from free-riding) is a context-dependent emergent phenomenon that arises when an individual benefits disproportionately from an interaction relative to the other participant(s) of the interaction. We study the phenomenon of free-loading at three levels: (i) its emergence as a dominant interaction strategy at the individual level; (ii) its occurrence in spontaneously formed dynamic collectives or ‘teams’; and (iii) its dominance at the global systemic level. For each of these three levels, we determine the effects of initial network topology on free-loading rate. The topologies considered include (i) random networks with uniform neighbourhood sizes; (ii) similarity networks with uniform neighbourhood sizes in which each agent’s neighbours are also the most similar to the agent (both cost-benefit and resources are considered); (iii) Barabasi-Albert networks with power-law distributed neighbourhood sizes; (iv) Non-uniform networks generated with preferential attachment according to similarity. We also consider associations between free-loading rate and other factors such as group size (at the group level) and group membership (at the agent level). In our network-based model, agent-group interactions represent spontaneous team (collective) formation between a set of agents. At each point in time, the sets of agents participating in collectives is selected depending on the relative costs and benefits of interaction to potential members. Heterogeneity is modelled by differences agents’ cost and benefit parameters, which also determine the payoff values for participating in a group interaction. For each agent-group interaction, a payoff matrix is dynamically generated as a function of the agent’s cost and benefit parameter values and the collective’s cost and benefit parameter values. We find that initial network topology and connectivity significantly affect the free-loading rate at all three levels (systemic, group and agent) and that free-loading rates at one level are not always coupled to free-loading rates at another. For example, it was found that the Barabasi-Albert network topology gave rise to groups tending to have comparatively lower rates of free-loading at the global and group levels but comparatively higher rates at the agent level. The different topologies also result in different linear associations between group size and free-loading at the group level, and between neighbourhood size and free-loading at the agent level. Our findings provide the basis for studying more fundamental relationships between network topologies and free-loading.
A Decimal Floating-Point Adder with Decoded Operands and a Decimal Leading-Zero Anticipator

The IEEE 754-2008 Standard for Floating-Point Arithmetic was officially approved this year. One of the most important revisions to IEEE 754-1985 is the introduction of decimal floating-point (DFP) formats and operations. Since IEEE 754-1985 was revised, major microprocessor vendors have been working on hardware designs and software libraries for decimal arithmetic. Because the new standard has been approved, many software vendors are planning to adapt the new decimal formats into their applications. Therefore, it is important to investigate efficient algorithms and hardware designs for common DFP arithmetic operations to improve the performance of these applications. This paper presents a novel DFP adder with decoded operands and a decimal leading-zero anticipator (LZA). The DFP adder is based on a previous DFP adder design with several new features, including a new internal format, an improved operand pre-correction stage, and a novel decimal LZA to obtain better timing for decimal addition and subtraction. Synthesis results show that the new DFP adder is roughly 14% faster than the previous design.
Graph based manifold regularized deep neural networks for automatic speech recognition

Deep neural networks (DNNs) have been successfully applied to a wide variety of acoustic modeling tasks in recent years. These include the applications of DNNs either in a discriminative feature extraction or in a hybrid acoustic modeling scenario. Despite the rapid progress in this area, a number of challenges remain in training DNNs. This paper presents an effective way of training DNNs using a manifold learning based regularization framework. In this framework, the parameters of the network are optimized to preserve underlying manifold based relationships between speech feature vectors while minimizing a measure of loss between network outputs and targets. This is achieved by incorporating manifold based locality constraints in the objective criterion of DNNs. Empirical evidence is provided to demonstrate that training a network with manifold constraints preserves structural compactness in the hidden layers of the network. Manifold regularization is applied to train bottleneck DNNs for feature extraction in hidden Markov model (HMM) based speech recognition. The experiments in this work are conducted on the Aurora-2 spoken digits and the Aurora-4 read news large vocabulary continuous speech recognition tasks. The performance is measured in terms of word error rate (WER) on these tasks. It is shown that the manifold regularized DNNs result in up to 37% reduction in WER relative to standard DNNs.
Evaluating experience-focused HCI

There is growing interest in experience-focused, rather than task-focused, HCI. Task-focused HCI has developed methods for creating and validating knowledge, but those methods may not be applicable or sufficient for experience-focused technology. In particular, new evaluation techniques to validate knowledge need to be created, discussed, and understood. I address this in three ways. First, it is important to understand the historical, technical and social factors that impact the evaluation criteria the community consider valid today. Second, I propose an ethnomethodological approach to evaluation that emphasizes the ways users use and make sense of technologies. And third, I demonstrate the validity of my approaches by means of several case studies.
De novo backbone scaffolds for protein design

In recent years, there have been significant advances in the field of computational protein design including the successful computational design of enzymes based on backbone scaffolds from experimentally solved structures. It is likely that large‐scale sampling of protein backbone conformations will become necessary as further progress is made on more complicated systems. Removing the constraint of having to use scaffolds based on known protein backbones is a potential method of solving the problem. With this application in mind, we describe a method to systematically construct a large number of de novo backbone structures from idealized topological forms in a top–down hierarchical approach. The structural properties of these novel backbone scaffolds were analyzed and compared with a set of high‐resolution experimental structures from the protein data bank (PDB). It was found that the Ramachandran plot distribution and relative γ‐ and β‐turn frequencies were similar to those found in the PDB. The de novo scaffolds were sequence designed with RosettaDesign, and the energy distributions and amino acid compositions were comparable with the results for redesigned experimentally solved backbones. Proteins 2010. © 2009 Wiley‐Liss, Inc.
A teaching/learning approach to CSCL

In this paper an integrated system to support an educational process called COSOFT (Computer Support for Face-to-face Teaching) is presented. It is intended for use by authors, teachers and students, who can use it to enhance the traditional ways of working inside and outside the classroom. The scenario for the system is the Computer-integrated Classroom (CiC), which is a traditional classroom in which computer technology has been added to support and enhance traditional teaching/learning activities and to enable new ones. The CiC is equipped with an electronic blackboard for the teacher and a personal computer for each student. The electronic blackboard and the personal computers are connected and to the Internet by a TCP/IP network. COSOFT is especially aimed to support the cooperative/collaborative use of computer based learning material by teachers and students upholding the following activities: presentation of learning material, planning and authoring of lesson units, discussion and cooperative problem-solving, student's individual work and problem solving, creation of new material during a lesson, and remote access to the learning material. The system uses open technology and it is extensible, allowing the incorporation of other tools.
Neuropeptide S and BDNF gene expression in the amygdala are influenced by social decision-making under stress

In a newly developed conceptual model of stressful social decision-making, the Stress-Alternatives Model (SAM; used for the 1st time in mice) elicits two types of response: escape or remain submissively. Daily (4d) aggressive social interaction in a neutral arena between a C57BL6/N test mouse and a larger, novel aggressive CD1 mouse, begin after an audible tone (conditioned stimulus; CS). Although escape holes (only large enough for smaller test animals) are available, and the aggressor is unremittingly antagonistic, only half of the mice tested utilize the possibility of escape. During training, for mice that choose to leave the arena and social interaction, latency to escape dramatically decreases over time; this is also true for control C57BL6/N mice which experienced no aggression. Therefore, the open field of the SAM apparatus is intrinsically anxiogenic. It also means that submission to the aggressor is chosen despite this anxiety and the high intensity of the aggressive attacks and defeat. While both groups that received aggression displayed stress responsiveness, corticosterone levels were significantly higher in animals that chose submissive coexistence. Although both escaping and non-escaping groups of animals experienced aggression and defeat, submissive animals also exhibited classic fear conditioning, freezing in response to the CS alone, while escaping animals did not. In the basolateral amygdala (BLA), gene expression of brain-derived neurotrophic factor (BDNF) was diminished, at the same time neuropeptide S (NPS) expression was significantly elevated, but only in submissive animals. This increase in submission-evoked NPS mRNA expression was greatest in the central amygdala (CeA), which coincided with decreased BDNF expression. Reduced expression of BDNF was only found in submissive animals that also exhibit elevated NPS expression, despite elevated corticosterone in all socially interacting animals. The results suggest an interwoven relationship, linked by social context, between amygdalar BDNF, NPS and plasma corticosterone.
Highly Sensitive to Their Regression Provides an Accurate Measure of Atherosclerotic Lesions Rich in Oxidized LDL and Is In Vivo Uptake of Radiolabeled MDA 2 , an Oxidation-Specific Monoclonal Antibody

To determine whether labeled antibodies against oxidized LDL (OxLDL) offer advantages for quantifying atherosclerosis, we compared in vivo aortic uptake of I-labeled MDA2, a monoclonal antibody against malondialdehyde-lysine epitopes), atherosclerotic surface area, and aortic weight in Watanabe heritable hyperlipidemic and New Zealand White rabbits and in low density lipoprotein receptor–deficient (LDLR ) and apolipoprotein E–deficient (apoE) mice. Absolute and specific uptakes of I-MDA2 were significantly greater in plaque than in normal aortas. Uptake of I-MDA2 significantly correlated with aortic weight and percent atherosclerotic surface area in rabbits and mice. To assess whether I-MDA2 uptake reflects changes in lesion content of OxLDL, in a separate study, extensive atherosclerosis was induced in 4 groups of LDLR 2/2 mice by feeding them a high fat/cholesterol diet for 6 months. A baseline group was euthanized at this time. The remaining groups were fed “regression” diets (chow or chow11% vitamin E10.05% vitamin C) or the high fat/cholesterol diet for 6 more months. When atherosclerosis was measured as percent surface area or aortic weight, there was strong progression in the high fat/cholesterol group, moderate progression in the chow group, and no progression in the chow 1vitamin E1vitamin C group compared with the baseline group. TheI-MDA2 method also yielded a significant increase in atherosclerosis in the high fat/cholesterol group but significant decreases in the chow and chow 1vitamin E1vitamin C groups. Immunocytochemistry showed fewer oxidation-specific epitopes in lesions from the chow and chow 1vitamin E1vitamin C groups. Thus, the uptake of I-MDA2 correlates well with traditional measures of atherosclerosis but also reflects reduced plaque OxLDL content after hypocholesterolemic intervention. (Arterioscler Thromb Vasc Biol . 2000;20:689-697.)
Quantifying Slopes with Digital E California : Effects of Resolution

Quant i f i ca t ion o f su r face slope angles is valuable in a wide variety of earth sciences. Slopes measured from digital elevation models (DEM’s) or other topographic data sets depend strongly on the length scale or window size used in the slope calculations. The spectrum of slope distributions as a function of length scale is related to the variation of relief as a function of scale, and may reflect the length scales of the processes acting to form the surface morphology. Small window sizes, approaching the DEM grid spacing, can yield reliable slope determinations if good quality data sets are available. There is a strong variation in the data quality among DEM’s, with a 3-arcsecond DEM poorly representing slopes in the Verdugo Hills, California area, The slopes measured from a standard 30-m DEM and high-resolution NA! YVJPL TOPSAR DEM match each other well at length-scales greater than 30 m, Hillslope means for the rugged Verdugo Hills change from 15° to 26° as the calculation window size decreases from 270 m to 15 m.
Effect of supplementation of yeast with bacteriocin and Lactobacillus culture on growth performance, cecal fermentation, microbiota composition, and blood characteristics in broiler chickens

Objective The aim of the present study was to investigate the effect of yeast with bacteriocin and Lactobacillus cultures (mixture of Lactobacillus agilis BCRC 10436 and Lactobacillus reuteri BCRC 17476) supplements, alone or in combination, on broiler chicken performance. Methods A total of 300, 1-d-old healthy broiler chickens were randomly divided into five treatment groups: i) basal diet (control), ii) basal diet+0.25% yeast (Saccharomyces cerevisiae) (YC), iii) basal diet+0.25% yeast with bacteriocin (BA), iv) basal diet+Lactobacillus cultures (LAB), and v) basal diet +0.25% yeast with bacteriocin+Lactobacillus cultures (BA+LAB). Growth performance, cecal microbiota, cecal fermentation products, and blood biochemistry parameters were determined when chickens were 21 and 35 d old. Results The supplementation of YC, BA, and BA+LAB resulted in a significantly better feed conversion rate (FCR) than that of the control group during 1 to 21 d (p<0.05). The LAB supplementation had a significant effect on the presence of Lactobacillus in the ceca at 35 d. None of the supplements had an effect on relative numbers of L. agilis and L. reuter at 21 d, but the BA supplementation resulted in the decrease of both Lactobacillus strains at 35 d. The BA+LAB supplementation resulted in higher short chain fatty acid (SCFA) in the ceca, but LAB supplementation significantly decreased the SCFA at 35 d (p<0.05). All treatments tended to decrease ammonia concentration in the ceca at 21 d, especially in the LAB treatment group. The BA supplementation alone decreased the triacylglycerol (TG) concentration significantly at 21 d (p<0.05), but the synergistic effect of BA and LAB supplementation was required to reduce the TG concentration at 35 d. The YC supplementation tended to increase the plasma cholesterol at 21 d and 35 d. However, the BA supplementation significantly decreased the cholesterol and low density lipoprotein cholesterol level at 35 d. In conclusion, the BA+LAB supplementation was beneficial to body weight gain and FCR of broiler chickens. Conclusion The effect of BA and LAB supplementation may be a result of the growth of lactic acid bacteria enhancement and physiological characterization of bacteriocin, and it suggests that the BA and LAB supplementation level or Lactobacillus strain selection should be integrated in future supplementation designs.