Miracle-dz/UniFAR-FTUs huggingface dataset:
Identifying structural domains in proteins.

Analysisofproteinstructurestypicallybeginswithdecompositionofthestructureintomorebasic units called structural domains. The underlying goal is to reduce a complex proteinstructuretoasetofsimpler,yetstructurallymeaningfulunits,eachofwhichcanbeanalyzedindependently. Structural semi-independence of domains is their hallmark: domains oftenhave compact structure that can fold (and sometimes function) independently. The totalnumber of distinct structural domains is currently hovering around one thousand: they arerepresented by the unique folds in SCOP classiﬁcation (Murzin et al., 1995) or uniquetopologies in CATH classiﬁcation (Orengo et al., 1997). Interestingly, this is what Chothiapredicted at a rather early stage of the Structural Genomics era (Chothia, 1992). Asigniﬁcantfractionofthesedomainsisuniversaltoalllifeforms,othersarekingdom-speciﬁcandyetothersareconﬁnedtosubgroupsofspecies(PontingandRussell,2002;Yang,and Doolittle, and Bourne, 2005). The enormous variety of protein structures is thenachievedthroughcombinationofvariousdomainswithinasinglestructure.This‘‘combin-ing’’ofdomainscan be achievedbycombiningtogether single domainpolypeptide chainswithin a noncovalently linked structure or by combining domains (via gene fusions/recombination) on a single polypeptide chain that folds into the ﬁnal structure (Bennett,Choe,andEisenberg,1994). Therearebeneﬁtstobothstrategies:theformercanbeseenasamoreeconomicandmodularapproachinwhichmanydifferentstructurescanbeputtogetherwith relatively few components within the cell. The latter, combining a speciﬁc set ofmodules within a single polypeptide chain, ensures that they are expressed together andlocalized in the same cells or cellular compartments (Tsoka and Ouzounis, 2000). Thischapterisconcernedwiththislattercase:thedecompositionofthemultidomainpolypeptidechain into structural domains.
Fuzzy Analysis in Pitch-Class Determination for Polyphonic Audio Key Finding

This paper presents a fuzzy analysis technique for pitch class determination that improves the accuracy of key finding from audio information. Errors in audio key finding, typically incorrect assignments of closely related keys, commonly result from imprecise pitch class determination and biases introduced by the quality of the sound. Our technique is motivated by hypotheses on the sources of audio key finding errors, and uses fuzzy analysis to reduce the errors caused by noisy detection of lower pitches, and to refine the biased raw frequency data, in order to extract more correct pitch classes. We compare the proposed system to two others, an earlier one employing only peak detection from FFT results, and another providing direct key finding from MIDI. All three used the same key finding algorithm (Chew’s Spiral Array CEG algorithm) and the same 410 classical music pieces (ranging from Baroque to Contemporary). Considering only the first 15 seconds of music in each piece, the proposed fuzzy analysis technique outperforms the peak detection method by 12.18% on average, matches the performance of direct key finding from MIDI 41.73% of the time, and achieves an overall maximum correct rate of 75.25% (compared to 80.34% for MIDI key finding).
Adiponectin and its association with bone mass accrual in childhood

Circulating adiponectin levels are inversely related to bone mineral density (BMD) in humans and animal models. Previous studies in humans have been confined largely to adult populations, and whether adiponectin influences bone mass accrual in childhood is unclear. We examined this question using the Avon Longitudinal Study of Parents and Children (ALSPAC) birth cohort by investigating relationships between circulating adiponectin levels at a mean age of 9.9 years, indices of bone mass as measured by total‐body dual‐energy X‐ray absorptiometry (DXA) at ages 9.9 and 15.5 years, and cortical bone parameters as measured by peripheral quantitative computed tomography (pQCT) of the midtibia at age 15.5 years. A total of 4927 children were included at age 9.9 years, of whom 97% and 90% of boys and girls, respectively, were in prepuberty or early puberty, as defined by Tanner stage 1–2. A total of 2754 children were included at age 15.5 years, of whom 95% and 97% of boys and girls, respectively, were in late puberty, as defined by Tanner stage 4–5. Circulating adiponectin was found to be related to fat mass, lean mass, and, to a lesser extent, height, so analyses were adjusted for these three variables to identify possible independent effects of adiponectin on bone development. Adiponectin was inversely related to total‐body‐less‐head bone mineral content (BMC; −3.0%), bone area (BA; −1.8%), BMC divided by BA (BMD; −4.8%), and BMC adjusted for BA by linear regression (aBMC; −5.6%), as measured at age 9.9 years (coefficients show change per doubling in adiponectin concentration, p < .001). Consistent with these results, inverse associations also were seen between adiponectin and cortical BMC (−4.8%) and cortical bone area (−4.7%), as measured by tibial pQCT at age 15.5 years (p < .001). Further pQCT results suggested that this inverse association of adiponectin with skeletal development predominantly involved a negative association with endosteal relative to periosteal expansion, as reflected by cortical thickness (−6.0%, p < .001). We conclude that, independent of fat mass, lean mass, and height, adiponectin is associated with lower bone mass in childhood predominantly owing to an influence on relative endosteal expansion. Since these associations were observed before and after puberty, this suggests that setting of adiponectin levels in midchildhood has the potential to exert long‐term effects on bone strength and fracture risk. © 2010 American Society for Bone and Mineral Research.
Baseline sympathetic nervous system activity predicts dietary weight loss in obese metabolic syndrome subjects.

CONTEXT The sympathetic nervous system is an important physiological modulator of basal and postprandial energy expenditure. OBJECTIVE Our objective was to investigate whether the variability of weight loss attained during hypocaloric dietary intervention is related to individual differences in baseline sympathetic drive and nutritional sympathetic nervous system responsiveness. PARTICIPANTS AND METHODS Untreated obese subjects (n = 42; body mass index = 32.1 ± 0.5 kg/m(2)), aged 57 ± 1 yr, who fulfilled Adult Treatment Panel III metabolic syndrome criteria participated in a 12-wk weight loss program using a modified Dietary Approaches to Treat Hypertension (DASH) diet. Muscle sympathetic nerve activity (MSNA) was measured by microneurography at rest and in a subset of subjects during a standard 75-g oral glucose tolerance test. RESULTS Weight loss (6.7 ± 0.5 kg) was independently predicted by baseline resting MSNA burst incidence (r = 0.38; P = 0.019), which accounted for 14.3% of the variance after adjustment for age and baseline body weight. Weight loss-resistant subjects in the lower tertile of weight loss (4.4 ± 0.3%) had significantly blunted MSNA responses to oral glucose at baseline compared with successful weight losers (9.6 ± 0.8%). Absolute Δ MSNA averaged -7 ± 2, -6 ± 5, and -3 ± 3 bursts per 100 heartbeats at 30, 60, and 90 min after glucose in the weight loss-resistant group. Corresponding values in the successful weight loss group were 9 ± 3, 12 ± 3, and 15 ± 4 bursts per 100 heartbeats (time × group interaction, P = 0.004). CONCLUSIONS These findings indicate that baseline sympathetic drive and nutritional sympathetic responsiveness may be important prognostic biological markers for weight loss outcome.
Effect of multiple dosing of ketoconazole on pharmacokinetics of midazolam, a cytochrome P-450 3A substrate in beagle dogs.

To evaluate effects of multiple dosing of ketoconazole (KTZ) on hepatic CYP3A, the pharmacokinetics of intravenous midazolam (MDZ, 0.5 mg/kg) before and during multiple dosing of KTZ were investigated in beagle dogs. KTZ tablets were given orally to dogs (n = 4) for 30 days (200 mg b.i.d.). With coadministration of KTZ, t(1/2beta) of MDZ were significantly increased both on day 1 (2-fold) and on day 30 (3-fold). Total body clearance (CL(tot)) of MDZ declined gradually during the first 5 days after the start of KTZ treatment, and thereafter CL(tot) appeared to reach a plateau phase (one-fourth), depending on plasma KTZ concentrations. The effects of KTZ on the biotransformation of MDZ were also investigated using dog liver microsomes (n = 5). The K(i) values of KTZ for MDZ 1'-hydroxylation and 4-hydroxylation were 0.0237 and 0.111 microM, respectively, indicating that KTZ extensively inhibits hepatic CYP3A activity in dogs. CL(tot) values estimated from in vitro K(i) values corrected by unbound fraction of KTZ and unbound concentrations of the drug in plasma were consistent with in vivo CL(tot) of MDZ. The results in this study suggest that KTZ treatment is necessary until plasma concentrations of the drug reach a steady state to evaluate the effect of multiple dosing of the drug on hepatic CYP3A in vivo. In addition, it is suggested that K(i) values corrected by unbound fraction of KTZ and unbound concentrations of the drug in plasma enable precise in vitro-in vivo scaling.
Subsign detection with region-growing from contrasted seeds

Speed limit determination systems for cars based on vision are more and more developed. Roadsign detection is nowadays a well managed problem. However, in some situations this information is not sufficient to know the speed limitation. Restrictions are sometimes applicable and specified by subsigns. These small rectangles often provide essential information about the applicability scope (vehicle type, condition, lane, etc.) of speed limits. We present an approach of subsign localization based on region growing with an initial step of seed selection using morphological reconstruction. A comparison is also performed with three other techniques based on edge, color and graph on two databases gathering French and German subsigns. The obtained subsign correct detection is above 65%.
Multiple-depth shadow maps

Traditional shadow maps store a single depth value per cell, leading to a binary outcome by the shadow test (either lit or in shadow), and are prone to produce aliased shadow borders. We present a new approach that produces better estimates of shadow percentages and, in combination with percentage closer filtering (PCF), reduces aliasing artifacts using smaller kernel sizes. The new algorithm extends the notions of shadow maps and shadow tests to support the representation of multiple depth values per shadow map cell, as well as multi-valued shadow tests. This new approach has the potential for hardware implementation, but can also be implemented exploiting the programmable capabilities of recent graphics cards.
Virtual Reality: Emerging Applications and Future Directions

Virtual reality is an emerging technology that has resulted in rapid expansion in the development of virtual immersive environments for use as educational simulations in schools, colleges and universities. This article presents an overview of virtual reality, describes a number of applications currently being used by special educators for personnel preparation in colleges and universities and for service delivery to children and adults with disabilities in K-12 schools and community services, and discusses possible future directions in virtual reality applications and their implications for rural special education.
THE RELATION BETWEEN WEIGHT, PERCEIVED PHYSICAL COMPETENCE AND BODY IMAGE IN EARLY ADOLESCENCE

Purpose.The aim of the present study is to explore the relation between perceived physical competence, body mass index and physical appearance esteem in early adolescence. Methods.A cross-sectional design, comprising 253 early adolescents from 11 to 13 years old (mean age = 12.32, SD = .57) was implemented. Hierarchical multiple regressions were used in order to identify direct and interaction effects. Results.Significant gender differences were found in both physical appearance esteem and contributive factors. The beneficial effect of perceived physical competence on physical appearance esteem is higher for girls compared to boys.
2D Conditional Random Fields for Web information extraction

The Web contains an abundance of useful semistructured information about real world objects, and our empirical study shows that strong sequence characteristics exist for Web information about objects of the same type across different Web sites. Conditional Random Fields (CRFs) are the state of the art approaches taking the sequence characteristics to do better labeling. However, as the information on a Web page is two-dimensionally laid out, previous linear-chain CRFs have their limitations for Web information extraction. To better incorporate the two-dimensional neighborhood interactions, this paper presents a two-dimensional CRF model to automatically extract object information from the Web. We empirically compare the proposed model with existing linear-chain CRF models for product information extraction, and the results show the effectiveness of our model.
Integrated motion planning and control for graceful balancing mobile robots

This paper presents an integrated motion planning and control framework that enables balancing mobile robots to gracefully navigate human environments. A palette of controllers called motion policies is designed such that balancing mobile robots can achieve fast, graceful motions in small, collision-free domains of the position space. The domains determine the validity of a motion policy at any point in the robot’s position state space. An automatic instantiation procedure that generates a motion policy library by deploying motion policies from a palette on a map of the environment is presented. A gracefully prepares relationship that guarantees valid compositions of motion policies to produce overall graceful motion is introduced. A directed graph called the gracefully prepares graph is used to represent all valid compositions of motion policies in the motion policy library. The navigation tasks are achieved by planning in the space of these gracefully composable motion policies. In this work, Dijsktra’s algorithm is used to generate a single-goal optimal motion policy tree, and its variant is used to rapidly replan the optimal motion policy tree in the presence of dynamic obstacles. A hybrid controller is used as a supervisory controller to ensure successful execution of motion policies and also successful switching between them. The integrated motion planning and control framework presented in this paper was experimentally tested on the ballbot, a human-sized dynamically stable mobile robot that balances on a single ball. The results of successful experimental testing of two navigation tasks, namely, point-point and surveillance motions are presented. Additional experimental results that validate the framework’s capability to handle disturbances and rapidly replan in the presence of dynamic obstacles are also presented.
Performance Evaluation, Portfolio Selection, and HARA Utility

Absract The main goal of this work is the generalization of the approach of Jobson and Korkie for funds performance evaluation. Therefore, the paper considers the portfolio selection problem of an investor who faces short sales restrictions when choosing among F different investment funds and assumes the investor’s utility function to be of the HARA type. A performance measure is developed and its relationship to previously proposed measures is discussed. Particular attention is given to the special case of cubic utility implying skewness preferences. Findings are illustrated by an empirical example.
Analysis of an on-line algorithm for solving large Markov chains

Algorithms for ranking of web pages such as Google Page-Rank assign importance scores according to a stationary distribution of a Markov random walk on the web graph. Although in the classical search scheme the ranking scores are pre-computed off-line, several challenging problems in contemporary web search, such as personalized search and search in entity graphs, require on-line PageRank computation. In this work we present a probabilistic point of view for an original on-line algorithm proposed by Abiteboul, Preda and Cobena [1]. According to this algorithm, at the beginning, each page receives an equal amount of 'cash', and every time when a page is visited by a random walk, it distributes its cash among its outgoing links. The PageRank score of a page is then proportional to the amount of cash transferred from this page. In this paper, instead of dealing with the variable 'cash', which is continuous, we create a two-dimensional discrete 'cat and mouse' Markov chain such that the amount of cash on each page can be expressed via probabilities for this new Markov chain. We also indicate further research directions, such as the analysis of the cat and mouse chain in the case when the cat's movements are described by a classical stochastic process such as the M/M/1 random walk.
A time series investigation of the oxygen isotopic composition of dissolved inorganic phosphate in Monterey Bay, California

We present a 2‐yr time series of the oxygen isotopic composition of dissolved inorganic phosphate (Δ18Op) in Monterey Bay, California. Δ18Op can serve as a proxy for phosphate utilization because its approach toward isotopic equilibrium is a function of the degree of biological phosphate cycling. When phosphate is extensively cycled by the biological community in the euphotic zone, the Δ18Op approaches isotopic equilibrium with surrounding water. Our results indicate that Δ18Op in the upper water column is consistently out of isotopic equilibrium with respect to seawater and fluctuates between the equilibrium value and the isotopic signatures of phosphate sources. This suggests that either phosphate is not extensively utilized or that the input of new phosphate to the bay exceeds the requirements of the biological community. Δ18Op is variable and linked to episodic upwelling events and the biotic response to these events. The greatest percent of phosphate oxygen exchange, and thus the greatest phosphate utilization relative to input, occurs at the locus of upwelling (Sta. M1), followed by the offshore (M2) and nearshore (C1) stations, respectively. During the highly productive upwelling season, phosphate turnover is greater than in the winter. Episodes of higher phosphate turnover, as indicated by peaks in d18Op, occur simultaneously throughout the upper 200 m of the water column and at all three stations, indicating that these events affect the bay on a large scale. Δ18Op data also suggest that deep water (≫500 m) may be a source of phosphate to the euphotic zone in Monterey Bay.
Learning with Skewed Class Distributions

Several aspects may influence the performance achieved by a classifier created by a Machine Learning system. One of these aspects is related to the dierence between the numbers of examples belonging to each class. When this dierence is large, the learning system may have diculties to learn the concept related to the minority class. In this work 1 , we discuss several issues related to learning with skewed class distributions, such as the relationship between cost-sensitive learning and class distributions, and the limitations of accuracy and error rate to measure the performance of classifiers. Also, we survey some methods proposed by the Machine Learning community to solve the problem of learning with imbalanced data sets, and discuss some limitations of these methods.
Get what you want from Internet using fuzzy k-means clustering algorithm

This paper proposed a new method of getting what you want from Internet using fuzzy k-means clustering algorithm. It used search engine to obtain relevant documents content, then adopted efficient Fuzzy k-means clustering algorithm to cluster all the sentences. The summary sentences were extracted by turns from the clusters. Experimental result shows that the proposed method can improve the performance of summary.
Building volumetric appearance models of fabric using micro CT imaging

The appearance of complex, thick materials like textiles is determined by their 3D structure, and they are incompletely described by surface reflection models alone. While volume scattering can produce highly realistic images of such materials, creating the required volume density models is difficult. Procedural approaches require significant programmer effort and intuition to design specialpurpose algorithms for each material. Further, the resulting models lack the visual complexity of real materials with their naturally-arising irregularities. This paper proposes a new approach to acquiring volume models, based on density data from X-ray computed tomography (CT) scans and appearance data from photographs under uncontrolled illumination. To model a material, a CT scan is made, resulting in a scalar density volume. This 3D data is processed to extract orientation information and remove noise. The resulting density and orientation fields are used in an appearance matching procedure to define scattering properties in the volume that, when rendered, produce images with texture statistics that match the photographs. As our results show, this approach can easily produce volume appearance models with extreme detail, and at larger scales the distinctive textures and highlights of a range of very different fabrics like satin and velvet emerge automatically---all based simply on having accurate mesoscale geometry.
Discovering Lexical Classes and Syntax : ( Report with Annotated Bibliography )

In most of the languages today, the sequence of words is quite restricted. It is quite obvious that an underlying structure which is, in general, abstract, generates such word orders. This underlying structure is basically the syntax of the language. Also, it is shown in previous researches that syntactic features are the most informative features in lexical class discovery such as verb classification. We want to design a framework that will be unsupervised and can induce lexical classes and syntax from the given data. We may further want to extend this framework for languages such as Hindi which is poor in
Asparaginase and glutaminase activities of bacteria.

SUMMARY: A test-tube method is described for the determinations of L-asparaginase and L-glutaminase in suspensions and extracts of bacteria. An automated modification of the method was used to determine the asparaginase activities of about 200 strains from 78 species and the glutaminase activities of 46 strains from 13 species. Both enzymes were widely distributed and, at pH 8.5, asparaginase was generally the more active. Asparaginase was exceptionally active in some species of Erwinia.
Generality and Speed in Nonblocking Dual Containers

Nonblocking dual data structures extend traditional notions of nonblocking progress to accommodate partial methods, both by bounding the number of steps that a thread can execute after its preconditions have been satisfied and by ensuring that a waiting thread performs no remote memory accesses that could interfere with the execution of other threads. A nonblocking dual container, in particular, is designed to hold either data or requests. An insert operation either adds data to the container or removes and satisfies a request; a remove operation either takes data out of the container or inserts a request. We present the first general-purpose construction for nonblocking dual containers, allowing any nonblocking container for data to be paired with almost any nonblocking container for requests. We also present new custom algorithms, based on the LCRQ of Morrison and Afek, that outperform the fastest previously known dual containers by factors of four to six.