Miracle-dz/UniFAR-FTUs huggingface dataset:
Geometric algorithms for the conformational analysis of long protein loops

The efficient filtering of unfeasible conformations would considerably benefit the exploration of the conformational space when searching for minimum energy structures or during molecular simulation. The most important conditions for filtering are the maintenance of molecular chain integrity and the avoidance of steric clashes. These conditions can be seen as geometric constraints on a molecular model. In this article, we discuss how techniques issued from recent research in robotics can be applied to this filtering. Two complementary techniques are presented: one for conformational sampling and another for computing conformational changes satisfying such geometric constraints. The main interest of the proposed techniques is their application to the structural analysis of long protein loops. First experimental results demonstrate the efficacy of the approach for studying the mobility of loop 7 in amylosucrase from Neisseria polysaccharea. The supposed motions of this 17‐residue loop would play an important role in the activity of this enzyme. © 2004 Wiley Periodicals, Inc. J Comput Chem 25: 956–967, 2004
Bank Income Smoothing, Ownership Concentration and the Regulatory Environment

We empirically examine whether the way a bank might use loan loss provisions to smooth its income is influenced by its ownership concentration and the regulatory environment. Using a panel of European commercial banks, we find evidence that banks with more concentrated ownership use discretionary loan loss provisions to smooth their income. This behavior is less pronounced in countries with stronger supervisory regimes or higher external audit quality. Banks with low levels of ownership concentration do not display such discretionary income smoothing behavior. This suggests the need to improve existing or implement new corporate governance mechanisms.
"Eigenlips" for robust speech recognition

We improve the performance of a hybrid connectionist speech recognition system by incorporating visual information about the corresponding lip movements. Specifically, we investigate the benefits of adding visual features in the presence of additive noise and crosstalk (cocktail party effect). Our study extends our previous experiments by using a new visual front end, and an alternative architecture for combining the visual and acoustic information. Furthermore, we have extended our recognizer to a multi-speaker, connected letters recognizer. Our results show a significant improvement for the combined architecture (acoustic and visual information) over just the acoustic system in the presence of additive noise and crosstalk. <<ETX>>
Developmental Effects and Spatial Hearing in Young Children With Normal-Hearing Sensitivity

Objectives: Previous research suggests that young children have significant difficulty recognizing speech in the presence of background noise as compared with older children and adults. However, limited research exists that examines the developmental effects of speech recognition in noise in separate age groups of young children, especially in a classroom setting. The lack of research may relate to the limited number of tests with multiple, equally intelligible lists in noise that are also appropriate for young children. As a result, the goals of the present study include investigating (1) effects of age and (2) benefits of spatial separation of speech and noise sources on the speech recognition in noise performance of young children with normal-hearing sensitivity. A secondary goal of the study was to establish the validity and reliability of the Phrases in Noise Test (PINT) for assessing the 50% correct speech-in-noise threshold of young children. Design: The investigators used a two-way repeated measures design to examine the main effects of age and spatial separation. Sixty-eight children in separate groups of 3-, 4-, 5-, and 6-year-olds and 17 adults completed two speech-recognition conditions with (1) speech and noise from the same loudspeaker at 0-degree azimuth (S0/N0) and (2) speech and noise from separate loudspeakers at 0- and 180-degree azimuth (S0/N180). Recruiting sites included local preschools and school districts for children and a university for adults. Results: The results of this investigation suggest that younger children (<4 years of age) have significantly poorer speech-in-noise thresholds than older children and adults, and 4- and 5-year-old children also have significantly poorer performance than adults when speech and noise are presented from the same spatial location. All participants obtained significant spatial release from masking. On a parent and teacher screening questionnaire to assess educational risk, five of 12 children with at-risk behaviors had poor speech-in-noise thresholds relative to their peers. When two lists of the PINT are used, the test seems to be a valid and reliable measure for assessing young children’s speech-in-noise thresholds. Conclusions: Young children exhibit significantly poorer speech recognition than do older children and adults in a classroom, especially when speech and noise are presented from the same location. Given the poor acoustics of typical classrooms, and the earlier age at which many children are educated, special modifications to classrooms may be necessary to improve listening through acoustic modifications or classroom amplification. A combination of a parent or teacher questionnaire and the PINT may be helpful in identifying children who are at risk for educational delays and listening difficulties in classrooms with typically poor acoustics.
GAUSSIAN PROCESSES AND NON-PARAMETRIC VOLATILITY FORECASTING

We provide a formulation of stochastic volatility based on Gaussian processes, a flexible framework for Bayesian nonlinear regression. The advantage of using Gaussian processes in this context is to place volatility forecasting within a regression framework; this allows a large number of explanatory variables to be used for forecasting, a task difficult with standard volatility-forecasting formulations. Our approach builds upon the range-based estimator of Alizadeh, Brandt, and Diebold (2002) to provide much greater accuracy than traditional close-to-close estimators using daily data. Experiments with high-frequency stock market data, using five-minute realized volatility as a benchmark, show that the approach significantly outperforms standard stochastic volatility and GARCH models in one-month-ahead out-of-sample volatility forecasting. It also shows promise for long-range (several months ahead) forecasting, an application that could prove useful in pricing long-dated options.
GQ(lambda): A general gradient algorithm for temporal-difference prediction learning with eligibility traces

A new family of gradient temporal-diﬀerence learning algorithms have recently been introduced by Sutton, Maei and others in which function approximation is much more straightforward. In this paper, we introduce the GQ( λ ) algorithm which can be seen as extension of that work to a more general setting including eligibility traces and oﬀ-policy learning of temporally abstract predictions. These extensions bring us closer to the ultimate goal of this work—the development of a universal prediction learning algorithm suitable for learning experientially grounded knowledge of the world. Eligibility traces are essential to this goal because they bridge the temporal gaps in cause and eﬀect when experience is processed at a temporally ﬁne resolution. Temporally abstract predictions are also essential as the means for representing abstract, higher-level knowledge about courses of action, or options. GQ( λ ) can be thought of as an extension of Q-learning. We extend existing convergence results for policy evaluation to this setting and carry out a forward-view/backward-view analysis to derive and prove the validity of the new algorithm.
Unsupervised Breast Masses Classification through Optimum-Path Forest

Computer-Aided Diagnosis (CAD) can be divided into two main categories: CADe (Computer-Aided Detection), which is focused on the detection of structures of interest, as well as to assist radiologists to find out signals of interest that might be hidden to human vision, and the CADx (Computer-Aided Diagnosis), which works as a second observer, being responsible to give an opinion on a specific lesion. In CADe - based systems, the identification of mammograms with and without masses is highly needed to reduce the false positive rates regarding the automatic selection of regions of interest. The main contribution of this study is to introduce the unsupervised classifier Optimum-Path Forest to identify breast masses, and to evaluate its performance against with two other unsupervised techniques (Gaussian Mixture Model and k-Means) using texture features from images obtained from a private dataset composed by 120 images with and without the presence of masses.
Construction and demolition waste indicators

The construction industry is one of the biggest and most active sectors of the European Union (EU), consuming more raw materials and energy than any other economic activity. Furthermore, construction waste is the commonest waste produced in the EU. Current EU legislation sets out to implement construction and demolition waste (CDW) prevention and recycling measures. However it lacks tools to accelerate the development of a sector as bound by tradition as the building industry. The main objective of the present study was to determine indicators to estimate the amount of CDW generated on site both globally and by waste stream. CDW generation was estimated for six specific sectors: new residential construction, new non-residential construction, residential demolition, non-residential demolition, residential refurbishment, and non-residential refurbishment. The data needed to develop the indicators was collected through an exhaustive survey of previous international studies. The indicators determined suggest that the average composition of waste generated on site is mostly concrete and ceramic materials. Specifically for new residential and new non-residential construction the production of concrete waste in buildings with a reinforced concrete structure lies between 17.8 and 32.9 kg m−2 and between 18.3 and 40.1 kg m−2, respectively. For the residential and non-residential demolition sectors the production of this waste stream in buildings with a reinforced concrete structure varies from 492 to 840 kg m−2 and from 401 to 768 kg/m−2, respectively. For the residential and non-residential refurbishment sectors the production of concrete waste in buildings lies between 18.9 and 45.9 kg/m−2 and between 18.9 and 191.2 kg/m−2, respectively.
Direct Estimation of Kinetic Parametric Images for Dynamic PET

Dynamic positron emission tomography (PET) can monitor spatiotemporal distribution of radiotracer in vivo. The spatiotemporal information can be used to estimate parametric images of radiotracer kinetics that are of physiological and biochemical interests. Direct estimation of parametric images from raw projection data allows accurate noise modeling and has been shown to offer better image quality than conventional indirect methods, which reconstruct a sequence of PET images first and then perform tracer kinetic modeling pixel-by-pixel. Direct reconstruction of parametric images has gained increasing interests with the advances in computing hardware. Many direct reconstruction algorithms have been developed for different kinetic models. In this paper we review the recent progress in the development of direct reconstruction algorithms for parametric image estimation. Algorithms for linear and nonlinear kinetic models are described and their properties are discussed.
Ecophys.Fish: A Simulation Model of Fish Growth in Time-Varying Environmental Regimes

Ecophys.Fish is a deterministic STELLA® model for simulating rates of fish growth in environmental regimes that have simultaneous temporal variation in food, oxygen, temperature, pH, and salinity. The purpose of this article is to introduce Ecophys.Fish to those who might want to use it as a framework or starting point for applications of their own. We believe our model, although focused in autecology, will prove useful at organizational levels both below and above the individual fish. Ecophys.Fish is a quantitatively explicit interpretation of concepts originally formalized by F.E. J. Fry, almost 60 years ago. Fry's “physiological classification of environment” and his concept of “metabolic scope for activity” were coupled with conventional bioenergetics to provide the model's theoretical basis. The model's inputs are initial size of fish, and time series of temperature, pH, dissolved-oxygen concentration (DO), salinity, and food availability and its energy content. Outputs are food consumption, oxygen consumption, waste production, energy content of fish biomass, and growth. Indirectly, the output is a measure of relative fitness of the fish-environment system to support fish growth. Two variants of the model represent the euryhaline red drum (Sciaenops ocellatus) and the freshwater bluegill (Lepomis macrochirus). Ecophys.Fish had its beginnings in laboratory experiments with juvenile red drum. These experiments enabled definition of functions and their parameterization, leading to a working model that effectively simulated growth of red drum in various pond and estuary trials with caged fish. Subsequently, Ecophys.Fish was converted to simulate growth rates of caged bluegill involved in stream ecoassays. The latter work confirmed the model's generality and the utility of automated routine respirometry for empirically estimating a key model parameter. Ecophys.Fish comprises an effective tool for resolving sources of variation in fish growth, even in natural systems with high levels of environmental variability. Moreover, the model has utility for probing biological and ecological mechanisms underlying fish growth and production. Finally, Ecophys.Fish is capable of producing rich hypotheses, e.g., 1) the optimum temperature for growth decreases whenever DO, food availability, or energy density of available food is limiting; 2) with unlimited DO and food availability, the optimum temperature for growth increases with increasing fish size but only when energy density of food is limiting; and, 3) when neither availability nor energy density of food is limiting, growth can be much faster under diel-cycling regimes of temperature and DO than under the optimum constant temperature/DO regime. Under Ecophys.Fish, environmental regimes that are best for survival are not necessarily those that are best for growth.
University of Huddersfield Repository Combinatorial Roles of Heparan Sulfate Proteoglycans and Heparan Sulfates in Caenorhabditis elegans Neural Development

Heparan sulfate proteoglycans (HSPGs) play critical roles in the development and adult physiology of all metazoan organisms. Most of the known molecular interactions of HSPGs are attributed to the structurally highly complex heparan sulfate (HS) glycans. However, whether a specific HSPG (such as syndecan) contains HS modifications that differ from another HSPG (such as glypican) has remained largely unresolved. Here, a neural model in C. elegans is used to demonstrate for the first time the relationship between specific HSPGs and HS modifications in a defined biological process in vivo. HSPGs are critical for the migration of hermaphrodite specific neurons (HSNs) as genetic elimination of multiple HSPGs leads to 80% defect of HSN migration. The effects of genetic elimination of HSPGs are additive, suggesting that multiple HSPGs, present in the migrating neuron and in the matrix, act in parallel to support neuron migration. Genetic analyses suggest that syndecan / sdn-1 and HS 6-O-sulfotransferase , hst-6 , function in a linear signaling pathway and glypican / lon-2 and HS 2-O- sulfotransferase , hst-2 , function together in a pathway that is parallel to sdn-1 and hst-6 . These results suggest core protein specific HS modifications that are critical for HSN migration. In C. elegans , the core protein specificity of distinct HS modifications may be in part regulated at the level of tissue specific expression of genes encoding for HSPGs and HS modifying enzymes. Genetic analysis reveals that there is a delicate balance of HS modifications and eliminating one HS modifying enzyme in a compromised genetic background leads to significant changes in the overall phenotype. These findings are of importance with the view of HS as a critical regulator of cell signaling in normal development and disease.
Theory and Evaluation of a Bayesian Music Structure Extractor

We introduce a new model for extracting end points of music structure segments, such as intro, verse, chorus, break and so forth, from recorded music. Our methods are applied to the problem of grouping audio features into continuous structural segments with start and end times corresponding as closely as possible to a ground truth of independent human structure judgements. Our work extends previous work on automatic summarization and structure extraction by providing a model for segment end-points posed in a Bayesian framework. Methods to infer parameters to the model using Expectation Maximization and Maximum Likelihood methods are discussed. The model identifies all the segments in a song, not just the chorus or longest segment. We discuss the theory and implementation of the model and evaluate the model in an automatic structure segmentation experiment against a ground truth of human judgements. Our results shows a segment boundary intersection rate break-even point of approximately 80%.
Dust Sublimation by Gamma-ray Bursts and Its Implications

The prompt optical flash recently detected accompanying GRB 990123 suggests that, for at least some γ-ray bursts (GRBs), γ-ray emission is accompanied by prompt optical-UV emission with luminosity L(1-7.5 eV) ≈ 1 × 1049(ΔΩ/4π) ergs s-1, where ΔΩ is the solid angle into which γ-ray and optical-UV emission is beamed. Such an optical-UV flash can destroy dust in the beam by sublimation out to an appreciable distance, ≈10 pc, and may clear the dust out of as much as ~107(ΔΩ/4π) M☉ of molecular cloud material on an apparent timescale of ~10 s. Detection of time-dependent extinction on this timescale would therefore provide strong constraints on the GRB source environment. Dust destruction implies that existing or future observations of fireballs that are not heavily reddened are not inconsistent with GRBs being associated with star-forming regions. In this case, however, if the initial flash is highly beamed, the expanding fireball would become reddened on a ~1 week timescale. If the optical depth due to dust beyond ≈8 pc from the GRB is 0.2 ≲ τV ≲ 2, most of the UV flash energy is converted to infrared (λ ≈ 1 μm) radiation with luminosity LIR ≈ 1041 ergs s-1 extending over an apparent duration of ≈20(1 + z)(ΔΩ/0.01) days. Dust infrared emission may already have been observed in GRB 970228 and GRB 980326 and may possibly explain their unusual late-time behavior.
A Neighborhood Analysis of the Consequences of Quercus suber Decline for Regeneration Dynamics in Mediterranean Forests

In forests, the vulnerable seedling stage is largely influenced by the canopy, which modifies the surrounding environment. Consequently, any alteration in the characteristics of the canopy, such as those promoted by forest dieback, might impact regeneration dynamics. Our work analyzes the interaction between canopy neighbors and seedlings in Mediterranean forests affected by the decline of their dominant species (Quercus suber). Our objective was to understand how the impacts of neighbor trees and shrubs on recruitment could affect future dynamics of these declining forests. Seeds of the three dominant tree species (Quercus suber, Olea europaea and Quercus canariensis) were sown in six sites during two consecutive years. Using a spatially-explicit, neighborhood approach we developed models that explained the observed spatial variation in seedling emergence, survival, growth and photochemical efficiency as a function of the size, identity, health, abundance and distribution of adult trees and shrubs in the neighborhood. We found strong neighborhood effects for all the performance estimators, particularly seedling emergence and survival. Tree neighbors positively affected emergence, independently of species identity or health. Alternatively, seedling survival was much lower in neighborhoods dominated by defoliated and dead Q. suber trees than in neighborhoods dominated by healthy trees. For the two oak species, these negative effects were consistent over the three years of the experimental seedlings. These results indicate that ongoing changes in species’ relative abundance and canopy trees’ health might alter the successional trajectories of Mediterranean oak-forests through neighbor-specific impacts on seedlings. The recruitment failure of dominant late-successional oaks in the gaps opened after Q. suber death would indirectly favor the establishment of other coexisting woody species, such as drought-tolerant shrubs. This could lead current forests to shift into open systems with lower tree cover. Adult canopy decline would therefore represent an additional factor threatening the recruitment of Quercus forests worldwide.
Homogenized sl(2)

This note studies a special case of Artin's projective geometry (Geometry of quantum planes, MIT, preprint, 1990) for noncommutative graded algebras. It is shown that (most of) the line modules over the homogenization of the enveloping algebra U(sl(2, C)) are in bijection with the lines lying on the quadrics that are the (closures of the) conjugacy classes in sl(2, C). Furthermore, these line modules are the homogenization of the Verma modules for sl((2, C)
The serosal mesothelium is a major source of smooth muscle cells of the gut vasculature

Most internal organs are situated in a coelomic cavity and are covered by a mesothelium. During heart development, epicardial cells (a mesothelium) move to and over the heart, undergo epithelial-mesenchymal transition (EMT), and subsequently differentiate into endothelial and vascular smooth muscle cells. This is thought to be a unique process in blood vessel formation. Still, structural and developmental similarities between the heart and gut led us to test the hypothesis that a conserved or related mechanism may regulate blood vessel development to the gut, which, similar to the heart, is housed in a coelomic cavity. By using a combination of molecular genetics, vital dye fate mapping, organ culture and immunohistochemistry, we demonstrate that the serosal mesothelium is the major source of vasculogenic cells in developing mouse gut. Our studies show that the gut is initially devoid of a mesothelium but that serosal mesothelial cells expressing the Wilm's tumor protein (Wt1) move to and over the gut. Subsequently, a subset of these cells undergoes EMT and migrates throughout the gut. Using Wt1-Cre genetic lineage marking of serosal cells and their progeny, we demonstrate that these cells differentiate to smooth muscle of all major blood vessels in the mesenteries and gut. Our data reveal a conserved mechanism in blood vessel formation to coelomic organs, and have major implications for our understanding of vertebrate organogenesis and vascular deficiencies of the gut.