Miracle-dz/UniFAR-FTUs huggingface dataset:
Minimization of polypeptide energy. I. Preliminary structures of bovine pancreatic ribonuclease S-peptide.

Because the problem of computing protein structures from a knowledge of the amino acid sequence is so complex, we have approached it by making many simplifying assumptions and then removing these assumptions in stages until a computer program could ultimately be developed to yield the structure of a protein. Thus, using a hard-sphere potential, it was possible to compute the allowed coinformations of dipeptides and tripeptides,l of helical structures,2 ' of a cyclic octapeptide,4 and of the cyclic decapeptide gramicidin-S.5 Subsequently, the hardsphere potential was replaced by more complete energy expressions, and energy contours were computed for several dipeptides6' I and helical structures. ' 8-10 Similar calculations have been reported by Ramachandran,1II 12 LiquoriI3' 14 and Flory.15, 16 In this paper, we make certain simplifying assumptions about the energies, and introduce the effect of the solvent (i.e., water). In addition, we report briefly on the exploration of several minimization techniques, and apply the most satisfactory one to the 20-residue N-terminus (S-peptide) of bovine pancreatic ribonuclease. Because of the problem of multiple apparent local minima, the structures reported here are to be regarded only as preliminary ones. In subsequent papers, we will report on energy minimization for some small polypeptides containing closed loops, and also on another minimization procedure which permits rapid minimization, starting with many arbitrary initial conformations. Calculation of the Energy. -Although we have shown that variations in bond lengths and bond angles affect the energy contours of dipeptides,7 we have not yet found it necessary to include this feature in calculations for small polypeptides; hence, the backbone and side-chain geometry were held fixed in the calculations reported in this paper. As before,9 a Lennard-Jones pairwise 6-12 potential function was used for the nonbonded interactions. However, in order to reduce the amount of computation, hydrogen atoms were not considered individually unless they can take part in a strong hydrogen bond. Instead, they were regarded as part of an extended "atom" such as a methylene group, etc. The coefficients of the attractive terms in the potentials were calculated by means of the Slater-Kirkwood equation,17 using the values of a and Neff given in Table 1. The coefficients of the repulsive terms were adjusted so as to minimize the pair-interaction energy when the interatomic distance was equal to the sum of the van der Waals radii as given in reference 15 or reference 20, plus 0.2 A (see ref. 16). This is equivalent to enlarging the van der Waals radii; the values of the enlarged radii are given in Table 1. Electrostatic interactions were computed by assigning partial charges to each atom and summing the contributions of all pairs, using Coulomb's law.9' 21 The partial charges were essentially those given elsewhere.21 Zero charge was assigned
Mitochondrial Import of the ADP/ATP Carrier: the Essential TIM Complex of the Intermembrane Space Is Required for Precursor Release from the TOM Complex

ABSTRACT The mitochondrial intermembrane space contains a protein complex essential for cell viability, the Tim9-Tim10 complex. This complex is required for the import of hydrophobic membrane proteins, such as the ADP/ATP carrier (AAC), into the inner membrane. Different views exist about the role played by the Tim9-Tim10 complex in translocation of the AAC precursor across the outer membrane. For this report we have generated a new tim10 yeast mutant that leads to a strong defect in AAC import into mitochondria. Thereby, for the first time, authentic AAC is stably arrested in the translocase complex of the outer membrane (TOM), as shown by antibody shift blue native electrophoresis. Surprisingly, AAC is still associated with the receptors Tom70 and Tom20 when the function of Tim10 is impaired. The nonessential Tim8-Tim13 complex of the intermembrane space is not involved in the transfer of AAC across the outer membrane. These results define a two-step mechanism for translocation of AAC across the outer membrane. The initial insertion of AAC into the import channel is independent of the function of Tim9-Tim10; however, completion of translocation across the outer membrane, including release from the TOM complex, requires a functional Tim9-Tim10 complex.
Melting Relations of MORB ^ Sediment Me ¤ langes in Underplated MantleWedge Plumes ; Implications for the Origin of Cordilleran-type

This paper gives the results of a set of laboratory experiments designed to analyse the petrological implications of mantle wedge plumesçlarge buoyant structures predicted by thermomechanical numerical modelling of subduction zones. A particular design of layered capsule was used to simulate the complex multilayer formed by intense flow within the mantle wedge as predicted by numerical models. A basaltic [mid-ocean ridge basalt (MORB)-derived amphibolite] component was sandwiched between two adjacent layers of a sedimentary (Bt-rich metagreywacke) component. Conditions were fixed at temperatures of 1000^12008C at pressures of 1·5^2·0 GPa. Our results suggest that significant volumes of hybrid, Cordilleran-type granodioritic magmas can be generated by sub-lithospheric partial melting of a mechanically mixed source. Partial melting of the end-members is not buffered, forming granitic (melting of metasediment) and trondhjemitic (melting of MORB) melts in high-variance assemblages Melt þ Grt þ Pl and Melt þ Grt þ Cpx, respectively. However, the composition of melts formed from partial melting of metasediment^MORB me¤ langes is buffered for sediment-to-MORB ratios ranging from 3:1 to 1:3, producing liquids of granodiorite to tonalite composition along a cotectic with the lower-variance phase assemblage MeltþGrtþCpxþPl. Our model explains the geochemical and isotopic characteristics of Cordilleran batholiths. In particular, it accounts for the observed decoupling between major element and isotopic compositions. Large variations in isotopic ratios can be inherited from a compositionally heterogeneous source; however, major element compositions are more strongly dependent on the temperature of melting rather than on the composition of the source.
Behavior-Level Observability Analysis for Operation Gating in Low-Power Behavioral Synthesis

Many techniques for power reduction in advanced RTL synthesis tools rely explicitly or implicitly on observability don’t-care conditions. In this article we propose a systematic approach to maximize the effectiveness of these techniques by generating power-friendly RTL descriptions in behavioral synthesis. This is done using operation gating, that is, explicitly adding a predicate to an operation based on its observability condition, so that the operation, once identified as unobservable at runtime, can be avoided using RTL power optimization techniques such as clock gating. We first introduce the concept of behavior-level observability and its approximations in the context of behavioral synthesis. We then propose an efficient procedure to compute an approximated behavior-level observability of every operation in a dataflow graph. Unlike previous techniques which work at the bit level in Boolean networks, our method is able to perform analysis at the word level, and thus avoids most computation effort with a reasonable approximation. Our algorithm exploits the observability-masking nature of some Boolean operations, as well as the select operation, and allows certain forms of other knowledge to be considered for stronger observability conditions. The approximation is proved exact for (acyclic) dataflow graphs when non-Boolean operations other than select are treated as black boxes. The behavior-level observability condition obtained by our analysis can be used to guide the operation scheduler to optimize the efficiency of operation gating. In a set of experiments on real-world designs, our method achieves an average of 33.9% reduction in total power; it outperforms a previous method by 17.1% on average and gives close-to-optimal solutions on several designs. To the best of our knowledge, this is the first time behavior-level observability analysis and optimization are performed during behavioral synthesis in a systematic manner. We believe that our idea can be applied to compiler transformations in general.
Morphological clocks in paleontology, and a mid-Cretaceous origin of crown Aves.

Birds are among the most diverse and intensivelystudied vertebrate groups, but many aspects of theirhigher-level phylogeny and evolution still remaincontroversial. One contentious issue concerns theantiquity of modern birds (=crown Aves): the ageof the most recent common ancestor of all livingbirds (Gauthier 1986). Very few Mesozoic fossilsare attributable to modern birds (e.g., Clarke et al.2005; Dyke and Kaiser 2011; Brocklehurst et al. 2012;Ksepka and Boyd 2012) suggesting that they diversiﬁedlargely or entirely in the early Paleogene, perhaps in theecologicalvacuumcreatedbytheextinctionofnon-aviandinosaurs, pterosaurs, and many archaic (stem) birds(e.g.,Longrichetal.2011). Incontrast,molecularstudiesindicate that modern birds commenced radiating deepwithin the Mesozoic, for example ∼130Ma(Cooperand Penny 1997; Haddrath and Baker 2012)or∼113 Ma(Jetz et al. 2012), with ratites, galliforms, anseriforms,shorebirds, and even passerines surviving acrossthe KPg boundary (∼66 Ma). The oldest moleculardates further imply an extraordinarily rapid earlybird evolution, with the modern birds appearingonly 20 myr after
Stable sparse channel estimation algorithm under non-Gaussian noise environments

Broadband frequency-selective fading channels usually exhibit the inherent sparse structure distribution in spread time-domain. By exploiting the sparsity, adaptive sparse channel estimation (ASCE) algorithms, e.g., least mean square with reweighted L1-norm constraint (LMS-RL1) algorithm, can bring a considerable performance gain under the assumption of additive white Gaussian noise (AWGN). In the scenarios of real wireless communication systems, however, channel estimation performance is often deteriorated by the unexpected non-Gaussian mixture noises which usually include AWGN and impulsive noises. To design stable communication systems, we propose sign LMS-RL1 (SLMS-RL1) channel estimation algorithm to remove the non-Gaussian noises and to exploit channel sparsity simultaneously. In addition, the regularization parameter (REPA) selection for SLMS-RL1 algorithm is proposed via Monte Carlo method. Simulation results are provided to corroborate our studies.
Development and Validation of an Automatic Segmentation Algorithm for Quantification of Intracerebral Hemorrhage

Background and Purpose— ABC/2 is still widely accepted for volume estimations in spontaneous intracerebral hemorrhage (ICH) despite known limitations, which potentially accounts for controversial outcome-study results. The aim of this study was to establish and validate an automatic segmentation algorithm, allowing for quick and accurate quantification of ICH. Methods— A segmentation algorithm implementing first- and second-order statistics, texture, and threshold features was trained on manual segmentations with a random-forest methodology. Quantitative data of the algorithm, manual segmentations, and ABC/2 were evaluated for agreement in a study sample (n=28) and validated in an independent sample not used for algorithm training (n=30). Results— ABC/2 volumes were significantly larger compared with either manual or algorithm values, whereas no significant differences were found between the latter (P<0.0001; Friedman+Dunn’s multiple comparison). Algorithm agreement with the manual reference was strong (concordance correlation coefficient 0.95 [lower 95% confidence interval 0.91]) and superior to ABC/2 (concordance correlation coefficient 0.77 [95% confidence interval 0.64]). Validation confirmed agreement in an independent sample (algorithm concordance correlation coefficient 0.99 [95% confidence interval 0.98], ABC/2 concordance correlation coefficient 0.82 [95% confidence interval 0.72]). The algorithm was closer to respective manual segmentations than ABC/2 in 52/58 cases (89.7%). Conclusions— An automatic segmentation algorithm for volumetric analysis of spontaneous ICH was developed and validated in this study. Algorithm measurements showed strong agreement with manual segmentations, whereas ABC/2 exhibited its limitations, yielding inaccurate overestimations of ICH volume. The refined, yet time-efficient, quantification of ICH by the algorithm may facilitate evaluation of clot volume as an outcome predictor and trigger for surgical interventions in the clinical setting.
Estimating the Number of Double-Strand Breaks Formed During Meiosis from Partial Observation

Analyzing the basic mechanism of DNA double-strand breaks (DSB) formation during meiosis is important for understanding sexual reproduction and genetic diversity. The location and amount of meiotic DSBs can be examined by using a common molecular biological technique called Southern blotting, but only a subset of the total DSBs can be observed; only DSB fragments still carrying the region recognized by a Southern blot probe are detected. With the assumption that DSB formation follows a nonhomogeneous Poisson process, we propose two estimators of the total number of DSBs on a chromosome: (1) an estimator based on the Nelson-Aalen estimator, and (2) an estimator based on a record value process. Further, we compared their asymptotic accuracy.
Deriving Semantic Sessions from Semantic Clusters

A important phase in any web personalization system is transaction identification. Recently a number of researches have been done to incorporate semantics of a website in representation of transactions. Building a hierarchy of concepts manually is time consuming and expensive. In this paper we intend to address these shortcomings. Our contribution is that we introduce a mechanism to automatically improve the representation of the user in the website using a comprehensive lexical semantic resource and semantic clusters. We utilize Wikipedia, the largest encyclopedia to date, as a rich lexical resource to enhance the automatic construction of vector model representation of user sessions. We cluster web pages based on their content with Hierarchical Unsupervised Fuzzy Clustering algorithms ,are effective methods, for exploring the structure of complex real data where grouping of overlapping and vague elements is necessary. Entries in web server logs are used to identify users and visit sessions, while web page or resources in the site are clustered based on their content and their semantic. Theses clusters of web documents are used to scrutinize the discovered web sessions in order to identify what we call sub-sessions. Each subsession have consistent goal. This process engendered to improving deriving semantic sessions from web site user page views. Our experiments show that proposed system significantly improves the quality of web personalization process.
Evidence of phonological processes in automatic recognition of children's speech

Automatic speech recognition (ASR) for children’s speech is more difﬁcult than for adults’ speech. A plausible explanation is that ASR errors are due to predictable phonological effects associated with language acquisition. We describe phone recognition experiments on hand labelled data for children aged between 5 and 9. A comparison of the resulting confusion matrices with those for adult speech (TIMIT) shows increased phone substitution rates for children, which correspond to some extent to established phonological phenomena. However these errors still only account for a relatively small proportion of the issue. This suggests that attempts to improve ASR accuracy on children’s speech by accommodating these phenomena, for exam-ple by changing the pronunciation dictionary, cannot solve the whole problem.
A Theory of Name Resolution with extended Coverage and Proofs

We describe a language-independent theory for name binding and resolution, suitable for programming languages with complex scoping rules including both lexical scoping and modules. We formulate name resolution as a two stage problem. First a language-independent scope graph is constructed using language-specific rules from an abstract syntax tree. Then references in the scope graph are resolved to corresponding declarations using a language-independent resolution process. We introduce a resolution calculus as a concise, declarative, and language-independent specification of name resolution. We develop a resolution algorithm that is sound and complete with respect to the calculus. Based on the resolution calculus we develop language-independent definitions of alpha-equivalence and rename refactoring. We illustrate the approach using a small example language with modules. In addition, we show how our approach provides a model for a range of name binding patterns in existing languages.
PRIVATE-IYE: A Framework for Privacy Preserving Data Integration

Data integration has been a long standing challenge to the database and data mining communities. This need has become critical in numerous contexts, including building e-commerce market places, sharing data from scientific research, and improving homeland security. However, these important activities are hampered by legitimate and widespread concerns of data privacy. It is necessary to develop solutions that enable integration of data, especially in the domains of national priorities, while effective privacy control of the data. In this paper, we present an architecture and key research issues for building such a privacy preserving data integration system called PRIVATE-IYE.
Contrasting hydraulic strategies in two tropical lianas and their host trees.

PREMISE OF THE STUDY Tropical liana abundance has been increasing over the past 40 yr, which has been associated with reduced rainfall. The proposed mechanism allowing lianas to thrive in dry conditions is deeper root systems than co-occurring trees, although we know very little about the fundamental hydraulic physiology of lianas. METHODS To test the hypothesis that two abundant liana species would physiologically outperform their host tree under reduced water availability, we measured rooting depth, hydraulic properties, plant water status, and leaf gas exchange during the dry season in a seasonally dry tropical forest. We also used a model to compare water use by one of the liana species and the host tree during drought. KEY RESULTS All species measured were shallowly rooted. The liana species were more vulnerable to embolism than host trees and experienced water potentials that were predicted to result in substantial hydraulic losses in both leaves and stems. Water potentials measured in host trees were not negative enough to result in significant hydraulic losses. Model results predicted the liana to have greater gas exchange than its host tree during drought and nondrought conditions. CONCLUSIONS The host tree species had a more conservative strategy for maintenance of the soil-to-leaf hydraulic pathway than the lianas it supported. The two liana species experienced embolism in stems and leaves, based on vulnerability curves and water potentials. These emboli were presumably repaired before the next morning. However, in the host tree species, reduced stomatal conductance prevented leaf or stem embolism.
Learning Multiscale Deep Features for High-Resolution Satellite Image Scene Classification

In this paper, we propose a multiscale deep feature learning method for high-resolution satellite image scene classification. Specifically, we first warp the original satellite image into multiple different scales. The images in each scale are employed to train a deep convolutional neural network (DCNN). However, simultaneously training multiple DCNNs is time-consuming. To address this issue, we explore DCNN with spatial pyramid pooling (SPP-net). Since different SPP-nets have the same number of parameters, which share the identical initial values, and only fine-tuning the parameters in fully connected layers ensures the effectiveness of each network, thereby greatly accelerating the training process. Then, the multiscale satellite images are fed into their corresponding SPP-nets, respectively, to extract multiscale deep features. Finally, a multiple kernel learning method is developed to automatically learn the optimal combination of such features. Experiments on two difficult data sets show that the proposed method achieves favorable performance compared with other state-of-the-art methods.
Full polarization high-resolution radar imaging based on multichannel joint sparse recovery

In this paper, a novel full polarization high-resolution ISAR imaging method based on multichannel joint sparse recovery is proposed. First, a definition of joint sparsity is given by exploiting the scattering characteristics of target in fully polarimetric channels. Then, a multichannel joint sparse recovery algorithm is proposed to reconstruct fully polarimetric radar images under the constraint of the joint sparsity. The proposed imaging method can not only provide high-resolution radar images with limited measurements, but also preserve the true polarimetric scattering characteristics of the target, which are beneficial for further applications. Finally, simulated experiments of the backhoe data verify the effectiveness of the proposed method.
Clonal Complexes and Diversity of Exotoxin Gene Profiles in Methicillin-Resistant and Methicillin-Susceptible Staphylococcus aureus Isolates from Patients in a Spanish Hospital

ABSTRACT Molecular epidemiology studies have allowed the identification of the methicillin (meticillin)-resistant (MRSA) and methicillin-susceptible (MSSA) clonal complexes (CCs) and clones of Staphylococcus aureus circulating in a Spanish hospital recently. Of 81 isolates tested, 32.1% were MRSA. Most of them carried staphylococcal cassette chromosome mec (SCCmec) IVc (88.5%) and belonged to CC5 (88.5%; multilocus sequence typing types ST125 [mainly associated with spa type t067], ST5, and ST228). A higher diversity was found among MSSA isolates (67.9%). Eighty percent shared the genetic background of major MRSA lineages (CC5 [38.2%; ST125 and ST5], CC30 [25.5%; ST30], CC45 [14.5%; ST45 and ST47], and CC8 [1.8%; ST8]), but CC12, CC15, CC51, and CC59 were also detected. Many exotoxin genes were present in each of the 81 isolates, independent of whether they were involved in sepsis (11 to 22) or other types of infections (13 to 21), and they appeared in 73 combinations. The relevant data are that (i) all isolates were positive for hemolysin and leukotoxin genes (98.8% for lukED and 25.9% for lukPV); (ii) all contained an enterotoxin gene cluster (egc with or without seu), frequently with one or more genes encoding classical enterotoxins; (iii) about half were positive for tst and 95% were positive for exfoliatin-encoding genes (eta, etb, and/or etd); and (iv) the four agr groups were detected, with agrII (55.6%) and agrIII (23.5%) being the most frequent. Taken together, results of the present study suggest a frequent acquisition and/or loss of exotoxin genes, which may be mediated by efficient intralineage transfer of mobile genetic elements and exotoxin genes therein and by eventual breakage of interlineage barriers.