Miracle-dz/UniFAR-FTUs huggingface dataset:
Protein conformational transitions explored by mixed elastic network models

We develop a mixed elastic network model (MENM) to study large‐scale conformational transitions of proteins between two (or more) known structures. Elastic network potentials for the beginning and end states of a transition are combined, in effect, by adding their respective partition functions. The resulting effective MENM energy function smoothly interpolates between the original surfaces, and retains the beginning and end structures as local minima. Saddle points, transition paths, potentials of mean force, and partition functions can be found efficiently by largely analytic methods. To characterize the protein motions during a conformational transition, we follow “transition paths” on the MENM surface that connect the beginning and end structures and are invariant to parameterizations of the model and the mathematical form of the mixing scheme. As illustrations of the general formalism, we study large‐scale conformation changes of the motor proteins KIF1A kinesin and myosin II. We generate possible transition paths for these two proteins that reveal details of their conformational motions. The MENM formalism is computationally efficient and generally applicable even for large protein systems that undergo highly collective structural changes. Proteins 2007. © 2007 Wiley‐Liss, Inc.
Relative Pose Estimation for Instrumented, Calibrated Imaging Platforms

Recent efforts in robust estimation of the two-view relation have fo- cused on uncalibrated cameras with no prior knowledge of pose. However, in practice robotic vehicles that perform image-based navigation and mapping typi- cally do carry a calibrated camera and pose sensors; this additional knowledge is currently not being exploited. This paper presents three contributions in using vision with instrumented and cal- ibrated platforms. First, we improve the performace of the correspondence stage by using uncertain measurements from egomotion sensors to constrain possible matches. Second, we assume wide-baseline conditions and propose Zernike mo- ments to describe affine invariant features. Third, we robustly estimate the essen- tial matrix with a new 6-point algorithm. Our solution is simpler than the minimal 5-point one and, unlike the linear 6-point solution, does not fail on planar scenes. While the contributions are general, we present structure and motion results from an underwater robotic survey.
Dental Stem Cells and their Applications in Dental Tissue Engineering

Tooth loss or absence is a common condition that can be caused by various pathological circumstances. The replacement of the missing tooth is important for medical and aesthetic reasons. Recently, scientists focus on tooth tissue engineering, as a potential treatment, beyond the existing prosthetic methods. Tooth engineering is a promising new therapeutic approach that seeks to replace the missing tooth with a bioengineered one or to restore the damaged dental tissue. Its main tool is the stem cells that are seeded on the surface of biomaterials (scaffolds), in order to create a biocomplex. Several populations of mesenchymal stem cells are found in the tooth. These different cell types are categorized according to their location in the tooth and they demonstrate slightly different features. It appears that the dental stem cells isolated from the dental pulp and the periodontal ligament are the most powerful cells for tooth engineering. Additional research needs to be performed in order to address the problem of finding a suitable source of epithelial stem cells, which are important for the regeneration of the enamel. Nevertheless, the results of the existing studies are encouraging and strongly support the belief that tooth engineering can offer hope to people suffering from dental problems or tooth loss.
Bookmark Hierarchies and Collaborative Recommendation

GiveALink.org is a social bookmarking site where users may donate and view their personal bookmark files online securely. The bookmarks are analyzed to build a new generation of intelligent information retrieval techniques to recommend, search, and personalize the Web. GiveALink does not use tags, content, or links in the submitted Web pages. Instead we present a semantic similarity measure for URLs that takes advantage both of the hierarchical structure in the bookmark files of individual users, and of collaborative filtering across users. In addition, we build a recommendation and search engine from ranking algorithms based on popularity and novelty measures extracted from the similarity-induced network. Search results can be personalized using the bookmarks submitted by a user. We evaluate a subset of the proposed ranking measures by conducting a study with human subjects.
Using Permutations to Enhance the Gain of RUQB Technique

Quantum key distribution (QKD) techniques usually suffer from a gain problem when comparing the final key to the generated pulses of quantum states. This research permutes the sets that RUQB (Abu-ayyash & Ajlouni, 2008) uses in order to increase the gain. The effect of both randomness and permutations are studied; While RUQB technique improves the gain of BB84 QKD by 5.5% it was also shown that the higher the randomness of the initial key the higher the gain that can be achieved, this work concluded that the use of around 7 permutations results in 30% gain recovery in an ideal situations.
High sensitivity of human leukocyte antigen-b*5701 as a marker for immunologically confirmed abacavir hypersensitivity in white and black patients.

BACKGROUND Although the human leukocyte antigen (HLA)-B*5701 is highly associated with a hypersensitivity reaction (HSR) to abacavir (ABC), variable sensitivities have been reported when clinical data alone have been used to define an ABC HSR. This study evaluated the sensitivity of detection of the HLA-B*5701 allele as a marker of ABC HSRs in both white and black patients, using skin patch testing to supplement clinical diagnosis. METHODS White and black patients, identified through chart review, were classified as having received a diagnosis of an ABC HSR based on clinical findings only (a clinically suspected ABC HSR) or based on clinical findings and a positive skin patch test result (an immunologically confirmed [IC] ABC HSR). Control subjects were racially matched subjects who tolerated ABC for >/=12 weeks without experiencing an ABC HSR. Patients and control subjects were tested for the presence of HLA-B*5701. Sensitivity, specificity, and odds ratios for the detection of HLA-B*5701 as a marker for an ABC HSR were calculated for white and black participants. RESULTS Forty-two (32.3%) of 130 white patients and 5 (7.2%) of 69 black patients who met the criteria for clinically suspected HSRs had IC HSRs. All 42 white patients with IC HSRs were HLA-B*5701 positive (sensitivity, 100%; odds ratio, 1945; 95% confidence interval, 110-34,352). Among all white patients with clinically suspected HSRs, sensitivity was 44% (57 of 130 patients tested positive for HLA-B*5701); specificity among white control subjects was 96%. Five of 5 black patients with IC HSRs were HLA-B*5701 positive (sensitivity, 100%; odds ratio, 900; 95% confidence interval, 38-21,045). Among black patients with clinically suspected HSRs, the sensitivity was 14% (10 of 69 tested positive for HLA-B*5701); specificity among black control subjects was 99%. CONCLUSIONS Although IC ABC HSRs are uncommon in black persons, the 100% sensitivity of HLA-B*5701 as a marker for IC ABC HSRs in both US white and black patients suggests similar implications of the association between HLA-B*5701 positivity and risk of ABC HSRs in both races.
Modeling of Wave Resonances in Low-Contrast Photonic Crystals

Coupled-mode equations are derived from Maxwell equations for modeling of low-contrast cubic-lattice photonic crystals in three spatial dimensions. Coupled-mode equations describe resonantly interacting Bloch waves in stop bands of the photonic crystal. We study the linear boundary-value problem for stationary transmission of four counter-propagating and two oblique waves on the plane. Well-posedness of the boundary-value problem is proved by using the method of separation of variables and generalized Fourier series. For applications in photonic optics, we compute integral invariants for transmission, reflection, and diffraction of resonant waves.
Couplings in Phase Domain Impedance Modeling of Grid-Connected Converters

The output impedance of a power converter plays an important role in the stability assessment of the converter. The impedance can be expressed in different frames such as the stationary frame (phase domain) or in the synchronous frame (dq domain). To treat the three-phase system like a single-phase system, the system can be divided into positive and negative sequences in the phase domain. This paper demonstrates that there exist couplings between the positive and negative sequences, even in a balanced system due to the PLL, which is important for synchronization. Further it will be shown that even though these couplings are very small in magnitude, they are important in the stability of the converter.
Micro/nanoscopic Characterizations of Epoxy-Silica Nanocomposites

Micro/nanoscopic properties of epoxy-silica nanocomposites are studied experimentally. The basic syntheses of epoxy-silica nanocomposites are introduced. Some micro/nanoscopic structure and characterizations of epoxy resin/silica nanocomposites, including the chemical elements, microstructure, the scattered state of the inorganic particles, and properties like elastic modulus and its hardness, are quantitatively analyzed using X-ray fluorescence spectral analysis, transmission electron microscope (TEM), and nanoindentation technique. These results will be useful for improving the synthesization technology and for optimizing the properties of epoxy resin-silica nanocomposites.
Transcribing handwritten text images with a word soup game

The major contribution presented here is the transformation of the tedious process of transcribing text images into an enjoyable game. A web-based application is composed by a word soup interface and a game engine that uses a system for automatic handwriting transcription as input to play the game. This WiP describes the rationale and design principles for the game, envisioning evaluation strategies and deriving insights for future developments.
Caveolin-1 Facilitates Mechanosensitive Protein Kinase B (Akt) Signaling In Vitro and In Vivo

Mechanotransduction represents an integral part of vascular homeostasis and contributes to vascular lesion formation. Previously, we demonstrated a mechanosensitive activation of phosphoinositide 3-kinase (PI3-K)/protein kinase B (Akt) resulting in p27Kip1 transcriptional downregulation and cell cycle entry of vascular smooth muscle cells (VSMC). In this study, we further elucidated the signaling from outside-in toward PI3-K/Akt in vitro and in an in vivo model of elevated tensile force. When VSMC were subjected to cyclic stretch (0.5 Hz at 125% resting length), PI3-K, Akt, and Src kinases were found activated. Disrupting caveolar structures with &bgr;-cyclodextrin or transfection of VSMC with caveolin-1 antisense oligonucleotides (ODN) prevented PI3-K and Akt activation and cell cycle entry. Furthermore, PI3-K and Akt were resistant to activation when Src kinases were inhibited pharmacologically or by overexpression of a kinase-dead c-Src mutant. &agr;V&bgr;3 integrins were identified to colocalize with PI3-K/caveolin-1 complexes, and blockade of &agr;V&bgr;3 integrins prevented Akt activation. The central role of caveolin-1 in mechanotransduction was further examined in an in vivo model of elevated tensile force. Interposition of wild-type (WT) jugular veins into WT carotid arteries resulted in a rapid Akt activation within the veins that was almost abolished when veins of caveolin-1 knockout (KO) mice were used. Furthermore, late neointima formation within the KO veins was significantly reduced. Our study provides evidence that PI3-K/Akt is critically involved in mechanotransduction of VSMC in vitro and within the vasculature in vivo. Furthermore, caveolin-1 is essential for the integrin-mediated activation of PI3-K/Akt.
Is Twitter a good enough social sensor for sports TV?

The globalization of TV programming (especially in the Sports and Reality segments) is leading to a bewildering amount of choice for TV watchers. The social currency around knowing what's happening in these programs as they happen combined with notable undulations in the interestingness of these programs leads to a navigation problem for the TV watcher. The pervasive use of Twitter in conjunction with TV watching makes it a potential sensor for real-time TV, and therefore a building block in solving the user problem of interstitially navigating to the most interesting program at any point in time. Given that users have to tune into shows with peak moments as soon as those peak moments happen, interstitial navigation has to be high enough performance to enable TV event detection and user tune in within tens of seconds of the event. The question being addressed in this paper is - Do Twitter's social sensing capabilities have sufficient precision and timeliness to cater to the `extreme' navigation needs of sports fans? And if so - how can we design a TV event detection framework that can be extended to multiple sports, and beyond sports. We focus on navigation for sports programming in the narrative, as an extremely demanding TV application that also has high market attractiveness. However, we anticipate that the ideas and architecture proposed herein apply to any TV programming that lends itself to interstitial viewing, and elicits a high level of real-time user participation in social networks.
Discrimination of Aliphatic Substrates by a Single Amino Acid Substitution in Bacillus badius and Bacillus sphaericus Phenylalanine Dehydrogenases

Replacement of glycine by serine at positions 123 and 124 of phenylalanine dehydrogenases from Bacillus badius and Bacillus sphaericus respectively strikingly decreased enzyme activity toward aromatic amino acids and resulted in an elevation of relative activity toward aliphatic amino acids. The mutant from B. badius preferentially dehydrogenated branched-chain amino acids, while that from B. sphaericus acted on amino acids with straight-chain amino acids.
Highly Selective and Ultrasensitive Turn-On Luminescence Chemosensor for Mercury (II) Determination Based on the Rhodamine 6G Derivative FC1 and Au Nanoparticles

A method for the detection and quantitation of Hg2+ in aqueous samples by fluorescence spectroscopy is presented. It consists of a turn-on sensor developed by coupling Gold nanoparticles (AuNPs) with the rhodamine 6G derivative FC1, in which the response is generated by a mercury-induced ring-opening reaction. The AuNPs were included in order to improve the sensitivity of the method towards the analyte, maintaining its high selectivity. The method was validated in terms of linearity, precision and accuracy, and applied to the quantitation of Hg2+ in Milli-Q and tap water with and without spiked analyte. The limit of detection and quantitation were 0.15 μg·L−1 and 0.43 μg·L−1, respectively, constituting a substantial improvement of sensitivity in comparison with the previously reported detection of Hg2+ with free FC1.
Statistical analyses of representation choice in level generation

This study demonstrates that representation choice in automatic map creation affects the characteristics of the map generated as well as showing that representation choice makes a statistically significant difference in the degree of satisfaction of the fitness functions used to drive map creation. This result is demonstrated with Tukeys HSD procedure and factor analysis. It was found that different representations are good at creating maps with specific characteristics. It also shows that there are significant differences in the maps that are created with different representations. This study is a companion to earlier qualitative research, providing a quantitative perspective on the impact of representation on automatic map creation.
Future Directions in Sleep and Developmental Psychopathology

It is critical for psychologists to gain a better understanding about the intersection between sleep and developmental psychopathology. However, while many strive to answer the question of whether sleep causes developmental psychopathology, or vice versa, ultimately the relationship between sleep and developmental psychopathology is complex and dynamic. This article considers future directions in the field of clinical child and adolescent psychology that go beyond this mechanistic question, highlighting areas important to address for clinicians and researchers who strive to better understand how best to serve children and adolescents with developmental psychopathology. Questions are presented about what is normal in terms of sleep across development, the role of individual variability in terms of sleep needs and vulnerability to sleep loss, and how sleep may serve as a risk or resilience factor for developmental psychopathology, concluding with considerations for interventions.
A Fully Integrated Bluetooth Low-Energy Transmitter in 28 nm CMOS With 36% System Efficiency at 3 dBm

We propose a new transmitter architecture for ultra-low power radios in which the most energy-hungry RF circuits operate at a supply just above a threshold voltage of CMOS transistors. An all-digital PLL employs a digitally controlled oscillator with switching current sources to reduce supply voltage and power without sacrificing its startup margin. It also reduces 1/f noise and supply pushing, thus allowing the ADPLL, after settling, to reduce its sampling rate or shut it off entirely during a direct DCO data modulation. The switching power amplifier integrates its matching network while operating in class-E/F2 to maximally enhance its efficiency at low voltage. The transmitter is realized in 28 nm digital CMOS and satisfies all metal density and other manufacturing rules. It consumes 3.6 mW/5.5 mW while delivering 0 dBm/3 dBm RF power in Bluetooth Low-Energy mode.
From protagonists to partners : Participative research in the corporate landscape

A critical perspective on the corporate landscape, especially corporate social responsibility, can arguably shed light on the increasing tensions between different corporate stakeholders. For stakeholders in a corporation are now commonly taken to include, not only investors, but also customers, employees, business suppliers and the local community. The paper has three parts. The first part situates the notion of corporate social responsibility within corporatist culture, and points to developments in the global corporate landscape that are indicative of a contemporary societal mood calling for higher levels of accountability and responsibility from corporations. The second part analyses the oppressive nature of stakeholder relationships in the corporate landscape, tracing how the work of Freire, Gramsci and Foucault lends different understandings to these relations between stakeholders. The third part of the paper illustrates how participative action research might be used to unsettle oppressive regimes in the tourism industry in general, and the gambling sector of that industry, in particular. The conclusion proposes a type of action research that envisages participant stakeholders engaging in their own emancipatory project in the context of prevailing oppressive corporatist relations. The paper therefore proposes that participative action research may open up opportunities for unsettling the dominant assumptions of economically driven stakeholders in the exploration of complex, competing stakeholder interests. In such engagements lie the potential for a shift
The Role of Cognitive Factors in the Rod-and-Frame Effect

We compared the contribution and the effectiveness of modulating the orientation perception of two types of visual information: the visual frame and the visual polarity of objects. In experiment 1, we examined the effect of a square frame, a mouse, an elephant, and a map of France on the apparent vertical. In the upright position, despite the presence of tilted individual component features, the visual objects had no illusory visual tilt effects. When tilted, these objects had a substantial effect on the direction that appeared to be vertical. However, rod-setting errors were smaller in the inducing objects than when observed with the frame display. In the second experiment, the results of experiment 1 were replicated with a meaningful circular contour—a porthole and a clock. The presence of the external circular contour did not abolish the illusion on the apparent vertical. Moreover, in experiment 3, a clock whose numbers were displaced and not tilted—to avoid the possible tilt influence of visual cues—was also able to deflect the subjective visual vertical. This finding suggests that through top–down processing shapes can act as a framework which serves as a reference influencing the perceived orientation of the inner objects.
Metaplasticity of amygdalar responses to the stress hormone corticosterone

High levels of corticosteroids (as circulate after stress) quickly and reversibly enhance hippocampal glutamatergic transmission via nongenomic actions requiring mineralocorticoid receptors. Subsequently, the hormone slowly and long-lastingly normalizes hippocampal cell function, through nuclear glucocorticoid receptors. Here we describe a rapid mineralocorticoid receptor-dependent enhancement of glutamatergic transmission in basolateral amygdala neurons. Contrary to the hippocampus, this rapid enhancement is long-lasting, potentially allowing an extended window for encoding of emotional aspects during stressful events. Importantly, the long-lasting change in state of amygdala neurons greatly affects the responsiveness to subsequent surges of corticosterone, revealing a quick suppression of glutamatergic transmission, which requires the glucocorticoid receptor. Responses of basolateral amygdala neurons to the stress hormone corticosterone can thus switch from excitatory to inhibitory, depending on the recent stress history of the organism.
Development of a Test Method That Will Allow Evaluation and Quantification of the Effects of Healing on Asphalt Mixture

Repeated traffic loading will result in accumulation of damage, but this damage will heal during periods of no traffic loading. Consequently, this healing will extend the fatigue life of the asphalt pavement. Traditional fatigue analysis does not consider this and, as a result, will often underpredict field fatigue life. In this study, a test was developed to evaluate the healing behavior of asphalt mixture, both dense-graded and open-graded, using the Superpave Indirect Tensile Test (IDT) testing system. The healing test comprises of two phases: a damage phase and a healing phase. The testing procedure consists of repeated loading damage tests (resilient modulus tests) during the damage phase followed by a healing phase during which resilient modulus tests are performed only periodically to measure modulus recovery (healing). A decrease in resilient modulus with an increasing number of load cycles is indicative of accumulation of microdamage during the damage phase. Recovery of resilient modulus during the healing phase is indicative of damage recovery or healing. Rate of healing was found to not be constant but rather changed with time at a decreasing rate for any given mixture. Since healing rate varies with time, a healing rate parameter was defined to allow for comparison between mixtures. Results showed that, in general, mixtures at higher temperatures healed at a faster rate than those at lower temperatures. Lastly, recommendations are made for continued development and validation of testing using the proposed healing test.