Miracle-dz/UniFAR-FTUs huggingface dataset:
High-Resolution Structure of the Histidine-Containing Phosphocarrier Protein (HPr) from Staphylococcus aureus and Characterization of Its Interaction with the Bifunctional HPr Kinase/Phosphorylase

ABSTRACT A high-resolution structure of the histidine-containing phosphocarrier protein (HPr) from Staphylococcus aureus was obtained by heteronuclear multidimensional nuclear magnetic resonance (NMR) spectroscopy on the basis of 1,766 structural restraints. Twenty-three hydrogen bonds in HPr could be directly detected by polarization transfer from the amide nitrogen to the carbonyl carbon involved in the hydrogen bond. Differential line broadening was used to characterize the interaction of HPr with the HPr kinase/phosphorylase (HPrK/P) of Staphylococcus xylosus, which is responsible for phosphorylation-dephosphorylation of the hydroxyl group of the regulatory serine residue at position 46. The dissociation constant Kd was determined to be 0.10 ± 0.02 mM at 303 K from the NMR data, assuming independent binding. The data are consistent with a stoichiometry of 1 HPr molecule per HPrK/P monomer in solution. Using transversal relaxation optimized spectroscopy-heteronuclear single quantum correlation, we mapped the interaction site of the two proteins in the 330-kDa complex. As expected, it covers the region around Ser46 and the small helix b following this residue. In addition, HPrK/P also binds to the second phosphorylation site of HPr at position 15. This interaction may be essential for the recognition of the phosphorylation state of His15 and the phosphorylation-dependent regulation of the kinase/phosphorylase activity. In accordance with this observation, the recently published X-ray structure of the HPr/HPrK core protein complex from Lactobacillus casei shows interactions with the two phosphorylation sites. However, the NMR data also suggest differences for the full-length protein from S. xylosus: there are no indications for an interaction with the residues preceding the regulatory Ser46 residue (Thr41 to Lys45) in the protein of S. xylosus. In contrast, it seems to interact with the C-terminal helix of HPr in solution, an interaction which is not observed for the complex of HPr with the core of HPrK/P of L. casei in crystals.
Bond stresses along plain steel reinforcing bars in pullout specimens

Although recent research has recognized the existence of relationships between bond stress, slip and bar force, mechanics-based analytical prediction models for bond of plain reinforcement based on pullout specimens have not yet been established. This study establishes mechanics-based relationships between bond stress, bar force, slip at the unloaded end of the bar, and slip along the length of plain steel reinforcing bars in pullout specimens. Two 200 mm (7.9 in.) diameter by 800 mm (31.5 in.) long pullout specimens reinforced with instrumented built-up hollow reinforcing bars were tested. The derived mechanics-based relationships show that bond stress is a function of relative bar slip, slip is a function of bar force, and bar force is a function of bond stress. It is shown both analytically and experimentally that bond stress magnitudes vary along the length of the bar at all applied loads. Maximum pullout resistance was observed just before slip initiated at the unloaded end of the bar, and the bond resistance subsequently reduced as slip increased. The location of the peak bond stress shifts from the loaded end toward the unloaded end of the specimen with increasing applied load. This study also demonstrates that a previously-developed theoretical two-step bond stress-slip model captures the essential features of bond behavior observed experimentally in pullout specimens once the authors accounted for the debonding adjacent to the loaded end of the specimen.
Assessment Methodology in Smart Cities Based on Public Value

Smart city is an approach to managing and coping with urban challenges in search for innovative solutions leading to better quality of life and sustainability in cities. Several initiatives have been undertaken, with a significant worldwide growth trend in the coming years. Such initiatives, however, may require non-trivial public investment, and failures resulting from them can have important consequences such as monetary loss, loss of reputation, reduced confidence and lack of public value. This article aims at setting a methodology in smart cities composed of a reference model and an assessment method from the Public Value perspective. It follows Design Science as its epistemological paradigm and Design Science Research as its method, uniting theoretical and methodological rigor as well as practical utility for society.
Red cell age and susceptibility to malaria during pregnancy

BACKGROUND Increased susceptibility to malaria in pregnancy is well recognized, and has generally been assumed to be due to hormonal changes resulting in altered immunity. Based on previous work demonstrating enhanced parasite growth in young normal and thalassemic red blood cells, we hypothesized that in pregnancy increased malaria susceptibility may be due, in part, to the increase in the population of young red cells. METHODS FC27 strain of Plasmodium falciparum was cultured in the red cells and sera from healthy primigravida pregnant (n=9) and non-pregnant (n=9) women. Red cells from both pregnant and non-pregnant women were each placed in three cultures containing the sera from pregnant, non-pregnant and pooled control samples. Cultures were set up in triplicate and incubated for 144 hours. Parasite development and growth were assessed by slide microscopy. RESULTS At 96 hours the median parasite growth in cells from pregnant samples (5.7%) was significantly better than that in the non-pregnant cells (4.8%) (p=0.01). There was no significant difference in parasite growth in cultures with pregnant and non-pregnant sera. As expected, there were significant differences in parameters measuring red cell age between the cells from pregnant and nonpregnant samples: median red cell creatine (11.09 mg/dl) versus (6.90 mg/dl) (p=0.004) and median reticulocyte count (2.3%) versus (1.4%) (p=0.0006). CONCLUSIONS These preliminary results are consistent with the hypothesis that an increased population of young red cells may contribute to increased malaria susceptibility during pregnancy.
Imitation Learning with a Value-Based Prior

The goal of imitation learning is for an apprentice to learn how to behave in a stochastic environment by observing a mentor demonstrating the correct behavior. Accurate prior knowledge about the correct behavior can reduce the need for demonstrations from the mentor. We present a novel approach to encoding prior knowledge about the correct behavior, where we assume that this prior knowledge takes the form of a Markov Decision Process (MDP) that is used by the apprentice as a rough and imperfect model of the mentor's behavior. Specifically, taking a Bayesian approach, we treat the value of a policy in this modeling MDP as the log prior probability of the policy. In other words, we assume a priori that the mentor's behavior is likely to be a high-value policy in the modeling MDP, though quite possibly different from the optimal policy. We describe an efficient algorithm that, given a modeling MDP and a set of demonstrations by a mentor, provably converges to a stationary point of the log posterior of the mentor's policy, where the posterior is computed with respect to the "value-based" prior. We also present empirical evidence that this prior does in fact speed learning of the mentor's policy, and is an improvement in our experiments over similar previous methods.
Simultaneous triple-registration of ictal SPECT, interictal SPECT and MR images for epilepsy studies: Method and validation

Subtraction of ictal and interictal SPECT images is known to be successful in localizing the seizure focus in presurgical evaluation of patients with partial epilepsy. Computer-aided method for producing subtraction ictal SPECT coregistered to MRI (SISCOM method) is commonly used. There are two registrations involved in SISCOM: between the ictal-interictal SPECT images, which was shown to be more critical, and between the ictal image and MRI. The aim of this paper is to improve registration accuracy of ictal-interictal registration in SISCOM by registering all three images (ictal, interictal SPECT, MRI) simultaneously. The results of the simulation study demonstrates that, in surface-based registration, triple-registration method results in smaller ictal-interictal SPECT registration error than the pairwise registration method (p<;0.05) for a range of cost-function parameter values.
Sintering of aluminium and its alloys

The conventional press-and-sinter powder metallurgy (P/M) technique is a unique cost-effective method for net shape or near net shape fabrication of complex aluminium parts. The chapter begins by providing a historical account of aluminium P/M and its application in North America, where the industry originated. It then reviews key issues of the press-and-sinter aluminium P/M technique and the science of sintering aluminium and its alloys under nitrogen, including the distinctive roles of magnesium and tin.
Flow Analysis during On-line and Radial Injection Applications in Permeability Measurements

In this study, a simple technique for revealing the key parameters (permeability, frontend kinetics) of the RTM process is developed. The variations in permeability during the technique lift the capillary effect, which is modeled for two configurations. The analysis of the front-end kinetics helps to identify the permeability tensor. The examination of the capillary number gives evidence of a non-saturated zone, characterized by a critical length.
ON THE DISCRETE-TIME H 1 FIXED-LAG SMOOTHING

This paper deals with the discrete-time H 1 xed-lag smoothing problem. Con- ventionally, this problem is solved by reducing it to a standard H 1 ltering problem for a higher order system that includes not only the actual system dynamics but also the delay caused by the smoothing lag. As the smoothing lag gets larger, such an approach may suffer from computational problems, especially due to the fact that a high dimensional Discrete Algebraic Riccati Equation (DARE) is to be solved. To overcome this disadvan- tage, in this paper, a new solution to this problem is derived in terms of one DARE of the same dimensions as the actual system dynamics. Copyright c 2002 IFAC
Effect of Renal Denervation on Neurohumoral Activation Triggering Atrial Fibrillation in Obstructive Sleep Apnea

Obstructive sleep apnea is characterized by repetitive collapses of the upper airway, negative thoracic pressure periods, and intermittent hypoxia, stimulating the autonomic nervous system. The increased sympathetic drive during obstructive sleep apnea results in postapneic blood pressure rises and neurohumoral activation potentially involved in the initiation and progression to permanent atrial fibrillation (AF). In a pig model mimicking obstructive sleep apnea, we studied the effects of repetitive obstructive respiratory events for 4 hours on the occurrence of spontaneous AF episodes, postapneic blood pressure rises, and neurohumoral activation. In addition, renal sympathetic denervation was performed to investigate the impact of the sympathetic nervous system. Repetitive obstructive respiratory events caused pronounced postapneic blood pressure rises, prolonged duration of spontaneous AF episodes triggered by spontaneous atrial beats, and increased plasma renin activity and aldosterone concentrations. This was associated with increased nicotinamide adenine dinucleotide phosphate-oxidase activity, reduced antioxidative capacity, and elevated expression of connective tissue growth factor, a redox-sensitive mediator of fibrosis. Renal sympathetic denervation inhibited postapneic blood pressure rises and decreased plasma renin activity and aldosterone concentrations. The occurrence and duration of spontaneous AF were reduced comparable with a combined pharmacological blockade of angiotensin receptor and &bgr;-adrenoceptor. Increased atrial oxidative stress, together with the activation of profibrotic pathways and intermittent hypoxia, was not attenuated after renal sympathetic denervation. Repetitive obstructive respiratory events triggered spontaneous AF, increased atrial oxidative stress, and activated profibrotic pathways in the atrium. Renal sympathetic denervation reduced spontaneous AF and postapneic blood pressure rises by combined reduction of sympathetic drive and components of the circulating renin–angiotensin system. However, the generation of atrial oxidative stress was not modulated.
Cryosurgery for recurrent carcinoma of the oral cavity.

Experience with cryosurgical techniques in the management of 64 patients with malignant tumors of the head and neck is reported with particular attention directed to 41 patients with recurrent tumors of the oral cavity following conventional therapy. The primary tumor was controlled in 16 patients while persistent disease resulted in the death of 21 others. There were four deaths in a total of 52 patients treated for cure, resulting in a mortality rate of 8%.
Elucidating glycosaminoglycan–protein–protein interactions using carbohydrate microarray and computational approaches

Glycosaminoglycan polysaccharides play critical roles in many cellular processes, ranging from viral invasion and angiogenesis to spinal cord injury. Their diverse biological activities are derived from an ability to regulate a remarkable number of proteins. However, few methods exist for the rapid identification of glycosaminoglycan–protein interactions and for studying the potential of glycosaminoglycans to assemble multimeric protein complexes. Here, we report a multidisciplinary approach that combines new carbohydrate microarray and computational modeling methodologies to elucidate glycosaminoglycan–protein interactions. The approach was validated through the study of known protein partners for heparan and chondroitin sulfate, including fibroblast growth factor 2 (FGF2) and its receptor FGFR1, the malarial protein VAR2CSA, and tumor necrosis factor-α (TNF-α). We also applied the approach to identify previously undescribed interactions between a specific sulfated epitope on chondroitin sulfate, CS-E, and the neurotrophins, a critical family of growth factors involved in the development, maintenance, and survival of the vertebrate nervous system. Our studies show for the first time that CS is capable of assembling multimeric signaling complexes and modulating neurotrophin signaling pathways. In addition, we identify a contiguous CS-E-binding site by computational modeling that suggests a potential mechanism to explain how CS may promote neurotrophin-tyrosine receptor kinase (Trk) complex formation and neurotrophin signaling. Together, our combined microarray and computational modeling methodologies provide a general, facile means to identify new glycosaminoglycan–protein–protein interactions, as well as a molecular-level understanding of those complexes.
OFDM channel estimation by singular value decomposition

A new approach to low-complexity channel estimation in orthogonal-frequency division multiplexing (OFDM) systems is proposed. A low-rank approximation is applied to a linear minimum mean-squared error (LMMSE) estimator that uses the frequency correlation of the channel. By using the singular value decomposition (SVD) an optimal low-rank estimator is derived, where performance is essentially preserved-even for low computational complexities. A fixed estimator, with nominal values for channel correlation and signal-to-noise ratio (SNR), is analysed. Analytical mean-squared error (MSE) and symbol-error rates (SER) are presented for a 16-QAM OFDM system.
Equitability, mutual information, and the maximal information coefficient

Significance Attention has recently focused on a basic yet unresolved problem in statistics: How can one quantify the strength of a statistical association between two variables without bias for relationships of a specific form? Here we propose a way of mathematically formalizing this “equitability” criterion, using core concepts from information theory. This criterion is naturally satisfied by a fundamental information-theoretic measure of dependence called “mutual information. ” By contrast, a recently introduced dependence measure called the “maximal information coefficient” is seen to violate equitability. We conclude that estimating mutual information provides a natural and practical method for equitably quantifying associations in large datasets. How should one quantify the strength of association between two random variables without bias for relationships of a specific form? Despite its conceptual simplicity, this notion of statistical “equitability” has yet to receive a definitive mathematical formalization. Here we argue that equitability is properly formalized by a self-consistency condition closely related to Data Processing Inequality. Mutual information, a fundamental quantity in information theory, is shown to satisfy this equitability criterion. These findings are at odds with the recent work of Reshef et al. [Reshef DN, et al. (2011) Science 334(6062):1518–1524], which proposed an alternative definition of equitability and introduced a new statistic, the “maximal information coefficient” (MIC), said to satisfy equitability in contradistinction to mutual information. These conclusions, however, were supported only with limited simulation evidence, not with mathematical arguments. Upon revisiting these claims, we prove that the mathematical definition of equitability proposed by Reshef et al. cannot be satisfied by any (nontrivial) dependence measure. We also identify artifacts in the reported simulation evidence. When these artifacts are removed, estimates of mutual information are found to be more equitable than estimates of MIC. Mutual information is also observed to have consistently higher statistical power than MIC. We conclude that estimating mutual information provides a natural (and often practical) way to equitably quantify statistical associations in large datasets.
SpaseLoc: An Adaptive Subproblem Algorithm for Scalable Wireless Sensor Network Localization

An adaptive rule-based algorithm, SpaseLoc, is described to solve localization problems for ad hoc wireless sensor networks. A large problem is solved as a sequence of very small subproblems, each of which is solved by semidefinite programming relaxation of a geometric optimization model. The subproblems are generated according to a set of sensor/anchor selection rules. Computational results compared with existing approaches show that the SpaseLoc algorithm scales well and provides excellent localization accuracy.
Rheology Study of Sugar Cane Bagasse Lignin-Added Phenol–Formaldehyde Adhesives

The rheological properties of sugar cane bagasse lignin–phenol formaldehyde (PF) (30% lignin – PF) resins were studied using oscillation tests. The bagasse lignin was introduced in the classic adhesive formulation in order to supply a part of PF. Rheological qualities of optimal lignin–PF (30% lignin – PF) resins and commercial PF resin were assessed by using a rotary rheometer (ARES). Dynamic rheological measurements, performed at low strain in the linear range, are useful to characterize the network properties of resins. The results obtained showed that the time sweep indicates excellent structural stability of optimal lignin–PF (30% lignin–PF) resins and commercial PF resin. The elastic modulus is greater than the viscous one showing a remarkable elastic character of the resins, and the performed frequency sweeps show a typical spectrum of a “weak gels” structure. The time dependence at 125°C shows that the optimum cure time is 7.5 min.
Mechanical and abrasive wear behavior of carbon fabric reinforced epoxy composite with and without fly ash cenospheres

Carbon fabric reinforced epoxy and carbon fabric reinforced epoxy containing different weight fraction of silane-treated fly ash cenospheres filled composites were cast, sectioned, and subjected to three-body abrasive wear tests for evaluating the abrasive wear behavior. Mechanical characterization was done and a comparison was made between the different samples. Abrasive wear tests were performed on a rubber wheel abrasion tester under different loads, abrading distances using quartz and silica sand as abrasives. The results showed that both unfilled carbon fabric reinforced epoxy and fly ash cenospheres filled carbon fabric reinforced epoxy composites exhibit differing magnitudes of wear volume loss, it being highest for unfilled carbon fabric reinforced epoxy composite. The data trends point to the fact that the wear volume and specific wear rate decreases with increasing fly ash cenospheres loading in carbon fabric reinforced epoxy composites. It was found that silane-treated fly ash cenospheres could effectively reduce the wear rate especially under silica sand as abrasives. To explain these differences, the worn surfaces were examined using scanning electron microscope and the features thus observed were correlated with the selected mechanical properties.
Effects of framework structure and coupling modification on the properties of mesoporous silica/poly(methyl methacrylate) composites

Mesoporous silicas (MPSs) with two-dimensional (2D) hexagonal framework (SBA-15) and worm-hole framework (MSU-J) were synthesized with poly(ethylene oxide-b-propylene oxide-b-ethylene oxide) (P123) and α,ω-polyoxypropylene diamine (D2000) as templates, respectively. Both SBA-15 and MSU-J were further modified with γ-(methacryloyloxy) propyl trimethoxy silane (MAPTS) via post-grafting to prepare organic mesoporous silicas (denoted SBA-15-G and MSU-J-G, respectively) with –C = C groups on the surface of mesopores. All mesoporous silicas were employed as filler to prepare improved poly(methyl methacrylate) (PMMA) composites with lower dielectric constant, higher thermal, and mechanical properties. It was found that all mesoporous silicas retained their mesostructure in MPS/PMMA composites to introduce a lot of voids into the composites. So, the dielectric constant of composites decreased with the loading of mesoporous silica and their organic derivatives increased. Also, all composites exhibited stabilized dielectric constant with lower value in comparison to pure PMMA over the whole frequency from 1 to 160 MHz. Specifically, with the addition of MPS to PMMA, the dielectric constants of the composite can be reduced from 2.91 of the pure PMMA to 2.73 and 2.64 by incorporating 4 wt% SBA-15 and 7 wt% MSU-J, respectively. All the composites exhibited improved mechanical properties, glass transmission temperature (Tg), and thermal stability in comparison to PMMA. All these differences in macro-properties are attributed to the different structure between MPS/PMMA composites and PMMA. MSU-J silica with the larger framework pore size provides the composite with the best improvement in dielectric, thermal, and mechanical properties.
Design and implementation of high-performance high-valency ling adders

Parallel prefix adders are used for efficient VLSI implementation of binary number additions. Ling architecture offers a faster carry computation stage compared to the conventional parallel prefix adders. Recently, Jackson and Talwar proposed a new method to factorize Ling adders, which helps to reduce the complexity as well as the delay of the adder further. This paper discusses the design and implementation details for such lower complexity, fast parallel prefix adders based on Ling theory of factorization. In particular, valency or radix, the number of inputs to a single node, is explored as a design parameter. Several low and high valency adders are implemented in 65 nm CMOS technology. Experimental results show that the high-valency Ling adders have superior area×delay characteristics over previously reported Ling-based or non-Ling adders for the same input size. Moreover, our 20-bit high valency adder has a better area×delay measurement than the previously-published 16-bit adders.