Miracle-dz/UniFAR-FTUs huggingface dataset:
NMR studies of Ca2+ binding to the regulatory domains of cardiac and E41A skeletal muscle troponin C reveal the importance of site I to energetics of the induced structural changes.

Ca2+ binding to the N-domain of skeletal muscle troponin C (sNTnC) induces an "opening" of the structure [Gagné, S. M. , et al. (1995) Nat. Struct. Biol. 2, 784-789], which is typical of Ca2+-regulatory proteins. However, the recent structures of the E41A mutant of skeletal troponin C (E41A sNTnC) [Gagné, S. M. , et al. (1997) Biochemistry 36, 4386-4392] and of cardiac muscle troponin C (cNTnC) [Sia, S. K. , et al. (1997) J. Biol. Chem. 272, 18216-18221] reveal that both of these proteins remain essentially in the "closed" conformation in their Ca2+-saturated states. Both of these proteins are modified in Ca2+-binding site I, albeit differently, suggesting a critical role for this region in the coupling of Ca2+ binding to the induced structural change. To understand the mechanism and the energetics involved in the Ca2+-induced structural transition, Ca2+ binding to E41A sNTnC and to cNTnC have been investigated by using one-dimensional 1H and two-dimensional {1H,15N}-HSQC NMR spectroscopy. Monitoring the chemical shift changes during Ca2+ titration of E41A sNTnC permits us to assign the order of stepwise binding as site II followed by site I and reveals that the mutation reduced the Ca2+ binding affinity of the site I by approximately 100-fold [from KD2 = 16 microM [sNTnC; Li, M. X. , et al. (1995) Biochemistry 34, 8330-8340] to 1.3 mM (E41A sNTnC)] and of the site II by approximately 10-fold [from KD1 = 1.7 microM (sNTnC) to 15 microM (E41A sNTnC)]. Ca2+ titration of cNTnC confirms that cNTnC binds only one Ca2+ with a determined dissociation constant KD of 2.6 microM. The Ca2+-induced chemical shift changes occur over the entire sequence in cNTnC, suggesting that the defunct site I is perturbed when site II binds Ca2+. These measurements allow us to dissect the mechanism and energetics of the Ca2+-induced structural changes.
PETRI NETS FOR TASK SUPERVISION IN HUMANOID ROBOTS

In contrast to industrial applications, humanoid robots (like ARMAR [1], see Figure 1) act in complex, permanently changing environments. Therefore, they require a fully functional control architecture for task planning, coordination, execution, and supervision. The function of such a supervision system is to detect occurring exceptional circumstances and if necessary to induce appropriate stabilization actions. Examples for exceptional circumstances within humanoid robots are collisions or new user commands during the execution of a task.
Comparison of User Ratings of Music in Copyright-free Databases and Onthe-market CDs

We have been conducting research to develop a music information retrieval system which retrieves music based on user preferences. In order to conduct evaluation experiments, it is necessary to accumulate an experiment set of music data, and collect user ratings of each music data included in this data set. Two music data sets were prepared for user evaluation: the RWC Popular Music Database, which is a collection of 100 copyright-free pop songs, and a collection of songs recorded in on-the-market CDs. Comparison of user ratings towards the songs in each data set shows that user ratings of the RWC songs were far lower than that of the songs in the other music data set. Based on this experience, the artists believe that the construction of a standard list of on-the-market CDs is necessary for the development of an entertaining MIR system.
Supplementary Document : Spatial-spectral Encoded Compressive Hyperspectral Imaging

Figure S. 1 shows the optical schematic of our prototype camera and some photographs of the prototype system. The parameters of each optical components are detailed in the primary document (Section 4.1). The objective lens is configured with a large f/# (small aperture size), which images the scene onto the diffraction grating. The axis of the relay components are tilted 28.7 degree with respect to the axis of the objective lens due to the blazing of the diffraction grating. The dispersed light is relayed by the 4f system to re-form the image plane. In order to achieve flexible adjustment of the mask−sensor distance and facilitate calibrations, another relay lens is added to relay the images onto the sensor. The attenuation mask printed with film is placed in front of the imaging plane (“virtual” sensor plane). We now analyse the tradeoffs between light efficiency and sensitivity in the spectral plane, and discuss on the parameter selection of the system design. The diffraction grating on the image plane maps the spectral dimension of the light to its angular dimension. A ray incident on the diffraction grating produces multiple diffracted outgoing rays in different directions with different spectral bands. This can be described by the grating equation:
Learning Near-Optimal Cost-Sensitive Decision Policy for Object Detection

Many object detectors, such as AdaBoost, SVM and deformable part-based models (DPM), compute additive scoring functions at a large number of windows scanned over image pyramid, thus computational efficiency is an important consideration beside accuracy performance. In this paper, we present a framework of learning cost-sensitive decision policy which is a sequence of two-sided thresholds to execute early rejection or early acceptance based on the accumulative scores at each step. A decision policy is said to be optimal if it minimizes an empirical global risk function that sums over the loss of false negatives (FN) and false positives (FP), and the cost of computation. While the risk function is very complex due to high-order connections among the two-sided thresholds, we find its upper bound can be optimized by dynamic programming (DP) efficiently and thus say the learned policy is near-optimal. Given the loss of FN and FP and the cost in three numbers, our method can produce a policy on-the-fly for Adaboost, SVM and DPM. In experiments, we show that our decision policy outperforms state-of-the-art cascade methods significantly in terms of speed with similar accuracy performance.
Learning Reward Modalities for Human-Robot-Interaction in a Cooperative Training Task

This paper proposes a novel method of learning a users preferred reward modalities for human-robot interaction through solving a cooperative training task. A learning algorithm based on a combination of adaptable pre-trained hidden Markov models and a computational model of classical conditioning is outlined. In a training task, where the desired outcome is known by an AIBO pet robot as well as its human instructor, the robot can freely explore human reward behavior. By this method, the robot is able to learn situated, user-specific reward behavior in the different modalities such as gestures, speech and interaction using the robot's built-in sensors. After the training phase, the learned reward behavior can be used as a basis for reinforcement learning of more complex tasks. A preliminary experimental study is presented, which investigates on the effects of restricting possible reward modalities, when teaching a pet robot. The results of the experiments suggest that being able to provide reward freely makes users give more reward compared to a scenario, where reward modalities are restricted. Moreover, the experiments showed that even if a restriction in possible reward modalities is introduced, users tend to give reward that does not conform to the restriction.
Distance Oracles for Sparse Graphs

Thorup and Zwick, in their seminal work, introduced the approximate distance oracle, which is a data structure that answers distance queries in a graph. For any integer k, they showed an efficient algorithm to construct an approximate distance oracle using space O(kn^{1+1/k}) that can answer queries in time O(k) with a distance estimate that is at most 2k-1 times larger than the actual shortest distance (this ratio is called the stretch). They proved that, under a combinatorial conjecture, their data structure is optimal in terms of space: if a stretch of at most 2k-1 is desired, then the space complexity is at least n^{1+1/k}. Their proof holds even if infinite query time is allowed: it is essentially an "incompressibility" result. Also, the proof only holds for dense graphs, and the best bound it can prove only implies that the size of the data structure is lower bounded by the number of edges of the graph. Naturally, the following question arises: what happens for sparse graphs? In this paper we give a new lower bound for approximate distance oracles in the cell-probe model. This lower bound holds even for sparse (polylog(n)-degree) graphs, and it is not an "incompressibility" bound: we prove a three-way tradeoff between space, stretch, and query time. We show that when the query time is t and the stretch is a, then the space S must be at least n^{1+1/Omega(a*t)} / lg n. This lower bound follows by a reduction from lopsided set disjointness to distance oracles, based on and motivated by recent work of Patrascu. Our results in fact show that for any high-girth regular graph, an approximate distance oracle that supports efficient queries for all subgraphs of G must obey this tradeoff. We also prove some lemmas that count sets of paths in high-girth regular graphs and high-girth regular expanders, which might be of independent interest.
What is the true resting potential of small cells?

instant, a direct consequence of the various ionic conductances and pumps or exchangers, with asymmetric ionic stoichiometries, which are present in the membrane and are active at that time. In addition to the membrane’s own ionic mechanisms, attempts to directly measure the membrane potential and conductance almost inevitably introduce another conductance (also called the shunt) which will influence to various degrees what is taken to be the potential of the cell. In giant axons, the membrane potential can be recorded between an external electrode and an electrode axially introduced into the axoplasm. In thin nerve and muscle fibres, the membrane potential can be recorded between an external electrode and an electrode located near an electrically isolated cut end of the fibre bathed with a solution producing no liquid junction potential with the cytoplasm. In these cases, the shunt resistance is sufficently greater than that of the membrane and has a negligible effect. In general, cells are too small to apply the above techniques, and the membrane potential is measured between an electrode in the extracellular solution and a thin microelectrode introduced into the cytoplasm through the plasma membrane. However, membrane potentials measured in this way may be disturbed by the low electrical resistance around the penetrating electrode. The membrane potential may also be measured electrically with the whole-cell or the perforated patch-clamp methods used in the zero current or the current clamp mode. In this case, the shunt resistance can be very much greater than with an impaling microelectrode. However, with very small cells or cells with membrane resistance in the order of GΩ, changes in the seal resistance (when changing from the cell-attached to the whole-cell or the perforated configuration) will alter the measured potential, which may also be disturbed by alterations of intracellular ion composition via the pipette
The Effect of Melatonin on Mitochondrial Function in Endotoxemia Induced by Lipopolysaccharide

This study examined the metabolism of free radicals in hepatic mitochondria of goats induced by lipopolysaccharide (LPS), and investigated the effects of melatonin (MT). Forty-eight healthy goats () were randomly selected and divided into four groups: saline control, LPS, MT+LPS and MT. The goats within each group were3 sacrificed either 3 or 6 h after treatment and the livers removed to isolate mitochondria. The respiration control ratio (RCR), the ADP:O ratio, the oxidative phosphorylation ratio (OPR), the concentration of and the activities of Complex I-IV were determined. The mitochondrial membrane potential () was analyzed by flow cytometry. The results showed that RCR, O/P and OPR of the LPS group decreased (p in Complex III increased (p. Interestingly, it is revealed that, in the MT+LPS group, the generation of increased firstly in 3 h, and then significantly (p were obviously improved compared to the control group. Conclusion: melatonin prevents damage caused by LPS on hepatic mitochondria of goats.
Stability Analysis of Filtered Mass-Spring Systems

Mass-spring systems simulations rely on the numerical integration method used for solving the resulting ordinary differential equations. Implicit schemes, which solve such equations, are unconditionally stable and are thus widely used. Part of this stability is due to force filtering which is inherent to the implicit formulation and is referred to artificial damping. We extract this artificial damping and we analyse frequencies. This analysis enables us to define a non arbitrary damping value and a stability criterion in accordance to filtering. This directly comes from a decrease of velocity vectors’ eigenvalues resulting in an increase of the time step in the same proportion. Moreover we applied a simple filtering model reproducing artificial damping to explicit schemes and results reveal an increase of the time step. Implementation of this method is straightforward for existing physically based simulators. Applications to cloth and fish animations are presented.
Hybrid Example-Based SMT: the Best of Both Worlds?

(Way and Gough, 2005) provide an in-depth comparison of their Example-Based Machine Translation (EBMT) system with a Statistical Machine Translation (SMT) system constructed from freely available tools. According to a wide variety of automatic evaluation metrics, they demonstrated that their EBMT system outperformed the SMT system by a factor of two to one. Nevertheless, they did not test their EBMT system against a phrase-based SMT system. Obtaining their training and test data for English--French, we carry out a number of experiments using the Pharaoh SMT Decoder. While better results are seen when Pharaoh is seeded with Giza++ word- and phrase-based data compared to EBMT sub-sentential alignments, in general better results are obtained when combinations of this 'hybrid' data is used to construct the translation and probability models. While for the most part the EBMT system of (Gough & Way, 2004b) outperforms any flavour of the phrase-based SMT systems constructed in our experiments, combining the data sets automatically induced by both Giza++ and their EBMT system leads to a hybrid system which improves on the EBMT system per se for French--English.
Eliciting comprehensive medication histories in the emergency department: the role of the pharmacist

The Australian Pharmaceutical Advisory Committee guidelines call for a detailed medication history to be taken at the first point of admission to hospital. Accurate medication histories are vital in optimising health outcomes and have been shown to reduce mortality rates. This study aimed to examine the accuracy of medication histories taken in the Emergency Department of the Royal Adelaide Hospital. Medication histories recorded by medical staff were compared to those elicited by a pharmacy researcher. The study, conducted over a six-week period, included 100 patients over the age of 70, who took five or more regular medications, had three or more clinical co-morbidities and/or had been discharged from hospital in three months prior to the study. Following patient interviews, the researcher contacted the patient’s pharmacist and GP for confirmation and completion of the medication history. Out of the 1152 medications recorded as being used by the 100 patients, discrepancies were found for 966 medications (83.9%). There were 563 (48.9%) complete omissions of medications. The most common discrepancies were incomplete or omitted dosage and frequency information. Discrepancies were mostly medications that treated dermatological and ear, nose and throat disorders but approximately 29% were used to treat cardiovascular disorders. This study provides support for the presence of an Emergency Department pharmacist who can compile a comprehensive and accurate medication history to enhance medication management along the continuum of care. It is recommended that the patient’s community pharmacy and GP be contacted for clarification and confirmation of the medication history.
Lifted coordinate descent for learning with trace-norm regularization

We consider the minimization of a smooth loss with trace-norm regularization, which is a natural objective in multi-class and multitask learning. Even though the problem is convex, existing approaches rely on optimizing a non-convex variational bound, which is not guaranteed to converge, or repeatedly perform singular-value decomposition, which prevents scaling beyond moderate matrix sizes. We lift the non-smooth convex problem into an infinitely dimensional smooth problem and apply coordinate descent to solve it. We prove that our approach converges to the optimum, and is competitive or outperforms state of the art.
Computing a centerpoint of a finite planar set of points in linear time

The notion of a centerpoint of a finite set of points in two and higher dimensions is a generalization of the concept of the median of a set of reals. In this paper we present a linear-time algorithm for computing a centerpoint of a set ofn points in the plane, which is optimal compared with theO(n log3n) complexity of the previously best-known algorithm. We use suitable modifications of the hamsandwich cut algorithm in [Me2] and the prune-and-search technique of Megiddo [Me1] to achieve this improvement.
LPVIOID- A LPV IDENTIFICATION TOOLBOX FOR MATLAB: RECENT AND NOVEL TECHNIQUES

In this paper a system identification toolbox for MATLAB is introduced, including a user friendly graphical user interface. The toolbox is appropriate for the identification of systems in discrete-time linear parameter varying (LPV) form. Using LPVIOID1 it is possible to identify input-output models in open-loop and closed-loop settings based on experimental data. It comprises several recent LPV identification techniques. Furthermore, a novel method for identifying unstable plants in closed-loop is proposed. The toolbox is equipped with several tools for model validation. Examples for illustration are included.
Dimensional Accuracy of Micro-Porous Metal Injection and Extrusion Molded Components Produced by Powder Space Holder Method

A production method for porous metal components has been developed by applying powder space holder (PSH) method to metal powder injection molding (MIM) process. The PSH-MIM method has an industrial advantage which is capable of net-shape manufacturing the micro-size porous metal products with complicated shapes and controlled porosity and pore size. In this study, a small impeller made of stainless steel 316L was manufactured by injection molding, and a plate specimen was produced by extrusion molding to evaluate the dimensional accuracy of the porous sintered parts produced by the PSH-MIM method. The effects of combinations of size and fraction of space holder particle on the dimensional deviation and its coefficient of variance were investigated. It was concluded that the PSH-MIM method could manufacture commercially micro-porous metal components with high dimensional accuracy.
Peculiarities of light scattering by nanoparticles and nanowires near plasmon resonance frequencies in weakly dissipating materials (invited)

Results related to the peculiarities of light scattering by nanoparticles and nanowires near plasmon resonance frequencies are reported. It is shown that the scattering problem for weakly dissipative media cannot be analyzed in the dipole approximation, in contrast to the classical Rayleigh scattering. A structure of the Poynting vector in the near field area is obtained. It is shown that small variations of the size parameter or/and the incident light frequency may lead to drastic transformations of the near field distribution.
Parallel Smoothed Aggregation Multigrid : Aggregation Strategies on Massively Parallel Machines

Algebraic multigrid methods offer the hope that multigrid convergence can be achieve (for at least some important applications) without a great deal of effort from engineers an scientists wishing to solve linear systems. In this paper we consider parallelization of the smoothe aggregation multigrid methods. Smoothed aggregation is one of the most promising algebraic multigrid methods. Therefore, eveloping parallel variants with both good convergence an efficiency properties is of great importance. However, parallelization is nontrivial due to the somewhat sequential aggregation (or grid coarsening) phase. In this paper, we discuss three different parallel aggregation algorithms an illustrate the advantages an disadvantages of each variant in terms of parallelism an convergence. Numerical results will be shown on the Intel Teraflop computer for some large problems coming from nontrivial codes: quasi-static electric potential simulation an a fluid flow calculation.
The Effects of Accelerated Heat and Light Aging on Textiles Marked with Fabric Marking Pens

Temporary fabric marking pens are popular products among quilters and home sewers. However, no published studies exist concerning long-term effects of temporary marking pens to help consumers make informed decisions. The purpose of this study was twofold: (1) to determine whether temporary marking pens in combination with ink removal treatments contribute to degradation or discoloration of fabrics over time, and (2) to determine whether marking pen ink that remains on fabric for 30 days can be successfully removed and thereby avoid discoloration of quilts or other home sewing projects. Specimens were marked with one of three brands of marking pen (Dritz, Clover and Crayola) and subjected to ink removal treatments (eraser pen, water, or no treatment), followed by heat or light aging. Changes in color and strength were measured. Results showed that the water immersion ink removal treatment was the most effective method for removing marking pen ink and was associated with much less discoloration than eraser pen ink removal treatments. Eraser pens caused statistically significant discoloration following both light and heat aging on both fabric types. They proved to be an undesirable ink removal treatment. Temporary marking pen inks, if rinsed out thoroughly using a water immersion treatment, do not result in discoloration or strength losses when exposed to heat and light aging. This suggests that consumers should use marking pens only if they launder their newly completed projects. Results also show that consumers may complete quilting and sewing projects over a period of several weeks without concern about ink removal because marked fabric specimens given a water immersion treatment within 30 days exhibited no more discoloration than the control specimens. Results of this study could influence the ink removal recommendations that manufacturers list on the packaging and the practices of quilters and home sewers who use the products.