Miracle-dz/UniFAR-FTUs huggingface dataset:
Extensive conformational searches of 13 representative dipeptides and an efficient method for dipeptide structure determinations based on amino acid conformers

Conformations of peptides are the basis for their property studies and the predictions of peptide structures are highly important in life science but very complex in practice. Here, thorough searches on the potential energy surfaces of 13 representative dipeptides by considering all possible combinations of the bond rotational degrees of freedom are performed using the density functional theory based methods. Careful analyses of the conformers of the 13 dipeptides and the corresponding amino acids reveal the connections between the structures of dipeptide and amino acids. A method for finding all important dipeptide conformers by optimizing a small number of trial structures generated by suitable superposition of the parent amino acid conformations is thus proposed. Applying the method to another eight dipeptides carefully examined by others shows that the new approach is both highly efficient and reliable by providing the most complete ensembles of dipeptide conformers and much improved agreements between the theoretical and experimental IR spectra. The method opens the door for the determination of the stable structures of all dipeptides with a manageable amount of effort. Preliminary result on the applicability of the method to the tripeptide structure determination is also presented. The results are the first step towards proving Anfinsen's hypothesis by revealing the relationships between the structures of the simplest peptide and its constituting amino acids. It implies that the structures of peptides are not only determined by their amino acid sequences, but also closely linked with the amino acid conformations. © 2009 Wiley Periodicals, Inc. J Comput Chem 2009
Translation elongation can control translation initiation on eukaryotic mRNAs

Synonymous codons encode the same amino acid, but differ in other biophysical properties. The evolutionary selection of codons whose properties are optimal for a cell generates the phenomenon of codon bias. Although recent studies have shown strong effects of codon usage changes on protein expression levels and cellular physiology, no translational control mechanism is known that links codon usage to protein expression levels. Here, we demonstrate a novel translational control mechanism that responds to the speed of ribosome movement immediately after the start codon. High initiation rates are only possible if start codons are liberated sufficiently fast, thus accounting for the observation that fast codons are overrepresented in highly expressed proteins. In contrast, slow codons lead to slow liberation of the start codon by initiating ribosomes, thereby interfering with efficient translation initiation. Codon usage thus evolved as a means to optimise translation on individual mRNAs, as well as global optimisation of ribosome availability.
The energy cost of fat and protein deposition in the rat

1. Measurements were made of energy balance by direct calorimetry, and of nitrogen balance in groups of lean and congenitally obese (‘fatty’) Zucker rats at body-weights of 200 and 350 g given a highly digestible semisynthetic diet at 14.0 or 18.4 g/rat per 24 h. 2. Losses of food energy and N in faeces were very small. The fatty rats lost much more N in urine than did lean rats. Despite this the proportion of gross energy that was metabolized was 0.92 for both fatty and lean rats. 3. In all trials, fatty rats lost a smaller proportion of metabolizable energy (ME) as heat and deposited less as protein than thin rats but deposited much more as fat. 4. The amounts of ME required to deposit 1 kJ of protein and 1 kJ of fat respectively were shown by regression analysis to be 2.25 (±0.16) and 1.36 (±0.06) kJ respectively. These values agree extremely closely with recent, more tentative, estimates based on assumptions as to maintenance requirement which the present experiments were able to circumvent. It may be concluded with confidence that the energy costs of depositing 1 g of protein or fat are almost identical at 53 kJ ME/g.
Prior streptozotocin treatment does not inhibit pancreas regeneration after 90% pancreatectomy in rats.

The effects of residual β-cell mass and glycemia on regeneration of endocrine pancreas after 90% pancreatectomy were investigated. Streptozotocin or buffer alone was injected into 4-wk-old male Lewis rats ( day 0). On day 7, varying numbers of syngeneic islets were transplanted under the kidney capsule to achieve varying degrees of glucose normalization. On day 14, a 90% pancreatectomy or sham pancreatectomy was performed. On day 19, rats were killed and the pancreas was fixed for quantitative morphometric determination of β-cell mass. Focal areas of regenerating pancreas were observed in all animals that underwent partial pancreatectomy. The percentage of remnant pancreas classified as foci was unaffected by streptozotocin treatment or by plasma glucose. Moderate to severe hyperglycemia did not promote regeneration of the pancreatic β-cell mass; rather the total endocrine cell mass was inversely related to the plasma glucose level ( r = -0.5, P < 0.01). These data suggest that the precursor population for both endocrine and exocrine tissue is not susceptible to damage by streptozotocin and that local effects of residual β-cell mass are not important to regeneration after a 90% pancreatectomy.
Estimation of Trustworthiness for P2P System in Collusive Attack

In the community of P2P, it is paid attention to try to control illegal behavior of the peer by managing the reputation of the peer. However, the implementation overhead was large, and the semantics of the trust model was indefinite in many of proposed methods. On the other hand, the trustworthiness estimation method by a simple, probabilistic technique, that is, by the maximum likelihood estimation is proposed. If this method is used, the problem concerning the semantics of the reliability model and the problem of the implementation overhead can be improved. However, the defense to a collusive attack is not proposed in this method. In this paper, it proposes the trust estimation method of the peer to give the defense to a collusive attack to the maximum likelihood estimation method. Moreover, peer's trustworthiness is correctly estimated though there is a collusive attack in this proposal method from the simulation result
Luminal acidification in K-replete OMCDi: inhibition of bicarbonate absorption by K removal and luminal Ba.

We have previously demonstrated that significant luminal acidification in the K-replete rabbit inner stripe of the outer medullary collecting duct (OMCDi) occurs via a renal H-K-adenosinetriphosphatase (H-K-ATPase) sensitive to several of the gastric H-K-ATPase inhibitors. To investigate further the mechanism of K-dependent luminal acidification in K-replete OMCDi, we examined the effects of luminal K removal, luminal addition of Ba in the presence and absence of luminal 5.0 nM bafilomycin A1 (BAF), and basolateral addition of Ba on net bicarbonate flux (JtCO2, pmol.mm-1.min-1) and transepithelial voltage (VT, mV). Removal of K from the perfusate inhibited JtCO2 by 74% (13.4 +/- 4.0 for control, 3.5 +/- 1.4 pmol.mm-1.min-1 for experimental, P < 0.05) and was statistically equivalent to the degree of inhibition previously observed under identical experimental conditions by either 10 microM Sch-28080 or 10 microM A-80915A. Approximately 50% inhibition of JtCO2 was observed following luminal application of 2.0 mM Ba2+, and the degree of inhibition was statistically equivalent regardless of whether BAF was present (12.2 +/- 2.7 for control, 6.0 +/- 1.4 pmol.mm-1.min-1 for 2.0 mM Ba2+, P < 0.05; 9.6 +/- 1.2 for control with 5 nM BAF, 5.7 +/- 1.3 pmol.mm-1.min-1 for 2.0 mM Ba2+ with 5 nM BAF, P < 0.05). Additionally, increasing the luminal concentration of Ba2+ from 2.0 to 4.0 mM resulted in no further inhibition of JtCO2 (8.5 +/- 1.7 for control, 3.9 +/- 1.3 pmol.mm-1.min-1 for 4.0 mM Ba2+, P = 0.05). (ABSTRACT TRUNCATED AT 250 WORDS)
An inertial motion capture framework for constructing body sensor networks

Motion capture is the process of measuring and subsequently reconstructing the movement of an animated object or being in virtual space. Virtual reconstructions of human motion play an important role in numerous application areas such as animation, medical science, ergonomics, etc. While optical motion capture systems are the industry standard, inertial body sensor networks are becoming viable alternatives due to portability, practicality and cost. This thesis presents an innovative inertial motion capture framework for constructing body sensor networks through software environments, smartphones and web technologies. The first component of the framework is a unique inertial motion capture software environment aimed at providing an improved experimentation environment, accompanied by programming scaffolding and a driver development kit, for users interested in studying or engineering body sensor networks. The software environment provides a bespoke 3D engine for kinematic motion visualisations and a set of tools for hardware integration. The software environment is used to develop the hardware behind a prototype motion capture suit focused on low-power consumption and hardware-centricity. Additional inertial measurement units, which are available commercially, are also integrated to demonstrate the functionality the software environment while providing the framework with additional sources for motion data. The smartphone is the most ubiquitous computing technology and its worldwide uptake has prompted many advances in wearable inertial sensing technologies. Smartphones contain gyroscopes, accelerometers and magnetometers, a combination of sensors that is commonly found in inertial measurement units. This thesis presents a mobile application that investigates whether the smartphone is capable of inertial motion capture by constructing a novel omnidirectional body sensor network. This thesis proposes a novel use for web technologies through the development of the Motion Cloud, a repository and gateway for inertial data. Web technologies have the potential to replace motion capture file formats with online repositories and to set a new standard for how motion data is stored. From a single inertial measurement unit to a more complex body sensor network, the proposed architecture is extendable and facilitates the integration of any inertial hardware configuration. The Motion Cloud’s data can be accessed through an application-programming interface or through a web portal that provides users with the functionality for visualising and exporting the motion data.
Markets with Simultaneous Signaling and Screening

We model markets with adverse selection as matching markets. In a given match the informed or the uniformed party is chosen to make a take-it-or-leave-it proposal. This allows to account for the simultaneous presence of signaling and screening. Moreover, the possibility to dissolve matches unsuccessfully allows to endogenize the distribution of types in the market. It will be shown that this approach overcomes the well-known trade-off between ensuring existence (in signaling games) and obtaining clear-cut results (in screening games).
Optimisation of friction-stir welding process using vibro-acoustic signal analysis

This paper presents a mathematical model to predict the tensile strength (TS) of friction-stir welded (FSW) AA1050 aluminium alloy joint. This model has been obtained from the optimisation of the parameters of models developed from vibro-acoustic signals produced during the process. The multiple response method was used to obtain the optimisation model. During experimental development, the process parameters selected to be assessed were rotation speed (RS), travel speed, and tool profile (TP). The TS of the welded joint and the root mean square (RMS) value of the vibro-acoustic signal in the frequency range of 3·2–6·4 kHz were analysed as response variables. In order to validate the model, the optimal values of the factors and responses are presented, showing their agreement with the experimental values obtained. This model can be used to develop and optimise the parameters of the automatic control of the FSW process, based on the vibro-acoustic signal generated.
The Reproductive Plan Language RPL2: Motivation, Architecture and Applications

The reproductive plan language RPL2 is a computer language designed to facilitate the writing, execution and modification of evolutionary algorithms. It provides a number of data parallel constructs appropriate to evol- utionary computing, facilitating the building of efficient parallel interpreters and compilers. This facility is exploited by the current interpreted implementa- tion. RPL2 supports all current structured population models and their hybrids at language level. Users can extend the system by linking against the supplied framework C-callable functions, which may then be invoked directly from an RPL2 program. There are no restrictions on the form of genomes, making the language particularly well suited to real-world optimisation problems and the production of hybrid algorithms. This paper describes the theoretical and prac- tical considerations that shaped the design of RPL2, the language, interpreter and run-time system built, and a suite of industrial applications that have used the system. 1 Motivation
The Structure and the Electrical Properties of Pb 0.95 La 0.05 [Zr x Ti (0.95–x) (Mo 1/3 ,In 2/3 ) 0.05 ] 0.9875 O 3 Ferroelectric Ceramics

The structural, the dielectric, and the piezoelectric properties of new ferroelectric Pb0.95La0.05[ZrxTi(0.95–x)(Mo1/3,In2/3)0.05]0.9875O3(0.46 ≤ x ≤ 0.55) ceramics have been investigated. All the samples were being sintered at a temperature ranging from 1000 to 1180℃ after being compacted in circular discs. The detailed structural and ferroelectric properties were carried out for sintered specimens. The results of X-ray diffraction showed that all the ceramics specimens have a perovskite phase. The phase structure of Pb0.95La0.05[ZrxTi(0.95–x)(Mo1/3,In2/3)0.05]0.9875O3 ceramics was transformed from the tetragonal to the rhombohedral, with an increase in the ratio of Zr/Ti in system. In the present system the MPB that coexists with the tetragonal and rhombohedral phases is a narrow composition region of x = 0.50 – 0.51. The scanning Electron Microscopy (SEM) showed an increase of the mean grain size when the sintering temperature was increased. The dielectric constant e and the coupling factor Kp reached the maximum values, while the mechanical quality factor Qm and the loss tangent reached the lowest values when x = 0.50. For the composition where x = 0.50, these properties include e = 5414 (at the Curie temperature), tangδ = 0.039, Kp = 0.67, Qm = 20 and a Curie temperature of 335℃.
An interval-censored model for predicting myopic regression after laser in situ keratomileusis.

PURPOSE A time-varying statistical model was proposed to predict the risk of regression toward myopia after laser in situ keratomileusis (LASIK) and to identify significant predictors within a time frame. METHODS A total of 615 eyes of 311 patients derived from a retrospective cohort who underwent LASIK in 2003 were analyzed. Refraction outcomes were recorded at 1 day, 1 week, and 1, 3, 6, 9, and 12 months or longer after LASIK. A cross-validated design was used, to split data into trained (n = 308) and validated (n = 307) data sets. These data sets were used in an interval-censored model to predict the probability of regression toward myopia and to assess the predictors including demographic features and preoperative and postoperative variables. RESULTS Myopia regression was observed in 164 (26.7%) of 615 eyes during the follow-up period of 12 months or longer after LASIK. Significant predictors for myopia regression after LASIK included preoperative manifest spherical equivalent (P = <0.0001), mean preoperative central corneal curvature (P = 0.001), size of optic zone (P = 0.0043), undercorrection (P = 0.04), and age (P = 0.0734). The risk of regression toward myopia after LASIK increased rapidly within 1 month, slowed down between 1 and 6 months, and became steady after 6 months, regardless of risk group. The risk of myopia regression up to 6 months after LASIK was 21% in average-risk eyes (based on all eyes). CONCLUSIONS The proposed interval-censored model was useful not only for predicting the probability of myopia regression after LASIK but also for identifying the evolution of patients within low, moderate, and high-risk groups.
Biometrics on visual preferences: A “pump and distill” regression approach

We present a statistical behavioural biometric approach for recognizing people by their aesthetic preferences, using colour images. In the enrollment phase, a model is learnt for each user, using a training set of preferred images. In the recognition/authentication phase, such model is tested with an unseen set of pictures preferred by a probe subject. The approach is dubbed “pump and distill”, since the training set of each user is pumped by bagging, producing a set of image ensembles. In the distill step, each ensemble is reduced into a set of surrogates, that is, aggregates of images sharing a similar visual content. Finally, LASSO regression is performed on these surrogates; the resulting regressor, employed as a classifier, takes test images belonging to a single user, predicting his identity. The approach improves the state-of-the-art on recognition and authentication tasks in average, on a dataset of 40000 Flickr images and 200 users. In practice, given a pool of 20 preferred images of a user, the approach recognizes his identity with an accuracy of 92%, and sets an authentication accuracy of 91% in terms of normalized Area Under the Curve of the CMC and ROC curve, respectively.
Safety and Efficacy of Rivaroxaban in Patients With Cardiac Implantable Electronic Devices: Observations From the ROCKET AF Trial

Background Although implantation of cardiac implantable electronic devices (CIEDs) in patients receiving warfarin is well studied, limited data are available on the use of oral factor Xa inhibitors in this setting. Methods and Results Using data from Rivaroxaban Once Daily Oral Direct Factor Xa Inhibition Compared with Vitamin K Antagonism for Prevention of Stroke and Embolism Trial in Atrial Fibrillation (ROCKET AF) (n=14 264), we compared baseline characteristics and clinical outcomes in patients with atrial fibrillation randomized to rivaroxaban versus warfarin who did and did not undergo CIED implantation or revision. In this post‐hoc, postrandomization, on‐treatment analysis, only the first intervention per patient was analyzed. During a median follow‐up of 2.2 years, 453 patients (242 rivaroxaban group; 211 warfarin group) underwent de novo CIED implantation (64.2%) or revision procedures (35.8%). Patients who received CIEDs were older, more likely to be male, and more likely to have past myocardial infarction, but had similar stroke risk compared to patients who did not receive CIEDs. Most patients who received a device had study drug interrupted for the procedure and did not receive bridging anticoagulation. During the 30‐day postprocedural period, 11 patients (4.55%) in the rivaroxaban group experienced bleeding complications compared with 15 (7.13%) in the warfarin group. Thromboembolic complications occurred in 3 patients (1.26%) in the rivaroxaban group and 1 (0.48%) in the warfarin group. Event rates were too low for formal hypothesis testing. Conclusions Bleeding and thromboembolic events were low in both rivaroxaban‐ and warfarin‐treated patients. Periprocedural use of oral factor Xa inhibitors in CIED implantation requires further study in prospective, randomized trials. Clinical Trial Registration URL: http://www.clinicaltrials. gov. Unique identifier: NCT00403767.
MODELLING PRIMARY RECRYSTALLIZATION IN fcc AND bcc METALS BY ORIENTED NUCLEATION AND GROWTH WITH THE STATISTICAL COMPROMISE MODEL

Statistical models of primary recrystallization are described. Particularly the superposition model and the compromise model must be distinguished. Both models are able to consider oriented nucleation, orientation dependence of driving force, and misorientation dependence of boundary mobility. The superposition model requires abundant nucleation, whereas the compromise model corresponds to sparse nucleation. In order to model the two-step recrystallization observed in low carbon steel the compromise model was generalized for the case of inhomogeneous (two-step) recrystallization. The compromise model was applied to the recrystallization textures of fcc-copper type and brass-type metals as well as to bcc-metals, i.e. low carbon steel. All these textures are well represented by the model on the basis of experimentally established input parameters, i.e. the growth laws 40°〈111〉, 27°
Systematic security evaluation method against C safe-error attacks

This paper proposes a systematic security evaluation of cryptographic hardware against C safe-error attacks. Using the graph representation of a design, we provide a simple and efficient method to detect possible C safe-errors. Exposing possible vulnerabilities at an early stage of a design process, this method avoids costly design re-spins and reduces time-to-market. As a proof of concept, we apply the method to two well-known exponentiation algorithms: square-and-multiply-always and the Montgomery ladder.
Exploring the role of visualization and engagement in computer science education

Visualization technology can be used to graphically illustrate various concepts in computer science. We argue that such technology, no matter how well it is designed, is of little educational value unless it engages learners in an active learning activity. Drawing on a review of experimental studies of visualization effectiveness, we motivate this position against the backdrop of current attitudes and best practices with respect to visualization use. We suggest a new taxonomy of learner engagement with visualization technology. Grounded in Bloom's well-recognized taxonomy of understanding, we suggest metrics for assessing the learning outcomes to which such engagement may lead. Based on these taxonomies of engagement and effectiveness metrics, we present a framework for experimental studies of visualization effectiveness. Interested computer science educators are invited to collaborate with us by carrying out studies within this framework.