Miracle-dz/UniFAR-FTUs huggingface dataset:
Structural Basis of the Induced-Fit Mechanism of 1,4-Dihydroxy-2-Naphthoyl Coenzyme A Synthase from the Crotonase Fold Superfamily

1, 4-Dihydroxy-2-naphthoyl coenzyme A (DHNA-CoA) synthase is a typical crotonase fold enzyme with an implicated role of conformational changes in catalysis. We have identified these conformational changes by determining the structures of its Escherichia coli and Synechocystis sp. PCC6803 orthologues in complex with a product analog. The structural changes include the folding of an active-site loop into a β-hairpin and significant reorientation of a helix at the carboxy terminus. Interestingly, a new interface is formed between the ordered loop and the reoriented helix, both of which also form additional interactions with the coenzyme A moiety of the ligand. Site-directed mutation of the amino acid residues involved in these ligand-induced interactions significantly diminishes the enzyme activity. These results suggest a catalytically essential induced-fit that is likely initiated by the enzyme-ligand interactions at the active site.
Contextual information access with Augmented Reality

We have developed a prototype platform for contextual information access in mobile settings. Objects, people, and the environment are considered as contextual channels or cues to more information. The system infers, based on gaze, speech and other implicit feedback signals, which of the contextual cues are relevant, retrieves more information relevant to the cues, and presents the information with Augmented Reality (AR) techniques on a handheld or head-mounted display. The augmented information becomes potential contextual cues as well, and its relevance is assessed to provide more information. In essence, the platform turns the real world into an information browser which focuses proactively on the information inferred to be the most relevant for the user. We present the first pilot application, a Virtual Laboratory Guide, and its early evaluation results.
Litmus tests for comparing memory consistency models: How long do they need to be?

Memory consistency litmus tests are small parallel programs that are designed to illustrate subtle differences between memory consistency models by exhibiting different outcomes for different models. In this paper, we show that for a class of memory models that is restricted yet expressive enough to include all store-atomic hardware memory models, litmus tests of a bounded size are sufficient for illustrating differences between memory consistency models in this class. We establish a bound of two threads and no more than six memory access instructions for differentiating litmus tests in this class of models. Thus, we can prove equivalence of two specification of memory consistency models in this class by exploring a bounded number of litmus tests. We build a tool for comparing memory models based on this result, and we use the tool to explore and map the space of this class of models.
Post-Elastic Behavior of Soil Profiles Under Earthquake Excitations

In order to take into account the non linear behaviour of soils in an earthquake response analysis, a visco-elasto-plastic model is used. The present study consists, firstly, in a rheological modelling of the soil material, assuming a completely undrained condition. Then, a space representation is done by using linear one-dimensional finite elements with two nodes. Damping is taken into account by the Rayleigh’s damping matrix. The seismic response is obtained in terms of accelerations at the free surface of each soil profile of the two studied sites: Garner Valley site (USA) and Dar El Beida site (Algeria), to base rock excitations. The soil profile behavior is influenced by the damping matrix model and the vibration level.
Collaborative Foraging Using a new Pheromone and Behavioral Model

we consider the problem of foraging with multiple agents, in which agents must collect disseminate resources in an unknown and complex environment. An efficient foraging should benefit from the presence of multiple agents, where cooperation between agents is a key issue for improvements. To do so, we propose a new distributed foraging mechanism. The aim is to adopt a new behavioral model regarding sources' affluence and pheromone's management. Simulations are done by considering agents as autonomous robots with goods transportation capacity, up to swarms that consist of 160 robots. Results demonstrate that the proposed model gives better results than c-marking agent model. Keywords—Collaborative foraging;reactive agents;digital pheromone;behavioral model.
Process Integration in Semantic Enterprise Application Integration: A Systematic Mapping

Enterprise Application Integration (EAI) plays an important role by linking heterogeneous applications to support business processes within and across organizations. Semantic conflicts often arise in this context and have to be addressed to a successful interoperation. Besides, to properly support business processes, integration should deal with processes integration and cover the process layer. In this paper, we present a systematic mapping that investigated aspects related to EAI, particularly, the use of ontologies to address semantics in integration at process layer. The results provide a panorama of the research in this area.
Incremental growth of deciduous tooth enamel

Deciduous tooth formation begins before birth and ends after birth. This makes it more difficult to construct a continuous developmental chronology for deciduous teeth than for permanent teeth. The discovery of the neonatal line in enamel and confirmation that it marks birth, allowed the expansion of deciduous dental chronologies, which until this time had been largely based on qualitative descriptions. The aim of this study was to use the daily incremental record in deciduous enamel to document rates of enamel formation and to use these data to produce regression equations that describe the average rates of deciduous enamel formation for each tooth type. These formulae can then be applied to all deciduous teeth even when daily increments are not visible, in order to estimate crown formation times and other events during crown development, as well as to determine the age at death where enamel formation has ceased prior to completion. In permanent teeth, rates of enamel formation vary between 2. 5μm per day at the EDJ to 6. 5μm per day at the enamel surface. Seventy deciduous ground sections were examined and it was established that the daily rates in deciduous enamel varied less, with regional weighted means for all tooth types ranging from 2. 85μm per day at the EDJ to 3. 40μm per day at the enamel surface with extreme outliers of 2.07 to 4. 97μm per day. The average daily incremental growth rate of enamel in deciduous teeth was calculated for each tooth type, the weighted mean of the apposition rate over both aspects (labial/buccal and lingual) and over all three regions (cervical, lateral and occlusal) for all tooth types was 3. 23μm per day. A key finding of this study was that there is a marked reduction in the enamel formation rate in the zone immediately following the neonatal line or following other accentuated striae assumed to be associated with stressful events. A catch-up phase usually followed these events, during which the previous rates recovered. These data provide clear evidence of enamel hypoplasia associated with both the birth process and other events that cause stress in perinatal life.
Runtime Security Verification for Itinerary-Driven Mobile Agents

We present a new approach to ensure the secure execution of itinerary-driven mobile agents, in which the specification of the navigational behavior of an agent is separated from the specification of its computational behavior. We empower each host with an access control policy so that the host will deny the access from an agent whose itinerary does not conform to the host's access control policy. A host uses model checking algorithms to check if the itinerary of the agent conforms to its access control policy written in mu-calculus, and if so, grant access permission. In order to address the state explosion problem for model checking itineraries, we propose an approach called model generation code. In this approach, instead of verifying the itinerary itself, a host actually checks the conservative models of a mobile agent. If a conservative model does not satisfy the host's access control policy, the mobile agent will provide refined models for further verification. Our preliminary results show that this is a practical and promising approach to ensure the secure execution of mobile agents
Does Financial Regulation Matter? Market Volatility and the US 1933/34 Acts 1

The impact of the US 1933/34 Acts, the …rst national …nancial regulation acts in the world, on …nancial markets have been under debates since Stigler (1964). Major …ndings in the literature is that …nancial regulation enacted by these laws is at best being ineective to improve …nancial markets until some recent studies imply indirectly that they could be eective. By studying daily returns of NYSE data from 1890 to 1970, this paper provides systematic evidence that the 1933/34 Acts have substantially reduced market volatilities after controlling for Great Depression eect and macroeco- nomic variables. Moreover, we show that even when we treat the existence and the date of the volatility changes as unknown, statistically identi…ed structural changes are fully consistent with the above results that the volatility reduction time coincide with the enacting of the Acts.
Bmc Musculoskeletal Disorders Elevated Levels of Β-catenin and Fibronectin in Three-dimensional Collagen Cultures of Dupuytren's Disease Cells Are Regulated by Tension in Vitro

Background: Dupuytren's contracture or disease (DD) is a fibro-proliferative disease of the hand that results in the development of scar-like, collagen-rich disease cords within specific palmar fascia bands. Although the molecular pathology of DD is unknown, recent evidence suggests that β-catenin may play a role. In this study, collagen matrix cultures of primary disease fibroblasts show enhanced contraction and isometric tension-dependent changes in β-catenin and fibronectin levels.
Chondrocyte Rather Than Osteoblast Conversion of Vascular Cells Underlies Medial Calcification in Uremic Rats

Objective—To investigate cell biological changes in calcified aortas of rats that experienced chronic renal failure. Methods and Results—Vascular smooth muscle cells have the potential to transdifferentiate to either chondrocytes or osteoblasts, depending on the molecular pathways that are stimulated. Uremia-related medial calcification was induced by feeding rats an adenine low-protein diet for 4 weeks. Aortic calcification was evaluated biochemically and histochemically and with in vivo micro–computed tomographic scanning. Immunohistochemistry and RT-PCR were applied to analyze the time-dependent aortic expression of molecules involved in the segregation between the chondrocyte versus osteoblast differentiation pathway. After 4 weeks, 85% of the uremic rats had developed distinct aortic medial calcification, which increased to severely calcified lesions during further follow-up. The calcification process was accompanied by a significant time-dependent increase in the expression of the chondrocyte-specific markers sex determining region Y-box 9 (sox9), collagen II, and aggrecan and a nonsignificant trend toward enhanced core binding factor alpha 1 (cbfa1), and collagen I. The expression of the osteoblast marker osterix and both lipoprotein receptor–related protein 6 and &bgr;-catenin, molecules of the wingless-type MMTV integration site family member (Wnt)/&bgr;-catenin pathway induced during osteoblast differentiation, was suppressed. Conclusion—In the aorta of uremic rats, medial smooth muscle cells acquire a chondrocyte rather than osteoblast phenotype during the calcification process.
Reading Digital Video Clocks

This paper presents an algorithm for reading digital video clocks reliably and quickly. Reading digital clocks from videos is difficult due to the challenges such as color variety, font diversity, noise, and low resolution. The proposed algorithm overcomes these challenges by using the novel methods derived from the domain knowledge. This algorithm first localizes the digits of a digital video clock and then recognizes the digits representing the time of digital video clock. It is a robust three-step algorithm. The first step is an efficient procedure that directly identifies the region of the second digit at a very low computational cost, which replaces the traditional tedious image processing procedure of identifying the second digit region. The success of the first step mainly leverages on the novel second-pixel periodicity method. Using the acquired second digit region as input, the second step is a clock digit localization procedure. It first acquires the colors of the digits of the digital video clock and performs the color conversion. Then it localizes the remaining clock digits. Finally, the last step is a clock digit recognition procedure. It first employs an enhanced digit-sequence recognition method to robustly recognize the digits on the second; it then adopts a deep learning procedure to recognize the remaining digits. The proposed algorithm is tested on a prepared benchmark of 1000 videos that is publicly available and the experimental results show that it can read digital video clocks with a 100% accuracy at a low computational cost.
Clean Answers over Dirty Databases: A Probabilistic Approach

The detection of duplicate tuples, corresponding to the same real-world entity, is an important task in data integration and cleaning. While many techniques exist to identify such tuples, the merging or elimination of duplicates can be a difficult task that relies on ad-hoc and often manual solutions. We propose a complementary approach that permits declarative query answering over duplicated data, where each duplicate is associated with a probability of being in the clean database. We rewrite queries over a database containing duplicates to return each answer with the probability that the answer is in the clean database. Our rewritten queries are sensitive to the semantics of duplication and help a user understand which query answers are most likely to be present in the clean database. The semantics that we adopt is independent of the way the probabilities are produced, but is able to effectively exploit them during query answering. In the absence of external knowledge that associates each database tuple with a probability, we offer a technique, based on tuple summaries, that automates this task. We experimentally study the performance of our rewritten queries. Our studies show that the rewriting does not introduce a significant overhead in query execution time. This work is done in the context of the ConQuer project at the University of Toronto, which focuses on the efficient management of inconsistent and dirty databases.
Significance of anchor speaker segments for constructing extractive audio summaries of broadcast news

Analysis of human reference summaries of broadcast news showed that humans give preference to anchor speaker segments while constructing a summary. Therefore, we exploit the role of anchor speaker in a news show by tracking his/her speech to construct indicative/informative extractive audio summaries. Speaker tracking is done by Bayesian information criterion (BIC) technique. The proposed technique does not require Automatic Speech Recognition (ASR) transcripts or human reference summaries for training. The objective evaluation by ROUGE showed that summaries generated by the proposed technique are as good as summaries generated by a baseline text summarization system taking manual transcripts as input and summaries generated by a supervised speech summarization system trained using human summaries. The subjective evaluation of audio summaries by humans showed that they prefer summaries generated by proposed technique to summaries generated by supervised speech summarization system.
Asymptomatic Norovirus Infection in Mexican Children

ABSTRACT Sixty-three children in periurban Mexico City were examined for the occurrence of asymptomatic norovirus (NoV) infection from June to August 1998. NoV was detected in 48 of 161 stool specimens (29.8%), with 31 children (49.2%) having at least one positive stool. Asymptomatic NoV infection occurred commonly during summertime in a Mexican pediatric population.
Origin-Bound Certificates: A Fresh Approach to Strong Client Authentication for the Web

Client authentication on the web has remained in the internet-equivalent of the stone ages for the last two decades. Instead of adopting modern public-key-based authentication mechanisms, we seem to be stuck with passwords and cookies. In this paper, we propose to break this stalemate by presenting a fresh approach to public-key-based client authentication on the web. We describe a simple TLS extension that allows clients to establish strong authenticated channels with servers and to bind existing authentication tokens like HTTP cookies to such channels. This allows much of the existing infrastructure of the web to remain unchanged, while at the same time strengthening client authentication considerably against a wide range of attacks. We implemented our system in Google Chrome and Google's web serving infrastructure, and provide a performance evaluation of this implementation.
Approaches Toward Combining Positron Emission Tomography with Magnetic Resonance Imaging

ii Co-Authorship Statement . iv Dedication . vi Table of Contents . vii List of Tables . xii List of Figures . xiii List of Appendices . xxv Preface . xxvi 1 Combining PET with MRI: An Introduction . 1 1.1 Why PET-MRI? 1 1.1.1 Principles of PET . 2 1.1.2 Principles of MRI . 5 1.1.3 The Complementary Roles of PET and MRI . 6 1.2 Technical Challenges for Combining PET with MRI . 6 1.2. 1 Sensitivity of PET Detectors to the MRI Environment . 7 1.2. 2 Attenuation Correction of PET Data . 8 1.2. 3 Design Considerations for MR Hardware . 10 1.3 Monte Carlo PET Simulation . 11 1.4 PET Detectors . 13 1.5 Developments in Combined PET-MRI . 16 1.6 Thesis Overview . 17 1.7 References . 23 2 Magnetic field exposure tests on a Siemens Inveon small animal PET system . 31
Future-based Static Analysis of Message Passing Programs

Message passing is widely used in industry to develop programs consisting of several distributed communicating components. Developing functionally correct message passing software is very challenging due to the concurrent nature of message exchanges. Nonetheless, many safety-critical applications rely on the message passing paradigm, including air traffic control systems and emergency services, which makes proving their correctness crucial. We focus on the modular verification of MPI programs by statically verifying concrete Java code. We use separation logic to reason about local correctness and define abstractions of the communication protocol in the process algebra used by mCRL2. We call these abstractions futures as they predict how components will interact during program execution. We establish a provable link between futures and program code and analyse the abstract futures via model checking to prove global correctness. Finally, we verify a leader election protocol to demonstrate our approach.
Analysis of a kinematic model for ion transport in rf plasma sheaths.

An idealized model for ion transport across an oscillating plasma sheath is analyzed to obtain insight into qualitative features of the ion energy distributions observed in low-pressure rf discharges. The sheath is characterized by a constant electric field over an extent that varies sinusoidally with time, and ions incident on it correspond to a monoenergetic flux independent of phase \ensuremath{\varphi} in the rf cycle. The dimensionless parameters \ensuremath{\alpha}=${\mathit{qV}}_{\mathit{s}}$/m${\mathrm{\ensuremath{\omega}}}^{2}$${\mathit{d}}^{2}$ and \ensuremath{\beta}=${\mathit{v}}_{0}$/\ensuremath{\omega}d (where d and ${\mathit{V}}_{\mathit{s}}$ are the mean sheath thickness and potential drop, \ensuremath{\omega} is the excitation frequency, and ${\mathit{v}}_{0}$ and q/m are the incoming ion speed and charge-to-mass ratio) govern the ion trajectories, which are found to divide into groups, delimited by two ``critical'' values of \ensuremath{\varphi}, that undergo N and N+1 encounters with the field. The first critical phase depends only weakly on \ensuremath{\beta}, whereas the second is sensitive to both \ensuremath{\alpha} and \ensuremath{\beta} and cycles continuously as these parameters diminish. Correspondingly, within the ``transition regime'' where \ensuremath{\alpha} and \ensuremath{\beta} are neither very small nor greater than (or comparable to) unity, the precise form of the incident-ion energy spectrum exhibits rapid variations, superposed on a systematic narrowing, as the frequency \ensuremath{\omega} is increased.
Simulation of a conductive shield plate for the focalization of transcranial magnetic stimulation in the rat

Transcranial Magnetic Stimulation (TMS) in the rat is a powerful tool for investigating brain function. However, the state-of-the-art experiments are considerably limited because the stimulation usually affects undesired anatomical structures. A simulation of a conductive shield plate placed between the coil stimulator and the rat brain during TMS is presented. The Finite Element (FE) method is used to obtain the 3D electric field distribution on a four-layer rat head model. The simulations show that the shield plate with a circular window can improve the focalization of stimulation, as quantitatively seen by computing the three-dimensional half power region (HPR). Focalization with the shield plate showed a clear compromise with the attenuation of the induced field. The results suggest that the shield plate can work as a helpful tool for conducting TMS rat experiments on specific targets.
Study of Electrical and Magnetic Properties of Praseodymium Samarium Doped Novel Magnesium Ferrite

The Praseodymium, Samarium doped novel Magnesium ferrite (Mg Prx Smy Fe2-x-y O4) was prepared by sol gel route and sintered in a microwave furnace. The nano size, structure and composition of Pr and Sm doped Magnesium ferrite ceramics was analyzed by X-ray diffraction and confirmed by SEM monographs. The elemental conformation was done by EDAX. The hysteresis property of this material was conformed through its hysteresis curves. The permeability of this material was calculated by using the magnetic saturation obtained from the hysteresis curves.The electrical measurements have been performed to determine the dielectric constant (r), dielectric loss (r) and loss tangent in the frequency range of 20KHz 20MHz. It is also found that the permittivity of these nano materials is being reduced with the increase in frequency.
BCI-FES training system design and implementation for rehabilitation of stroke patients

A BCI-FES training platform has been designed for rehabilitation on chronic stroke patients to train their upper limb motor functions. The conventional functional electrical stimulation (FES) was driven by userspsila intention through EEG signals to move their wrist and hand. Such active participation was expected to be important for motor rehabilitation according to motor relearning theory. The common spatial pattern (CSP) algorithm was applied as one pre-processing step in brain-computer interface (BCI) module to search for the optimal spatial projection direction after brain reorganization. The pre- and post- clinical assessment was conducted to identify the possible functional improvement after the training. Two chronic stroke subjects attended this pilot study and the error rate of the BCI control was less than 20% after training of 10 sessions. This implementation showed the feasibility for stroke patients to accomplish the BCI triggered FES rehabilitation training.