Miracle-dz/UniFAR-FTUs huggingface dataset:
Origin and Diversification of TRIM Ubiquitin Ligases

Most proteins of the TRIM family (also known as RBCC family) are ubiquitin ligases that share a peculiar protein structure, characterized by including an N-terminal RING finger domain closely followed by one or two B-boxes. Additional protein domains found at their C termini have been used to classify TRIM proteins into classes. TRIMs are involved in multiple cellular processes and many of them are essential components of the innate immunity system of animal species. In humans, it has been shown that mutations in several TRIM-encoding genes lead to diverse genetic diseases and contribute to several types of cancer. They had been hitherto detected only in animals. In this work, by comprehensively analyzing the available diversity of TRIM and TRIM-like protein sequences and evaluating their evolutionary patterns, an improved classification of the TRIM family is obtained. Members of one of the TRIM subfamilies defined, called Subfamily A, turn to be present not only in animals, but also in many other eukaryotes, such as fungi, apusozoans, alveolates, excavates and plants. The rest of subfamilies are animal-specific and several of them originated only recently. Subfamily A proteins are characterized by containing a MATH domain, suggesting a potential evolutionary connection between TRIM proteins and a different type of ubiquitin ligases, known as TRAFs, which contain quite similar MATH domains. These results indicate that the TRIM family emerged much earlier than so far thought and contribute to our understanding of its origin and diversification. The structural and evolutionary links with the TRAF family of ubiquitin ligases can be experimentally explored to determine whether functional connections also exist.
Delay distribution dependent stability criteria for discrete-time systems with interval time-varying delay

This paper studies the stability problem for discrete-time systems with interval time-varying delay. By dividing delay interval into two subintervals, a delay-dependent exponential stability criterion is obtained based on Lyapunov stability theory and reciprocally convex lemma. Furthermore, by assuming that the distribution of time-varying delay is known, the difference of Lyapunov functional is allowed to have positive upper bound for the value of time-varying delay in one subinterval, and a new delay distribution dependent stability criterion is obtained. The obtained result is also extended to cope with the robust delay distribution dependent stability problem for uncertain time-varying delay systems. All the obtained criteria are presented in terms of Linear Matrix Inequalities (LMIs). Finally one numerical example is given to show the effectiveness of the proposed method.
A robust RAM-THP architecture for downlink multiuser MISO transmission with user scheduling

A robust RAM-THP architecture for Zero-Forcing Tomlinson-Harashima Precoding (ZF-THP) for multi-user transmission in a multiple-input-single-output (MU-MISO) system is proposed with user scheduling and Convolutional Turbo Coding (CTC). The proposed architecture is developed to improve the rate of the system. A semi-optimal user-selection scheme is considered to make the aggregate channel matrix used by ZF-THP full rank and increase the robustness of THP under channel estimation error. The impact of the imperfect channel state information (CSI) due to block transmission is also considered. Simulation results reveal that the proposed scheduling procedure significantly improves the BER performance of the system especially in high SNR regime.
Successful Pregnancies after the Treatment of a Thymic Carcinoid

The present report describes the case of a woman diagnosed with an adrenocorticotropic hormone- (ACTH-) secreting thymic carcinoid associated with Cushing's syndrome. Treatment consisted of tumour resection and 131-I-meta-iodobenzylguanidine (MIBG) therapy. In spite of her iatrogenic menopausal state she twice became pregnant and delivered two healthy babies but developed recurrences during both pregnancies. The last recurrence presented as a primary breast cancer. Despite poor prognosis our patient survived for eleven years. To our knowledge this is the first report of successful pregnancy and delivery in a patient with a thymic carcinoid.
Changing time: Possible effects on peak electricity generation

This article considers the possible effects on electricity costs of implementing The Brighter Evenings Bill, 2012, which would move Ireland to Central European Time (CET). The results suggest that such a change would produce very limited savings in peak demand for electricity and possibly some increase in off peak electricity costs. Moving time zone in the other direction would result in some limited savings on both counts. The effects of changing time zone on the cost of electricity would be likely to be small so that other considerations are likely to be more important in any such decision. Corresponding Author: john.fitzgerald@esri.ie 1 This material is based upon works supported by the Science Foundation Ireland under Grant No. 09/SRC/E1780. Support was also provided by the ESRI Energy Policy Research Centre. ESRI working papers represent un-refereed work-in-progress by researchers who are solely responsible for the content and any views expressed therein. Any comments on these papers will be welcome and should be sent to the author(s) by email. Papers may be downloaded for personal use only. Working Paper No. 486 July 2014
Synchronization and Storage Models for Multimedia Objects

A technique is presented for the formal specification and modeling of multimedia composition with respect to intermedia timing. The proposed model is based on the logic of temporal intervals and timed Petri nets. A strategy is evinced for constructing a database schema to facilitate data storage and retrieval of media elements based on the temporal relationship established by the proposed modeling tool. An algorithm which allows the retrieval of media elements from the constructed database in a manner which preserves the temporal requirements of the initial specification is presented. Using the proposed model, the synchronization requirements of complex structures of temporally related objects can be easily specified. >
A Design and Implementation of Information Service Architecture for Resource-Constraint Devices in Internet of Things

Billions of smart devices will be connected to the Internet to form the Internet of Things. The core value of IoT (Internet of Things) is to supply information services through the huge amounts of devices. Most of sensors, actors and terminal equipment such as mobile phones are resource-constrained in battery, bandwidth, storage and computation ability. Accordingly, we propose an information service architecture for IoT, which is a four-layer design including perception layer, network layer, service layer and process layer. We compare the data transmission methods in a resource-constrained condition and find that REST (Representational State Transfer) technology is more suitable. We analyze the device discovery process, and we implement the information service of image searching and video sharing based on the proposed architecture by using Restful technology.
Inflation Expectations and Learning about Monetary Policy

Divers indicateurs donnent a penser que les attentes d'inflation evoluent plus lentement que l'inflation observee. En outre, dans bien des cas, ils se revelent entaches de biais lorsqu'on les soumet aux tests usuels d'absence de biais. Le rejet de ces tests est parfois interprete comme une refutation de l'hypothese de rationalite des attentes. Les auteurs […]
A variational calculus framework for motion planning

We argue that it is advantageous to formulate motion planning as a variational problem. In this way, a unified framework for addressing redundancy, constraints, and optimality is obtained. An efficient numerical method is proposed for solving the motion planning problem in the variational form. The approach is illustrated on the problem of motion planning for systems that change dynamic equations at discrete time instants as they move. A technique is described for computing a motion plan when the sequence of dynamic equations describing the motion is known. Finally, a motion plan for a simple grasping task, a typical representative of this class of systems, is computed.
A Methodology and Tool for Concurrent Fault Injection

As the speed of microprocessors tails off, utilizing multiple processing cores per chip is becoming a common way for developers to achieve higher performance. However , writing concurrent programs can be a big challenge because of common concur-rency faults. Because concurrency faults are hard to detect and reproduce, traditional testing techniques are not suitable. New techniques are needed, and these must be assessed. A typical method for assessing testing techniques is to embed faults in programs using mutation tools, and assess the ability of techniques to detect these. Although mutation testing techniques can be used to represent common faults, approaches for representing concurrency faults have not been created. In this paper, we introduce a methodology for injecting mutations related to concurrency faults, focus-ing on four common concurrency fault patterns as mutant operators. We implement the approach in the Eclipse IDE. We empirically study our approach's effectiveness by using it to seed various types of concurrency faults based on the four fault patterns in a set of programs. This approach generates many times more mutants than can be seeded by hand. We then execute the original programs and these mutants. We characterize the mutants in terms of detectability as part of our study. The results show that using the proposed tool, concurrent fault injection tool (CFIT) is feasible and efficient. iii ACKNOWLEDGMENTS I would like to thank my two advisors. Dr. Gregg Rothermel and Dr.Witty Srisa-an for their invaluable guidance, support and encouragement over the past few years. Dr. Gregg Rothermel led me into a wonderful research area and taught me how to do rigorous research. As a good mentor, he provided me with valuable advice all the time and gave me advice and support when I ran into trouble in my life. I would like to thank him for everything he did for me. Dr. Witty Srisa-an has also had a great influence on me. He led me into the gorgeous system's area and taught me how to be a good programmer. I would like to thank him for his infinite encouragement and patience. Without him, I can not imagine how I could achieve the goal that I previously thought was not possible. All his advising and mentoring are valuable to me and I will remember it now and forever. I do not know how I can possibly thank him enough. I hope I can repay him by making him …
Assessing recording delays in general practice records to inform near real‐time vaccine safety surveillance using the Clinical Practice Research Datalink (CPRD)

Near real‐time vaccine safety surveillance (NRTVSS) is an option for post‐licensure vaccine safety assessment. NRTVSS requires timely recording of outcomes in the database used. Our main objective was to examine recording delays in the Clinical Practice Research Datalink (CPRD) for outcomes of interest for vaccine safety to inform the feasibility of NRTVSS using these data. We also evaluated completeness of recording and further assessed reporting delays for hospitalized events in CPRD.
Leaky Wave Antenna Realization by Composite Right/Left-Handed Transmission Line

This paper presents a realization of composite right/left handed transmission lines using coupled microstrip lines. This structure exploits the advantages of the microstrip lines, while increases the coupling by a ∞oating conductor at the ground plane. The performance of this composite right/left-handed line is demonstrated by both simulated and measured results, and they show good agreement. The designed line has broad bandwidth with low losses and small size. A novel dominant mode leaky wave antenna design, using the previous structure, is presented with backward to forward scanning capability.
Quality Preferences by using H . 2 . 4 . k Spatial Databases

A spatial preference query ranks objects based on the qualities of features in their spatial neighborhood. For example, using a real estate agency database of flats for lease, a customer may want to rank the flats with respect to the appropriateness of their location, defined after aggregating the qualities of other features (e.g., rest aurants, cafes, hospital, market, etc.) within their spatial neighborhood. Such a neighborhood concept can be specified by the user via different functions. It can be an explicit circular region within a given distance from the flat. Another intuitive definition is to assign higher weights to the features based on their proximity to the flat. In this paper, we formally define spatial preference queries and propose appropriate indexing techniques and search algorithms for them. Extensive evaluation of our methods on both real and synthetic data reveals that an optimized branch-and-bound solution is efficient and robust with respect to different parameters. I. Introduction There is a growing interest in spatial data mining in many different areas such as transportation, ecology, epidemiology, etc. Many algorithms to extract knowledge from such data have been proposed in the literature. One of the main problems is that only a few of these algorithms are implemented in toolkits which support the whole discovery process. In spatial/geographic databases data are stored in different relations (e.g. cities, rivers, roads), which need to be spatially joined in order to find novel and useful patterns in data mining. This step is normally performed in data preprocessing, and basically manually, since there is no available free and open source toolkit which automates this step. The result is that effort and time is required from the data mining user, which is usually neither an expert in geographic databases nor in data mining. It is stated that between 60 and 80 percent of the time and effort in the whole discovery process is required for data preparation [Addrians and Zantinge 1996]. Another problem is that data mining algorithms produce large amounts of outputs, mainly the association rule mining technique. In spatial data mining this problem increases significantly. Besides the large number of patterns, many are well known a priori, because of the natural geographic dependences intrinsic to geographic data [Bogorny et al 2006a, 2006b]. Many solutions for spatial data mining have been proposed in the literature, but only a few consider data preparation aspects. Most approaches extend query languages with …
Multiple Pairwise Sequences Alignments with Needleman-Wunsch Algorithm on GPU

Pairwise sequence alignment is the method to find the best matching piece for two sequences. It can be either local which return the most similar subsequence or global which return the alignment of whole sequence. Nowadays, the number of genetic sequences increases exponentially so that it becomes a challenge to analyze and understand those data. The cutting-edge parallel architectures provide lots of opportunities to ace the problem. The Graphical Processing Unit (GPU) is becoming an appealing choice for accelerating these processes. In this paper, we will explore multiple pairwise sequence alignment with Needleman-Wunsch algorithm, which is the fundamental method for global alignment. Our proposed method levers the parallelism between different pairs and void the unnecessary data copy to achieve 2X speedup for data transfer and 2.9X acceleration ratio for kernel execution.
Hybrid Personalized Recommended Model Based on Genetic Algorithm

Amount of customer and product is huge and variant. It usually decreases the accuracy of personalized recommender system. To solve this problem, a hybrid model is proposed to integrate outputs produced by every recommender at the basis of genetic algorithm. According to features of recommend task, weight vectors are constructed to represent different forecasting performances of each recommender. Then, the hybrid problem is translated into optimizing problem about weight vectors. Fitness function is designed based on forecasting accuracy, and a selecting strategy is constructed to avoid pre-mature of GA. Experiments express the proposed model has higher capability than traditional method.
Anonymization of Set-Valued Data via Top-Down, Local Generalization

Set-valued data, in which a set of values are associated with an individual, is common in databases ranging from market basket data, to medical databases of patients' symptoms and behaviors, to query engine search logs. Anonymizing this data is important if we are to reconcile the conflicting demands arising from the desire to release the data for study and the desire to protect the privacy of individuals represented in the data. Unfortunately, the bulk of existing anonymization techniques, which were developed for scenarios in which each individual is associated with only one sensitive value, are not well-suited for set-valued data. In this paper we propose a top-down, partition-based approach to anonymizing set-valued data that scales linearly with the input size and scores well on an information-loss data quality metric. We further note that our technique can be applied to anonymize the infamous AOL query logs, and discuss the merits and challenges in anonymizing query logs using our approach.
Differential Sensitivity of Letters, Numbers, and Symbols to Character Transpositions

This study was designed to explore whether the human visual system has different degrees of tolerance to character position changes for letter strings, digit strings, and symbol strings. An explicit perceptual matching task was used (same–different judgment), and participants' electrophysiological activity was recorded. Materials included trials in which the referent stimulus and the target stimulus were identical or differed either by two character replacements or by transposing two characters. Behavioral results showed clear differences in the magnitude of the transposed-character effect for letters as compared with digit and symbol strings. Electrophysiological data confirmed this observation, showing an N2 character transposition effect that was only present for letter strings. An earlier N1 transposition effect was also found for letters but was absent for symbols and digits, whereas a later P3 effect was found for all types of string. These results provide evidence for a position coding mechanism that is specific to letter strings, that was most prominent in an epoch between 200 and 325 msec, and that operates in addition to more general-purpose position coding mechanisms.
Carotenoids from Foods of Plant, Animal and Marine Origin: An Efficient HPLC-DAD Separation Method

Carotenoids are important antioxidant compounds, present in many foods of plant, animal and marine origin. The aim of the present study was to describe the carotenoid composition of tomato waste, prawn muscle and cephalothorax and avian (duck and goose) egg yolks through the use of a modified gradient elution HPLC method with a C30 reversed-phase column for the efficient separation and analysis of carotenoids and their cis-isomers. Elution time was reduced from 60 to 45 min without affecting the separation efficiency. All-trans lycopene predominated in tomato waste, followed by all-trans-β-carotene, 13-cis-lutein and all-trans lutein, while minor amounts of 9-cis-lutein, 13-cis-β-carotene and 9-cis-β-carotene were also detected. Considering the above findings, tomato waste is confirmed to be an excellent source of recovering carotenoids, especially all-trans lycopene, for commercial use. Xanthophylls were the major carotenoids of avian egg yolks, all-trans lutein and all-trans zeaxanthin in duck and goose egg yolk, respectively. In the Penaeus kerathurus prawn, several carotenoids (zeaxanthin, all-trans-lutein, canthaxanthin, cryptoxanthin, optical and geometrical astaxanthin isomers) were identified in considerable amounts by the same method. A major advantage of this HPLC method was the efficient separation of carotenoids and their cis-isomers, originating from a wide range of matrices.
Community-Acquired Pneumonia Due to Pandemic A(H1N1)2009 Influenzavirus and Methicillin Resistant Staphylococcus aureus Co-Infection

Background Bacterial pneumonia is a well described complication of influenza. In recent years, community-onset methicillin-resistant Staphylococcus aureus (cMRSA) infection has emerged as a contributor to morbidity and mortality in patients with influenza. Since the emergence and rapid dissemination of pandemic A(H1N1)2009 influenzavirus in April 2009, initial descriptions of the clinical features of patients hospitalized with pneumonia have contained few details of patients with bacterial co-infection. Methodology/Principal Findings Patients with community–acquired pneumonia (CAP) caused by co-infection with pandemic A(H1N1)2009 influenzavirus and cMRSA were prospectively identified at two tertiary hospitals in one Australian city during July to September 2009, the period of intense influenza activity in our region. Detailed characterization of the cMRSA isolates was performed. 252 patients with pandemic A(H1N1)2009 influenzavirus infection were admitted at the two sites during the period of study. Three cases of CAP due to pandemic A(H1N1)2009/cMRSA co-infection were identified. The clinical features of these patients were typical of those with S. aureus co-infection or sequential infection following influenza. The 3 patients received appropriate empiric therapy for influenza, but inappropriate empiric therapy for cMRSA infection; all 3 survived. In addition, 2 fatal cases of CAP caused by pandemic A(H1N1)2009/cMRSA co-infection were identified on post–mortem examination. The cMRSA infections were caused by three different cMRSA clones, only one of which contained genes for Panton-Valentine Leukocidin (PVL). Conclusions/Significance Clinicians managing patients with pandemic A(H1N1)2009 influenzavirus infection should be alert to the possibility of co-infection or sequential infection with virulent, antimicrobial-resistant bacterial pathogens such as cMRSA. PVL toxin is not necessary for the development of cMRSA pneumonia in the setting of pandemic A( H1N1) 2009 influenzavirus co-infection.
Imaging neuron-glia interactions in the enteric nervous system

The enteric nervous system (ENS) is a network of neurons and glia within the wall of the gastrointestinal tract that is able to control many aspects of digestive function independently from the central nervous system. Enteric glial cells share several features with astrocytes and are closely associated with enteric neurons and their processes both within enteric ganglia, and along interconnecting fiber bundles. Similar to other parts of the nervous system, there is communication between enteric neurons and glia; enteric glial cells can detect neuronal activity and have the machinery to intermediate neurotransmission. However, due to the close contact between these two cell types and the particular characteristics of the gut wall, the recording of enteric glial cell activity in live imaging experiments, especially in the context of their interaction with neurons, is not straightforward. Most studies have used calcium imaging approaches to examine enteric glial cell activity but in many cases, it is difficult to distinguish whether observed transients arise from glial cells, or neuronal processes or varicosities in their vicinity. In this technical report, we describe a number of approaches to unravel the complex neuron-glia crosstalk in the ENS, focusing on the challenges and possibilities of live microscopic imaging in both animal models and human tissue samples.