Miracle-dz/UniFAR-FTUs huggingface dataset:
Advanced optical simulation of scintillation detectors in GATE V8.0: first implementation of a reflectance model based on measured data

Typical PET detectors are composed of a scintillator coupled to a photodetector that detects scintillation photons produced when high energy gamma photons interact with the crystal. A critical performance factor is the collection efficiency of these scintillation photons, which can be optimized through simulation. Accurate modelling of photon interactions with crystal surfaces is essential in optical simulations, but the existing UNIFIED model in GATE is often inaccurate, especially for rough surfaces. Previously a new approach for modelling surface reflections based on measured surfaces was validated using custom Monte Carlo code. In this work, the LUT Davis model is implemented and validated in GATE and GEANT4, and is made accessible for all users in the nuclear imaging research community. Look-up-tables (LUTs) from various crystal surfaces are calculated based on measured surfaces obtained by atomic force microscopy. The LUTs include photon reflection probabilities and directions depending on incidence angle. We provide LUTs for rough and polished surfaces with different reflectors and coupling media. Validation parameters include light output measured at different depths of interaction in the crystal and photon track lengths, as both parameters are strongly dependent on reflector characteristics and distinguish between models. Results from the GATE/GEANT4 beta version are compared to those from our custom code and experimental data, as well as the UNIFIED model. GATE simulations with the LUT Davis model show average variations in light output of <2% from the custom code and excellent agreement for track lengths with R2 > 0.99. Experimental data agree within 9% for relative light output. The new model also simplifies surface definition, as no complex input parameters are needed. The LUT Davis model makes optical simulations for nuclear imaging detectors much more precise, especially for studies with rough crystal surfaces. It will be available in GATE V8.0.
Partially Dynamic Algorithms for Distributed Shortest Paths and their Experimental Evaluation

In this paper, we study the dynamic version of the distributed all-pairs shortest paths problem. Most of the solutions given in the literature for this problem, either (i) work under the assumption that before dealing with an edge operation, the algorithm for the previous operation has to be terminated, that is, they are not able to update shortest paths concurrently, or (ii) concurrently update shortest paths, but their convergence can be very slow (possibly infinite). In this paper we propose a partially dynamic algorithm that overcomes most of these limitations. In particular, it is able to concurrently update shortest paths and in many cases its convergence is quite fast. These properties are highlighted by an experimental study whose aim is to show the effectiveness of the proposed algorithms also in the practical case.
An empirical framework for comparing effectiveness of testing and property-based formal analysis

Today, many formal analysis tools are not only used to provide certainty but are also used to debug software systems - a role that has traditional been reserved for testing tools. We are interested in exploring the complementary relationship as well as tradeoffs between testing and formal analysis with respect to debugging and more specifically bug detection. In this paper we present an approach to the assessment of testing and formal analysis tools using metrics to measure the quantity and efficiency of each technique at finding bugs. We also present an assessment framework that has been constructed to allow for symmetrical comparison and evaluation of tests versus properties. We are currently beginning to conduct experiments and this paper presents a discussion of possible outcomes of our proposed empirical study.
Pharmacokinetic and pharmacodynamic evaluation of donepezil for the treatment of Alzheimer's disease

Introduction: Donepezil is a highly selective acetylcholinesterase inhibitor and one of the only four drugs currently approved for treatment of Alzheimer's dementia. Providing high bioavailability and a very long half-time, donepezil is regarded as effective and well tolerable in Alzheimer's disease patients, even in difficult clinical conditions such as hepatic or renal impairment. It moderately improves cognitive and global functioning scores in patients with mild to moderate Alzheimer's disease over the course of 6 – 12 months, with open-label extension studies suggesting effects of even longer duration. Areas covered: We summarized relevant pharmacokinetic, pharmacodynamic, clinical trial and neuroimaging data of donepezil. A literature search was performed in the PubMed database; articles published until October 2013 have been considered for this review. Moreover, references from original work and reviews have been searched for further relevant literature. Expert opinion: Donepezil is one of the most frequently prescribed anti-dementia drugs. The recent additional approval of the 23 mg formulation will expand its use in patients with moderate to severe Alzheimer's disease. After numerous Phase III study failures of novel disease-modifying drugs for Alzheimer's disease, donepezil is likely going to stay a first-line therapeutic option in Alzheimer's disease in the upcoming years.
The Arabidopsis BAP1 and BAP2 Genes Are General Inhibitors of Programmed Cell Death1[OA]

Here we identify the BAP1 and BAP2 genes of Arabidopsis (Arabidopsis thaliana) as general inhibitors of programmed cell death (PCD) across the kingdoms. These two homologous genes encode small proteins containing a calcium-dependent phospholipid-binding C2 domain. BAP1 and its functional partner BON1 have been shown to negatively regulate defense responses and a disease resistance gene SNC1. Genetic studies here reveal an overlapping function of the BAP1 and BAP2 genes in cell death control. The loss of BAP2 function induces accelerated hypersensitive responses but does not compromise plant growth or confer enhanced resistance to virulent bacterial or oomycete pathogens. The loss of both BAP1 and BAP2 confers seedling lethality mediated by PAD4 and EDS1, two regulators of cell death and defense responses. Overexpression of BAP1 or BAP2 with their partner BON1 inhibits PCD induced by pathogens, the proapototic gene BAX, and superoxide-generating paraquat in Arabidopsis or Nicotiana benthamiana. Moreover, expressing BAP1 or BAP2 in yeast (Saccharomyces cerevisiae) alleviates cell death induced by hydrogen peroxide. Thus, the BAP genes function as general negative regulators of PCD induced by biotic and abiotic stimuli including reactive oxygen species. The dual roles of BAP and BON genes in repressing defense responses mediated by disease resistance genes and in inhibiting general PCD has implications in understanding the evolution of plant innate immunity.
HCRL at NTCIR-11 MedNLP-2 Task

year's MedNLP-2 (1) has two tasks: Extraction task (Task 1) and Normalization task (Task 2). We tested both machine learning based methods and an ad-hoc rule-based method for the two tasks. For the Extraction Task, a two-stage approach (first, the machine learning based method is applied to identify c tags, and second, the rule-based method is applied to modality features) obtained higher results. For the Normalization Task, the machine learning based method obtained higher results for training data, but the simple pattern-matching method obtained higher results for test data.
Determination of the in vivo prebiotic potential of a maize-based whole grain breakfast cereal: a human feeding study.

Epidemiological studies have shown an inverse relationship between risk of CVD and intake of whole grain (WG)-rich food. Regular consumption of breakfast cereals can provide not only an increase in dietary WG but also improvements to cardiovascular health. Various mechanisms have been proposed, including prebiotic modulation of the colonic microbiota. In the present study, the prebiotic activity of a maize-derived WG cereal (WGM) was evaluated in a double-blind, placebo-controlled human feeding study (n 32). For a period of 21 d, healthy men and women, mean age 32 (sd 8) years and BMI 23·3 (sd 0·58) kg/m2, consumed either 48 g/d WG cereal (WGM) or 48 g placebo cereal (non-whole grain (NWG)) in a crossover fashion. Faecal samples were collected at five points during the study on days 0, 21, 42, 63 and 84 (representing at baseline, after both treatments and both wash-out periods). Faecal bacteriology was assessed using fluorescence in situ hybridisation with 16S rRNA oligonucleotide probes specific for Bacteroides spp. , Bifidobacterium spp. , Clostridium histolyticum/perfringens subgroup, Lactobacillus-Enterococcus subgroup and total bacteria. After 21 d consumption of WGM, mean group levels of faecal bifidobacteria increased significantly compared with the control cereal (P = 0·001). After a 3-week wash-out period, bifidobacterial levels returned to pre-intervention levels. No statistically significant changes were observed in serum lipids, glucose or measures of faecal output. In conclusion, this WG maize-enriched breakfast cereal mediated a bifidogenic modulation of the gut microbiota, indicating a possible prebiotic mode of action.
Noncoding RNAs of the Mammalian Testis

Abstract: In eukaryotic cells, the vast majority of transcribed sequences are extragenic with no known functions. Translin is a DNA/RNA‐binding protein involved in mRNA transport and translation in postmeiotic male germ cells. In an effort to identify meiotic target RNAs of Translin, reversible RNA protein cross‐linking and immunoprecipitations with an affinity purified antibody to Translin were performed. Four new meiotically expressed mRNAs and one noncoding RNA with Translin binding sites were identified. Following sequencing, the noncoding RNA, Nct1, was 100% identical to a site on mouse chromosome 2. A second partially homologous sequence, Nct2, was detected nearby. Nct 1 and 2 contained sequences identical to piRNAs. Nct1 and 2 appear to be male germ cell‐specific transcripts and are predominantly detected in pachytene spermatocytes. Focusing on the abundant single‐copy PIWI‐interacting RNA (piRNA), germline small RNA (gsRNA10) (the gsRNA10 sequence is identical to 29 nt in Nct1), we find that gsRNA10 increases greatly as spermatogenesis proceeds with concomitant decreases in Nct1 and 2. The piRNA gsRNA10 binds to the germ cell‐specific Y‐box protein, MSY2, but not to Translin. Although the size of the primary transcript(s) encoding the piRNAs in the locus on chromosome 2 is not known, we propose that Nct1 and 2 are part of a piRNA precursor.
Performance Evaluation of Algorithms for Newspaper Article Identification

A typical modern newspaper recognition system operates in distinct phases: i) page segmentation (also called page decomposition or zoning), that is the process of decomposing a page into its structural and logical units (called regions or zones), ii) region (or zone) labeling, where the previously identified units are labeled according to their types (title, text, images, and lines), iii) article identification (or tracking or clustering), in which all the units that belong to a single article are clustered together, and iv) read order identification, in which each item in an article is assigned its reading order inside the article. So far, in the literature, several works appeared describing algorithms and metrics for the first two phases, i.e. page segmentation and region labeling, that indeed play a crucial role in the whole process, however, few results focused on article identification, that is a difficult task mainly due to the rich and complex variety of newspapers layouts. In this paper we propose a methodology to evaluate news-papers article identification algorithms, our approach is based on well-established tools from graph theory: in particular, we reduce the newspaper article clustering problem to a specific graph clustering problem, that is therefore evaluated using the appropriate coverage and performance measures. The advantages of our approach are twofold: on one side, the proposed measures correctly detects that not all the errors are equals, i.e. some errors are worse than others, and the scores are assigned properly. On the other side, we show how to reverse the reduction, in order to exploit the large number of graph clustering algorithm available: indeed, given a graph clustering algorithm, to obtain a full working newspaper article identification algorithm we only need to define a similarity measure between units in the article. We provide some examples, using a specifically designed dataset. Finally, we would like to point out that both our dataset, together with its ground-truth base, and the software tool, that implements the proposed approach, are freely available.
Contactin Associates with Na+ Channels and Increases Their Functional Expression

Contactin (also known as F3, F11) is a surface glycoprotein that has significant homology with the β2 subunit of voltage-gated Na+ channels. Contactin and Na+channels can be reciprocally coimmunoprecipitated from brain homogenates, indicating association within a complex. Cells cotransfected with Na+ channel Nav1.2α and β1 subunits and contactin have threefold to fourfold higher peak Na+ currents than cells with Nav1.2α alone, Nav1.2/β1, Nav1.2/contactin, or Nav1.2/β1/β2. These cells also have a correspondingly higher saxitoxin binding, suggesting an increased Na+ channel surface membrane density. Coimmunoprecipitation of different subunits from cell lines shows that contactin interacts specifically with the β1 subunit. In the PNS, immunocytochemical studies show a transient colocalization of contactin and Na+ channels at new nodes of Ranvier forming during remyelination. In the CNS, there is a particularly high level of colocalization of Na+ channels and contactin at nodes both during development and in the adult. Contactin may thus significantly influence the functional expression and distribution of Na+ channels in neurons.
View-Driven Deduplication with Active Learning

Visual analytics systems such as Tableau are increasingly popular for interactive data exploration. These tools, however, do not currently assist users with detecting or resolving potential data quality problems including the well-known deduplication problem. Recent approaches for deduplication focus on cleaning entire datasets and commonly require hundreds to thousands of user labels. In this paper, we address the problem of deduplication in the context of visual data analytics. We present a new approach for record deduplication that strives to produce the cleanest view possible with a limited budget for data labeling. The key idea behind our approach is to consider the impact that individual tuples have on a visualization and to monitor how the view changes during cleaning. With experiments on nine different visualizations for two real-world datasets, we show that our approach produces significantly cleaner views for small labeling budgets than state-of-the-art alternatives and that it also stops the cleaning process after requesting fewer labels.
Metabolic Drug-Drug Interaction Potential of Macrolactin A and 7-O-Succinyl Macrolactin A Assessed by Evaluating Cytochrome P450 Inhibition and Induction and UDP-Glucuronosyltransferase Inhibition In Vitro

ABSTRACT Macrolactin A (MA) and 7-O-succinyl macrolactin A (SMA), polyene macrolides containing a 24-membered lactone ring, show antibiotic effects superior to those of teicoplanin against vancomycin-resistant enterococci and methicillin-resistant Staphylococcus aureus. MA and SMA are currently being evaluated as antitumor agents in preclinical studies in Korea. We evaluated the potential of MA and SMA for the inhibition or induction of human liver cytochrome P450 (CYP) enzymes and UDP-glucuronosyltransferases (UGTs) in vitro to assess their safety as new molecular entities. We demonstrated that MA and SMA are potent competitive inhibitors of CYP2C9, with Ki values of 4.06 μM and 10.6 μM, respectively. MA and SMA also weakly inhibited UGT1A1 activity, with Ki values of 40.1 μM and 65.3 μM, respectively. However, these macrolactins showed no time-dependent inactivation of the nine CYPs studied. In addition, MA and SMA did not induce CYP1A2, CYP2B6, or CYP3A4/5. On the basis of an in vitro-in vivo extrapolation, our data strongly suggested that MA and SMA are unlikely to cause clinically significant drug-drug interactions mediated via inhibition or induction of most of the CYPs involved in drug metabolism in vivo, except for the inhibition of CYP2C9 by MA. Similarly, MA and SMA are unlikely to inhibit the activity of UGT1A1, UGT1A4, UGT1A6, UGT1A9, and UGT2B7 enzymes in vivo. Although further investigations will be required to clarify the in vivo interactions of MA with CYP2C9-targeted drugs, our findings offer a clearer understanding and prediction of drug-drug interactions for the safe use of MA and SMA in clinical practice.
Closing the gap between ASIC and custom: an ASIC perspective

We investigate the differences in speed between application-specific integrated circuits and custom integrated circuits when each are implemented in the same process technology, with some examples in 0.25 micron CMOS. We first attempt to account for the elements that make the performance different and then examine ways in which tools and methodologies may close the performance gap between application-specific integrated circuits and custom circuits.
Application of Digital Imaging Technique in Electrical Charge Tomography System for Image Reconstruction Validation

Image reconstruction in electrical charge tomography is vital and has not been widely studied. There are three methods introduced before namely linear back projection, filter back projection and least square methods. These normally face with ill-posed problem and its solution is unstable and inaccuracy. In this paper, the new image reconstruction method has been introduced to reconstruct the image cross-section of material in gravity mode conveyor pipeline. Numerical analysis result indicated that this algorithm is efficient to overcome the numerical instability. Instead of image reconstruction process, validation the accuracy of the image is very important. It would be parts of verify process to the new image reconstruction method. In this system, digital imaging technique is used to interrogate the flow in pipeline around sensing area using CCD camera. The result between image reconstruction by new method and image captured by CCD camera will be compared.
Learning to satisfy

This paper investigates a class of learning problems called learning satisfiability (LSAT) problems, where the goal is to learn a set in the input (feature) space that satisfies a number of desired output (label/response) constraints. LSAT problems naturally arise in many applications in which one is interested in the class of inputs that produce desirable outputs, rather than simply a single optimum. A distinctive aspect of LSAT problems is that the output behavior is assessed only on the solution set, whereas in most statistical learning problems output behavior is evaluated over the entire input space. We present a novel support vector machine (SVM) algorithm for solving LSAT problems and apply it to a synthetic data set to illustrate the impact of the LSAT formulation.
A Reliable and Power Efficient Beacon Structure for Cognitive Radio Systems

In this paper, an energy efficient structure for beacon signal transmission is proposed for incumbent wireless microphone protection in a cognitive radio system. The proposed structure consists of two consecutive parts: synchronization with index and synchronization with payload, transmitted as in-phase and quadrature components respectively. As opposed to the current beacon design, it can achieve more reliable and balanced error protection for the beacon components, while keeping the system complexity low.
SOFT CLUSTERING BASED EXPOSITION TO MULTIPLE DICTIONARY BAG OF WORDS

Object classification is a highly important area of computer vision and has many applications including robotics, searching images, face recognition, aiding visually impaired people, censoring images and many more. A new common method of classification that uses features is the Bag of Words approach. In this method a codebook of visual words is created using various clustering methods. For increasing the performance Multiple Dictionaries BoW (MDBoW) method that uses more visual words from different independent dictionaries instead of adding more words to the same dictionary was implemented using hard clustering method. Nearest-neighbor assignments are used in hard clustering of features. A given feature may be nearly the same distance from two cluster centers. For a typical hard clustering method, only the slightly nearer neighbor is selected to represent that feature. Thus, the ambiguous features are not well-represented by the visual vocabulary. To address this problem, soft clustering model based Multiple Dictionary Bag of Visual words for image classification is implemented with dictionary generated using modified Fuzzy C-means algorithm using R1 norm. A performance evaluation on images has been done by varying the dictionary size. The proposed method works better when the number of topics and the number of images per topics are more. The results obtained indicate that multiple dictionary bag of words model using fuzzy clustering increases the recognition performance than the baseline method.
Towards a suite of software configuration management metrics

Software Configuration Management (SCM) is an important support activity in software development. However, its transparent nature as a service that makes life easier for others and as an insurance against disasters, often makes it difficult to justify investments in tools and processes that apparently do not have any direct return. We have made a first step towards establishing a model for showing the return on investment in SCM, making the costs and benefits explicit. In this paper, we also sketch how we plan to take the next important step and establish a set of metrics that can be used to manage and tune the SCM processes and tools.
Index of Dirac operators and classification of topological insulators

Real and complex Clifford bundles and Dirac operators defined on them are considered. By using the index theorems of Dirac operators, table of topological invariants is constructed from the Clifford chessboard. Through the relations between K-theory groups, Grothendieck groups and symmetric spaces, the periodic table of topological insulators and superconductors is obtained. This gives the result that the periodic table of real and complex topological phases is originated from the Clifford chessboard and index theorems.
Development and Supervision during Practicum Placement: A Comparative Study.

Abstract The authors conducted a comparative study of the supervision of student teachers and student counselors and their development. The authors were interested in whether student practicum progress and practicum supervisory strategies are consistent with a developmental model. Findings for the progress of student counselors were consistent with a developmental model; those for student teachers were not. Supervision strategies for the supervision of both student counselors and student teachers were consistent with a developmental model. The authors suggest inservice training in supervision for cooperating teachers and additional research to validate inservice training strategies.