Miracle-dz/UniFAR-FTUs huggingface dataset:
Replay detection in broadcasting sports video

An effective replay detection method for broadcasting sports videos is proposed in this paper. The algorithm is composed of logos detection and replay recognition. Firstly, a logo-template is automatically extracted from logo-transition at the beginning of a video. It is further used to detect the other logos in the same video. Then, with taking logos as boundaries, the video can be divided into replay and non-replay segments. To identify replay segments, an SVM classifier with mid-level features is utilized. Experiments demonstrate the effectiveness of this method.
More BLAST for the buck.

Time and money—they are the essential, yet most often, the limiting factors in people’s lives. Sequence comparisons via computer searches are certainly no different. For the sequence similarity search, time is determined by how long it takes to compare your sequence of interest to the burgeoning sequence information available, whereas matches found are the currency. Of course, not just any sequence match is worthwhile—only matches that are likely to have biological significance; your money should be worth something. To obtain such matches requires a program that is both sensitive (able to pick up relevant matches of weak similarity) and selective (provide a list of matches that are all biologically relevant). The balance between these two can greatly increase the time it takes to run a program—too high a sensitivity and it will take too much time and produce too many nonbiologically relevant sequences; too low a sensitivity and the program will run much faster, but meaningful matches may be lost. The BLAST program has been the primary method for doing database searches to detect related sequences for the purpose of classifying proteins into functional families and identifying unknown functional units. Now, a paper by Altschul et al. (1997) provides modifications to the current algorithms in the BLAST program that save the user time and provide far greater return on the investment.
Genome Sequences of Listeria monocytogenes Strains Responsible for Cheese- and Cooked Ham Product-Associated Swiss Listeriosis Outbreaks in 2005 and 2011

ABSTRACT The complete genome sequences of three Listeria monocytogenes serotype 1/2a strains, Lm 3136, Lm 3163, and Lm N1546, which were responsible for listeriosis outbreaks in 2005 and 2011 in Switzerland, are presented here.
Incidental maxillary sinus findings in orthodontic patients: a radiographic analysis using cone-beam computed tomography (CBCT).

UNLABELLED To determine the frequency of incidental maxillary sinus findings using cone-beam computed tomography (CBCT) images made for orthodontic purposes. SETTING AND SAMPLE POPULATION One hundred thirty-nine consecutive CBCTs from 134 patients treated at the Department of Orthodontics and Dentofacial Orthopedics, University of Bern, Bern, Switzerland. Indications for CBCT imaging included the localization of impacted teeth and root resorption related to impacted teeth. MATERIAL AND METHODS POPULATION: Two experienced observers reviewed the CBCT scans (fields of view: 4 × 4/6 × 6/8 × 8 cm) and recorded all incidental maxillary sinus findings according to standardized categories. The patient's age and gender, the size of the field of view, the season of CBCT image taking, and the thickness of the Schneiderian membrane were evaluated to identify potential influencing factors. RESULTS In 65 CBCTs (46.8%), incidental maxillary sinus findings were found (interrater classification agreement of 95.7%/95% CI: 90.9-97.9%). Three types of incidental findings were diagnosed: flat mucosal thickening (23.7%), polypoid mucosal thickening (19.4%), and signs of acute sinusitis (3.6%). There was no correlation between the field of view of the CBCT and the number of incidental findings inside the field. There was no correlation between the season during which the CBCT was made and the number of incidental findings. The mean thickness of the mucosal lining in the maxillary sinus was 1.58 mm (95% CI: 1.17-1.98 mm). CONCLUSIONS A high percentage of the CBCTs made for orthodontic diagnostic purposes exhibit incidental maxillary sinus findings not associated with the primary indication.
Bioluminescence imaging allows measuring CD8 T cell function in the liver

In vivo evaluation of CD8 T cell effector (cytotoxic T lymphocyte [CTL]) function in peripheral organs such as the liver is currently not possible but would greatly improve our understanding of local immune regulation, because simple determination of antigen‐specific CTL numbers does not predict the outcome of immune responses. In particular, measurement of alanine aminotransferase serum levels is not sensitive enough to detect T cell immunity against low numbers of target hepatocytes. We developed a procedure that detects virus‐specific effector function of CTLs in the liver after simultaneous adenoviral transfer of reporter and immune target genes into hepatocytes, followed by bioluminescence imaging of reporter genes. Bioluminescence imaging enabled detection of as few as 10,000 infected hepatocytes in vivo, and even more importantly, quantification of antiviral effector function of as few as 50,000 CTLs. Conclusion: Our results provide evidence that low numbers of antigen‐specific CTLs are sufficient to control viral gene expression and eliminate viral infection from hepatocytes. The experimental system established here is a highly sensitive method to simultaneously detect viral infection of hepatocytes and to quantify antiviral CTL function in the liver in vivo and will help in characterizing principles of hepatic immune regulation. (HEPATOLOGY 2010;51:1430–1437)
Extraction of protein interaction information from unstructured text using a context-free grammar

MOTIVATION As research into disease pathology and cellular function continues to generate vast amounts of data pertaining to protein, gene and small molecule (PGSM) interactions, there exists a critical need to capture these results in structured formats allowing for computational analysis. Although many efforts have been made to create databases that store this information in computer readable form, populating these sources largely requires a manual process of interpreting and extracting interaction relationships from the biological research literature. Being able to efficiently and accurately automate the extraction of interactions from unstructured text, would greatly improve the content of these databases and provide a method for managing the continued growth of new literature being published. RESULTS In this paper, we describe a system for extracting PGSM interactions from unstructured text. By utilizing a lexical analyzer and context free grammar (CFG), we demonstrate that efficient parsers can be constructed for extracting these relationships from natural language with high rates of recall and precision. Our results show that this technique achieved a recall rate of 83.5% and a precision rate of 93.1% for recognizing PGSM names and a recall rate of 63.9% and a precision rate of 70.2% for extracting interactions between these entities. In contrast to other published techniques, the use of a CFG significantly reduces the complexities of natural language processing by focusing on domain specific structure as opposed to analyzing the semantics of a given language. Additionally, our approach provides a level of abstraction for adding new rules for extracting other types of biological relationships beyond PGSM relationships. AVAILABILITY The program and corpus are available by request from the authors.
PER1 rs3027172 Genotype Interacts with Early Life Stress to Predict Problematic Alcohol Use, but Not Reward-Related Ventral Striatum Activity

Increasing evidence suggests that the circadian and stress regulatory systems contribute to alcohol use disorder (AUD) risk, which may partially arise through effects on reward-related neural function. The C allele of the PER1 rs3027172 single nucleotide polymorphism (SNP) reduces PER1 expression in cells incubated with cortisol and has been associated with increased risk for adult AUD and problematic drinking among adolescents exposed to high levels of familial psychosocial adversity. Using data from undergraduate students who completed the ongoing Duke Neurogenetics Study (DNS) (n = 665), we tested whether exposure to early life stress (ELS; Childhood Trauma Questionnaire) moderates the association between rs3027172 genotype and later problematic alcohol use (Alcohol Use Disorders Identification Test) as well as ventral striatum (VS) reactivity to reward (card-guessing task while functional magnetic resonance imaging data were acquired). Initial analyses found that PER1 rs3027172 genotype interacted with ELS to predict both problematic drinking and VS reactivity; minor C allele carriers, who were also exposed to elevated ELS reported greater problematic drinking and exhibited greater ventral striatum reactivity to reward-related stimuli. When gene × covariate and environment × covariate interactions were controlled for, the interaction predicting problematic alcohol use remained significant (p < 0.05, corrected) while the interaction predicting VS reactivity was no longer significant. These results extend our understanding of relationships between PER1 genotype, ELS, and problematic alcohol use, and serve as a cautionary tale on the importance of controlling for potential confounders in studies of moderation including gene × environment interactions.
Social Media and Multiple Sclerosis in the Posttruth Age

Over the last few decades, patients have increasingly been searching for health information on the Internet. This aspect of information seeking is really important, especially for people affected by chronic pathologies and require lifelong treatment and management. These people are usually very well informed about the disease, but are nonetheless vulnerable to hopes of being cured or saved, often amplified by misinformation, myths, legends, and therapies that are not always scientifically proven. Many studies suggest that some individuals prefer to rely on the Internet as their main source of information, often hindering the patient-doctor relationship. This is why a professional approach is imperative in this posttruth age, in order to maintain confidentiality, honesty, and trust in the medical profession.
High-order Deep Neural Networks for Learning Multi-Modal Representations

In multi-modal learning, data consists of multiple modalities, which need to be represented jointly to capture the real-world ’concept’ that the data corresponds to (Srivastava & Salakhutdinov, 2012). However, it is not easy to obtain the joint representations reflecting the structure of multi-modal data with machine learning algorithms, especially with conventional neural networks. This is because the information which consists of multiple modalities has distinct statistical properties and each modality has a different kind of representation and correlational structure (Srivastava & Salakhutdinov, 2012). Also, noise exists in information from multi-modal input, which makes the information unreliable and inaccurate (Ernst & Di Luca, 2011).
Optimization of Purification of Human Cell‐Free mRNA from Plasma

Cell‐free RNA has a potential for diagnosis and prognosis of many diseases. Our aim was to optimize a commercially available QIAamp UltraSens Virus Kit (Qiagen, Hilden, Germany) for isolation of mRNA from human plasma. The amount of carrier RNA to bind plasma mRNA, the centrifugal force to pellet the mRNA–carrier RNA complex, the incubation time for proteolysis, and the centrifugal force to bind mRNA to the silica gel membrane were modified in order to maximize the yield of isolated mRNA. The isolated cell‐free mRNA was detected for cycA using TaqMan real‐time quantitative RT‐PCR. The lowest threshold cycle (Ct) was obtained with the use of 4.0 μL of carrier RNA. Pelleting with a centrifugal force of 1500 ×g yielded the lowest Ct, but caused difficulties in resuspending the pellet. Therefore, we suggest using a lower centrifugal force of 1300 ×g. The duration of proteolysis had no effect on Ct. To bind mRNA to the silica gel membrane, a centrifugal force of 5000 ×g is recommended. Our results show that the UltraSens Virus Kit is an appropriate choice for isolating mRNA from human plasma, with imprecision expressed as coefficient of variation below 2%.
Depth Properties of scaled attachment random recursive trees

We study depth properties of a general class of random recursive trees where each node i attaches to the random node \documentclass{article} \usepackage{mathrsfs, amsmath, amssymb}\pagestyle{empty} \begin{document} \begin{align*}\left\lfloor iX_i\right\rfloor\end{align*} \end{document} and X0,…,Xn is a sequence of i.i. d. random variables taking values in [0,1). We call such trees scaled attachment random recursive trees (sarrt). We prove that the typical depth Dn, the maximum depth (or height) Hn and the minimum depth Mn of a sarrt are asymptotically given by Dn ∼μ‐1 log n, Hn ∼ αmax log n and Mn ∼ αmin log n where μ,αmax and αmin are constants depending only on the distribution of X0 whenever X0 has a density. In particular, this gives a new elementary proof for the height of uniform random recursive trees Hn ∼ elog n that does not use branching random walks. © 2011 Wiley Periodicals, Inc. Random Struct. Alg. , 2011
Flexural properties of polyamide versus injection-molded polymethylmethacrylate denture base materials

Although polymethylmethacrylate is the most commonly used denture base resin, its limitation of compromised flexibility has promoted the use of nylon-based denture resins. Aims: The purpose of this study is to evaluate and compare flexural strength and flexural modulus of two commercially available nylon-based flexible denture base materials, Valplast and Lucitone FRS, and injection-molded SR Ivocap polymethylmethacrylate denture base resin. Materials and Methods: A total of 15 samples of each group (Group A, B, C [Valplast, Lucitone FRS, SR Ivocap]) were prepared. All the samples were subjected to three-point bending test on an Instron Universal Testing machine to test their flexural strength and flexural modulus. Results: The results were statistically analyzed using SPSS Version 12. The difference in flexural modulus and flexural strength of all the three groups was statistically significant, P < 0.05. Conclusion: The mean flexural modulus of Valplast was significantly lower than Lucitone FRS, indicating that Valplast is less rigid, more flexible than Lucitone FRS, and hence more useful in conditions where flexibility in denture base is desired. SR Ivocap displayed flexural strength comparable with Lucitone, but less than Valplast.
Searching Sexual Predators in Social Network Dialogues

In this paper we propose a two-step technique for detecting sexual predators from social network dialogues. One step for detecting dialogues in which a sexual predators participates, and the second step is for detecting, from the whole dialogue users, the one that is the sexual predator. From the three different supervised classifier employed, Random Forests obtained the best results in the first step, whereas Neural Networks performed best in the second step.
An agent-based semantic Web department content management system

The semantic Web promises to bring the Web to its full potential by standardizing the protocols for metadata. It enables a knowledge-based Web to provide a qualitatively new level of service. It also provides intelligent access to heterogeneous, distributed information, which enabling both software agents and human users to exchange information. This paper presents architecture of an agent-based semantic Web department content management system. This system is called aSDMS and is designed for managing a typical department at a higher education institute. The system extracts information from existing department resources, such as the department's Website (e.g. the home page of the department), course catalogue and professor's personal Web pages. A set of ontologies representing information used by students and faculty members is described, where resource description framework (RDF) and RDF schema (RDFS) is used. The user of this system is able to navigate and edit the information through a Web interface. This paper discusses the semantic Web technology within the context of higher education. The feasibility and the potential of adopting the semantic Web technologies to improve department content management are demonstrated by implementing a prototype, using RDF Gateway.
Understanding the privacy implications of using context-based awareness cues in social networks

Information from the physical world is increasingly being digitalized and shared in social networks. We share our locations, tag photos and add different kinds of informal awareness cues about the physical world to our online communities. In this paper, we investigate the privacy implications of shared context cues in social networking services. We present an experimental mobile application, which allows users to add different descriptions of context information to their Facebook and Twitter status updates. The application was used by 12 persons during a two-week user trial using their own devices and Facebook accounts. The results indicate that user-defined abstractions of context items were often preferred over more accurate indicators due to privacy concerns or discomfort in sharing. We also found out that using shared context from friends in vicinity needs careful design to overcome the extended privacy implications.
A Consciousness-based Control System for a Simulated Autonomous Vehicle

This work describes the application of the Baars-Franklin Architecture (BFA), an artificial consciousness approach, to synthesize a control system for an autonomous vehicle. The BFA was reported in the literature as a successful control system to different kinds of agents: CMattie, IDA and CTS. In this paper, BFA is for the first time applied for controlling an autonomous vehicle. Firstly we introduce the theoretical foundations of this approach for the development of a conscious agent. Then we explain the architecture of our agent and at the end we discuss the results and first impressions of this approach. Keywords— artificial consciousness, intelligent systems, autonomous vehicle, multi-agent systems Resumo— Este trabalho descreve a aplicação da Arquitetura Baars-Franklin (BFA), uma abordagem de consciência artificial, para sintetizar um sistema de controle para um véıculo autônomo. A arquitetura BFA é reportada na literatura como um caso de sucesso no controle de diferentes tipos de agentes: CMattie, IDA e CTS. Neste artigo, a BFA é utilizada pela primeira vez no controle de um véıculo autônomo. Inicialmente, introduzimos os fundamentos teóricos desta abordagem para o desenvolvimento de um agente consciente. Em seguida, explicamos a arquitetura utilizada em nosso agente e por final discutimos os resultados e as primeiras impressões no uso desta abordagem. Palavras-chave— consciência artificial, sistemas inteligentes, véıculo autônomo, sistemas multi-agentes
Determining the subcellular location of new proteins from microscope images using local features

MOTIVATION Evaluation of previous systems for automated determination of subcellular location from microscope images has been done using datasets in which each location class consisted of multiple images of the same representative protein. Here, we frame a more challenging and useful problem where previously unseen proteins are to be classified. RESULTS Using CD-tagging, we generated two new image datasets for evaluation of this problem, which contain several different proteins for each location class. Evaluation of previous methods on these new datasets showed that it is much harder to train a classifier that generalizes across different proteins than one that simply recognizes a protein it was trained on. We therefore developed and evaluated additional approaches, incorporating novel modifications of local features techniques. These extended the notion of local features to exploit both the protein image and any reference markers that were imaged in parallel. With these, we obtained a large accuracy improvement in our new datasets over existing methods. Additionally, these features help achieve classification improvements for other previously studied datasets. AVAILABILITY The datasets are available for download at http://murphylab.web. cmu.edu/data/. The software was written in Python and C++ and is available under an open-source license at http://murphylab.web. cmu.edu/software/. The code is split into a library, which can be easily reused for other data and a small driver script for reproducing all results presented here. A step-by-step tutorial on applying the methods to new datasets is also available at that address. CONTACT murphy@cmu.edu SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
Neuroprotective effect of Citrus unshiu immature peel and nobiletin inhibiting hydrogen peroxide-induced oxidative stress in HT22 murine hippocampal neuronal cells

Background: Oxidative stress-induced cell damage is common in the etiology of several neurobiological disorders, including Alzheimer's disease and Parkinson's disease. In a case study, nobiletin-rich Citrus reticulata peels could prevent the progression of cognitive impairment in donepezil-preadministered Alzheimer's disease patients. Objective: In this study, we investigated the effects and underlying mechanism of nobiletin and Citrus unshiu immature peel (CUIP) water extract, which contains nobiletin as a major compound, on hydrogen peroxide-induced oxidative stress in HT22 cells, a murine hippocampal neuronal model. Materials and Methods: HT22 cells were treated with hydrogen peroxide in the presence or absence of various concentrations of CUIP and nobiletin. Cytotoxicity and apoptotic protein levels were measured by 3-(4,5-dimethythiazol-2-yl)-2,5-diphenyl tetrazolium bromide assay and Western blotting. Results: Pretreatment with CUIP and nobiletin inhibited cell death due to hydrogen peroxide. Hydrogen peroxide-induced the expression of phospho-Jun N-terminal kinases (p-JNK) and p-p38 proteins in HT22 cells; however CUIP and nobiletin suppressed p-JNK and p-p38 without changing JNK or p38. Regarding apoptosis, caspase 3, B-cell lymphoma 2 (Bcl-2), and Bax protein expression was determined. CUIP and nobiletin suppressed caspase 3 and Bax expression, but they induced Bcl-2 expression in HT22 cells. Conclusion: These results show that CUIP and nobiletin can protect against hydrogen peroxide-induced cell death in HT22 neurons via mitogen-activated protein kinases and apoptotic pathways.