Miracle-dz/UniFAR-FTUs huggingface dataset:
One gene, two transcripts: isolation of an alternative transcript encoding for the autoantigen La/SS-B from a cDNA library of a patient with primary Sjogrens' syndrome

A cDNA library was prepared from peripheral blood lymphocytes of an autoimmune patient with primary Sjogrens' syndrome. The cDNA library was screened with the patients own autoimmune serum being monospecific for the nuclear autoantigen La/SS-B. Thereby an alternative type of La mRNA was identified that differed from the known La mRNA due to an exchange of the exon 1. Sequencing of the genomic region between the exons 1 and 2 showed that the alternative 5'-end is a part of the intron. In addition, the presence of an alternative promoter site, which exists within the intron downstream of the exon 1, became evident. In consequence, the alternative La mRNA is the result of a promoter switching combined with an alternative splicing mechanism. In the intron, further transcription factor binding sites, including a NF- kappa B element, were identified leading to the suggestion that the expression of the gene encoding for the nuclear autoantigen La/SS-B alters in dependence on disease conditions.
Robust image watermarking using dual tree complex wavelet transform based on Human Visual System

In this paper, we proposed an image watermarking algorithm based on Human Visual System's perceptual model in the dual tree complex wavelet domain. We took advantages of the regular and the complex wavelets (perfect reconstruction, approximate shift invariance, and good directional selectivity) for watermark embedding. Firstly we applied the JND (Just Noticeable Difference) to control the watermark embedding strength. Then the host image was decomposed into six sub-bands by the 4-level dual tree complex wavelet transform. We embedded the watermark sequence into the six subbands with the same JND value. Lastly the watermark was extracted by comparing the host image coefficients and the watermarked image coefficients. Experimental results confirm that the proposed method was robust against geometric distortions, Gaussian noise, JPEG compression and Gaussian low pass filtering attacks.
Targeting Toll-Like Receptors : a step closer to effective recombinant subunit vaccines

The control and prevention of infectious diseases through immunization is one of the greatest achievements of modern medicine since Edward Jenner pioneered smallpox vaccination. However, future challenges in improving the efficacy of existing vaccines, development of new prophylactic vaccines for infectious diseases and therapeutic immunization for noninfectious diseases require extensive work to reveal key components of the molecular immune mechanism involved. Successful activation of innate immune response is a prerequisite for successful immunization and activation of adaptive immunity. Innate immune system comprises numerous evolutionary conserved pattern-recognition receptors (PRRs) that bind structural components shared by many pathogens. Upon binding the ligand, cascade reaction results in de novo gene expression required for immediate immune response by innate immunity and the activation of specific immune response mediated by the humoral and cellular mediators. Appropriate selection of specific pattern-recognition receptor ligands (adjuvants) enables formulation of the next generation vaccines, with controlled minimal adverse symptoms and efficient adaptive immunity development. DISCOVERY OF PATHOGEN RECOGNITION
Adaptive control using multiple models switching and tuning

The purpose of this paper is to marry the two concepts of multiple model adaptive control and safe adaptive control. In its simplest form, multiple model adaptive control involves a supervisory switching among one of a finite number of controllers as more is learnt about the plant, until one of the controllers is finally selected and remains unchanged. Safe adaptive control is concerned with ensuring that when the controller is changed the closed-loop is never unstable. This paper introduces a receding horizon multiple model, switching and tuning control scheme based on an on-line redesign of the controller. This control scheme has a natural two-stage adaptive control algorithm: identification of the closest model and design of the control law. The computational complexity aspects of this approach to adaptive control are discussed briefly. A nonlinear system is used to illustrate the ideas
Leaf Classification from Boundary Analysis

1 Abstract In this project, I will analyze the boundary curves of leaf images to recognize and classify leaves by species. The input leaf boundary curve will be decomposed into a wavelet bases, which will then be compared to the decomposition of all sample s in the database, and the closest matches will be returned. The inner-distance measure will also be computed and compared at multiple scales. This project is constructed to complement an existing leaf classification system which uses general leaf geometry, and not pure boundary i nformation, to recognize leaf species.
Improved Discovery of Molecular Interactions in Genome-Scale Data with Adaptive Model-Based Normalization

Background High throughput molecular-interaction studies using immunoprecipitations (IP) or affinity purifications are powerful and widely used in biology research. One of many important applications of this method is to identify the set of RNAs that interact with a particular RNA-binding protein (RBP). Here, the unique statistical challenge presented is to delineate a specific set of RNAs that are enriched in one sample relative to another, typically a specific IP compared to a non-specific control to model background. The choice of normalization procedure critically impacts the number of RNAs that will be identified as interacting with an RBP at a given significance threshold – yet existing normalization methods make assumptions that are often fundamentally inaccurate when applied to IP enrichment data. Methods In this paper, we present a new normalization methodology that is specifically designed for identifying enriched RNA or DNA sequences in an IP. The normalization (called adaptive or AD normalization) uses a basic model of the IP experiment and is not a variant of mean, quantile, or other methodology previously proposed. The approach is evaluated statistically and tested with simulated and empirical data. Results and Conclusions The adaptive (AD) normalization method results in a greatly increased range in the number of enriched RNAs identified, fewer false positives, and overall better concordance with independent biological evidence, for the RBPs we analyzed, compared to median normalization. The approach is also applicable to the study of pairwise RNA, DNA and protein interactions such as the analysis of transcription factors via chromatin immunoprecipitation (ChIP) or any other experiments where samples from two conditions, one of which contains an enriched subset of the other, are studied.
Structure-based Mining of Hierarchical Media Data , Meta-Data , and Ontologies

{candan, jong.wook. kim huan.liu, reshma.suvarna} @asu.edu ABSTRACT Users now have access to unprecedented amounts of media data, but it is increasingly difficult to integrate relevant media from multiple and diverse sources. The functioning of a multimodal integration system requires metadata, such as ontologies, that describe media resources and media components. Such metadata are generally application dependent and this can cause difficulties when media needs to be shared across application domains. There is a need for a mechanism that can relate the common and uncommon terms and media components. In this paper, we develop an algorithm to mine and automatically discover mappings in hierarchical media data, meta-data, and ontologies, using the structural information inherent in these types of data. We evaluate the performance of this algorithm for various parameters using both synthetic and real data collections and show that the structure based mining of relationships provides high degrees of precision.
Dietary Polyphenol Supplementation Prevents Alterations of Spatial Navigation in Middle-Aged Mice

Spatial learning and memory deficits associated with hippocampal synaptic plasticity impairments are commonly observed during aging. Besides, the beneficial role of dietary polyphenols has been suggested as potential functional food candidates to prevent this memory decline. Indeed, polyphenols could potentiate the signaling pathways of synaptic plasticity underlying learning and memory. In this study, spatial learning deficits of middle-aged mice were first highlighted and characterized according to their navigation patterns in the Morris water maze task. An eight-week polyphenol-enriched diet, containing a polyphenol-rich extract from grape and blueberry (PEGB; from the Neurophenols Consortium) with high contents of flavonoids, stilbenes and phenolic acids, was then successful in reversing these age-induced effects. The use of spatial strategies was indeed delayed with aging whereas a polyphenol supplementation could promote the occurrence of spatial strategies. These behavioral results were associated with neurobiological changes: while the expression of hippocampal calmodulin kinase II (CaMKII) mRNA levels was reduced in middle-aged animals, the polyphenol-enriched diet could rescue them. Besides, an increased expression of nerve growth neurotrophic factor (NGF) mRNA levels was also observed in supplemented adult and middle-aged mice. Thus these data suggest that supplementation with polyphenols could be an efficient nutritional way to prevent age-induced cognitive decline.
Extreme recoils: impact on the detection of gravitational waves from massive black hole binaries

Recent numerical simulations of the coalescence of highly spinning massive black hole binaries (MBHBs) suggest that the remnant can suffer a recoil velocity of the order of few thousand km s−1. We study here, by means of dedicated simulations of black hole build-up, how such extreme recoils could affect the cosmological coalescence rate of MBHBs, placing a robust lower limit for the predicted number of gravitational wave (GW) sources detectable by future space-borne missions (such as the Laser Interferometer Space Antenna, LISA). We consider two main routes for black hole formation: one where seeds are light remnants of Population III stars (≃102 M⊙), and one where seeds are much heavier (≳104 M⊙), formed via the direct gas collapse in primordial nuclear discs. We find that extreme recoil velocities do not compromise the efficient MBHB detection by LISA. If seeds are already massive and/or relatively rare, the detection rate is reduced by only ∼15 per cent. The number of detections drops substantially (by ∼60 per cent) if seeds are instead light and abundant, but in this case the number of predicted coalescences is so high that at least ∼10 sources in a three-year observation are guaranteed.
On completeness of the Ribaucour transformations for triply orthogonal curvilinear coordinate systems in R^3

In this paper we solve positively the problem of (local) density of solutions of the (2+1)-dimentional integrable system describing triply orthogonal curvilinear coordinates in R^3 (a (2+1)-dimensional generalization of the 3-wave system) obtainable from a given initial solution with consecutive B\"acklund transformations (called Ribaucour transformations in classical differential geometry) in the space of all solutions of the system in question.
QTrace: a framework for customizable full system instrumentation

This work presents QTrace, an open-source instrumentation extension API for QEMU (1) that can instrument unmodified applications and OS binaries for uni- and multi-processor systems. QTrace facilitates the development of custom, full-system instrumentation tools for the X86 guest architecture enabling statistics collection and program execution studies including system-level code. This paper: illustrates QTrace's API through instrumentation examples, discusses how QEMU was modified to implement QTrace, explains the validation testing procedures, shows QTrace's usefulness in comparison to a user-level binary instrumentation tool in workloads that spend significant time in the kernel, and illustrates that QTrace does not impose a significant performance penalty. Experiments show that for an instruction count plug-in, QTrace is 12.2X slower than PIN [2], a user-level only instrumentation tool, and 4.1X faster than BOCHS [3], a full-system emulator. QTrace without instrumentation performs similarly to the un-modified QEMU.
Determination of RhD zygosity: comparison of a double amplification refractory mutation system approach and a multiplex real-time quantitative PCR approach.

BACKGROUND Rh isoimmunization and hemolytic disease of the newborn still occur despite the availability of Rh immunoglobulin. For the prenatal investigation of sensitized RhD-negative pregnant women, determination of the zygosity of the RhD-positive father has important implications. The currently available molecular methods for RhD zygosity assessment, in general, are technically demanding and labor-intensive. Therefore, at present, rhesus genotype assessment is most commonly inferred from results of serological tests. The recent elucidation of the genetic structure of the prevalent RHD deletion in Caucasians, as well as the development of real-time PCR, allowed us to explore two new approaches for the molecular determination of RhD zygosity. METHODS Two methods for RhD zygosity determination were developed. The first was based on the double Amplification Refractory Mutation System (double ARMS). The second was based on multiplex real-time quantitative PCR. For the double ARMS assay, allele-specific primers were designed to directly amplify the most prevalent RHD deletion found in RhD-negative individuals in the Caucasian population. The multiplex real-time quantitative PCR assay, on the other hand, involved coamplification and quantification of RHD-specific sequences in relation to a reference gene, albumin, in a single PCR reaction. A ratio, DeltaCt, based on the threshold cycle, was then determined and reflects the RHD gene dosage. RESULTS The allele-specific primers of the double ARMS assay reliably amplified the RHD-deleted allele and therefore accurately distinguished homozygous from heterozygous RhD-positive samples. The results were in complete concordance with serological testing. For the multiplex real-time quantitative PCR assay, the DeltaCt values clearly segregated into two distinct populations according to the RHD gene dosage, with mean values of 1.70 (SD, 0.17) and 2.62 (SD, 0.29) for the homozygous and heterozygous samples, respectively (P: <0.001, t-test). The results were in complete concordance with the results of serological testing as well as with the double ARMS assay. CONCLUSION Double ARMS and real-time quantitative PCR are alternative robust assays for the determination of RhD zygosity.
Estimated reduction of energy consumption related to mobility in urban renewal projects

The urban sprawl that characterizes most European cities relies highly on the use of private motor vehicle. As a result, there is a prominent increase in the energy consumption of the built environment. Therefore, the densification of existing urban areas located near public transportation is an interesting alternative to dispersed urbanization, provided that such process goes together with an offer of local services and facilities to promote the use of soft mobility. Analysis at neighborhood scale allows studying the influence of infrastructures, facilities and services on daily mobility choices. This analysis should create direct insights into how the combination of global and local parameters related to mobility infrastructures and urban developments affect mobility energy consumption. The latter can be calculated by two main different methods: the macro-scale methods, which are based on parameters defining the city, and the micro-scale methods, which use accurate data from individuals and infrastructures. The present paper shows an application of a novel intermediate method at neighborhood level developed by the Swiss Society of Engineers and Architects (SIA) to estimate the energy consumption related to mobility and attributed to buildings. The analysis of induced mobility by different urban renewal scenarios of an existing neighborhood in Lausanne, Switzerland, shows the importance of the number of car parks and of the human density (residents or jobs per square meter) as key factors related to mobility energy planning. Results also highlight the significant impact of changes in behavior, in terms of chosen mean of transportation and covered distances, on the potential for energy savings.
Activity of the Monocarboxylate Transporter 1 Inhibitor AZD3965 in Small Cell Lung Cancer

Purpose: The monocarboxylate transporter 1 (MCT1) inhibitor, AZD3965, is undergoing phase I evaluation in the United Kingdom. AZD3965 is proposed, via lactate transport modulation, to kill tumor cells reliant on glycolysis. We investigated the therapeutic potential of AZD3965 in small cell lung cancer (SCLC) seeking rationale for clinical testing in this disease and putative predictive biomarkers for trial use. Experimental Design: AZD3965 sensitivity was determined for seven SCLC cell lines, in normoxia and hypoxia, and for a tumor xenograft model. Proof of mechanism was sought via changes in intracellular/tumor lactate. Expression of MCT1 and related transporter MCT4 was assessed by Western blot analysis. Drug resistance was investigated via MCT4 siRNAi and overexpression. The expression and clinical significance of MCT1 and MCT4 were explored in a tissue microarray (TMA) from 78 patients with SCLC. Results: AZD3965 sensitivity varied in vitro and was highest in hypoxia. Resistance in hypoxia was associated with increased MCT4 expression. In vivo, AZD3965 reduced tumor growth and increased intratumor lactate. In the TMA, high MCT1 expression was associated with worse prognosis (P = 0.014). MCT1 and hypoxia marker CA IX expression in the absence of MCT4 was observed in 21% of SCLC tumors. Conclusions: This study provides a rationale to test AZD3965 in patients with SCLC. Our results suggest that patients with tumors expressing MCT1 and lacking in MCT4 are most likely to respond. Clin Cancer Res; 20(4); 926–37. ©2013 AACR.
Health wearables in adolescents: implications for body satisfaction, motivation and physical activity

ABSTRACT Significant proportions of adolescents do not meet recommended physical activity levels. Finding new ways to motivate adolescents to be active is important for physical and psychological well-being. Health and fitness wearables such as the Fitbit have the potential to motivate young people to be active. The aim of this study is to explore if wearing a Fitbit for 5 weeks impacted adolescents’ (14–15 year olds) body satisfaction, physical activity motivation and objective physical activity. The study was conducted with 62 (38 boys, 24 girls) pupils aged 14–15, from five high school physical education classes, in one high school in the United Kingdom. Pupils wore a Fitbit Charge HR for 5 weeks. Pupils wore an accelerometer for 7 days pre and post the 5-week period to explore changes in physical activity levels. Pupils also completed pre-post-test questionnaires to measure body satisfaction and physical activity motivation. Data were analysed using a repeated measures Multivariate Analysis of Variance to explore differences in scores between time and sex. After wearing the Fitbit, the pupils experienced declines in autonomous motivation and increases in both amotivation and controlled motivation, but these differences were not significant. In line with these negative motivational outcomes, pupils engaged in significantly less moderate to vigorous physical activity after wearing the Fitbit. Significant increases in body satisfaction were also experienced by pupils after wearing the Fitbit. These findings suggest that without support Fitbits may make pupils less motivated to be active and decrease the physical activity levels of adolescents.
Context-Aware Coordination of Cascaded Machine Translations Supervisor Professor

Recently more and more people communicate through the Internet, and machine translators are used as communication tools between peoples who cannot speak their partners' mother language. Since English is a hub language of development of language resources like machine translators or bilingual dictionaries, combining multiple machine translators via English enables intercultural communication and collaboration between non-English languages. To combine multiple machine translators, problems interfering communication sometimes occur. Cascaded machine translators often yield mistranslations due to inconsistency of word selections, even if all translators are combined correctly and each translation result is correct. This is because each translator considers each input sentence only. This phenomenon is a big problem for both multi-hop translation cascading multiple translators and machine translator-mediated communication. Then, coordination of cascaded machine translators is needed. For resolution of such problems, this research addresses following issues. In order to examine whether the sense of translated sentence is different from the one of the source sentence, equivalent terms of all languages is required. Equivalent terms between two languages is developed as bilingual dictionaries between lots of languages, while that of more than three languages is developed manually among parts of languages. Therefore this research aims to generate multilingual equivalent terms automatically from existing language resources. Coordination of translators, that is, consistent word selections, can be realized by extracting context and propagating it to machine translators. Context is extracted from the source sentence or whole document including the source sentence. The sense of translated sentence is kept consistent by ii selecting translated words which suit propagated context. Methods of extracting context are proposed in previous researches. This research assumes that the context is already extracted, and focuses on the coordination by propagating extracted context. To solve these two issues, this research proposed following solutions. This research proposed the method to obtain multilingual equivalent terms by combining multiple bilingual dictionaries. Relations between words and translated words are represented as a graph, and equivalent terms are obtained by using the structure of it. If simply combining multiple dictionaries, there are some cases where multiple terms which do not share the same sense are also obtained. Such error can be prevented by considering the structure of the graph. This research proposed a method to coordinate cascaded machine translators so as to select translated words based on the context which was propagated using multilingual equivalent terms. Each context extracted from the sentence is represented in …
Mediated digraphs and quantum nonlocality

A digraphD = (V ,A) is mediated if for each pair x, y of distinct vertices ofD, eitherxy ∈ A or yx ∈ A or there is a vertex z such that bothxz, yz ∈ A. For a digraphD, −(D) is the maximum indegree of a vertex in D. Thenth mediation number (n) is the minimum of −(D) over all mediated digraphs onn vertices. Mediated digraphs and (n) are of interest in the study of quantum nonlocality. We obtain a lower bound f (n) for (n) and determine infinite sequences of values of n for which (n)= f (n) and (n)>f (n), respectively. We derive upper bounds for (n) and prove that (n)= f (n)(1+ o(1)). We conjecture that there is a constant c such that (n) f (n) + c. Methods and results of design theory and number theory are used. © 2005 Elsevier B.V. All rights reserved.