Miracle-dz/UniFAR-FTUs huggingface dataset:
An Inducible Transgenic Mouse Model for Immune Mediated Hepatitis Showing Clearance of Antigen Expressing Hepatocytes by CD8+ T Cells

The liver has the ability to prime immune responses against neo antigens provided upon infections. However, T cell immunity in liver is uniquely modulated by the complex tolerogenic property of this organ that has to also cope with foreign agents such as endotoxins or food antigens. In this respect, the nature of intrahepatic T cell responses remains to be fully characterized. To gain deeper insight into the mechanisms that regulate the CD8+ T cell responses in the liver, we established a novel OVA_X_CreERT2 mouse model. Upon tamoxifen administration OVA antigen expression is observed in a fraction of hepatocytes, resulting in a mosaic expression pattern. To elucidate the cross-talk of CD8+ T cells with antigen-expressing hepatocytes, we adoptively transferred Kb/OVA257-264-specific OT-I T cells to OVA_X_CreERT2 mice or generated triple transgenic OVA_X CreERT2_X_OT-I mice. OT-I T cells become activated in OVA_X_CreERT2 mice and induce an acute and transient hepatitis accompanied by liver damage. In OVA_X_CreERT2_X_OT-I mice, OVA induction triggers an OT-I T cell mediated, fulminant hepatitis resulting in 50% mortality. Surviving mice manifest a long lasting hepatitis, and recover after 9 weeks. In these experimental settings, recovery from hepatitis correlates with a complete loss of OVA expression indicating efficient clearance of the antigen-expressing hepatocytes. Moreover, a relapse of hepatitis can be induced upon re-induction of cured OVA_X_CreERT2_X_OT-I mice indicating absence of tolerogenic mechanisms. This pathogen-free, conditional mouse model has the advantage of tamoxifen inducible tissue specific antigen expression that reflects the heterogeneity of viral antigen expression and enables the study of intrahepatic immune responses to both de novo and persistent antigen. It allows following the course of intrahepatic immune responses: initiation, the acute phase and antigen clearance.
Building a Domain Knowledge Base from Wikipedia: a Semi-supervised Approach

Knowledge bases are becoming indispensable to software engineering and knowledge engineering. However, the existing domain knowledge bases are always artificially construct- ed and small-scale. In this paper, we propose a semi-supervised approach to domain concepts detection and software engineering knowledge base construction from Wikipedia. First, the approach selects domain relevant tags from Stackoverflow. Then, it matches Wikipedia entities and expands the concept set through an improved label propagation algorithm. A rule-based method is designed to discover semantic relations including relate, subclassOf and equal by analyzing structural information of Wikipedia. A relation derivation mechanism is presented to optimize the relation set. We finally construct SEBase, a domain- specific knowledge base of software engineering. Experimental results show the high accuracy of the integrated concepts and relations. Compared with other knowledge bases, SEBase has the widest coverage of concepts and relations in software engineering.
Blocks at your fingertips: Blurring the line between blocks and text in GP

Visual blocks languages offer many advantages to the beginner or "casual" programmer. They eliminate syntax issues, allow the user to work with logical program chunks, provide affordances such as drop-down menus, and leverage the fact that recognition is easier than recall. However, as users gain experience and start creating larger programs, they encounter two inconvenient properties of pure blocks languages: blocks take up more screen real-estate than textual languages and dragging blocks from a palette is slower than typing. This paper describes three experiments in blurring the line between blocks and textual code in GP, a new blocks language for casual programmers currently under development.
Fast Deconvolution for Motion Blur Along the Blurring Paths

In this paper, we propose a deconvolution method which removes the motion blur along the blurring paths. The 2-D blurred image is transformed into 1-D horizontal blurred vectors along the blurring paths. Hence, the deconvolution of stacked horizontal blurred vectors is implemented in an iterative deconvolution process by a 1-D image restoration method that saves computation time. The deconvolution process is usually implemented in the frequency domain by fast Fourier transform (FFT). The computation time of FFT used in the 1-D image restoration method for the blurred vectors is about two-fifths of that of 2-D FFT used in the common image restoration method. To get stacked horizontal blurred vectors, we first incorporate orthogonal Chebyshev polynomial into the proposed method to extract pixels along the blurring paths. Then, we expand horizontal blurred vectors smoothly to reduce boundary artifacts. At last, we add a nonquadratic regularization term to the Richardson-Lucy algorithm, which adaptively penalizes the image gradients, to avoid oversmoothing of details. Experimental results for real motion-blurred images demonstrate that our approach runs much faster than the 2-D deblurring algorithm, while achieving as high restoration accuracy and visual perception as the 2-D deconvolution algorithm.
Magnetic resonance imaging for adaptive cobalt tomotherapy: A proposal

Magnetic resonance imaging (MRI) provides excellent soft tissue contrast for oncology applications. We propose to combine a MRI scanner with a helical tomotherapy (HT) system to enable daily target imaging for improved conformal radiation dose delivery to a patient. HT uses an intensity-modulated fan-beam that revolves around a patient, while the patient slowly advances through the plane of rotation, yielding a helical beam trajectory. Since the use of a linear accelerator to produce radiation may be incompatible with the pulsed radiofrequency and the high and pulsed magnetic fields required for MRI, it is proposed that a radioactive Cobalt-60 (60Co) source be used instead to provide the radiation. An open low field (0.25 T) MRI system is proposed where the tomotherapy ring gantry is located between two sets of Helmholtz coils that can generate a sufficiently homogenous main magnetic field. It is shown that the two major challenges with the design, namely acceptable radiation dose rate (and therefore treatment duration) and moving parts in strong magnetic field, can be addressed. The high dose rate desired for helical tomotherapy delivery can be achieved using two radiation sources of 220TBq (6000Ci) each on a ring gantry with a source to axis-of-rotation distance of 75 cm. In addition to this, a dual row multi-leaf collimator (MLC) system with 15 mm leaf width at isocentre and relatively large fan beam widths between 15 and 30 mm per row shall be employed. In this configuration, the unit would be well-suited for most pelvic radiotherapy applications where the soft tissue contrast of MRI will be particularly beneficial. Non-magnetic MRI compatible materials must be used for the rotating gantry. Tungsten, which is non-magnetic, can be used for primary collimation of the fan-beam as well as for the MLC, which allows intensity modulated radiation delivery. We propose to employ a low magnetic Cobalt compound, sycoporite (CoS) for the Cobalt source material itself. Rotational delivery is less susceptible to problems related to the use of a low energy megavoltage photon source while the helical delivery reduces the negative impact of the relatively large penumbra inherent in the use of Cobalt sources for radiotherapy. On the other hand, the use of a 60Co source ensures constant dose rate with gantry rotation and makes dose calculation in a magnetic field as easy as the range of secondary electrons is limited. The MR-integrated Cobalt tomotherapy unit, dubbed ‘MiCoTo,’ uses two independent physical principles for image acquisition and treatment delivery. It would offer excellent target definition and will allow following target motion during treatment using fast imaging techniques thus providing the best possible input for adaptive radiotherapy. As an additional bonus, quality assurance of the radiation delivery can be performed in situ using radiation sensitive gels imaged by MRI.
Functional Characterization of Spliceosomal Introns and Identification of U2, U4, and U5 snRNAs in the Deep-Branching Eukaryote Entamoeba histolytica

ABSTRACT Pre-mRNA splicing is essential to ensure accurate expression of many genes in eukaryotic organisms. In Entamoeba histolytica, a deep-branching eukaryote, approximately 30% of the annotated genes are predicted to contain introns; however, the accuracy of these predictions has not been tested. In this study, we mined an expressed sequence tag (EST) library representing 7% of amoebic genes and found evidence supporting splicing of 60% of the testable intron predictions, the majority of which contain a GUUUGU 5′ splice site and a UAG 3′ splice site. Additionally, we identified several splice site misannotations, evidence for the existence of 30 novel introns in previously annotated genes, and identified novel genes through uncovering their spliced ESTs. Finally, we provided molecular evidence for the E. histolytica U2, U4, and U5 snRNAs. These data lay the foundation for further dissection of the role of RNA processing in E. histolytica gene expression.
A Novel Even & Odd-Mode Symmetric Circuit Decomposition Method

This paper presents a novel method using the principles of even-odd mode analysis to derive the scattering parameters of the even-mode and odd-mode circuit decompositions of a symmetric circuit solely from its known scattering parameters. This eliminates the need for the microwave designer to perform additional simulations to obtain the even-mode and odd-mode circuits once the full circuit S-parameters are known. The technique is especially attractive in the case of Monolithic Microwave Integrated Circuit (MMIC) design where the additional simulations typically require a EM (3D) simulator. The utility of the method is highlighted by analyzing the odd-mode circuit of a MMIC PA power combiner.
‘Higher than Einstein’: constructions of going to university among working-class non-participants

Despite a vast increase in numbers in higher education, the lower socio-economic groups continue to be under-represented. Many reasons have been put forward for this: they include institutional and financial factors; low academic achievement and aspirations; lack of knowledge of HE; and perceptions of universities as élitist. While a number of studies have identified knowledge and perceptions of HE as factors that may deter working-class groups from aspiring to go to university, there has been limited investigation of the views of those who do not enter HE. This study focuses on constructions of going to university among young working-class non-participants. Drawing on data collected in focus groups, it analyses the discourses used in talking about entry qualifications, financial arrangements, studying at university and students. It is suggested that these young working-class people are to some extent aware of the hierarchy of HE entry routes and institutions and that they believe that the openings most easily accessible to them constitute a second rate form of HE.
A desistance paradigm for offender management

In an influential article published in the British Journal of Social Work in 1979, Anthony Bottoms and Bill McWilliams proposed the adoption of a ‘non-treatment paradigm’ for probation practice. Their argument rested on a careful and considered analysis not only of empirical evidence about the ineffectiveness of rehabilitative treatment but also of theoretical, moral and philosophical questions about such interventions. By 1994, emerging evidence about the potential effectiveness of some intervention programmes was sufficient to lead Peter Raynor and Maurice Vanstone to suggest significant revisions to the ‘non-treatment paradigm’. In this article, it is argued that a different but equally relevant form of empirical evidence—that derived from desistance studies—suggests a need to re-evaluate these earlier paradigms for probation practice. This reevaluation is also required by the way that such studies enable us to understand and theorize both desistance itself and the role that penal professionals might play in supporting it. Ultimately, these empirical and theoretical insights drive us back to the complex interfaces between technical and moral questions that preoccupied Bottoms and McWilliams and that should feature more prominently in contemporary debates about the futures of ‘offender management’ and of our penal systems.
Central Nervous System Tuberculosis: A Forgotten Diagnosis

Introduction:Early diagnosis and treatment of central nervous system (CNS) tuberculosis (TB) are very important because of its high morbidity and mortality characteristics. However, the clinical symptoms, laboratory and neuroimaging findings of CNS TB are nonspecific, no matter whether they are the common form, tuberculous meningitis (TBM), or the rare form, intracranial tuberculomas. We report a case of TBM with miliary pattern of intracranial tuberculomas, although the initial diagnosis was masked by an atypical neuropsychiatric presentation, cerebrospinal fluid (CSF) finding, and other medical comorbidity. Case Report:A 51-year-old man was brought to the emergency room due to a traffic accident. The initial impression was Wernicke encephalopathy due to his alcohol use history and the clinical triad. After admission, fever and mental confusion lead to the suspicion of CNS infection. Although the initial CSF analysis was inconclusive, the miliary pattern of intracranial tuberculomas was highly suspected by brain magnetic resonance imaging finding. The diagnosis of TBM and miliary TB was finally confirmed by positive CSF and sputum culture of Mycobacterium tuberculosis. The patient had a good response to standard antituberculous therapy, although paradoxical expansion of cerebral tuberculomas occurred during treatment. Conclusions:TB is still a major public health problem in the world, and there is a rising tendency of extrapulmonary TB incidences in the developed countries. Because of the high mortality and treatable characteristics of CNS TB, physicians should be familiar with it and keep the diagnosis in mind.
Mobile cross-media visualisations made from building information modelling data

The advent of Building Information Modelling (BIM) provides geometry data that can be easily used for visualisations. We present six demonstrators made from the same data using similar workflows. They cover different categories of mobile devices, ranging from head-mounted displays to smartphones and tablets with inside-out positional tracking. They showcase cross-media visualisations depending on the device capabilities, which vary from a sophisticated car-based AR-setup, over wired and wireless VR, to see-through AR on smart glasses, and video-based AR on tablets.
RELATIONSHIP BETWEEN SACRAL SKIN BLOOD FLOW OSCILLATIONS AND VASODILATORY FUNCTIONS IN PEOPLE AT RISK FOR PRESSURE ULCERS

The role of microvascular function in the risk for pressure ulcers can be assessed by studying the changes of skin blood flow oscillations (BFO) in response to causative factors of pressure ulcers such as local heating [1]. Previous studies, using either Fourieror wavelet-based spectral analysis, provide essential contributions to the understanding of the control mechanisms of BFO [2]. Wavelet analysis of skin BFO reveals five characteristic frequencies, associated with endothelial metabolic activities, sympathovagal neurogenic activities, vascular myogenic activities, breathing movements, and heart beats. This method allows clinicians and researchers to non-invasively assess microvascular dysfunction in various pathological populations. However, wavelet analysis is a linear method and cannot characterize the nonlinear properties embedded in BFO of the cardiovascular system. The cardiovascular system is a complex, nonlinear dynamical system, and skin blood flow regulation is therefore a nonlinear process [3].
A Low-Complexity Layered Decoding Algorithm for LDPC Codes

A Low-complexity Layered Decoding Algorithm for LDPC Codes is proposed. Our modified algorithm reduces the number of operations in variable nodes to lower LDPC decoder power consumption. The modified parts of LDPC decoder architecture is also described. Simulation results show that comparing with SPA and MSA, our algorithm reducing the number of operations nearly to 60% with little performance loss.
Variance reduction by using separate genuine- impostor statistics in multimodal biometrics

In this paper, we propose some novel normalization and fusion techniques for biometric matching score level fusion in person verification. While conventional matching score level fusion methods use global score statistics, we consider in this work both genuine and impostor statistics separately. Performing a joint mean normalization of the separate monomodal scores, multimodal scores with less separate variance than the monomodal ones are obtained. Furthermore, a weighting method has been designed in order to minimize the variance sum of the separate multimodal statistics. This method obtains a minor sum of genuine and impostor variances for the multimodal biometric than that of the monomodal ones. The results obtained in speech and face scores fusion upon POLYCOST and XM2VTS databases show that the proposed normalization and fusion techniques provide better results than the conventional methods.
Interface Language, User Language and Success Rates in the European Library

In this paper, TEL 2010 action logs are analyzed with a particular focus on the impact of language (user native language and interface language) on the success of a search session. Particular user actions are defined as success indicators for searches and sessions are divided into "successful" and "unsuccessful" sessions with respect to their outcomes. Two approaches for studying the impact of the language of the search interface are pursued: (1) the effect of concurrent language choice when associating the user language (determined by IP address) with the interface language and (2) the consequences of interface language changes during a session. The challenges of country and language identification via IP addresses are also discussed.
Scientific Method and the Appraisal of Religion

In looking for criteria by which to assess religious conceptual systems, many philosophers have turned for help to scientific methodology. Perhaps this is because they felt philosophers of science were themselves looking in the right epistemological direction, and had a viable way of describing what they saw. Richard Swinburne has provided a strong, sustained treatment of the application of scientific method to religious truth claims, in The Existence of God. He there makes use of what he sees as ‘the close similarities which exist between religious theories and large-scale scientific theories’ in assessing the epistemic status of belief in God. The goal of this paper will be to give enough of Swinburne's position to see what criteria might be plucked therefrom, to subject both the criteria and the underlying methodology to scrutiny, and to assess where one must go from here in appraising the truth-claims of religion.
I. The Neurocognitive Profile of Williams Syndrome: A Complex Pattern of Strengths and Weaknesses

The rare, genetically based disorder, Williams syndrome (WMS), produces a constellation of distinctive cognitive, neuroanatomical, and electrophysiological features which we explore through the series of studies reported here. In this paper, we focus primarily on the cognitive characteristics of WMS and begin to forge links among these characteristics, the brain, and the genetic basis of the disorder. The distinctive cognitive profile of individuals with WMS includes relative strengths in language and facial processing and profound impairment in spatial cognition. The cognitive profile of abilities, including what is typical for individuals with WMS is discussed, but we also highlight areas of variability across the group of individuals with WMS that we have studied. Although the overall cognitive abilities (IQs) of individuals with WMS are typically in the mild-to-moderate range of mental retardation, the peaks and valleys within different cognitive domains make this syndrome especially intriguing to study across levels. Understanding the brain basis (and ultimately the genetic basis) for higher cognitive functioning is the goal we have begun to undertake with this line of interdisciplinary research.
A Parallel Algorithm for Mining Maximal Cohesive Subgraphs

Robust and scalable techniques for mining patterns or subgraphs in protein protein interaction (PPI) networks can help identify functionally relevant and coherent subnetworks. Recently, researchers have focused on integrating genes attributes with the protein-protein interaction networks for mining connected subnetworks whose genes are similar in a subset of attributes. However, most of the proposed approaches assume that these subnetworks are dense. While detecting dense and cohesive subnetworks is desirable, the density factor can prevent these algorithms from reporting highly cohesive subgraphs which are not particularly dense. In this paper, we propose a parallel algorithm for mining maximal cohesive subgraphs from node-attributed networks. Experiments on two real interaction networks and gene expression attributes demonstrate the eﬀectiveness of the proposed algorithm. Moreover, biological enrichment analysis of the reported patterns show that the patterns are biologically relevant and enriched with known biological processes and KEGG pathways.
Measurement information processing in Functional Magnetic Resonance Imaging

Functional Magnetic Resonance Imaging (fMRI) is one of the main techniques for the in vivo diagnosis of physiological and psychological diseases. During the data acquisition, alterations may intervene causing uncertainty in the diagnosis. Therefore, many preprocessing techniques are developed to reduce the alteration effects. Since today there is no consensus on standard procedure to perform the fMRI preprocessing, many correction techniques and evaluation metrics are used. The different preprocessing procedures give different information to the clinicians. Different diagnosis will be provided if the used preprocessing procedure is not completely known and then the preprocessed data are not correctly interpreted. The aim of the paper is to provide an overview of the fMRI preprocessing procedures in order to stimulate the interest of the scientific community (i) to develop and experiment new and advanced techniques for efficiency and accuracy improvement, and (ii) to attain an unified procedure.