Miracle-dz/UniFAR-FTUs huggingface dataset:
Differential Requirements for Conserved E2 Binding Sites in the Life Cycle of Oncogenic Human Papillomavirus Type 31

ABSTRACT Human papillomavirus (HPV) E2 proteins regulate viral replication by binding to sites in the upstream regulatory region (URR) and by complex formation with the E1 origin recognition protein. In the genital HPV types, the distribution and location of four E2 binding sites (BS1 to BS4) which flank a single E1 binding site are highly conserved. We have examined the roles of these four E2 sites in the viral life cycle of HPV type 31 (HPV31) by using recently developed methods for the biosynthesis of papillomaviruses from transfected DNA templates (M. G. Frattini et al., Proc. Natl. Acad. Sci. USA 93:3062–3067, 1996). In transient assays, no single site was found to be necessary for replication, and mutation of the early promoter-proximal site (BS4) led to a fourfold increase in replication. Cotransfection of the HPV31 wild-type (HPV-wt) and mutant genomes with expression vectors revealed that E1 stimulated replication of HPV31-wt as well as the HPV31-BS1, -BS2, and -BS3 mutants. In contrast, increased expression of E2 decreased replication of these genomes. Replication of the HPV31-BS4 mutant genome was not further increased by cotransfection of E1 expression vectors but was stimulated by E2 coexpression. In stably transfected normal human keratinocytes, mutation of either BS1, BS3, or BS4 resulted in integration of viral genomes into host chromosomes. In contrast, mutation of BS2 had no effect on stable maintenance of episomes or copy number. Following growth of stably transfected lines in organotypic raft cultures, the differentiation-dependent induction of late gene expression and amplification of viral DNA of the BS2 mutant was found to be similar to that of HPV31-wt. We were unable to find a role for BS2 in our assays for viral functions. We conclude that at least three of the four E2 binding sites in the URRs of HPVs are essential for the productive viral life cycle. The specific arrangement of E2 binding sites within the URR appears to be more important for viral replication than merely the number of sites.
The relationship between contextual processing, intrusive imagery and hallucination proneness

Aims: This study tested the hypothesis that hallucinations exist on a continuum with intrusive imagery and that contextual processing underlies this relationship. The study hypothesised that weak contextual (allocentric) processing would correlate with intrusive images that are vivid, sensory and possess a strong sense of nowness. Further, that hallucination-proneness would also be associated with a weaker contextual system either directly or indirectly via the presence of intrusive imagery. Method: A cross-sectional, correlation design was employed using a general population sample. 55 participants completed a virtual environment task that probed allocentric and egocentric processing and memory. An intrusive interview paradigm and measures assessing predisposition to psychotic experiences were also employed. Results: Weaker allocentric processing was associated with intrusive images with a greater sense of “nowness”. Both egocentric and allocentric systems were related to the sensory attributes of intrusive imagery. Predisposition to hallucinations was associated with greater “nowness” of intrusive imagery and post-hoc findings demonstrated a relationship between weaker allocentric processing and more extreme cases on the hallucination scale. Conclusion: The findings supported some of the hypotheses, which have clinical implications with regard to understanding psychotic features within traumatised individuals and the development of psychosis more widely. Limitations and further areas of research are discussed.
The many faces of facial nerve schwannoma.

BACKGROUND AND PURPOSE The imaging appearance of facial nerve schwannomas (FNSs) has been described as an enhancing tubular mass (using T1-enhanced MR) within an enlarged facial nerve canal (using CT). The purpose of this study is to identify how often the FNS imaging findings conform to this description and determine whether there are underlying anatomic explanations for the discrepant imaging appearances identified. MATERIALS AND METHODS The clinical, pathologic, and radiologic records of 24 FNS in 23 patients were retrospectively reviewed. Each FNS was evaluated for location along the facial nerve. The lesions were cataloged by facial nerve segment with the imaging characteristics of each segment described. RESULTS The average age at time of first imaging was 39 years (age range, 10-70 years). Eighteen (71%) of the 24 FNSs were pathologically confirmed, while the others were determined intraoperatively or diagnostically by the presence of both enlargement of the facial nerve canal and enhancement on contrast-enhanced T1 MR examination. The most common location was in the geniculate fossa (83%), followed by the labyrinthine and tympanic segments of the facial nerve (both 54%). The most common clinical presentation was facial neuropathy (42%). CONCLUSION The classic description of FNS on enhanced T1 MR is that of a well-circumscribed fusiform enhancing mass along the course of the intratemporal facial nerve with bone algorithm CT showing sharply defined bony canal enlargement. Modern imaging techniques, however, demonstrate the importance of the surrounding anatomic landscape, leading to various imaging appearances. Lesions traversing the labyrinthine segment can demonstrate a dumbbell appearance. When FNSs track along the greater superficial petrosal nerve, they may present as a round mass projecting up into the middle cranial fossa. FNS of the tympanic segment of the facial nerve preferentially pedunculate into the middle ear cavity, clinically presenting as a middle ear mass. When the mastoid segment of the facial nerve is involved, irregular and "invasive" tumor margins seen on MR can be explained on CT as tumor breaking into surrounding mastoid air cells.
High performance LU factorization for non-dedicated clusters

This paper describes an implementation of parallel LU factorization. The focus is to achieve high performance on non-dedicated clusters, where the number of available computing resources may be arbitrary and even dynamically changing. We accommodate joining/leaving processes by describing the algorithm in the Phoenix programming model. We achieve high performance in this setting by a combination of techniques including a latency tolerant communication and data partitioning that achieves both load balance and small communication volume for arbitrary and dynamically changing number of processors. We observed 130 GFlops with 128 processes on a 70-node dual 2.4GHz Xeon cluster, at matrix size = 46080. This performance is comparable to that of the High Performance Linpack (HPL). When cluster nodes are loaded by background processes, our implementation surpasses HPL.
Interactive Experiences and Contextual Learning in Museums

Inspired by the work of John Falk and Lynn Dierking, this article examines the characteristics of museum visitors and their museum experiences in order to provide recommendations for more meaningful learning experiences for future visitors. A recent shifting agenda in museum missions is discussed in respect to its visitors according to the following variables: demographic, psychographic, personal and cultural history, and environmental. Also included are visitor behaviors in relation to time, attention, label reading, and social factors. To investigate museum visitors' experiences, Falk and Dierking's (1992, 2000) Interactive Experience Model and Contextual Model of Learning are explored as means for elaborating on the nature of museum experiences and learning. Recent empirical studies also are examined in order to illustrate new responsive methodologies for engaging museum visitors. In conclusion, it is emphasized that museums can be effective public educational institutions when they meet the needs and expectations of a diverse population of visitors.
Online identification of frequently executed acyclic paths by leveraging data stream algorithms

Most of the traditional path profilers simply generate a path-frequency table that records the raw frequencies of each path. The compiler is supposed to carry out the herculean task of mining this table for frequently executed paths to drive aggressive profile-guided optimizations. This begs a question: why cannot profilers themselves identify these frequent paths --- produce information that can be consumed directly by the optimizers? The essential theme of this paper is that the sequence of acyclic paths emitted by a classic Ball-Larus profiler can be viewed as a data-stream: this enables an online extraction of any required statistics (like the frequently executed paths) on the profile information without requiring storage and update of the huge path-frequency tables generated by a long-running program. We adapt a classic data stream algorithm for finding majority elements in a stream (by Karp et al.) for our use, essentially by enabling optimizations that exploit the properties of paths generated off a Ball-Larus profiler. We instantiate our ideas by building an efficient path profiler that identifies all acyclic paths frequented above a user-provided threshold percentage of all executed paths.
Noninvasive Detection of Radiation-Induced Optic Neuropathy by Manganese-Enhanced MRI

Abstract Ryu, S. , Brown, S. L. , Kolozsvary, A. , Ewing, J. R. and Kim, J. H. Noninvasive Detection of Radiation-Induced Optic Neuropathy by Manganese-Enhanced MRI. Radiat. Res. 157, 500–505 (2002). Available imaging techniques have a limited ability to detect radiation-induced injury of the normal brain. In particular, there is no noninvasive method available for detection of structural or functional neuronal damage induced by radiation. This study was designed to determine whether MRI enhanced using the neuronal track tracer MnCl2 can detect radiation-induced optic neuropathy. A single dose of radiation (35 Gy) was delivered to produce optic neuropathy in Fischer 344 rats by using a stereotactic method with a 6-mm dorsoventral secondary collimator. At 6 months after irradiation, MRI was performed in 1-mm sections using a 7-T magnetic field with the neuronal tracer MnCl2 injected into the vitreous of the eye 24 h prior to imaging. The rats were then killed humanely for a histological study with hematoxylin and eosin, glial fibrillary acidic protein (Gfap) for the detection of astrocytic activity, Luxol Fast Blue/Periodic Acid Schiff (LFB/PAS) for the detection of myelinization status, and Bielschowski silver stain for axon status. In nonirradiated control animals, T1-weighted MRI with manganese vitreous injection revealed an optic nerve track that was brightly enhanced from the orbit to the optic chiasm. In the irradiated animals, there was clear evidence of the damage at the optic chiasm and optic nerves, with loss of axon and demyelinization within the site of irradiation upon histological examination. T1-weighted MRI with manganese vitreous injection showed an enhancing optic nerve posterior to the orbit. However, this enhancement disappeared at the site of irradiation. The area of loss of manganese contrast on the MRI scan correlated well with the area of histological abnormality showing axonal degeneration and demyelinization. Radiation-induced optic neuropathy was thus detected noninvasively by MRI with the antegrade neuronal tracer manganese, which exhibited negative contrast enhancement by causing loss of signal. This study represents the first demonstration of MR imaging of radiation-induced neuronal damage and could provide a means to explore the biological and functional integrity of neuronal pathways.
An updated checklist of aquatic plants of Myanmar and Thailand

Abstract The flora of Tropical Asia is among the richest in the world, yet the actual diversity is estimated to be much higher than previously reported. Myanmar and Thailand are adjacent countries that together occupy more than the half the area of continental Tropical Asia. This geographic area is diverse ecologically, ranging from cool-temperate to tropical climates, and includes from coast, rainforests and high mountain elevations. An updated checklist of aquatic plants, which includes 78 species in 44 genera from 24 families, are presented based on floristic works. This number includes seven species, that have never been listed in the previous floras and checklists. The species (excluding non-indigenous taxa) were categorized by five geographic groups with the exception of to reflect the rich diversity of the countries' floras.
Paragraph Acquisition and Selection for List Question Using Amazon’s Mechanical Turk

Creating more fine-grained annotated data than previously relevent document sets is important for evaluating individual components in automatic question answering systems. In this paper, we describe using the Amazon's Mechanical Turk (AMT) to judge whether paragraphs in relevant documents answer corresponding list questions in TREC QA track 2004. Based on AMT results, we build a collection of 1300 gold-standard supporting paragraphs for list questions. Our online experiments suggested that recruiting more people per task assures better annotation quality. In order to learning true labels from AMT annotations, we investigated three approaches on two datasets with different levels of annotation errors. Experimental studies show that the Naive Bayesian model and EM-based GLAD model can generate results highly agreeing with gold-standard annotations, and dominate significantly over the majority voting method for true label learning. We also suggested setting higher HIT approval rate to assure better online annotation quality, which leads to better performance of learning methods.
Intelligibility detection of pathological speech using asymmetric sparse kernel partial least squares classifier

Pathological speech usually refers to the voice disorders resulting from atypicalities in voice and/or in the articulatory mechanisms due to disease, illness or other physical problem in the speech production system. It may increase unhealthy social behavior and voice abuse, and dramatically affect the patients' quality of life. Therefore, automatic intelligibility detection of pathological speech has an important role in the opportune treatment of pathological voices. This paper proposes to use asymmetric sparse kernel partial least squares classifier (ASKPLSC) for intelligibility detection of pathological speech. The proposed approach achieves an unweighted accuracy (UA) of 74.0%, which is 7.34% relative improvement of baseline system of an UA of 68.90% for the Pathology Sub-Challenge of INTERSPEECH 2012 Speaker Trait Challenge.
In Vitro Susceptibilities of Isolates of Sporothrix schenckii to Itraconazole and Terbinafine

ABSTRACT Thirty isolates of the yeast form of Sporothrix schenckii were evaluated for in vitro susceptibility to itraconazole and terbinafine by the recommended NCCLS modified technique (M27-A2). The MICs of itraconazole obtained oscillated between 0.062 and 4.0 μg/ml, and those of terbinafine oscillated between 0.007 and 0.50 μg/ml; therefore, terbinafine showed greater in vitro activity.
Control design of matrix converter system

The presented paper deals with matrix converter induction motor drive with emphasis on the PWM modulation strategy design. The special digital control system was used. This system consists of two personal computers. The first one serves for monitoring purposes only, the second one is equipped with a common interface card and works in real time. The most of the contemporary modulation strategies are able to provide practically sinusoidal waveforms of the input and output currents with negligible low order harmonics, and to control the input displacement factor. Sophisticated pulse width modulation strategies in terms of various optimization criteria are known in case of indirect frequency converters, whereas both the inverter and the rectifier can be operated with pulse width modulation. The instantaneous state of both the output and the input converter waveforms depends at any time on the switch state of the converter power switches. Suitable switch states sequence of the nine matrix converter switches can be indirectly derived from the given switch states sequence of the twelve switchers of the indirect frequency converter. Attention is paid to overmodulation possibilities, too.
Glial response during cuprizone-induced de- and remyelination in the CNS: lessons learned

Although astrogliosis and microglia activation are characteristic features of multiple sclerosis (MS) and other central nervous system (CNS) lesions the exact functions of these events are not fully understood. Animal models help to understand the complex interplay between the different cell types of the CNS and uncover general mechanisms of damage and repair of myelin sheaths. The so called cuprizone model is a toxic model of demyelination in the CNS white and gray matter, which lacks an autoimmune component. Cuprizone induces apoptosis of mature oligodendrocytes that leads to a robust demyelination and profound activation of both astrocytes and microglia with regional heterogeneity between different white and gray matter regions. Although not suitable to study autoimmune mediated demyelination, this model is extremely helpful to elucidate basic cellular and molecular mechanisms during de- and particularly remyelination independently of interactions with peripheral immune cells. Phagocytosis and removal of damaged myelin seems to be one of the major roles of microglia in this model and it is well known that removal of myelin debris is a prerequisite of successful remyelination. Furthermore, microglia provide several signals that support remyelination. The role of astrocytes during de- and remyelination is not well defined. Both supportive and destructive functions have been suggested. Using the cuprizone model we could demonstrate that there is an important crosstalk between astrocytes and microglia. In this review we focus on the role of glial reactions and interaction in the cuprizone model. Advantages and limitations of as well as its potential therapeutic relevance for the human disease MS are critically discussed in comparison to other animal models.
Comparison of the Incidence of Parenchymal Hematoma and Poor Outcome in Patients with Carotid Terminus Occlusion Treated with Intra-Arterial Urokinase Alone or with Combined IV rtPA and Intra-Arterial Urokinase

BACKGROUND AND PURPOSE: Patients with acute CTO generally have a poor prognosis, despite IV or IA thrombolytic treatment. The goal of this study was to analyze the results of patients with CTO who had IA urokinase treatment with or without initial IV rtPA based on a bridging protocol. MATERIALS AND METHODS: Sixteen consecutive patients with acute ischemic stroke due to CTO who had combined IV and IA or a single IA thrombolytic treatment were enrolled. The baseline characteristics and prognosis were described. The patients who did and did not develop a PH shortly after treatment were compared. RESULTS: The mean age was 66.4 years, and the median initial NIHSS score was 17. The median dose of IA urokinase was 320,000 U, and recanalization (TICI grade II-III) was achieved in 12 patients (75%). However, 5 patients died and 10 patients had poor prognosis with mRS 5–6 at discharge. Six patients (37.5%) with a PH had a higher NIHSS score 1 day after treatment (26.7 versus 13.6, P = .002), and they had more frequent mortality (66.7% versus 10.0%, P = .018) and worse prognosis (mRS 5–6; 100% versus 40%, P = .016) at discharge than patients without PH. CONCLUSIONS: Patients with CTO who received IA urokinase treatment based on a bridging protocol had a poor prognosis. The development of PH might affect this outcome.
Confirmation strategy for document retrieval systems with spoken dialog interface

Adequate confirmation is indispensable in spoken dialog systems to eliminate misunderstandings caused by speech recognition errors. Spoken language also inherently includes redundant expressions such as disfluency and out-of-domain phrases, which do not contribute to task achievement. It is easy to define a set of keywords to be confirmed for conventional database query tasks, but not straightforward in general document retrieval tasks. In this paper, we propose two statistical measures for identifying portions to be confirmed. A relevance score (RS) represents matching degree with the document set. A significance score (SS) detects portions that consequently affect the retrieval results. With these measures, the system can generate confirmation prior to and posterior to the retrieval, respectively. The strategy is implemented and evaluated with retrieval from software support knowledge base of 40K entries. It is shown that the proposed strategy using the two measures is more efficient than using the conventional confidence measure.
The drive fatigue pattern monitor for haul truck drivers in surface mining operations

Haul trucks are one of the most important transportations in the operations of large surface mines. The traffic accidents involved haul trucks result in serious damages on the vehicles, even the loss of the drivers' lives. Drive fatigue is one of the key features that cause traffic accidents in surface mining operations. The light varies and driver's behaviors in the cabin increase the difficulties of drive fatigue monitoring. This paper developed the haul truck driver fatigue monitoring prealarm methodologies using real-time, non-intrusive machine vision technologies. It detected and tracked the driver's face by using AdaBoost algorithm. It extracted the key features of driver's eyes by template matching algorithm. This paper improved the SNAKE algorithms in the monitored image processing and pattern recognition, which increased the efficiency of the fatigue detection under the light variations and different driver's gestures. It observed the eye's closure duration and calculated the cumulative total percentage of a particular time (PERCLOS) to determine the driver's fatigue status. This research was applied to a driver of the haul truck in a coal mine. The detection results indicate that it can identify the driver's fatigue. The further research of the drive fatigue monitoring will increase the reliability and reduce uncertainty in surface mining operations.
Emerging trends in recent research on motivation in learning contexts

At the conclusion of this book, it becomes clear that the case for understanding and researching motivation in learning contexts is strong. Overall, and despite different theoretical underpinnings, units of analysis and research foci, a number of common trends emerge across the fourteen chapters. Six conceptual shifts in the way research seems to be evolving, and eight methodological implications are discussed in turn, with reference to material from different chapters. Given the richness of the contributors, referencing is obviously limited and illustrative.