Miracle-dz/UniFAR-FTUs huggingface dataset:
Identification of Caspase Cleavage Sites in KSHV Latency-Associated Nuclear Antigen and Their Effects on Caspase-Related Host Defense Responses

Kaposi’s sarcoma-associated herpesvirus (KSHV), also known as human herpesvirus-8, is the causative agent of three hyperproliferative disorders: Kaposi’s sarcoma, primary effusion lymphoma (PEL) and multicentric Castleman’s disease. During viral latency a small subset of viral genes are produced, including KSHV latency-associated nuclear antigen (LANA), which help the virus thwart cellular defense responses. We found that exposure of KSHV-infected cells to oxidative stress, or other inducers of apoptosis and caspase activation, led to processing of LANA and that this processing could be inhibited with the pan-caspase inhibitor Z-VAD-FMK. Using sequence, peptide, and mutational analysis, two caspase cleavage sites within LANA were identified: a site for caspase-3 type caspases at the N-terminus and a site for caspase-1 and-3 type caspases at the C-terminus. Using LANA expression plasmids, we demonstrated that mutation of these cleavage sites prevents caspase-1 and caspase-3 processing of LANA. This indicates that these are the principal sites that are susceptible to caspase cleavage. Using peptides spanning the identified LANA cleavage sites, we show that caspase activity can be inhibited in vitro and that a cell-permeable peptide spanning the C-terminal cleavage site could inhibit cleavage of poly (ADP-ribose) polymerase and increase viability in cells undergoing etoposide-induced apoptosis. The C-terminal peptide of LANA also inhibited interleukin-1beta (IL-1β) production from lipopolysaccharide-treated THP-1 cells by more than 50%. Furthermore, mutation of the two cleavage sites in LANA led to a significant increase in IL-1β production in transfected THP-1 cells; this provides evidence that these sites function to blunt the inflammasome, which is known to be activated in latently infected PEL cells. These results suggest that specific caspase cleavage sites in KSHV LANA function to blunt apoptosis as well as interfere with the caspase-1-mediated inflammasome, thus thwarting key cellular defense mechanisms.
Manuscript Submitted to the Ieee Transactions on Circuits and Systems for Video Technology a New Fast and Eecient Image Codec Based on Set Partitioning in Hierarchical Trees

Embedded zerotree wavelet (EZW) coding, introduced by Shapiro 1], is a very eeective and computationally simple technique for image compression. Here we offer an alternative explanation of the principles of its operation, so that the reasons for its excellent performance can be better understood. These principles are partial ordering by magnitude with a set partitioning sorting algorithm, ordered bit plane transmission, and exploitation of self-similarity across diierent scales of an image wavelet transform. Moreover, we present a new and diierent implementation which provides even better performance than the extension of the EZW described in 6], which surpassed that in 1]. The image coding results, calculated from actual le sizes and images reconstructed by the decoding algorithm, are either comparable to or surpass previous results obtained through much more sophisticated and computationally complex methods. In addition, the new coding and decoding procedures are extremely fast, and they can be made even faster, with only small loss in performance, by omitting entropy coding of the bit stream by arithmetic code.
Similar-Part Approximation Using Invariant Feature Descriptors

This thesis describes the implementation of a new algorithm for identifying similar parts in multiple images. Visual words of Scale Invariant Feature Transform descriptors are used to describe parts of images and Locality Sensitive Hashing is utilized for quick similar-part lookup. This algorithm proves very effective on identical items of different sizes and rotations, and moderately effective on similar yet unidentical items of the same class. Suggestions are made for apply this approximation to building object grammars. Further exploration on feature descriptors and distance functions are needed for better performance accuracy.
Revising Z: semantics and logic

Note to editor/referees: We provide full details of proofs in this draft. Naturally we would envisage most of this being removed from a published version. However, even with all proofs removed, the paper is around 30 pages long (in the jounal style). With a sensible amount of proof detail it is 34 pages long. We appreciate that the nominal upper bound for papers is currently 20 pages. One possible solution would be to reform this draft into two papers of 17 pages: roughly breaking the material at the end of the current section 5. Your advice would be appreciated. Abstract. We introduce a simple speciication logic Z C comprising a logic and semantics (in ZF set theory). We then provide an interpretation for (a rational reconstruction of) the speciication language Z within Z C. As a result we obtain a sound logic for Z , including the schema calculus. A consequence of our formalisation is a critique of a number of concepts used in Z. We demonstrate that the complications and confusions which these concepts introduce can be avoided without compromising expressibility.
Seasonal selection and resource dynamics in a seasonally polyphenic butterfly

Seasonal polyphenisms are widespread in nature, yet the selective pressures responsible for their evolution remain poorly understood. Previous work has largely focussed either on the developmental regulation of seasonal polyphenisms or putative ‘top‐down’ selective pressures such as predation that may have acted to drive phenotypic divergence. Much less is known about the influence of seasonal variation in resource availability or seasonal selection on optimal resource allocation. We studied seasonal variation in resource availability, uptake and allocation in Araschnia levana L. , a butterfly species that exhibits a striking seasonal colour polyphenism consisting of predominantly orange ‘spring form’ adults and black‐and‐white ‘summer form’ adults. ‘Spring form’ individuals develop as larvae in the late summer, enter a pupal diapause in the fall and emerge in the spring, whereas ‘summer form’ individuals develop directly during the summer months. We find evidence for seasonal declines in host plant quality, and we identify similar reductions in resource uptake in late summer, ‘spring form’ larvae. Further, we report shifts in the body composition of diapausing ‘spring form’ pupae consistent with a physiological cost to overwintering. However, these differences do not translate into detectable differences in adult body composition. Instead, we find minor seasonal differences in adult body composition consistent with augmented flight capacity in ‘summer form’ adults. In comparison, we find much stronger signatures of sex‐specific selection on patterns of resource uptake and allocation. Our results indicate that resource dynamics in A. levana are shaped by seasonal fluctuations in host plant nutrition, climatic conditions and intraspecific interactions.
3-GHz Silicon Photodiodes Integrated in a 0.18-$\mu$m CMOS Technology

A new PIN photodiode (PD) structure with deep n-well (DNW) fabricated in an epitaxial substrate complementary metal-oxide-semiconductor (epi-CMOS) process is presented. The DNW buried inside the epitaxial layer intensifies the electric field deep inside the epi-layer significantly, and helps the electrons generated inside the epi-layer to drift faster to the cathode. Therefore, this new structure reduces the carrier transit time and enhances the PD bandwidth. A PD with an area of 70 times 70 mum2 fabricated in a 0.18-mum epi-CMOS achieves 3-dB bandwidth of 3.1 GHz in the small signal and 2.6 GHz in the large signal, both with a 15-V bias voltage and 850-nm optical illumination. The responsivity is measured 0.14 A/W, corresponding to a quantum efficiency of 20%, at low bias. The responsivity increases to 0.4 A/W or 58% quantum efficiency at 16.2-V bias in the avalanche mode.
Quaternary structure of the specific p53–DNA complex reveals the mechanism of p53 mutant dominance

The p53 tumour suppressor is a transcriptional activator that controls cell fate in response to various stresses. p53 can initiate cell cycle arrest, senescence and/or apoptosis via transactivation of p53 target genes, thus preventing cancer onset. Mutations that impair p53 usually occur in the core domain and negate the p53 sequence-specific DNA binding. Moreover, these mutations exhibit a dominant negative effect on the remaining wild-type p53. Here, we report the cryo electron microscopy structure of the full-length p53 tetramer bound to a DNA-encoding transcription factor response element (RE) at a resolution of 21 Å. While two core domains from both dimers of the p53 tetramer interact with DNA within the complex, the other two core domains remain available for binding another DNA site. This finding helps to explain the dominant negative effect of p53 mutants based on the fact that p53 dimers are formed co-translationally before the whole tetramer assembles; therefore, a single mutant dimer would prevent the p53 tetramer from binding DNA. The structure indicates that the Achilles’ heel of p53 is in its dimer-of-dimers organization, thus the tetramer activity can be negated by mutation in only one allele followed by tumourigenesis.
A Hybrid Dynamical Extension of Averaging

We extend a smooth dynamical systems averaging technique to a class of hybrid systems with a limit cycle that is particularly relevant to the synthesis of stable legged gaits. After introducing a definition of hybrid averageability sufficient to recover the classical result, we provide a simple illustration of its applicability to legged locomotion and conclude with some rather more speculative remarks concerning the prospects for further generalization of these ideas.
Proxy Tk: a java applet user interface toolkit for Tcl

Proxy Tk allows a Tcl program to provide a highly interactive web-browser user interface, without requiring the end user to download additional software. It uses a thin client design, where a server-side Tcl application communicates with a very small generic Java applet running in the browser, sending it commands to create and modify widgets, and receiving events from the user. A Tk-like layer encapsulates the communication protocols to provide a familiar programming paradigm, and allow easy porting of existing code.
Time-reversal-based imaging and inverse scattering of multiply scattering point targets

The treatment of time-reversal imaging of multiply scattering point targets developed by the present authors in Gruber et al. [“Time-reversal imaging with multiple signal classification considering multiple scattering between the targets,” J. Acoust. Soc. Am. , 115, 3042–3047 (2004)] is reformulated and extended to the estimation of the target scattering strengths using the Foldy–Lax multiple scattering model. It is shown that the time-reversal multiple signal classification (MUSIC) pseudospectrum computed using the background Green function as the steering vector yields accurate estimates of the target locations, even in the presence of strong multiple scattering between the targets, and that the target scattering strengths are readily computed from the so-determined target locations using a nonlinear iterative algorithm. The paper includes computer simulations illustrating the theory and algorithms presented in the paper.
Document Summarization and Classification using Concept and Context Similarity Analysis

2 ABSTRACT: "Document summarization and classification using concept and context similarity analysis'' deals with an information retrieval task, which aims at extracting a condensed version of the original document. A document summary is useful since it can give an overview of the original document in a shorter period of time. The main goal of a summary is to present the main ideas in a document/set of documents in a short and readable paragraph. Classification is a data mining function that assigns items in a collection to target categories of the documents. Context sensitive document indexing model based on the Bernoulli model of randomness is used for document summarization process. The lexical association between terms is used to produce a context sensitive weight to the document terms. The context sensitive indexing weights are used to compute the sentence similarity matrix and as a result, the sentences are presented in such a way that the most informative sentences appear on the top of the summary, making a positive impact on the quality of the summary
Incremental support vector machine for unlabeled data classification

Due to the wide proliferation of the Internet and telecommunication, huge amount of information has been produced as digital data format. It is impossible to classify this information with one's own hand one by one in many realistic problems, so that the research on automatic text classification has been grown. Machine learning technologies have applied in text classification. However, the traditional statistic machine learning technologies require large number of labeled training examples to learn accurately. To obtain enough training examples, we have to label on these huge training examples by hand. This paper presents a supervised learning algorithm based on support vector machine (SVM) to classify text documents more accurately by using unlabeled documents to augment available labeled training examples. Experimental results indicate that the classification with unlabeled examples using SVM is superior to the conventional classification,with labeled examples.
Peptide nucleic acid (PNA): its medical and biotechnical applications and promise for the future

Synthetic molecules that can bind with high sequence specificity to a chosen target in a gene sequence are of major interest in medicinal and biotechnological contexts. They show promise for the development of gene therapeutic agents, diagnostic devices for genetic analysis, and as molecular tools for nucleic acid manipulations. Peptide nucleic acid (PNA) is a nucleic acid analog in which the sugar phosphate backbone of natural nucleic acid has been replaced by a synthetic peptide backbone usually formed from N‐(2‐amino‐ethyl)‐glycine units, resulting in an achiral and uncharged mimic. It is chemically stable and resistant to hydrolytic (enzymatic) cleavage and thus not expected to be degraded inside a living cell. PNA is capable of sequence‐specific recognition of DNA and RNA obeying the Watson‐Crick hydrogen bonding scheme, and the hybrid complexes exhibit extraordinary thermal stability and unique ionic strength effects. It may also recognize duplex homopurine sequences of DNA to which it binds by strand invasion, forming a stable PNA–DNA–PNA triplex with a looped‐out DNA strand. Since its discovery, PNA has attracted major attention at the interface of chemistry and biology because of its interesting chemical, physical, and biological properties and its potential to act as an active component for diagnostic as well as pharmaceutical applications. In vitro studies indicate that PNA could inhibit both transcription and translation of genes to which it has been targeted, which holds promise for its use for antigene and antisense therapy. However, as with other high molecular mass drugs, the delivery of PNA, involving passage through the cell membrane, appears to be a general problem. —Ray, A. , Norden, B. Peptide nucleic acid (PNA): its medical and biotechnical applications and promise for the future. FASEB J. 14, 1041–1060 (2000)
Qualitative Modeling of Object Behaviour in the Dynamic Vision System

The subject of this paper is cognitive analysis of the dynamic scene: on the base of the identified motions of objects and calculated trajectory attributes we need to analyse, evaluate and reconstruct behaviours implementing artificial intelligence methods. Dynamic scene analysis has traditionally been quantitative and typically generates large amounts of temporally evolving data. Recently, increasing interest has been shown in higher-level approaches to representing and reasoning with such data using conceptual and qualitative approaches. One motivation for the present work was the desire to apply qualitative spatio-temporal reasoning techniques to real-world dynamic scene analysis. The system presented in the paper uses the qualitative modelling method, based on the model of space and time and incomplete domain background knowledge, in the process of discovering qualitative behaviour patterns. The resulting qualitative model of the dynamic scene is the base for the comparative analysis, data interpretation and system simulation.
Joint Time-Frequency Domain Proportional Fair Scheduler with HARQ for 3GPP LTE Systems

This paper explores the potential gain of joint diversity in both frequency domain and time domain which can be exploited to achieve spectral efficiency gains whilst simultaneously facilitating QoS/fairness in an OFDMA system (particularly in 3GPP Long Term Evolution (LTE)). The performance of several joint time-frequency schedulers is investigated. Simulation results show that joint time frequency schedulers achieve significantly superior performance compared to a more conventional time domain (only) proportional fair scheduler. The joint schemes show promising throughput gain while meeting stringent fairness criteria.
Higher-Order Confidence Intervals for Stochastic Programming using Bootstrapping

We present a novel approach based on bootstrap for constructing confidence intervals for the optimal value of a stochastic programming problem. We propose a statistical estimator of the optimal value and prove under some regularity conditions of the stochastic problem that the probability coverage of the confidence intervals based on our estimator converges almost one order faster than the standard estimates. This feature allows the construction of accurate and reliable confidence intervals for applications affording only a small number of samples. The good convergence properties are demonstrated with two numerical examples.
A Study of Speech Pauses for Multilingual Time-Scaling Applications

In this paper we present a study of silent speech pauses at three different speaking rates, based on the analysis of four hours of read speech in six European languages. Our results confirm earlier observations by Campione et al. [1] that the logarithmic duration of the pauses can be well approximated by a bi-Gaussian distribution and we found this also to be true at slow and fast speaking rates. Our analysis further shows that, as far as the long speech pauses are concerned, similar strategies for speaking slowly or rapidly are used in all languages considered. For speaking slowly, speakers increase the total amount of pauses and they effectively use a wider range of pause durations. Overall, however, besides using more pauses, there appeared to be no striking change in the average pause duration, nor in the variance of the distribution of the pause durations. For speaking rapidly, speakers decrease the amount of pauses used and they refrain from using the longest pauses that occur in their normal speech. Overall, this results in a lower average duration of the pauses and a smaller variance of the pause durations.
Risk‐Sensitive Control and an Optimal Investment Model

We consider an optimal investment model in which the goal is to maximize the long‐term growth rate of expected utility of wealth. In the model, the mean returns of the securities are explicitly affected by the underlying economic factors. The utility function is HARA. The problem is reformulated as an infinite time horizon risk‐sensitive control problem. We study the dynamic programming equation associated with this control problem and derive some consequences of the investment problem.
The Current Role of Carotid Duplex Ultrasonography in the Management of Carotid Atherosclerosis: Foundations and Advances

The management of atherosclerotic carotid occlusive disease for stroke prevention has entered a time of dramatic change. Improvements in medical management have begun to challenge traditional interventional approaches to asymptomatic carotid stenosis. Simultaneously, carotid artery stenting (CAS) has emerged as an alternative to carotid endarterectomy (CE). Finally, multiple factors beyond degree of stenosis and symptom status now mitigate clinical decision making. These factors include brain perfusion, plaque morphology, and patency of intracranial collaterals (circle of Willis). With all of these changes, it seems prudent to review the role of carotid duplex ultrasonography in the management of atherosclerotic carotid occlusive disease for stroke prevention. Carotid duplex ultrasonography (CDU) for initial and serial imaging of the carotid bifurcation remains an essential component in the management of carotid bifurcation disease. However, correlative axial imaging modalities (computer tomographic angiography (CTA) and contrast-enhanced magnetic resonance angiography (CE-MRA)) increasingly aid in the assessment of individual stroke risk and are important in treatment decisions. The purpose of this paper is twofold: (1) to discuss foundations and advances in CDU and (2) to evaluate the current role of CDU, in light of other imaging modalities, in the clinical management of carotid atherosclerosis.
Automatic audio segmentation using the Generalized Likelihood Ratio

This paper presents a novel technique for segmenting an audio stream into homogeneous regions according to speaker identities, background noise, music, environmental and channel conditions. Audio segmentation is useful in audio diarization systems, which aim to annotate an input audio stream with information that attributes temporal regions of the audio into their specific sources. The segmentation method introduced in this paper is performed using the Generalized Likelihood Ratio (GLR), computed between two adjacent sliding windows over preprocessed speech. This approach is inspired by the popular segmentation method proposed by the pioneering work of Chen and Gopalakrishnan, using the bayesian information criterion (BIC) with an expanding search window. This paper will aim to identify and address the shortcomings associated with such an approach. The result obtained by the proposed segmentation strategy is evaluated on the 2002 rich transcription (RT-02) Evaluation dataset, and a miss rate of 19.47% and a false alarm rate of 16.94% is achieved at the optimal threshold.