Miracle-dz/UniFAR-FTUs huggingface dataset:
Processing/Activation of At Least Four Interleukin-1β Converting Enzyme–like Proteases Occurs during the Execution Phase of Apoptosis in Human Monocytic Tumor Cells

Identification of the processing/activation of multiple interleukin-1β converting enzyme (ICE)–like proteases and their target substrates in the intact cell is critical to our understanding of the apoptotic process. In this study we demonstrate processing/activation of at least four ICE-like proteases during the execution phase of apoptosis in human monocytic tumor THP.1 cells. Apoptosis was accompanied by processing of Ich-1, CPP32, and Mch3α to their catalytically active subunits, and lysates from these cells displayed a proteolytic activity with kinetics, characteristic of CPP32/Mch3α but not of ICE. Fluorescence-activated cell sorting was used to obtain pure populations of normal and apoptotic cells. In apoptotic cells, extensive cleavage of Ich-1, CPP32, and Mch3α was observed together with proteolysis of the ICE-like protease substrates, poly (ADP-ribose) polymerase (PARP), the 70-kD protein component of U1 small nuclear ribonucleoprotein (U170K), and lamins A/B. In contrast, no cleavage of CPP32, Mch3α or the substrates was observed in normal cells. In cells exposed to an apoptotic stimulus, some processing of Ich-1 was detected in morphologically normal cells, suggesting that cleavage of Ich-1 may occur early in the apoptotic process. The ICE-like protease inhibitor, benzyloxycarbonyl-Val-Ala-Asp (OMe) fluoromethyl ketone (Z-VAD.FMK), inhibited apoptosis and cleavage of Ich-1, CPP32, Mch3α, Mch2α, PARP, U1-70K, and lamins. These results suggest that Z-VAD.FMK inhibits apoptosis by inhibiting a key effector protease upstream of Ich-1, CPP32, Mch3α, and Mch2α. Together these observations demonstrate that processing/activation of Ich-1, CPP32, Mch3α, and Mch2α accompanies the execution phase of apoptosis in THP.1 cells. This is the first demonstration of the activation of at least four ICE-like proteases in apoptotic cells, providing further evidence for a requirement for the activation of multiple ICE-like proteases during apoptosis.
Centering in-the-Large: Computing Referential Discourse Segments

We specify an algorithm that builds up a hierarchy of referential discourse segments from local centering data. The spatial extension and nesting of these discourse segments constrain the reachability of potential antecedents of an anaphoric expression beyond the local level of adjacent center pairs. Thus, the centering model is scaled up to the level of the global referential structure of discourse. An empirical evaluation of the algorithm is supplied.
Three-dimensional image visualization methods for hyperthemia treatment planning system

In order to reduce the risk of themoseeds hyperthemia clinical operation, an intuitive 3-D virtual patient needs to be reconstructed by the preoperative treatment planning system. The reconstruct results can supply the geometric physiological information of lesions and their surrounding tissues to form an optimal operation planning. In this study, the construction of 3D image intuitive environment of diagnosis and treatment in the system was investigated. On the basis of 2-D DICOM medical images, the 3-D data field was established and visually rendered, and the methods of volume rendering and surface rendering were correspondingly investigated. Results show that these two algorithms can provide specific rendering models for different organs. Volume rendering method can show good effects for 3-D body visualization and real-time interaction, and surface rendering method can extract iso-surface models to support tissue segmentation display and build thermal dose field.
Why you follow: a classification scheme for twitter follow links

Twitter is used for various purposes, such as, information publishing/gathering, open discussions, and personal communications. As a result, there are various types of follow links. In this paper, we propose a scheme for classifying follow links according to the followers' intention. The scheme consists of three axes: user-orientation, content-orientation, and mutuality. The combination of these three axes can classify most major types of follow links. Our experimental results suggest that the type of a follow link does not solely depend on the type of the followee nor solely on the type of the follower. The results also suggest that the proposed three axes are highly independent of one another.
Epiphenomenal Grammar Acquisition with GSG

As a step toward conversational systems that allow for a more natural human-computer interaction, we rep6r~ on GSG, a system that, while providing a natural-l~nguage interface to a variety of applications, engages in clarification dialogues with the end user through which new semantic mappings are dynamically acquired. GsG exploits taskand language-dependent information but is fully taskand language-independent in its architecture and strategies.
NLPR at TREC 2005: HARD Experiments

1 Overview It is the third time that Chinese Information Processing Group of NLPR takes part in TREC. In the past, we participated in Novelty track and Robust track, in which we had evaluated our two key notions: Window-based Retrieval Algorithm and Result Emerging Strategy [1][2]. This year we focus on investigating the significance of relevance feedback, so HARD track is our best choice. HARD2005 is very different from that in the past two years. Firstly, Metadata is removed from topic description so that the topic description in HARD is the same as that of Robust track. Secondly, passage retrieval is cancelled this year. The paper introduces our work on HARD Track in TREC 2005, mainly (1) we propose a new feature selection method for query expansion in relevance feedback; (2) we adopt some query expansion methods. Our paper is organized as follows. Section 2 introduces our system, a new term selection algorithm for query expansion, and our clarification forms. Section 3 presents our query expansion methods. In section 4 experimental results are given, and finally we conclude our work in section 5. As to the retrieval model, Lemur toolkit developed by UMASS and CMU includes six different retrieval models [3]. In order to facilitate our work, we use Okapi BM25 [4][5] as the retrieval model, which is based on the probability model of Robertson and Sparck Jones. The formula is described as follow: 3 1 2 3 (1) (1) | | k qtf k tf avdl dl w k Q K tf k qtf avdl dl + + − = + ⋅ ⋅ + + + (1) 1 ((1) /) K k b b dl avdl = − + ⋅
Histone Deacetylase 3 Is Critical in Endothelial Survival and Atherosclerosis Development in Response to Disturbed Flow

Background— Histone deacetylase 3 (HDAC3) is known to play a crucial role in the differentiation of endothelial progenitors. The role of HDAC3 in mature endothelial cells, however, is not well understood. Here, we investigated the function of HDAC3 in preserving endothelial integrity in areas of disturbed blood flow, ie, bifurcation areas prone to atherosclerosis development. Methods and Results— En face staining of aortas from apolipoprotein E–knockout mice revealed increased expression of HDAC3, specifically in these branching areas in vivo, whereas rapid upregulation of HDAC3 protein was observed in endothelial cells exposed to disturbed flow in vitro. Interestingly, phosphorylation of HDAC3 at serine/threonine was observed in these cells, suggesting that disturbed flow leads to posttranscriptional modification and stabilization of the HDAC3 protein. Coimmunoprecipitation experiments showed that HDAC3 and Akt form a complex. Using a series of constructs harboring deletions, we found residues 136 to 206 of HDAC3 to be crucial in this interaction. Enforced expression of HDAC3 resulted in increased phosphorylation of Akt and upregulation of its kinase activity. In line with these findings, knockdown of HDAC3 with lentiviral vectors (shHDAC3) led to a dramatic decrease in cell survival accompanied by apoptosis in endothelial cells. In aortic isografts of apolipoprotein E–knockout mice treated with shHDAC3, a robust atherosclerotic lesion was formed. Surprisingly, 3 of the 8 mice that received shHDAC3-infected grafts died within 2 days after the operation. Miller staining of the isografts revealed disruption of the basement membrane and rupture of the vessel. Conclusions— Our findings demonstrated that HDAC3 serves as an essential prosurvival molecule with a critical role in maintaining the endothelial integrity via Akt activation and that severe atherosclerosis and vessel rupture in isografted vessels of apolipoprotein E–knockout mice occur when HDAC3 is knocked down.
On Solvability of Boundary Value Problems in Elastoplasticity

In the paper the existence of a solution to the three dimensional elastoplastic problem with the Prandtl-Reuss constitutive law and the Neumann boundary conditions is obtained. The proof is based on a suitable combination of the parabolic regularization of equations and the penalty method for the elastoplastic yield condition. The method is applied in the case of the domain with smooth boundary as well as in the case of an interior crack. It is shown that the weak solutions to the elastoplastic problem satisfying the variational inequality meet all boundary conditions.
Wide-area long-range unidirectional sensor (WALRUS) network

Networks consisting of low-cost wireless sensors have been the subject of extensive research, with applications ranging from environmental monitoring to building control systems, to name a few. In this paper we consider networks intended to provide wide area coverage of one or more physical, chemical or biological parameters. We envision a target average data rate per sensor of 1-5 bps and transmission ranges of up to 100 m. Unlike conventional networks, the goal of wide-area parameter characterization can be achieved even with less than 100% node reliability, a feature that allows us to propose a novel ultra-low-cost architecture based on redundant sensors. To achieve the low-cost goal, sensor nodes include no receivers, and they transmit their information to a central reader using radio backscatter. This communication modality makes it possible to achieve a few years of battery life with small and inexpensive batteries. Performance impact due to absence of individual reception acknowledgement in this unidirectional communication channel is offset mainly by transmitter spatial diversity achieved through deployment of additional nodes. We describe the design of the system and its components, and analyze its performance characteristics
Articulated Model Detection in Range Images

We present a method for detecting the placement of complex articulated models in 3D partial view range images. Specifically, we detect the placement of the parts of an articulated model in a scene. This is a difficult task because the object can be substantially occluded by clutter or portions may not be observed. Our approach uses detectors to provide initial location hypotheses for parts. We expand upon these hypotheses, using a mechanism for dealing with missing parts. We then create a probabilistic model to determine the most likely placement of parts based on individual and pairwise potentials. We devise efficient scoring mechanisms to evaluate placements and provide these potentials. During a post processing phase we further refine our results, providing the final pose of the model in the scene. In this thesis, I present our algorithm and results of successfully running it on two data sets of objects of 15 or more parts.
Performance of typical children on the Sensory Profile: an item analysis.

OBJECTIVES The purpose of this study was to obtain data about typical children on the 99-item Sensory Profile, a newly developed tool derived from sensory history items reported in the literature and designed to assess children's responses to commonly occurring sensory events. METHOD Parents of 64 typical children 3 to 10 years of age completed the Sensory Profile; parents used a five-point Likert scale to report the percentage of time their children engaged in each behavior. Researchers then analyzed these percentages to determine differences by age and gender. RESULTS Sixty-seven of the items on the Sensory Profile were found to be uncommon for these typical children. On further analysis with a multivariate analysis of variance and appropriate follow-up procedures, one item was more common for younger children, and four items were more common for girls. CONCLUSION Two thirds of the items on the Sensory Profile were uncommon for typical children and thus may contribute useful information about children with disabilities who respond to these sensory events.
A BSP approach to composite network analysis

The pervasive availability of personal devices such as smartphones, smartwatches, and in-car navigation systems combined with the widespread acceptance of social networks has resulted in an explosion of data about individuals and their interactions in the society. The presence of multiple social networks such as FaceBook, Twitter, and Google Plus results in fragmentation of an individual's online presence. As such, the notion of interacting multiple networks or composite networks is gaining popularity. In this paper, we present a first-of-a-kind framework to analyze such composite networks in an efficient and scalable manner. We propose to use the BSP programming model to analyze composite networks and show the inportance of analyzing such composite networks as opposed to individual networks separately through preliminary experiments on realworld data.
The MIT Alewife Machine

A variety of models for parallel architectures, such as shared memory, message passing, and data flow, have converged in the recent past to a hybrid architecture form called distributed shared memory (DSM). Alewife, an early prototype of such DSM architectures, uses hybrid software and hardware mechanisms to support coherent shared memory, efficient user level messaging, fine grain synchronization, and latency tolerance. Alewife supports up to 512 processing nodes connected over a scalable and cost effective mesh network at a constant cost per node. Four mechanisms combine to achieve Alewife's goals of scalability and programmability: software extended coherent shared memory provides a global, linear address space; integrated message passing allows compiler and operating system designers to provide efficient communication and synchronization; support for fine grain computation allows many processors to cooperate on small problem sizes; and latency tolerance mechanisms-including block multithreading and prefetching-mask unavoidable delays due to communication. Extensive results from microbenchmarks, together with over a dozen complete applications running on a 32-node prototype, demonstrate that integrating message passing with shared memory enables a cost efficient solution to the cache coherence problem and provides a rich set of programming primitives. Our results further show that messaging and shared memory operations are both important because each helps the programmer to achieve the best performance for various machine configurations.
Privacy Enhancing Technologies for the Internet III : Ten Years Later ∗

In 1997 with Wagner and Brewer, and again in 2002, we looked at the hen-current state of privacy-enhancing technologies (PETs) for the Internet. [ 27, 26] Now, in 2007, we take a third look. Technologies to help users maintain their privacy online ar e as important today as ever before—if not more so. Identity theft is the fastest-growing crime in the US tod ay [47] and it is all too easy for would-be identity thieves to harvest personal information from the o nline trails Internet users leave every day. Losses of large databases of personal information are an almost dai ly occurrence [2]; for example, retailers’ servers are penetrated [44], databases are traded between g over ment and private companies [36] and laptops containing social security numbers are stolen [35] .
Content Augmentation for Mixed-Mode News Broadcasts

Rich News, a system that augments news broadcasts with textual content, is described. The system identifies individual stories in news broadcasts, and annotates them with related content from the World Wide Web. The web content is subsequently semantically analysed, and used to produce summary information for each news story. This content can then be delivered to users as part of an interactive television broadcast, or used to create semantically enhanced electronic programme guides. It also enables sophisticated search and browsing of news stories via a web interface. Rich News could be deployed either by broadcasters, or on digital video recorders in viewers’ homes, and allows the creation of new personalized media experiences that integrate television and web content into one unified viewing experience.
Sum-of-squares Lower Bounds for Planted Clique

Finding cliques in random graphs and the closely related "planted" clique variant, where a clique of size k is planted in a random G(n,1/2) graph, have been the focus of substantial study in algorithm design. Despite much effort, the best known polynomial-time algorithms only solve the problem for k = Θ(√n). In this paper we study the complexity of the planted clique problem under algorithms from the Sum-Of-Squares hierarchy. We prove the first average case lower bound for this model: for almost all graphs in G(n,1/2), r rounds of the SOS hierarchy cannot find a planted k-clique unless k ≥ (√n/log n)1/rCr. Thus, for any constant number of rounds planted cliques of size no(1) cannot be found by this powerful class of algorithms. This is shown via an integrability gap for the natural formulation of maximum clique problem on random graphs for SOS and Lasserre hierarchies, which in turn follow from degree lower bounds for the Positivestellensatz proof system. We follow the usual recipe for such proofs. First, we introduce a natural "dual certificate" (also known as a "vector-solution" or "pseudo-expectation") for the given system of polynomial equations representing the problem for every fixed input graph. Then we show that the matrix associated with this dual certificate is PSD (positive semi-definite) with high probability over the choice of the input graph.This requires the use of certain tools. One is the theory of association schemes, and in particular the eigenspaces and eigenvalues of the Johnson scheme. Another is a combinatorial method we develop to compute (via traces) norm bounds for certain random matrices whose entries are highly dependent; we hope this method will be useful elsewhere.
EFFECT OF DIET ON CONDITION INDICES IN BLACK-TAILED JACKRABBITS

Changes in blood, urine and physical condition indices in 23 adult male black-tailed jackrabbits (Lepus californicus) with ad libitum feeding and 25% feed restriction were measured over a 2 wk period from 30 May to 12 June 1988. Feed restricted jackrabbits had (1) lower posttrial body weights and kidney fat indices, (2) higher femur marrow fat, serum bilirubin and cortisol concentrations, and adrenal cortex width, and (3) depressed immune function. No single index alone could best measure the nutritional status of these jackrabbits.
Phase transformations in rapid thermal processed lead zirconate titanate

The crystallization kinetics of the pyrochlore to perovskite phase transformation in lead zirconate titanate (PZT) thin films have been analyzed using rapid thermal processing (RTP). Sol-gel PZT thin films, fabricated on platinum electrodes, were annealed at 550 °C to 650 °C with hold times ranging from 1 s to 5 min. Glancing angle x-ray diffraction (XRD) was used for depth profiling to identify the location of phases in the films. Transmission electron microscopy (TEM) provided information on grain structure, nucleation, and growth. The phase information was correlated to the ferroelectric and dielectric properties. The perovskite phase nucleated in the pyrochlore phase throughout the film thickness, and at 650 °C the transformation was complete in 15 s. Fast growing (100) PZT nucleated at the platinum and consumed a small-grained matrix until a columnar structure was obtained. A ramp rate of 100 °C/s was sufficiently fast to prevent transformation during heating and allowed the direct application of an Avrami model for transformation kinetics. An activation energy of 610 kJ/mol was determined.
Revving up Natural Killer Cells and Cytokine-Induced Killer Cells Against Hematological Malignancies

Natural killer (NK) cells belong to innate immunity and exhibit cytolytic activity against infectious pathogens and tumor cells. NK-cell function is finely tuned by receptors that transduce inhibitory or activating signals, such as killer immunoglobulin-like receptors, NK Group 2 member D (NKG2D), NKG2A/CD94, NKp46, and others, and recognize both foreign and self-antigens expressed by NK-susceptible targets. Recent insights into NK-cell developmental intermediates have translated into a more accurate definition of culture conditions for the in vitro generation and propagation of human NK cells. In this respect, interleukin (IL)-15 and IL-21 are instrumental in driving NK-cell differentiation and maturation, and hold great promise for the design of optimal NK-cell culture protocols. Cytokine-induced killer (CIK) cells possess phenotypic and functional hallmarks of both T cells and NK cells. Similar to T cells, they express CD3 and are expandable in culture, while not requiring functional priming for in vivo activity, like NK cells. CIK cells may offer some advantages over other cell therapy products, including ease of in vitro propagation and no need for exogenous administration of IL-2 for in vivo priming. NK cells and CIK cells can be expanded using a variety of clinical-grade approaches, before their infusion into patients with cancer. Herein, we discuss GMP-compliant strategies to isolate and expand human NK and CIK cells for immunotherapy purposes, focusing on clinical trials of adoptive transfer to patients with hematological malignancies.
Just-in-time query retrieval over partially indexed data on structured P2P overlays

Structured peer-to-peer (P2P) overlays have been successfully employed in many applications to locate content. However, they have been less effective in handling massive amounts of data because of the high overhead of maintaining indexes. In this paper, we propose PISCES, a Peer-based system that Indexes Selected Content for Efficient Search. Unlike traditional approaches that index all data, PISCES identifies a subset of tuples to index based on some criteria (such as query frequency, update frequency, index cost, etc.). In addition, a coarse-grained range index is built to facilitate the processing of queries that cannot be fully answered by the tuple-level index. More importantly, PISCES can adaptively self-tune to optimize the subset of tuples to be indexed. That is, the (partial) index in PISCES is built in a Just-In-Time (JIT) manner. Beneficial tuples for current users are pulled for indexing while indexed tuples with infrequent access and high maintenance cost are discarded. We also introduce a light-weight monitoring scheme for structured networks to collect the necessary statistics. We have conducted an extensive experimental study on PlanetLab to illustrate the feasibility, practicality and efficiency of PISCES. The results show that PISCES incurs lower maintenance cost and offers better search and query efficiency compared to existing methods.