Miracle-dz/UniFAR-FTUs huggingface dataset:
A Lagrangian optimization approach to complexity-constrained TSVQ

We present a new variable rate tree-structured vector quantizer (TSVQ) design algorithm, in which the complexity-distortion tradeoff is explicitly managed using a Lagrangian optimization approach. The algorithm is greedy and uses subvector distortion measures to lower the encoding complexity. We show that we can obtain low complexity encoders for the Gauss-Markov source with similar distortion to that observed on standard variable rate TSVQ.
E-cadherin-mediated interactions of thymic epithelial cells with CD103+ thymocytes lead to enhanced thymocyte cell proliferation

Cadherins are a family of cell adhesion molecules that mainly mediate homotypic homophilic interactions, but for E-cadherin, heterophilic interactions with the integrin αE(CD103)β7 have also been reported. In the human thymus, where thymocytes develop in close contact with thymic stromal cells, E-cadherin expression was detected on thymic epithelial cells. By immunofluorescence staining, the strongest expression of E-cadherin was observed on medullary thymic epithelial cells. These cells also express cytosolic catenins, which are necessary to form functional cadherin-catenin complexes. Regardless of their developmental stage, human thymocytes do not express E-cadherin, indicating that homophilic interactions cannot occur. Flow cytometric analysis revealed that the E-cadherin ligand CD103 is expressed on subpopulations of the early CD4- CD8- double-negative and of the more mature CD8+ single-positive thymocytes. Using an in vitro cell adhesion assay, double-negative and CD8+ single-positive thymocytes adhered strongly to isolated thymic epithelial cells. These adhesive interactions could be inhibited by antibodies against E-cadherin or CD103. CD8+ thymocytes showed a proliferative response when incubated with thymic epithelial cells. This mitogenic effect was inhibited by antibodies against CD103, which strongly indicates a direct involvement of the adhesive ligand pair CD103—E-cadherin in human thymocyte cell proliferation.
A case for document management functions on the Web

eb technology and applications are growing at a rate unprecedented for computer-based information technology. In 1996, Zona Research projected Weband Internet-related revenue would double in 1997 and then grow about 30–50% through 1999. Company intranets—using the Web to support an organization’s internal information needs—are expected to be the fastest growing component of that market. Yet, despite its impressive growth and apparent success, the immaturity of Web technology may be the most significant factor preventing its more widespread usage and adoption. This article looks at the use of the Web to support organizational work within one Fortune 500 company—Xerox Corp.—to better understand the technology’s limitations. The term “Web” has three common connotations: the physical network of servers and gateways, the actual information or content contained in the distributed web of links and nodes, and the Internet technology—an Internet operating system or computing environment with its tools—that is applied to the first two connotations. Another articulation views the Web as an interface, most often graphical, with the Internet. This article relies heavily on the second and third connotations. Like many companies, Xerox is rapidly expanding its internal Web. It has more than 200 servers and supports over 20,000 employees with Web browsers. These numbers have grown exponentially over the past year and are expected to continue to grow rapidly for the next several years. What is of particular interest in this article is that this internal Web, as an environment for supporting organizational work, is falling short of our expectations and hopes in significant ways. We suspect that our experiences are not unique, and therefore, in the interest of accelerating others’ learning, we share these experiences and our analysis of them. This article is not a proper case study [6], but rather a reflective account by three Web users (the authors). We address the following questions by examining and analyzing a sampling of Xerox’s successful and less-than-successful Web applications:
Mode effects in cultural domain analysis: comparing pile sort data collected via internet versus face-to-face interviews

Abstract This article tests whether collecting pile-sort data online produces results similar to those obtained with face-to-face methods. We collected pile sorts from 227 university students in the cultural domain of emotions. To test for mode and design effects, we randomly assigned participants to face-to-face or internet modes and to either a 15- or 30-item sort. We found no evidence of mode effects in semantic structure, but the level of agreement among respondents varied by mode, depending on the number of items in the task. Agreement was higher among online respondents in the 15-item task but among face-to-face respondents in the 30-item one. Because the central purpose of pile sorting is to elicit semantic structure, we conclude that online data collection is a viable option for most researchers, but the mode effect in level of agreement implies that other design elements may affect comparability of face-to-face and web-based methods.
Predicting Search Satisfaction Metrics with Interleaved Comparisons

The gold standard for online retrieval evaluation is AB testing. Rooted in the idea of a controlled experiment, AB tests compare the performance of an experimental system (treatment) on one sample of the user population, to that of a baseline system (control) on another sample. Given an online evaluation metric that accurately reflects user satisfaction, these tests enjoy high validity. However, due to the high variance across users, these comparisons often have low sensitivity, requiring millions of queries to detect statistically significant differences between systems. Interleaving is an alternative online evaluation approach, where each user is presented with a combination of results from both the control and treatment systems. Compared to AB tests, interleaving has been shown to be substantially more sensitive. However, interleaving methods have so far focused on user clicks only, and lack support for more sophisticated user satisfaction metrics as used in AB testing. In this paper we present the first method for integrating user satisfaction metrics with interleaving. We show how interleaving can be extended to (1) directly match user signals and parameters of AB metrics, and (2) how parameterized interleaving credit functions can be automatically calibrated to predict AB outcomes. We also develop a new method for estimating the relative sensitivity of interleaving and AB metrics, and show that our interleaving credit functions improve agreement with AB metrics without sacrificing sensitivity. Our results, using 38 large-scale online experiments en- compassing over 3 billion clicks in a web search setting, demonstrate up to a 22% improvement in agreement with AB metrics (constituting over a 50% error reduction), while maintaining sensitivity of one to two orders of magnitude above the AB tests. This paves the way towards more sensitive and accurate online evaluation.
Methodological Framework: Discovering Foods or Nutrients with a Causative Influence on Body Weight in Free-Living Settings

A significant increase in food availability has been implicated in the worldwide obesity epidemic, and there is significant interest in understanding if specific foods may contribute to weight gain or aid in weight loss. Many foods have been studied in controlled laboratory studies or short-term studies, and these findings are often the basis for food-based public health recommendations to reduce or prevent obesity. Unfortunately, often these findings are not applicable to free-living settings where many interacting factors influence energy balance and body weight. Therefore, a proposed set of evidence criteria for making a food-based public health recommendation to reduce or prevent obesity is outlined and discussed herein, to serve as a basis for future committee or panel discussion and formalization. Using these criteria as a basis for making strong evidence-based recommendations will improve the state of science and policy in this area.
MigBSP: A Novel Migration Model for Bulk-Synchronous Parallel Processes Rescheduling

We have developed a model called MigBSP that controls processes rescheduling in BSP (Bulk Synchronous Parallel)applications. A BSP application is composed by one or more supersteps, each one containing both computation and communication phases followed by a synchronization barrier. Since the barrier waits for the slowest process, MigBSP’s final idea is to adjust the processes location in order to reduce the supersteps’ times. Considering the scope of the BSP model, the novel ideas of MigBSPare: (i) combination of three metrics - Memory, Computation and Communication - to measure the potential of migration of each BSP process; (ii) use of both Computation and Communication Patterns to control processes’ regularity;(iii) adaptation regarding the periodicity to launch the processes rescheduling. This paper describes MigBSP and presents some experimental results and related work.
Operational coastal ocean forecasting in the Eastern Mediterranean : implementation and evaluation

Operational coastal ocean forecasting in the Eastern Mediterranean: implementation and evaluation G. Zodiatis, R. Lardner, D. R. Hayes, G. Georgiou, S. Sofianos, N. Skliris, and A. Lascaratos Oceanography Centre, University of Cyprus, P.O. Box 20537, 1678 Nicosia, Cyprus Applied Physics Dept., Ocean Physics Modelling Group, University of Athens, Greece Received: 28 March 2006 – Accepted: 27 April 2006 – Published: 8 June 2006 Correspondence to: D. R. Hayes (dhayes@ucy.ac.cy)
Astronomical Data Analysis and Sparsity: From Wavelets to Compressed Sensing

Wavelets have been used extensively for several years now in astronomy for many purposes, ranging from data filtering and deconvolution to star and galaxy detection or cosmic-ray removal. More recent sparse representations such as ridgelets or curvelets have also been proposed for the detection of anisotropic features such as cosmic strings in the cosmic microwave background. We review in this paper a range of methods based on sparsity that have been proposed for astronomical data analysis. We also discuss the impact of compressed sensing, the new sampling theory, in astronomy for collecting the data, transferring them to earth or reconstructing an image from incomplete measurements.
Mobile P2P queries over temporal data

In this paper we evaluate the performance a mobile P2P query processing framework, where peers issue location-dependent range queries and receive temporal data. We consider an environment where stationary objects generate temporal data and peers issue location-dependent range queries. We evaluate this framework by varying the constraints of range queries and measure their effect on three metrics: percentage of queries satisfied, fraction of data received and query response time. From our simulations, we make two key observations: the range query constraints have no impact on the performance metrics beyond a certain threshold and the temporal nature of data drastically limits the mobility benefits (traditionally exploited by mobile P2P query systems). We also present scenarios where a mobile P2P query processing framework can be used to satisfy location-dependent range queries.
VARIUS: A Model of Parameter Variation and Resulting Timing Errors for Microarchitects ∗

As VLSI technology continues to scale, parameter variation is about to pose a major challenge to high-performance processor de-sign. In particular, within-die variation is directly detrimental to a processor’s frequency and leakage power. To gain an understanding of this problem, this paper starts out by proposing a microarchitecture-aware model for parameter variation. It includes both random and systematic effects. It is partially calibrated with empirical data and uses a few intuitive parameters. Then, we extend the framework to model timing errors caused by parameter variation. This model yields the failure rate of microarchitectural blocks as a function of frequency and the amount of variation. With the combination of the variation model and the error model, we have VARIUS , a comprehensive model that is capable of producing detailed statistics of timing errors as a function of different process parameters and operating conditions. We propose possible applications of VAR-IUS to microarchitectural research.
Ant Colony Optimization-Based Fault-Aware Routing in Mesh-Based Network-on-Chip Systems

The advanced deep submicrometer technology increases the risk of failure for on-chip components. In advanced network-on-chip (NoC) systems, the failure constrains the on-chip bandwidth and network throughput. Fault-tolerant routing algorithms aim to alleviate the impact on performance. However, few works have integrated the congestion-, deadlock-, and fault-awareness information in channel evaluation function to avoid the hotspot around the faulty router. To solve this problem, we propose the ant colony optimization-based fault-aware routing (ACO-FAR) algorithm for load balancing in faulty networks. The behavior of an ant colony while facing an obstacle (failure in NoC) can be described in three steps: 1) encounter; 2) search; and 3) select. We implement the corresponding mechanisms as: 1) notification of fault information; 2) path searching mechanism; and 3) path selecting mechanism. With proposed ACO-FAR, the router can evaluate the available paths and detour packets through a less-congested fault-free path. The simulation results show that this paper has higher throughput than related works by 29.1%-66.5%. In addition, ACO-FAR can reduce the undelivered packet ratio to 0.5%-0.02% and balance the distribution of traffic flow in the faulty network.
TIDE: An Intelligent Home-Based Healthcare Information & Diagnostic Environment

The 21st century promises to usher in an era of Internet based healthcare services--Tele-Healthcare. Such services augur well with the on-going paradigm shift in healthcare delivery patterns, i.e. patient centred services as opposed to provider centred services and wellness maintenance as opposed to illness management. This paper presents a Tele-Healthcare info-structure TIDE--an 'intelligent' wellness-oriented healthcare delivery environment. TIDE incorporates two WWW-based healthcare systems: (1) AIMS (Automated Health Monitoring System) for wellness maintenance and (2) IDEAS (Illness Diagnostic & Advisory System) for illness management. Our proposal comes from an attempt to rethink the sources of possible leverage in improving healthcare; vis-à-vis the provision of a continuum of personalised home-based healthcare services that emphasise the role of the individual in self health maintenance.
Non-linear Mapping for Improved Identification of 1300+ Languages

Non-linear mappings of the form P (ngram)γ and log(1+τP (ngram)) log(1+τ) are applied to the n-gram probabilities in five trainable open-source language identifiers. The first mapping reduces classification errors by 4.0% to 83.9% over a test set of more than one million 65-character strings in 1366 languages, and by 2.6% to 76.7% over a subset of 781 languages. The second mapping improves four of the five identifiers by 10.6% to 83.8% on the larger corpus and 14.4% to 76.7% on the smaller corpus. The subset corpus and the modified programs are made freely available for download at http://www.cs. cmu.edu/∼ralf/langid.html.
Loss of STAT3 in Lymphoma Relaxes NK Cell-Mediated Tumor Surveillance

The transcription factors and proto-oncogenes STAT3 and STAT5 are highly activated in hematological malignancies and represent promising therapeutic targets. Whereas the importance of STAT5 as tumor promoter is beyond doubt, the role of STAT3 in hematological cancers is less well understood. Both, enforced as well as attenuated expression of STAT3 were reported in hematopoietic malignancies. Recent evidence implicates STAT3 as key player for tumor immune surveillance as it both mediates the production of and response to inflammatory cytokines. Here we investigated the effects of STAT3 deletion in a BCR/ABL-induced lymphoma model, which is tightly controlled by natural killer (NK) cells in vivo. Upon STAT3 deletion tumor growth is significantly enhanced when compared to STAT3-expressing controls. The increased tumor size upon loss of STAT3 was accompanied by reduced NK cell infiltration and decreased levels of the cytokine IFN-γ and the chemokine RANTES. Upon transplantation into NK cell-deficient mice differences in lymphoma size were abolished indicating that STAT3 expression in the tumor cells controls NK cell-dependent tumor surveillance. Our findings indicate that STAT3 inhibition in lymphoma patients will impair NK cell-mediated tumor surveillance, which needs to be taken into account when testing STAT3 inhibitors in preclinical or clinical trials.
A spectral clustering approach to optimally combining numericalvectors with a modular network

We address the issue of clustering numerical vectors with a network. The problem setting is basically equivalent to constrained clustering by Wagstaff and Cardie and semi-supervised clustering by Basu et al., but our focus is more on the optimal combination of two heterogeneous data sources. An application of this setting is web pages which can be numerically vectorized by their contents, e.g. term frequencies, and which are hyperlinked to each other, showing a network. Another typical application is genes whose behavior can be numerically measured and a gene network can be given from another data source.We first define a new graph clustering measure which we call normalized network modularity, by balancing the cluster size of the original modularity. We then propose a new clustering method which integrates the cost of clustering numerical vectors with the cost of maximizing the normalized network modularity into a spectral relaxation problem. Our learning algorithm is based on spectral clustering which makes our issue an eigenvalue problem and uses k-means for final cluster assignments. A significant advantage of our method is that we can optimize the weight parameter for balancing the two costs from the given data by choosing the minimum total cost. We evaluated the performance of our proposed method using a variety of datasets including synthetic data as well as real-world data from molecular biology. Experimental results showed that our method is effective enough to have good results for clustering by numerical vectors and a network.
Geometric Point Pattern Matching in the Knuth-Morris-Pratt Way

Given finite sets P and T of points in the Euclidean space R d ,t he point pattern matching problem studied in this paper is to find all translations f ∈ R d such that P + f ⊆ T. A fast search algorithm with some variants is presented for point patterns P that have regular grid-like geometric shape. The algorithm is analogous to the Knuth-Morris-Pratt algorithm of string matching. The time requirement of the search is O(r|T | )w herer is the grid dimension of P. Pattern P has grid dimension r = 1 if it consists of evenly spaced points on a line. In general, a pattern P is an r-dimensional grid if it has for some p ∈ P and e1,. ,er ∈ R d and positive integers m1,. ,mr ar epresentationP = {p +i1e1 + ·· ·+irer | 0 ≤ ij ≤ mj } where the ij 's are integers. Both P and T are given to the search algorithm in the lexicographic order.
Mapping accessible chromatin regions using Sono-Seq

Disruptions in local chromatin structure often indicate features of biological interest such as regulatory regions. We find that sonication of cross-linked chromatin, when combined with a size-selection step and massively parallel short-read sequencing, can be used as a method (Sono-Seq) to map locations of high chromatin accessibility in promoter regions. Sono-Seq sites frequently correspond to actively transcribed promoter regions, as evidenced by their co-association with RNA Polymerase II ChIP regions, transcription start sites, histone H3 lysine 4 trimethylation (H3K4me3) marks, and CpG islands; signals over other sites, such as those bound by the CTCF insulator, are also observed. The pattern of breakage by Sono-Seq overlaps with, but is distinct from, that observed for FAIRE and DNase I hypersensitive sites. Our results demonstrate that Sono-Seq can be a useful and simple method by which to map many local alterations in chromatin structure. Furthermore, our results provide insights into the mapping of binding sites by using ChIP–Seq experiments and the value of reference samples that should be used in such experiments.
Local Modelling by SOM partitioning and linear regression for Ecological Modelling

EXTENDED ABSTRACT Global modelling approaches construct a single model that covers all of the training data or data used to describe a system. However, for many problems, especially in the natural sciences, the system under consideration is best understood in terms of a number of distinct states, with different patterns and processes operating for each state. The issue of state-based modelling, where different models are constructed for different states, brings in several issues that need to be addressed, including: how are the states determined, how are they represented, how does the modelling of the system determine which states are appropriate during some phase of modelling, and how are state transitions determined.
Fast assessment of the correlation between coverage-like genomic features and its statistical significance

The modern high-throughput sequencing methods provide massive amounts of genome-focused, DNA-positioned data. This data is often represented as a function of the DNA coordinate (e.g. coverage). The genome-or chromosome-wide correlations between data from diﬀerent sources may provide information about functional biological interrelation of the investigated features, e.g., trancription and histone modiﬁcation. The task to compute the correlation was already successfully solved for interval annotations ([1]) as well as for coverage (functional) data ([2], [3], [4]). The key idea of the correlation studies is that two features that are similarly distributed along a chromosome may be functionally related. The point we are addressing here is a that peaks of dependent functional features can be located in a similar, although somewhat diﬀerent, way. To account for these similarities, we propose here a fast method for calculation of kerneled correlation between two numeric annotations of the genome. The kernel represents the mutual position of related features; e.g., a Gaussian shape corresponds to ’somewhere around’, etc.
Activating Expression Life Cycle by Automatic Draft Generation and Interactive Creation

In this research, we propose the expression life cycle model which consists of liquidization and crystallization of expressions. We believe that activating this cycle will enrich and widen our views of thinking and feeling. After providing a framework for activating the cycle by automatic draft generation and interactive creation processes, the preliminary practices and prototypes are introduced.