Miracle-dz/UniFAR-FTUs huggingface dataset:
Apotopes and the biliary specificity of primary biliary cirrhosis

Primary biliary cirrhosis (PBC) is characterized by antimitochondrial antibodies (AMAs), directed to the E2 component of the pyruvate dehydrogenase complex (PDC‐E2). Notwithstanding the presence of mitochondria in virtually all nucleated cells, the destruction in PBC is limited to small intrahepatic bile ducts. The reasons for this tissue specificity remain unknown, although biliary epithelial cells (BECs) uniquely preserve the PDC‐E2 epitope following apoptosis. Notably, PBC recurs in an allogeneic transplanted liver, suggesting generic rather than host PBC–specific susceptibility of BEC. We used cultured human intrahepatic BECs (HIBECs) and other well‐characterized cell lines, including, HeLa, CaCo‐2 cells, and nontransformed human keratinocytes and bronchial epithelial cells, to determine the integrity and specific localization of PDC‐E2 during induced apoptosis. All cell lines, both before and after apoptosis, were tested with sera from patients with PBC (n = 30), other autoimmune liver and rheumatic diseases (n = 20), and healthy individuals (n = 20) as well as with a mouse monoclonal antibody against PDC‐E2 and AMA with an immunoglobulin A isotype. PDC‐E2 was found to localize unmodified within apoptotic blebs of HIBECs, but not within blebs of various other cell lineages studied. The fact that AMA‐containing sera reacted with PDC‐E2 on apoptotic BECs without a requirement for permeabilization suggests that the autoantigen is accessible to the immune system during apoptosis. Conclusion: Our data indicate that the tissue (cholangiocyte) specificity of the autoimmune injury in PBC is a consequence of the unique characteristics of HIBECs during apoptosis and can be explained by exposure to the immune system of intact immunoreactive PDC‐E2 within apoptotic blebs. (HEPATOLOGY 2009.)
A Method for Fast States Estimation of Multi-function Radar Based on Syntactic Derivation of Parse Chart

Stochastic Context-Free Grammars (SCFG) have promising application prospect in the field of Multi-Function Radars (MFR) states recognition and threat estimation, which entails the fast learning of the probability of radar grammar production based on training data. Conventional learning algorithms are limited in practical application for their high computational complexity. A new fast learning algorithm for the probability of MFR grammar is proposed in this paper in light of a reformulated and delicate SCGF modeling of the MFR signal generation mechanism. The proposed algorithm first pre-compute Cocke-Younger-Kasami(CKY) parsing chart for each training sequence, and then the probability of radar grammar production is estimated with modified Inside-Outside(IO) algorithm based on the aforementioned parsing chart. The computational complexity and accuracy of the algorithm are also analyzed in detail. Simulation results show that the algorithm could fast estimate production rule probabilities with favorable estimation accuracy, and compared with the conventional IO or Viterbi Score (VS) algorithm, more than a half operation time can be reduced.
Experimental/clinical evaluation of EIT image reconstruction with ℓ1 data and image norms

Electrical impedance tomography (EIT) image reconstruction is ill-posed, and the spatial resolution of reconstructed images is low due to the diffuse propagation of current and limited number of independent measurements. Generally, image reconstruction is formulated using a regularized scheme in which ℓ2 norms are preferred for both the data misfit and image prior terms due to computational convenience which result in smooth solutions. However, recent work on a Primal Dual-Interior Point Method (PDIPM) framework showed its effectiveness in dealing with the minimization problem. ℓ1 norms on data and regularization terms in EIT image reconstruction address both problems of reconstruction with sharp edges and dealing with measurement errors. We aim for a clinical and experimental evaluation of the PDIPM method by selecting scenarios (human lung and dog breathing) with known electrode errors, which require a rigorous regularization and cause the failure of reconstructions with ℓ2 norm. Results demonstrate the applicability of PDIPM algorithms, especially ℓ1 data and regularization norms for clinical applications of EIT showing that ℓ1 solution is not only more robust to measurement errors in clinical setting, but also provides high contrast resolution on organ boundaries.
SandCanvas: a multi-touch art medium inspired by sand animation

Sand animation is a performance art technique in which an artist tells stories by creating animated images with sand. Inspired by this medium, we have developed a new multi-touch digital artistic medium named SandCanvas that simplifies the creation of sand animations. SandCanvas also goes beyond traditional sand animation with tools for mixing sand animation with video and replicating recorded free-form hand gestures. In this paper, we analyze common sand animation hand gestures, present SandCanvas's intuitive UI, and describe implementation challenges we encountered. We also present an evaluation with professional and novice artists that shows the importance and unique affordances of this new medium.
Directed Information, Causal Estimation, and Communication in Continuous Time

A notion of directed information between two continuous-time processes is proposed. A key component in the definition is taking an infimum over all possible partitions of the time interval, which plays a role no less significant than the supremum over “space” partitions inherent in the definition of mutual information. Properties and operational interpretations in estimation and communication are then established for the proposed notion of directed information. For the continuous-time additive white Gaussian noise channel, it is shown that Duncan's classical relationship between causal estimation error and mutual information continues to hold in the presence of feedback upon replacing mutual information by directed information. A parallel result is established for the Poisson channel. The utility of this relationship is demonstrated in computing the directed information rate between the input and output processes of a continuous-time Poisson channel with feedback, where the channel input process is constrained to be constant between events at the channel output. Finally, the capacity of a wide class of continuous-time channels with feedback is established via directed information, characterizing the fundamental limit on reliable communication.
A three-valued characterization for strong equivalence of logic programs

In this work we present additional results related to the property of strong equivalence of logic programs. This property asserts that two programs share the Same set of stable models, even under the addition of new rules. As shown in a recent work by Lifschitz, Pearce and Valverde, strong equivalence can be simply reduced to equivalence in the logic of <i>Here-and-There </i> (HT). In this paper we provide an alternative based on 3-valued logic, using also, as a first step, a classical logic charaterization. We show that the 3-valued encoding provides a direct interpretation for nested expressions but, when moving to an unrestricted syntax, it generally yields different results from HT.
Differential on-line sensor calibration [light intensity sensor example]

We have developed an on-line calibration scheme that employs a single source as the external stimulus that creates differential sensor readings used for calibration. The technique utilizes the maximal likelihood principle and a nonlinear system optimization solver to derive the calibration function of arbitrary complexity and accuracy. The approach is intrinsically localized and we present two variants: i) one where only two neighboring sensors have to communicate in order to conduct calibration; ii) one where a provably minimum amount of communication is achieved. We evaluate the techniques using traces from light sensors recorded by deployed sensors, and statistical evaluations are conducted in order to obtain the interval of confidence to support all the results.
Expression of vascular permeability factor (vascular endothelial growth factor) by epidermal keratinocytes during wound healing

Persistent microvascular hyperpermeability to plasma proteins even after the cessation of injury is a characteristic but poorly understood feature of normal wound healing. It results in extravasation of fibrinogen that clots to form fibrin, which serves as a provisional matrix and promotes angiogenesis and scar formation. We present evidence indicating that vascular permeability factor (VPF; also known as vascular endothelial growth factor) may be responsible for the hyperpermeable state, as well as the angiogenesis, that are characteristic of healing wounds. Hyperpermeable blood vessels were identified in healing split-thickness guinea pig and rat punch biopsy skin wounds by their capacity to extravasate circulating macromolecular tracers (colloidal carbon, fluoresceinated dextran). Vascular permeability was maximal at 2-3 d, but persisted as late as 7 d after wounding. Leaky vessels were found initially at the wound edges and later in the subepidermal granulation tissue as keratinocytes migrated to cover the denuded wound surface. Angiogenesis was also prominent within this 7-d interval. In situ hybridization revealed that greatly increased amounts of VPF mRNA were expressed by keratinocytes, initially those at the wound edge, and, at later intervals, keratinocytes that migrated to cover the wound surface; occasional mononuclear cells also expressed VPF mRNA. Secreted VPF was detected by immunofluoroassay of medium from cultured human keratinocytes. These data identify keratinocytes as an important source of VPF gene transcript and protein, correlate VPF expression with persistent vascular hyperpermeability and angiogenesis, and suggest that VPF is an important cytokine in wound healing.
Selective Requirement of Myosin Light Chain 2v in Embryonic Heart Function*

Two major myosin light chain 2 isoforms are coexpressed in the early stages of murine cardiogenesis, a cardiac ventricular isoform and a cardiac atrial isoform, each of which is tightly regulated in a muscle cell-type-specific manner during embryogenesis (Chien, K. R., Zhu, H., Knowlton, K. U., Miller-Hance, W., van Bilsen, M., O’Brien, T. X., and Evans, S. M. (1993) Annu. Rev. Physiol. 55, 77–95). We have disrupted myosin light chain 2v gene in mice and monitored in vivo cardiac function in living myosin light chain 2v −/− embryos. The mutant embryos die at approximately embryonic day 12.5. In mutant ventricles, the myosin light chain 2a protein level is increased and reaches levels comparable to the myosin light chain 2v in the ventricles of wild type littermates and is appropriately incorporated into the thick filaments of mutant embryonic hearts. However, despite the substitution of myosin light chain 2a, ultrastructural analysis revealed defects in sarcomeric assembly and an embryonic form of dilated cardiomyopathy characterized by a significantly reduced left ventricular ejection fraction in mutant embryos compared with wild type littermates. We conclude that myosin light chain 2v may have a unique function in the maintenance of cardiac contractility and ventricular chamber morphogenesis during mammalian cardiogenesis and that a chamber-specific combinatorial code for sarcomeric assembly may exist that ultimately requires myosin light chain 2v in ventricular muscle cells.
The Annotation Graph Toolkit: Software Components for Building Linguistic Annotation Tools

Annotation graphs provide an efficient and expressive data model for linguistic annotations of time-series data. This paper reports progress on a complete software infrastructure supporting the rapid development of tools for transcribing and annotating time-series data. This general-purpose infrastructure uses annotation graphs as the underlying model, and allows developers to quickly create special-purpose annotation tools using common components. An application programming interface, an I/O library, and graphical user interfaces are described. Our experience has shown us that it is a straightforward task to create new special-purpose annotation tools based on this general-purpose infrastructure.
Opinion fluctuations and persistent disagreement in social networks

We study a tractable opinion dynamics model that generates long-run disagreements and persistent opinion fluctuations. Our model involves an inhomogeneous stochastic gossip process of continuous opinion dynamics in a society consisting of two types of agents: regular agents, who update their beliefs according to information that they receive from their social neighbors; and stubborn agents, who never update their opinions and might represent leaders, political parties or media sources attempting to influence the beliefs in the rest of the society. When the society contains stubborn agents with different opinions, the belief dynamics never lead to a consensus (among the regular agents). Instead, beliefs in the society almost surely fail to converge, the belief profile keeps on oscillating in an ergodic fashion, and it converges in law to a non-degenerate random vector.
Simultaneous Identification of Potential Pathogenicity Factors of Mycoplasma agalactiae in the Natural Ovine Host by Negative Selection

ABSTRACT Mycoplasmas possess complex pathogenicity determinants that are largely unknown at the molecular level. Mycoplasma agalactiae serves as a useful model to study the molecular basis of mycoplasma pathogenicity. The generation and in vivo screening of a transposon mutant library of M. agalactiae were employed to unravel its host colonization factors. Tn4001mod mutants were sequenced using a novel sequencing method, and functionally heterogeneous pools containing 15 to 19 selected mutants were screened simultaneously through two successive cycles of sheep intramammary infections. A PCR-based negative selection method was employed to identify mutants that failed to colonize the udders and draining lymph nodes in the animals. A total of 14 different mutants found to be absent from ≥95% of samples were identified and subsequently verified via a second round of stringent confirmatory screening where 100% absence was considered attenuation. Using this criterion, seven mutants with insertions in genes MAG1050, MAG2540, MAG3390, uhpT, eutD, adhT, and MAG4460 were not recovered from any of the infected animals. Among the attenuated mutants, many contain disruptions in hypothetical genes, implying their previously unknown role in M. agalactiae pathogenicity. These data indicate the putative role of functionally different genes, including hypothetical ones, in the pathogenesis of M. agalactiae. Defining the precise functions of the identified genes is anticipated to increase our understanding of M. agalactiae infections and to develop successful intervention strategies against it.
Effect of Precursor on Antifouling Efficacy of Vertically-Oriented Graphene Nanosheets

Antifouling efficacy of graphene nanowalls, i.e., substrate-bound vertically-oriented graphene nanosheets, has been demonstrated against biofilm-forming Gram-positive and Gram-negative bacteria. Where graphene nanowalls are typically prepared using costly high-temperature synthesis from high-purity carbon precursors, large-scale applications demand efficient, low-cost processes. The advancement of plasma enabled synthesis techniques in the production of nanomaterials has opened a novel and effective method for converting low-cost natural waste resources to produce nanomaterials with a wide range of applications. Through this work, we report the rapid reforming of sugarcane bagasse, a low-value by-product from sugarcane industry, into high-quality vertically-oriented graphene nanosheets at a relatively low temperature of 400 °C. Electron microscopy showed that graphene nanowalls fabricated from methane were significantly more effective at preventing surface attachment of Gram-negative rod-shaped Escherichia coli compared to bagasse-derived graphene, with both surfaces showing antifouling efficacy comparable to copper. Attachment of Gram-positive coccal Staphylococcus aureus was lower on the surfaces of both types of graphene compared to that on copper, with bagasse-derived graphene being particularly effective. Toxicity to planktonic bacteria estimated as a reduction in colony-forming units as a result of sample exposure showed that both graphenes effectively retarded cell replication.
On convergence of numerical schemes for hyperbolic conservation laws with stiff source terms

We deal in this study with the convergence of a class of numerical schemes for scalar conservation laws including stiff source terms. We suppose that the source term is dissipative but it is not necessarily a Lipschitzian function. The convergence of the approximate solution towards the entropy solution is established for first and second order accurate MUSCL and for splitting semi-implicit methods.
Multilevel and Session Variability Compensated Language Recognition: ATVS-UAM Systems at NIST LRE 2009

This paper presents the systems submitted by the ATVS Biometric Recognition Group to the 2009 Language Recognition Evaluation (LRE'09), organized by NIST. New challenges included in this LRE edition can be summarized by three main differences with respect to past evaluations. First, the number of languages to be recognized expanded to 23 languages from 14 in 2007, and 7 in 2005. Second, the data variability has been increased by including telephone speech excerpts extracted from Voice of America (VOA) radio broadcasts through Internet in addition to conversational telephone speech (CTS). The third difference was the volume of data, involving in this evaluation up to 2 terabytes of speech data for development, which is an order of magnitude greater than past evaluations. LRE'09 thus required participants to develop robust systems able not only to successfully face the session variability problem but also to do it with reasonable computational resources. ATVS participation consisted of state-of-the-art acoustic and high-level systems focussing on these issues. Furthermore, the problem of finding a proper combination and calibration of the information obtained at different levels of the speech signal was widely explored in this submission. In this paper, two original contributions were developed. The first contribution was applying a session variability compensation scheme based on factor analysis (FA) within the statistics domain into a SVM-supervector (SVM-SV) approach. The second contribution was the employment of a novel back-end based on anchor models in order to fuse individual systems prior to one-versus-all calibration via logistic regression. Results both in development and evaluation corpora show the robustness and excellent performance of the submitted systems, exemplified by our system ranked second in the 30-second open-set condition, with remarkably scarce computational resources.
Proteins with RNA Chaperone Activity: A World of Diverse Proteins with a Common Task—Impediment of RNA Misfolding

Proteins with RNA chaperone activity are ubiquitous proteins that play important roles in cellular mechanisms. They prevent RNA from misfolding by loosening misfolded structures without ATP consumption. RNA chaperone activity is studied in vitro and in vivo using oligonucleotide- or ribozyme-based assays. Due to their functional as well as structural diversity, a common chaperoning mechanism or universal motif has not yet been identified. A growing database of proteins with RNA chaperone activity has been established based on evaluation of chaperone activity via the described assays. Although the exact mechanism is not yet understood, it is more and more believed that disordered regions within proteins play an important role. This possible mechanism and which proteins were found to possess RNA chaperone activity are discussed here.
Prefetch-based dynamic row buffer management for LPDDR2-NVM devices

LPDDR2-NVM has been announced as an industry standard to efficiently interface with non-volatile memory devices such as phase change memory (PCM). This standard interface has been adopted in most commercial PCM devices. In this paper, we devise a prefetch-based dynamic row buffer management that targets the LPDDR2-NVM devices for enhancing performance with almost negligible implementation overhead. Our extensive simulations with timing parameters from the industry's commercial PCM devices demonstrate that the proposed method enhances the performance of memory systems up to 11.3% when compared with the static optimum configuration with fairly low-cost overheads.
Global food and trade dimensions of groundwater governance

About 22% of water use in the world is for producing export products. The overdraft of many aquifers is partially related to incentives to produce for the world market and the fact that water scarcity is not properly priced and therefore not reflected in the price of traded commodities. This chapter aims to discuss the relation between the global economy and unsustainable water use, with a focus on groundwater and global food demand. Unsustainable groundwater use isn’t a local problem only, because increasingly global markets and companies and consumers worldwide depend on the products derived from unsustainable water supplies. There is a need to collaborate internationally in introducing forces or incentives to drive towards more sustainable groundwater use. Possible arrangements discussed are an international water pricing protocol, but also the institutionalization of groundwater footprint caps that reflect maximum sustainable abstraction levels and an international product label reflecting sustainability of water use.
Token-based Performance Modeling for 2 D and 3 D Infrared Search and Track Processing

The purpose of this study was to develop and evaluate a new VHDL-based performance modeling capability for multiprocessor systems. The framework for this methodology involved modeling the following system aspects: processor characterization, task modeling, network characterization, and data set size. Initially, all aspects are specified at a high (or abstract) level, and eventually become specified at a detailed level through the process of verification and refinement of design assumptions. Processor characterization involves modeling the processor’s speed, instruction set, and memory hierarchy. Task modeling is concerned with the execution time and instruction mix of software tasks within the system. Network characterization models bus protocols, topology, and bandwidths. Data set size refers to how much data is represented by the tokens used in the models. In this study, we applied and evaluated this methodology using both twodimensional (2D) and three-dimensional (3D) infrared search and track (IRST) algorithms. Two different candidate processors were investigated: IBM PowerPC and Texas Instruments TMS320C80. For the 2D IRST algorithm, the abstract and detailed performance modeling results were obtained for both processors using partitioned data and pipelined algorithmic approaches. The PowerPC abstract performance modeling results were quite close compared to those for the TMS320C80. For the 3D IRST algorithm, abstract performance models for pipelined and parallelized implementations on the PowerPC were developed. These models examined the feasibility of the implementations, the potential risk areas, and laid the groundwork for detailed performance modeling. In short, this methodology provided a good approach to rapidly explore the performance of various system designs.