Miracle-dz/UniFAR-FTUs huggingface dataset:
Polymeric meshes induce zonal regulation of matrix metalloproteinase‐2 gene expression by macrophages and fibroblasts

Matrix metalloproteinase‐2 (MMP‐2) is a key regulator in wound healing that orchestrates tissue remodeling. In the present study the spatial and temporal distribution of MMP‐2 gene transcription, protein synthesis, and enzymatic activity were analyzed following polymeric mesh (polyglactin, polypropylene) im‐plantation in transgenic reporter mice harboring MMP‐2 regulatory sequences ‐1686/+423 or ‐1241/ +423. Polymers induced MMP‐2 promoter activity in macrophages within the foreign body granuloma via sequences ‐ 1686/+ 423 with concomitantly up‐regulated protein synthesis and enzymatic activity. Macro‐phages distant from mesh filaments exhibited low MMP‐2 expression levels. Fibroblasts surrounding mesh material displayed strong MMP‐2 gene transcription independent of the included promoter sequences, whereas fibroblasts without close contact to mesh material had low MMP‐2 synthesis rates due to silencing activity of sequences ‐1686/ ‐1241. In vitro studies support a cellular crosstalk concept, as macrophages trans‐repressed MMP‐2 gene transcription in fibroblasts. The zonal and cell‐specific regulation of MMP‐2 gene transcription illuminates an intimate cellular crosstalk in foreign body reaction that may provide a new approach for mesh modification. —Jansen, P. L. , Kever, M. , Rosch, R. , Krott, E. , Jansen, M. , Alfonso‐Jaume, A. , Dooley, S. , Klinge, U. , Lovett, D. H. , Mertens, P. R. Polymeric meshes induce zonal regulation of matrix metalloproteinase‐2 gene expression by macrophages and fibroblasts. FASEB J. 21, 1047–1057 (2007)
reacTIVision: a computer-vision framework for table-based tangible interaction

This article provides an introductory overview to first-time users of the reacTIVision framework -- an open-source cross-platform computer-vision framework primarily designed for the construction of table-based tangible user interfaces. The central component of the framework is a standalone application for fast and robust tracking of fiducial markers in a real-time video stream. The framework also defines a transport protocol for efficient and reliable transmission of object states via a local or wide area network. In addition, the distribution includes a collection of client example projects for various programming environments that allow the rapid development of unique tangible user interfaces. This article also provides a discussion of key points relevant to the construction of the necessary table hardware and surveys some projects that have been based on this technology.
A review on scaling of earthquake faults

Scaling of earthquake faults is important not only for earthquake physics but also seismic hazard assessment. There have been many studies about this topic. It is significant to compile, review, and discuss those studies. This work reviews the observations and modeling of scaling of fault parameters, including the fault length (L), fault width (W), fault area (A), average displacement (Do), maximum displacement (Dmax), seismic moment (Mo), and static stress drop (Δσ). Major issues for reviewing in this work are: (1) assumptions of constant Δσ, of earthquakes and self-similarity of faults; (2) the Land W-models; (3) the L-Do and L-Dmax scaling relationships; (4) the Mo-Do and Mo-Dmax scaling relationships; (5) the Do-A scaling relationships; (6) the Mo-A scaling relationships; (7) the L-W scaling relationship; (8) the Mo-L and Mo-W scaling relationships; and (9) modeling of the Mo-L scaling based on the onedimensional spring-slider model in the presence of velocity-weakening friction. Article history:
A Block-Based Blind Source Separation Approach With Equilateral Triangular Microphone Array

In this paper we describe a method for multiple speech sources separation using an equilateral triangular microphone array. Firstly, the azimuths of horizontal plane are divided into many units and the spatial features of some directions observed by the microphone array are modeled precisely. Secondly, the input mixing signals are segmented into blocks, and then the number of active speakers and their directions are estimated in each block. Thirdly, the pre-trained model with the nearest azimuth to each speaker is adapted to obtain a precise model, which is then used for time-frequency binary mask estimation. Finally, we separate every source appeared in each block and concatenate those sounds from same unit to reproduce the whole stream. The experiments are set up in a real meeting room. The results show that our method can separate multiple speech sources correctly with low distortion, and are competitive with the total un-blind separation results.
SVM for hyperspectral images classification based on 3D spectral signature

Hyperspectral imaging sensors acquire images in hundreds of continuous narrow spectral bands spanning the visible to infrared spectrum which led to obtain hyperspectral image with high spectral resolution. Thus each object presented in the image can be identified from their spectral response. The classification of multi-temporal hyperspectral image is a challenge task due to the problem of spectral variation over the time. In fact, many factors can affect the spectral signature of object like weather and climatic effects, so two images taken on the same area but at different times and under different conditions can lead to different spectral signatures for the same objects. This observation has fostered the idea of adopting 3D representation of spectral signature to classify multi-temporal hyperspectral image. The main objective of this representation is to have for each object a compact model which illustrate their spectral variation over the time, it represent the variation of reflectance as a function of time and spectral waveband. In this paper, we propose a new approach for multi-temporal hyperspectral image classification based on 3D spectral signature to solve the problem of spectral variation. This approach consist, foremost, to represent each pixel of classified image by a 3D spectral signature after the application of the powerful 3D modeling method "Non-uniform Rational Basis Spline" (NURBS), after, to apply local shape descriptor "spherical harmonic decomposition" to extract spectral features from each 3D spectral signature and, finally, to classify the image by means of supervised classifier "Support Vector Machines (SVMs)" with Radial Basis Function (RBF) kernel. To evaluate this approach, we used a series of multi-temporal hyperspectral "hyperion" images.
Prevalence of Oral Mucosal Disorders in Diabetes Mellitus Patients Compared with a Control Group

Chronic hyperglycemia is associated with impaired wound healing and higher susceptibility to infections. It is unclear whether patients with diabetes mellitus (DM) present more oral mucosal disorders compared to control groups. The objectives were to compare (a) the prevalence rates of oral mucosal disorders in the DM and non-DM population and (b) the prevalence rates of specific disorders in the DM and non-DM population. Full-text articles were included if they met the following inclusion criteria: (a) they must be original articles from scientific journals, (b) they must be only cross-sectional studies in English, (c) the prevalence of oral mucosal disorders in DM patients must be evaluated, (d) results must be compared with a healthy control group, and (e) oral mucosal disorders must be specified in DM and non-DM group. All studies showed higher prevalence of oral mucosal disorders in DM patients in relation to non-DM population: 45–88% in type 2 DM patients compared to 38.3–45% in non-DM groups and 44.7% in type 1 DM patients compared to 25% in non-DM population. Tongue alterations and denture stomatitis were the most frequent significant disorders observed. The quality assessment following the Joanna Briggs Institute (JBI) Prevalence Critical Appraisal Tool showed the low quality of the existing studies.
PERFORMANCE ANALYSIS OF THE RANDOM EARLY DETECTION ALGORITHM

In this article we consider a finite queue with its arrivals controlled by the random early detection algorithm. This is one of the most prominent congestion avoidance schemes in the Internet routers. The aggregate arrival stream from the population of transmission control protocol sources is locally considered stationary renewal or Markov modulated Poisson process with general packet length distribution. We study the exact dynamics of this queue and provide the stability and the rates of convergence to the stationary distribution and obtain the packet loss probability and the waiting time distribution. Then we extend these results to a two traffic class case with each arrival stream renewal. However, computing the performance indices for this system becomes computationally prohibitive. Thus, in the latter half of the article, we approximate the dynamics of the average queue length process asymptotically via an ordinary differential equation. We estimate the error term via a diffusion approximation. We use these results to obtain approximate transient and stationary performance of the system. Finally, we provide some computational examples to show the accuracy of these approximations.
Lower Bounds for Testing Digraph Connectivity with One-Pass Streaming Algorithms

In this note, we show that three graph properties—strong connectivity, acyclicity, and reachability from a vertex <inline-formula><tex-math notation="LaTeX">$s$</tex-math><alternatives> <inline-graphic xlink:href="miglervondollen-ieq1-2854761.gif"/></alternatives></inline-formula> to all vertices—each require a working memory of <inline-formula><tex-math notation="LaTeX">$\Omega (\epsilon m)$ </tex-math><alternatives><inline-graphic xlink:href="miglervondollen-ieq2-2854761.gif"/></alternatives></inline-formula> on a graph with <inline-formula><tex-math notation="LaTeX">$m$</tex-math><alternatives> <inline-graphic xlink:href="miglervondollen-ieq3-2854761.gif"/></alternatives></inline-formula> edges to be determined correctly with probability greater than <inline-formula><tex-math notation="LaTeX">$(1+\epsilon)/2$</tex-math> <alternatives><inline-graphic xlink:href="miglervondollen-ieq4-2854761.gif"/></alternatives></inline-formula>.
Detection and Resolution of Aspect Interactions in Workflows

Workflow systems have become a popular means of automating processes in many domains. Current workflow languages, however, provide only limited modularization mechanisms, and thus suffer from a lack of separation of concerns. Inspired by aspect-oriented research, several extensions to workflow languages have been developed which allow modularizing workflow concerns into separate aspects. Unfortunately, these extensions suffer from similar feature interaction problems as general-purpose aspect-oriented programming languages. In previous work, we have outlined a strategy for managing such interactions. This technical report extends and applies these ideas to workflows. Control flow policies are specified using high-level predicates, and are verified by translating both these predicates and the workflows on which they are specified to DFAs. By computing the intersection between a policy DFA and a workflow DFA, we can determine whether a given policy holds for a given workflow.
Verification of parameterized hierarchical state machines using action language verifier

Action language verifier (ALV) is an infinite-state symbolic model checker. ALV can verify (or falsify, by generating counter-examples) temporal logic properties of systems that can be modeled using a combination of Boolean logic and linear arithmetic expressions on Boolean, enumerated and (possibly unbounded) integer variables and parameterized integer constants. In this paper, we apply ALV to the verification of parameterized hierarchical state machine specifications. We extend the standard notation for hierarchical state machines by introducing primitives for explicit specification of asynchronous processes and their finite and parameterized instantiations. We define the formal semantics of these primitives, where the states of the parameterized processes are mapped to integer variables using the counting abstraction technique. We apply the presented approach to the specification and analysis of an airport ground traffic controller and verify several correctness properties of this specification using ALV.
Colorectal liver metastasis thymidylate synthase staining correlates with response to hepatic arterial floxuridine.

We assessed whether intensity of colorectal liver metastasis staining with the thymidylate synthase (TS) antibody TS106 predicted response to hepatic arterial infusion (HAI) of floxuridine chemotherapy. Liver metastasis biopsies were taken during laparotomy for hepatic arterial cannulation and stained using the TS106 monoclonal antibody. Staining intensity was designated at histological examination by two independent assessors as either "high" or "low. " Patients were treated by HAI, and liver metastasis response was assessed by comparison of computed tomography scan tumor volume before and after 4 months of treatment. A significant correlation (Fisher's exact test, P = 0.01) was noted between partial response to HAI and TS106 staining intensity in patients with colorectal liver metastases. Seventy-five percent of patients with evidence of a partial response had low TS staining compared with 29% of nonresponders. There was a significant difference (Fisher's exact test, P = 0.01) in the proportion of low (9 of 16) compared with high (3 of 20) TS staining tumors in which a partial response occurred. There was no significant difference (logrank test, P = 0.4) in survival from hepatic cannulation and HAI treatment of high (median, 322 days; interquartile range, 236-411) compared with low (median, 335 days; interquartile range, 301-547) TS staining patients. This study demonstrates an inverse correlation between TS immunohistochemical staining intensity in colorectal liver metastases and response to HAI. The results suggest that a prospective assessment of TS staining intensity in colorectal liver metastases would be useful to determine whether this method can be used to define patients who will benefit from HAI chemotherapy.
A real options approach to a classical capacity expansion problem

Some authors, considering deterministic or stochastic demand patterns and different forecasting formulations, have studied the classical problem of optimally meeting a growing demand for capacity, over an infinite horizon. With this approach, only investment costs discounted with a predefined interest rate are considered in the analysis. Adding other expenditures and revenues, managers usually estimate the discounted cash flow of the project, and assume the organization will follow a predetermined plan when investing, regardless of how events unfold in the future. The real options approach, on the other hand, introduces the possibility of incorporating other decision alternatives in the economic analysis, such as the option of waiting or postponing, abandoning, switching, etc. In this paper we first review the classical capacity expansion models. Then, the concepts and properties of the real options approach, with emphasis on the Black-Scholes equation, are briefly discussed. Finally, an application example is presented and discussed.
Image enhancement using second generation wavelet super resolution

A pressure relief device for a sealed system is provided. The device includes a negative pressure support that is engageable with the system. A seal is disposed between the support and the system such that a negative pressure differential created in the system acts on the seal to move the seal away from the negative pressure support. A wire connects the seal to the support. The wire is configured to break, thereby releasing the seal, when the seal is exposed to a negative pressure differential having a predetermined level. The device may also include a positive pressure support disposed between the seal and the negative pressure support. The positive pressure support prevents the seal from releasing until the system experiences a positive pressure differential of a predetermined level. The device may also include a sensor that indicates when the seal has released.
Software Selection and Configuration in Mobile Environments: A Utility-Based Approach

Users of low-power mobile computing platforms make ad hoc decisions when choosing software components among alternatives and configuring those components. We propose applying utility-theoretic models, which can help determine optimal allocation of scarce resources to applications given the user’s utility and application resource usage. We believe that taking into consideration resource consumption and applying microeconomic models has the potential of improving the user’s satisfaction with the system. In this paper, we formula te the problem, demonstrate the use of a microeconomics-based model on a simple version of the problem, and list possible solutions. Further, we identify issues typical of mobile environments that are not addressed by existing research, and propose ways of tackling these issues.
Discrepancy Games

We investigate a game played on a hypergraph H = ( V, E ) by two players, Balancer and Unbalancer. They select one element of the vertex set V alternately until all vertices are selected. Balancer wins if at the end of the game all edges e ∈ E are roughly equally distributed between the two players. We give a polynomial time
Estimation of Character Diagram from Open Movie Database Using Markov Logic Network

In this paper, we propose the estimation method of interpersonal relationships of characters from movie script databases on the Web using Markov Logic Network. By using Markov Logic Network, we can infer while allowing the violation of rules. In experiments, we confirmed that our proposed method can estimate favors between the characters in a movie with a precision of 69.8%.
Novel Membrane-Bound eIF2α Kinase in the Flagellar Pocket of Trypanosoma brucei

ABSTRACT Translational control mediated by phosphorylation of the alpha subunit of the eukaryotic initiation factor 2 (eIF2α) is central to stress-induced programs of gene expression. Trypanosomatids, important human pathogens, display differentiation processes elicited by contact with the distinct physiological milieu found in their insect vectors and mammalian hosts, likely representing stress situations. Trypanosoma brucei, the agent of African trypanosomiasis, encodes three potential eIF2α kinases (TbeIF2K1 to -K3). We show here that TbeIF2K2 is a transmembrane glycoprotein expressed both in procyclic and in bloodstream forms. The catalytic domain of TbeIF2K2 phosphorylates yeast and mammalian eIF2α at Ser51. It also phosphorylates the highly unusual form of eIF2α found in trypanosomatids specifically at residue Thr169 that corresponds to Ser51 in other eukaryotes. T. brucei eIF2α, however, is not a substrate for GCN2 or PKR in vitro. The putative regulatory domain of TbeIF2K2 does not share any sequence similarity with known eIF2α kinases. In both procyclic and bloodstream forms TbeIF2K2 is mainly localized in the membrane of the flagellar pocket, an organelle that is the exclusive site of exo- and endocytosis in these parasites. It can also be detected in endocytic compartments but not in lysosomes, suggesting that it is recycled between endosomes and the flagellar pocket. TbeIF2K2 location suggests a relevance in sensing protein or nutrient transport in T. brucei, an organism that relies heavily on posttranscriptional regulatory mechanisms to control gene expression in different environmental conditions. This is the first membrane-associated eIF2α kinase described in unicellular eukaryotes.
Rhetorical Structure Theory in Natural Language Generation

1 Introduction This paper is a survey of some literature on the use of Rhetorical Structure Theory (RST) (Mann and Thompson, 1988) for text generation, some of which can also be of use for building RST trees from texts for summarisation purposes. Several researchers have suggested the use of RST trees for summarisation, e.g. The organisation of the RST trees, then, depends on the input. If the input is a text, the organisation is signalled by the author and interpreted by the analyser. If the input is a knowledge base, the organisation is guided by the relations present in the knowledge base and the communicative goal guiding the analysis. Although many of the methods in RST summarisation deals with text as input, they could equally well be applied to RST trees generated from a knowledge base. This technique could be used for situations where the same text base has to be displayed in many ways, and the generation process is requiring a lot of resources. The processes of parsing and generating RST trees also have much in common, and therefore can profit from each other, sharing theories, resources and techniques. The paper is organised as follows: Section 2 gives a short introduction to RST. Section 3 focuses on the position of RST in the architecture of generation systems. In Section 4, some issues concerning the top-level organisation of texts are discussed, and in Section 5, the more detailed planning, such as choice of discourse markers and clause ordering, is under scrutiny. is based on the analyses of over hundred texts. Mann and Thompson claim that it is possible to analyse the majority of text types in terms of a hierarchical tree of rhetorical relations (see, for example, Figure 1). The analysis is based on the assumption that some text units are more central (salient) to the text than others, and that the other units are given to support the reader's belief in them. The central units are named nuclei, and the supporting units are named satellites. Rhetorical relations are described in terms of schemas, i.e. the way in which one or more satellites (or nuclei) are related to the current nucleus. It is also assumed that a relation that holds between two text spans also holds between the nuclei of those text spans. The application of a particular schema to a couple of text units is restricted by a number …
Simultaneously Segmenting Multiple Gene Expression Time Courses by Analyzing Cluster Dynamics

We present a new approach to segmenting multiple time series by analyzing the dynamics of cluster formation and rearrangement around putative segment boundaries. This approach finds application in distilling large numbers of gene expression profiles into temporal relationships underlying biological processes. By directly minimizing information-theoretic measures of segmentation quality derived from Kullback-Leibler (KL) divergences, our formulation reveals clusters of genes along with a segmentation such that clusters show concerted behavior within segments but exhibit significant regrouping across segmentation boundaries. The results of the segmentation algorithm can be summarized as Gantt charts revealing temporal dependencies in the ordering of key biological processes. Applications to the yeast metabolic cycle and the yeast cell cycle are described.