Miracle-dz/UniFAR-FTUs huggingface dataset:
Constructing and Refining Large-Scale Railway Models Represented by Petri Nets

A new method for rapid construction of large-scale executable railway models is presented. Computer systems for railway systems suffer from poor integration and lack of explicit understanding of the large amount of static and dynamic information in the railway. In this paper, we give solutions to both problems. It is shown how a component-oriented approach makes it easy to construct and refine basic railway models by effective methods, such that a variety of models with important properties can be maintained within the same framework. Basic railway nets are refined into several new kinds: nets that are safe, permit collision detection, include time, and are sensitive to its surroundings. Since the underlying implementation language is Petri nets, large expressibility is combined with simplicity, and in addition, the analysis of the behavior of railway models comes gently.
Evidence of a molecular boundary lubricant at snakeskin surfaces

During slithering locomotion the ventral scales at a snake's belly are in direct mechanical interaction with the environment, while the dorsal scales provide optical camouflage and thermoregulation. Recent work has demonstrated that compared to dorsal scales, ventral scales provide improved lubrication and wear protection. While biomechanic adaption of snake motion is of growing interest in the fields of material science and robotics, the mechanism for how ventral scales influence the friction between the snake and substrate, at the molecular level, is unknown. In this study, we characterize the outermost surface of snake scales using sum frequency generation (SFG) spectra and near-edge X-ray absorption fine structure (NEXAFS) images collected from recently shed California kingsnake (Lampropeltis californiae) epidermis. SFG's nonlinear optical selection rules provide information about the outermost surface of materials; NEXAFS takes advantage of the shallow escape depth of the electrons to probe the molecular structure of surfaces. Our analysis of the data revealed the existence of a previously unknown lipid coating on both the ventral and dorsal scales. Additionally, the molecular structure of this lipid coating closely aligns to the biological function: lipids on ventral scales form a highly ordered layer which provides both lubrication and wear protection at the snake's ventral surface.
Mutated K‐rasAsp12 promotes tumourigenesis in ApcMin mice more in the large than the small intestines, with synergistic effects between K‐ras and Wnt pathways

K‐ras mutations are found in 40–50% of human colorectal adenomas and carcinomas, but their functional contribution remains incompletely understood. Here, we show that a conditional mutant K‐ras mouse model (K‐rasAsp12/Cre), with transient intestinal Cre activation by β‐Naphthoflavone (β‐NF) treatment, displayed transgene recombination and K‐rasAsp12 expression in the murine intestines, but developed few intestinal adenomas over 2 years. However, when crossed with ApcMin/+ mice, the K‐rasAsp12/Cre/ApcMin/+ offspring showed acceleration of intestinal tumourigenesis with significantly changed average lifespan (P < 0.05) decreased to 18.4 ± 5.4 weeks from 20.9 ± 4.7 weeks (control ApcMin/+ mice). The numbers of adenomas in the small intestine and large intestine were significantly (P < 0.01) increased by 1.5‐fold and 5.7‐fold, respectively, in K‐rasAsp12/Cre/ApcMin/+ mice compared with ApcMin/+ mice, with the more marked increase in adenoma prevalence in the large intestine. To explore possible mechanisms for K‐rasAsp12 and ApcMin co‐operation, the Mitogen‐activated protein kinase (Mapk), Akt and Wnt signalling pathways, including selected target gene expression levels, were evaluated in normal large intestine and large intestinal tumours. K‐rasAsp12 increased activation of Mapk and Akt signalling pathway targets phospho‐extracellular signal‐regulated kinase (pErk) and pAkt, and increased relative expression levels of Wnt pathway targets vascular endothelial growth factor (VEGF), gastrin, cyclo‐oxygenase 2 (Cox2) and T‐cell lymphoma invasion and metastasis 1 (Tiam1) in K‐rasAsp12/Cre/ApcMin/+ adenomas compared with that of ApcMin/+ adenomas, although other Wnt signalling pathway target genes such as Peroxisome proliferator‐activated receptor delta (PPARd), matrix metalloproteinase 7 (MMP7), protein phosphatase 1 alpha (PP1A) and c‐myc remained unchanged. In conclusion, intestinal expression of K‐rasAsp12 promotes mutant Apc‐initiated intestinal adenoma formation in vivo more in the large intestine than the small intestine, with evidence of synergistic co‐operation between mutant K‐ras and Apc involving increased expression of some Wnt‐pathway target genes.
PDGF ligand and receptor gene expression during repair of arterial injury

Smooth muscle cells (SMC) in rat carotid artery leave the quiescent state and proliferate after balloon catheter injury, but the signals for mitogenesis are not known. In this study, the possibility that cells within damaged arteries produce a growth factor that could act locally to stimulate SMC replication and repair was examined. We found that the genes for PDGF-A and -B (ligand) and PDGF receptor (alpha and beta subunits) were expressed in normal and injured carotid arteries and were independently regulated during repair of carotid injury. Two phases of PDGF ligand and receptor gene expression were observed: (a) In the early stage, a large decrease in PDGF beta-receptor mRNA levels preceded 10- to 12-fold increases in PDGF-A transcript abundance in the first 6 h after wounding. No change in PDGF alpha-receptor or PDGF-B gene expression was found at these times. (b) In the chronic phase, 2 wk after injury, neointimal tissue had lower levels of PDGF alpha- receptor mRNA (threefold) and higher levels of PDGF beta-receptor mRNA (three- to fivefold) than did restored media. Moreover, in situ hybridization studies identified a subpopulation of neointimal SMC localized at or near the luminal surface with a different pattern of gene expression than the underlying carotid SMC. Luminal SMC were strongly positive for PDGF-A and PDGF beta-receptor transcripts, while showing little or no hybridization for PDGF-B or PDGF alpha-receptor. Immunohistochemical studies showed strongly positive staining for PDGF- A in SMC along the luminal surface. These data show that changes in PDGF ligand and receptor expression occur at specific times and locations in injured carotid artery and suggest that these changes may play a role in regulating arterial wound repair.
Development of a New Methodology for Screening of Human Immunodeficiency Virus Type 1 Microbicides Based on Real-Time PCR Quantification

ABSTRACT Potential topical retrovirucides or vaginal microbicides against human immunodeficiency virus type 1 (HIV-1) include nonnucleoside reverse transcriptase inhibitors (NNRTIs). To be successful, such agents have to be highly active against cell-free virions. In the present study, we developed a new real-time PCR-based assay to measure the natural endogenous reverse transcription (NERT) activity directly on intact HIV-1 particles in the presence of reverse transcriptase (RT) inhibitors. We further evaluated the permeability to nevirapine (NVP) and efavirenz (EFV) and their retention within nascent viral particles. We also demonstrated the NVP and EFV inhibitory effects on NERT activity and the impact of resistance mutations measured directly by this new strategy. Furthermore, the results showed a clear correlation between NERT activity and classical infectivity assays. The 50% inhibitory concentrations (IC50s) of NVP and EFV were demonstrated to be up to 100-fold higher for cell-free than for cell-associated virions, suggesting that cell-free virions are less permeable to these drugs. Our results suggest that NVP and EFV penetrate both the envelope and the capsid of HIV-1 particles and readily inactivate cell-free virions. However, the characteristics of these NNRTIs, such as lower permeability and lower retention during washing procedures, in cell-free virions reduce their efficacies as microbicides. Here, we demonstrate the usefulness of the NERT real-time PCR as an assay for screening novel antiretroviral compounds with unique mechanisms of action.
Gabexate Mesilate Inhibits Colon Cancer Growth, Invasion, and Metastasis by Reducing Matrix Metalloproteinases and Angiogenesis

Gabexate mesilate (GM), a synthetic protease inhibitor, has an antiproteinase activity on various types of plasma serine proteases. However, its role on matrix metalloproteinases (MMPs) has not been identified. In this study, we investigated the effect of GM on MMPs and on the invasion and metastasis of human colon cancer cell lines and neoangiogenesis. The activities of MMPs secreted from these cells were significantly reduced by GM but unaffected by the serine protease inhibitor aprotinin. GM directly inhibited purified progelatinase A derived from T98G human glioblastoma cells. In vitro, GM significantly reduced the invasive ability of colon cancer cells but not cellular motility, whereas aprotinin affected neither. Liver metastatic ability and tumorigenic potential in nude mice were remarkably reduced on treatment with GM. Immunohistochemical analysis of GM-treated tumors in mice showed a marked increase in apoptosis and a significant reduction in tumor angiogenesis. Human umbilical vein endothelial cell proliferation, tube formation, and neoangiogenesis in the rabbit cornea and Matrigel implanted in mice were significantly inhibited by GM. These results suggest that GM is a novel inhibitor of MMPs and that it may inhibit the invasion and metastasis of human colon cancer cells by blocking MMPs and neoangiogenesis.
SyDiG: uncovering Synteny in Distant Genomes

Current methods for detecting synteny work well for genomes with high degrees of inter- and intra-species chromosomal homology, such as mammals. This paper presents a new algorithm for synteny computation that is well suited to genomes covering a large evolutionary span. It is based on a three-step process: identification of initial microsyntenic homologous regions, extension of homologous boundaries and reconstruction of syntenic blocks by identification of groups of homologous genomic segments that are conserved in every subject genome. Our method performs as well as GRIMM-Synteny on mammalian genomes, and outperforms it for clades with much greater evolutionary distances such as the Hemiascomycetous yeasts.
Differential projections of the infralimbic and prelimbic cortex in the rat

The medial prefrontal cortex has been associated with diverse functions including attentional processes, visceromotor activity, decision‐making, goal‐directed behavior, and working memory. The present report compares and contrasts projections from the infralimbic (IL) and prelimbic (PL) cortices in the rat by using the anterograde anatomical tracer, Phaseolus vulgaris‐leucoagglutinin. With the exception of common projections to parts of the orbitomedial prefrontal cortex, olfactory forebrain, and midline thalamus, PL and IL distribute very differently throughout the brain. Main projection sites of IL are: 1) the lateral septum, bed nucleus of stria terminalis, medial and lateral preoptic nuclei, substantia innominata, and endopiriform nuclei of the basal forebrain; 2) the medial, basomedial, central, and cortical nuclei of amygdala; 3) the dorsomedial, lateral, perifornical, posterior, and supramammillary nuclei of hypothalamus; and 4) the parabrachial and solitary nuclei of the brainstem. By contrast, PL projects at best sparingly to each of these structures. Main projection sites of PL are: the agranular insular cortex, claustrum, nucleus accumbens, olfactory tubercle, the paraventricular, mediodorsal, and reuniens nuclei of thalamus, the capsular part of the central nucleus and the basolateral nucleus of amygdala, and the dorsal and median raphe nuclei of the brainstem. As discussed herein, the pattern of IL projections is consistent with a role for IL in the control of visceral/autonomic activity homologous to the orbitomedial prefrontal cortex of primates, whereas those of PL are consistent with a role for PL in limbic‐cognitive functions homologous to the dorsolateral prefrontal cortex of primates. Synapse 51:32–58, 2004. © 2003 Wiley‐Liss, Inc.
What's 'choice' got to do with it?: avatar selection differences between novice and expert players of World of Warcraft and Rift

It's a now familiar refrain among both players and academics that healing is a 'feminine' activity and tanking a 'masculine' one within Massively Multiplayer Online Games. In this paper we present data from a multi-site study of World of Warcraft and Rift that examines this stereotype across novice and expert players. Our findings suggest that gender role stereotyping is progressively internalized as players become more competent in their gameworld of choice, with experts being more likely than novices to adopt this convention in their avatar selection.
Coarse Blobs or Fine Edges? Evidence That Information Diagnosticity Changes the Perception of Complex Visual Stimuli

Efficient categorizations of complex visual stimuli require effective encodings of their distinctive properties. However, the question remains of how processes of object and scene categorization use the information associated with different perceptual spatial scales. The psychophysics of scale perception suggests that recognition uses coarse blobs before fine scale edges, because the former is perceptually available before the latter. Although possible, this perceptually determined scenario neglects the nature of the task the recognition system must solve. If different spatial scales transmit different information about the input, an identical scene might be flexibly encoded and perceived at the scale that optimizes information for the considered task-i.e., the diagnostic scale. This paper tests the hypothesis that scale diagnosticity can determine scale selection for recognition. Experiment 1 tested whether coarse and fine spatial scales were both available at the onset of scene categorization. The second experiment tested that the selection of one scale could change depending on the diagnostic information present at this scale. The third and fourth experiments investigated whether scale-specific cues were independently processed, or whether they perceptually cooperated in the recognition of the input scene. Results suggest that a mandatory low-level registration of multiple spatial scales promotes flexible scene encodings, perceptions, and categorizations.
Non-negative matrix factorization based illumination robust meanshift tracking

Object tracking is a critical task in surveillance and activity analysis. One main issue in tracking is illumination variation. We propose a method which is robust to illumination by incorporating a feature that is less variant to illumination. The proposed feature is a reflectance histogram obtained using sparsity constrained non-negative matrix factorization (NMFsc). Using NMFsc, illumination and reflectance components are separated in each frame of the input video. The obtained reflectance histogram is used as feature vector in a meanshift framework for target tracking. We also use an adaptive target model to handle target appearance changes. Experimental results using standard benchmark videos show that the proposed scheme can lead to better tracking in challenging illumination scenarios, when compared to several existing algorithms.
Shared learning in supply networks: evidence from an emerging market supply network

Purpose – Firms face the challenge of developing learning capabilities that enable them to work as part of an effective business network. While an extensive literature examines learning capabilities within the firm, little attention has been given to shared learning that occurs between networked firms. This study aims to explore how a manufacturer and businesses services provider learn to develop their supply network. Specifically, this research investigates four areas of shared learning that are central to supply network success, and discusses the development of shared learning capabilities within a supply network. Design/methodology/approach – The paper presents an in-depth, longitudinal case study of a supply network that involves an engineering company and two business services suppliers. Findings – The study suggests that developing shared learning capabilities in four key areas is imperative for network success: business relationships, customers’ desired values, firm boundaries, and network structures. Furthermore, there are three distinct types of shared learning that were common to all four areas of shared learning identified. These are: strategic shared learning, operational shared learning, and exchange shared learning. Research limitations/implications – The research findings are based on a single case study. Additional research across multiple case studies is needed in order to verify the findings reported. Practical implications – The four learning areas have significant managerial implications for the way managers develop mechanisms to capture and share learning associated with developing supply networks. Originality/value – This research addresses a gap in the literature concerning the areas of learning capabilities for developing a supply network. The findings are important to research and practice with regard to how companies develop learning capabilities.
CD4 engagement induces Fas antigen‐dependent apoptosis of T cells in vivo

CD4 is a T lymphocyte receptor for major histocompatibility complex class II antigens. It is referred to as coreceptor because it synergizes with the T cell receptor for antigen when both receptors become engaged simultaneously. We show here in mice that when engaged by antibody independently of the T cell antigen receptor, CD4 induces T cells to undergo apoptosis. Several features of this process were identified. The expression of an intact Fas protein is a requirement for CD4‐mediated T cell death. Mice homozygous for the lpr mutation which are defective in the expression of Fas and in their ability to delete lymphocytes apoptotically fail to delete anti‐CD4‐reactive T cells. Sessile anti‐CD4‐reactive T cells leave their homing environment in lymphoid organs and modulate their cell surface molecules, e.g. CD2, CD3, CD4. A massive influx of lymphoid cells with null‐cell phenotype occurs in the blood where they begin to reexpress cell surface markers. With their arrival in the circulation, anti‐CD4‐reactive T cells develop features of DNA degradation typical of apoptosis. More than one third of the circulating lymphoid cells show apoptotic features 7–8 h after anti‐CD4 injection. Their frequency declines subsequently presumably due to their physical disintegration via shedding of apoptotic bodies and phagocytosis. Our data show that when not obliged to the activation process by the antigen receptor, CD4 can mediate deletion signals. Thus, besides functioning as coreceptor with the antigen receptor, CD4 has a function of its own in facilitating the induction of apoptosis.
Title: Understanding Expressive Action Laboratory Where Thesis Will Be Done: Mit Media Lab Vision and Modeling Group

Brief Statement of the Problem: User interfaces make measurements of the user and use those measurements to give the user control over some abstract domain. The sophistication of these measurements range from the trivial keyclick to the most advanced perceptual interface system. Once the measurements are acquired the system usually attempts to extract some set of features as the first step in a pattern recognition system that will convert those measurements into whatever domain of control the application provides. Those features are usually chosen for mathematical convenience or to satisfy an ad hoc notion of invariance. The expressivity of any such interface is limited by the user's ability to overcome the reality of their bodies and perform in this arbitrary feature space. The fact that people are embodied places powerful constraints on their motion. An appropriate model of this embodiment allows a perceptual system to separate the necessary aspects of motion from the purposeful aspects of motion. The necessary aspects are a result of physics, and are predictable. The purposeful aspects are the direct result of a person attempting to express themselves through the motion of their bodies. By taking this one thoughtful step closer to the original intentions of the user, we open the door to better interfaces. Understanding embodiment is the key to perceiving expressive motion.
Long‐term Mapping Techniques for Ship Hull Inspection and Surveillance using an Autonomous Underwater Vehicle

This paper reports on a system for an autonomous underwater vehicle to perform in situ, multiple session hull inspection using long‐term simultaneous localization and mapping (SLAM). Our method assumes very little a priori knowledge, and it does not require the aid of acoustic beacons for navigation, which is a typical mode of navigation in this type of application. Our system combines recent techniques in underwater saliency‐informed visual SLAM and a method for representing the ship hull surface as a collection of many locally planar surface features. This methodology produces accurate maps that can be constructed in real‐time on consumer‐grade computing hardware. A single‐session SLAM result is initially used as a prior map for later sessions, where the robot automatically merges the multiple surveys into a common hull‐relative reference frame. To perform the relocalization step, we use a particle filter that leverages the locally planar representation of the ship hull surface, and a fast visual descriptor matching algorithm. Finally, we apply the recently developed graph sparsification tool, generic linear constraints, as a way to manage the computational complexity of the SLAM system as the robot accumulates information across multiple sessions. We show results for 20 SLAM sessions for two large vessels over the course of days, months, and even up to three years, with a total path length of approximately 10.2 km.
Novel copy number variants and major limb reduction malformation: Report of three cases

Limb reduction malformations are highly heterogeneous in their clinical presentation and so, predicting the underlying mutation on a clinical basis can be challenging. Molecular karyotyping is a powerful genomic tool that has quickly become the mainstay for the study of children with malformation syndromes. We describe three patients with major limb reduction anomalies in whom pathogenic copy number variants were identified on molecular karyotyping. These include a patient with hypoplastic phalanges and absent hallux bilaterally with de novo deletion of 11.9 Mb on 7p21.1–22.1 spanning 63 genes including RAC1, another patient with severe Holt–Oram syndrome and a large de novo deletion 2.2 Mb on 12q24.13–24.21 spanning 20 genes including TBX3 and TBX5, and a third patient with acheiropodia who had a nullizygous deletion of 102 kb on 7q36.3 spanning LMBR1. We discuss the potential of these novel genomic rearrangements to improve our understanding of limb development in humans. © 2016 Wiley Periodicals, Inc.
Quality of life after surgery for rectal cancer with special reference to pelvic floor dysfunction

Aim Conventional outcomes such as survival, tumour recurrence and complication rates after surgery for rectal cancer have been rigorously assessed, but the importance of maintaining quality of life (QOL) after surgery for rectal cancer has received less attention. The aim of the current study was to analyse QOL and the occurrence of pelvic dysfunction after the surgical treatment of rectal cancer.