Miracle-dz/UniFAR-FTUs huggingface dataset:
Constitutive activation of Rho proteins by CNF-1 influences tight junction structure and epithelial barrier function

The apical-most epithelial intercellular junction, referred to as the tight junction (TJ), regulates paracellular solute flux in diverse physiological and pathological states. TJ affiliations with the apical filamentous actin (F-actin) cytoskeleton are crucial in regulating TJ function. F-actin organization is influenced by the Rho GTPase family, which also controls TJ function. To explore the role of Rho GTPases in regulating TJ structure and function, we utilized Escherichia coli cytotoxic necrotizing factor-1 (CNF-1) as a tool to activate constitutively Rho, Rac and Cdc42 signaling in T84 polarized intestinal epithelial monolayers. The biological effects of the toxin were polarized to the basolateral membrane, and included profound reductions in TJ gate function, accompanied by displacement of the TJ proteins occludin and zonula occludens-1 (ZO-1), and reorganization of junction adhesion molecule-1 (JAM-1) away from the TJ membrane. Immunogold electron microscopy revealed occludin and caveolin-1 internalization in endosomal/caveolar-like structures in CNF-treated cells. Immunofluorescence/confocal microscopy suggested that a pool of internalized occludin went to caveolae, early endosomes and recycling endosomes, but not to late endosomes. This provides a novel mechanism potentially allowing occludin to evade a degradative pathway, perhaps allowing efficient recycling back to the TJ membrane. In contrast to the TJ, the characteristic ring structure of proteins in adherens junctions (AJs) was largely preserved despite CNF-1 treatment. CNF-1 also induced displacement of a TJ-associated pool of phosphorylated myosin light chain (p-MLC), which is normally also linked to the F-actin contractile machinery in epithelial cells. The apical perjunctional F-actin ring itself was maintained even after toxin exposure, but there was a striking effacement of microvillous F-actin and its binding protein, villin, from the same plane. However, basal F-actin stress fibers became prominent and cabled following basolateral CNF-1 treatment, and the focal adhesion protein paxillin was tyrosine phosphorylated. This indicates differences in Rho GTPase-mediated control of distinct F-actin pools in polarized cells. Functionally, CNF-1 profoundly impaired TJ/AJ assembly in calcium switch assays. Re-localization of occludin but not E-cadherin along the lateral membrane during junctional reassembly was severely impaired by the toxin. A balance between activity and quiescence of Rho GTPases appears crucial for both the generation and maintenance of optimal epithelial barrier function. Overactivation of Rho, Rac and Cdc42 with CNF-1 seems to mirror key barrier-function disruptions previously reported for inactivation of RhoA.
Expression of uPA and its receptor by both neoplastic and stromal cells during xenograft invasion

Recent studies have shown that molecules involved in generation and regulation of extracellular proteolytic activity are often expressed by non‐malignant stromal cells during human cancer invasion. We have studied the expression of the urokinase‐type plasminogen activator and the urokinase‐type plasminogen activator cell‐surface receptor in xenografts of human MDA‐MB‐231 mammary carcinoma cells growing invasively in nude mice. Northern analysis showed the presence of both human and mouse urokinase‐type plasminogen activator and urokinase‐type plasminogen activator receptor mRNA in tumor extracts. By in situ hybridization, mRNA for human urokinase‐type plasminogen activator and its receptor was detected in virtually all the cancer cells, while mouse urokinase‐type plasminogen activator and urokinase‐type plasminogen activator receptor mRNA was expressed by tumor‐infiltrating fibroblast‐like and macrophage‐like cells. In invasive areas the cells expressing the 2 murine mRNAs were either the same or located immediately adjacent to each other. This model system has several advantages for studies of the mechanism by which cancer cells induce or recruit stromal cells to produce molecules involved in proteolysis. © 1994 Wiley‐Liss, Inc.
Gait recognition based on wavelet features with spectral regression kernel discriminant analysis

This paper has proposed gait recognition approach for analyzing and classifying human identification under carrying a bag and wearing a clothing thus improving recognition performances. The proposed method is based on detail wavelet features extracted from the Haar-wavelet decomposition of dynamic areas in the Gait Energy Image (GEI). Spectral Regression Kernel Discriminant Analysis (SRKDA) is then applied to the extracted feature vector in order to reduce its dimensionality by selecting only the most relevant and discriminate features. The CASIA Gait database under variations of clothing and carrying conditions for different viewing angles was used to evaluated the proposed method using a k-NN classifier and has yielded an attractive performance of up to 93% in terms of identification Rate (IR) at rank-1 when compared to similar and existing state-of-the-art methods.
mixed meal in type 2 diabetes Regulation of endogenous glucose production after a

[PDF] [Full Text] [Abstract] , November 1, 2008; 295 (5): E1132-E1141. Am J Physiol Endocrinol Metab Bouwman, Matthew J. Watt, Joseph Proietto, Jenny M. Favaloro and Sofianos Andrikopoulos Sherley Visinoni, Barbara C. Fam, Amy Blair, Christian Rantzau, Benjamin J. Lamont, Russell the liver Increased glucose production in mice overexpressing human fructose-1,6-bisphosphatase in [PDF] [Full Text] [Abstract] 2008; 31 (11): 2183-2187. Dia Care and David B. Dunger Mary E. Pennant, Leslie J.C. Bluck, M. Loredana Marcovecchio, Burak Salgin, Roman Hovorka Insulin Administration and Rate of Glucose Appearance in People With Type 1 Diabetes [PDF] [Full Text] [Abstract] , April , 2009; 329 (1): 102-111. J Pharmacol Exp Ther Véniant Y. Lau, Jin Wang, Yue-Sheng Li, Tom Boone, Richard A. Lindberg, Sylvia Hu and Murielle M. Renée Komorowski, Cheng Zhang, Jennifer J. Patel, Dorothy Caughey, Gary S. Elliott, Yvonne Hai Yan, Wei Gu, Jie Yang, Vivian Bi, Yuqing Shen, Eunkyung Lee, Katherine A. Winters, Glucose Homeostasis in Mice and Monkeys Fully Human Monoclonal Antibodies Antagonizing the Glucagon Receptor Improve [PDF] [Full Text] [Abstract] , May , 2009; 32 (5): 866-872. Dia Care Rizza Ananda Basu, Chiara Dalla Man, Rita Basu, Gianna Toffolo, Claudio Cobelli and Robert A. Postprandial Glucose Metabolism Effects of Type 2 Diabetes on Insulin Secretion, Insulin Action, Glucose Effectiveness, and [PDF] [Full Text] [Abstract] , December , 2009; 331 (3): 871-881. J Pharmacol Exp Ther Richard A. Lindberg and Murielle M. Véniant Atangan, Glenn Sivits, David Hill, Jie Yang, Vivian Bi, Yuqing Shen, Sylvia Hu, Tom Boone, Wei Gu, Hai Yan, Katherine A. Winters, Renée Komorowski, Steven Vonderfecht, Larissa and Hyperglucagonemia -Cell Hyperplasia α Causes Sustained Improvement in Glycemic Control, with Reversible Long-Term Inhibition of the Glucagon Receptor with a Monoclonal Antibody in Mice
Activation of HIV Transcription by the Viral Tat Protein Requires a Demethylation Step Mediated by Lysine-specific Demethylase 1 (LSD1/KDM1)

The essential transactivator function of the HIV Tat protein is regulated by multiple posttranslational modifications. Although individual modifications are well characterized, their crosstalk and dynamics of occurrence during the HIV transcription cycle remain unclear. We examine interactions between two critical modifications within the RNA-binding domain of Tat: monomethylation of lysine 51 (K51) mediated by Set7/9/KMT7, an early event in the Tat transactivation cycle that strengthens the interaction of Tat with TAR RNA, and acetylation of lysine 50 (K50) mediated by p300/KAT3B, a later process that dissociates the complex formed by Tat, TAR RNA and the cyclin T1 subunit of the positive transcription elongation factor b (P-TEFb). We find K51 monomethylation inhibited in synthetic Tat peptides carrying an acetyl group at K50 while acetylation can occur in methylated peptides, albeit at a reduced rate. To examine whether Tat is subject to sequential monomethylation and acetylation in cells, we performed mass spectrometry on immunoprecipitated Tat proteins and generated new modification-specific Tat antibodies against monomethylated/acetylated Tat. No bimodified Tat protein was detected in cells pointing to a demethylation step during the Tat transactivation cycle. We identify lysine-specific demethylase 1 (LSD1/KDM1) as a Tat K51-specific demethylase, which is required for the activation of HIV transcription in latently infected T cells. LSD1/KDM1 and its cofactor CoREST associates with the HIV promoter in vivo and activate Tat transcriptional activity in a K51-dependent manner. In addition, small hairpin RNAs directed against LSD1/KDM1 or inhibition of its activity with the monoamine oxidase inhibitor phenelzine suppresses the activation of HIV transcription in latently infected T cells. Our data support the model that a LSD1/KDM1/CoREST complex, normally known as a transcriptional suppressor, acts as a novel activator of HIV transcription through demethylation of K51 in Tat. Small molecule inhibitors of LSD1/KDM1 show therapeutic promise by enforcing HIV latency in infected T cells.
ROS, Notch, and Wnt Signaling Pathways: Crosstalk between Three Major Regulators of Cardiovascular Biology

Reactive oxygen species (ROS), traditionally viewed as toxic by-products that cause damage to biomolecules, now are clearly recognized as key modulators in a variety of biological processes and pathological states. The development and regulation of the cardiovascular system require orchestrated activities; Notch and Wnt/β-catenin signaling pathways are implicated in many aspects of them, including cardiomyocytes and smooth muscle cells survival, angiogenesis, progenitor cells recruitment and differentiation, arteriovenous specification, vascular cell migration, and cardiac remodelling. Several novel findings regarding the role of ROS in Notch and Wnt/β-catenin modulation prompted us to review their emerging function in the cardiovascular system during embryogenesis and postnatally.
Question-Directed Reasoning With Relation-Aware Graph Attention Network for Complex Question Answering Over Knowledge Graph

Complex knowledge graph question answering (KGQA) aims at answering natural language questions by entities retrieving from a knowledge graph (KG). Recently, the relation path-based models have shown the unique advantage for complex KGQA. However, these existing models ignore the dependency between different relation paths, which leads to aimless reasoning over the KG. To resolve this issue, we propose the question-directed reasoning with relation-aware graph attention network (QRGAT) that encodes the reasoning process as a reasoning graph. The relation-aware GAT can recognize neighbor entities along with the corresponding relations for each entity. With the relation-aware GAT stacked in multiple layers, it can collaboratively capture the dependency of different relation paths for each entity. The question-directed reasoning utilizes the information learned by the relation-aware GAT to solve the aimless reasoning on the KG by constructing a reasoning graph. Extensive experiments demonstrate that our QRGAT outperforms the baseline models on both popular datasets WebQuestionsSP and ComplexWebQuestions. Compared with the strong GNN-based baseline NSM$_{+h}$, our QRGAT achieves the performance improvements of 2.3% on WebQuestionsSP and 3.6% on ComplexWebQuestions by the metric Hits@1.
Examining the association between media coverage of organ donation and organ transplantation rates

Abstract: Research addressing the organ shortage in the USA has examined multiple factors influencing one's decision to become an organ donor. One of these research lines addresses media coverage of organ donation. The present investigation seeks to advance this research line by examining the association between organ donation media coverage and organ transplantation rates. A content analysis spanning January 1990 to December 2005 of three television networks reveals an overall positive association between coverage and transplantation rates. The implications of our findings are discussed along with recommendations for practitioners and advocates alike.
Sources of Uncertainty in the Meridional Pattern of Climate Change

We employ a moist energy balance model (MEBM), representing atmospheric heat transport as the diffusion of near‐surface moist static energy, to evaluate sources of uncertainty in the meridional pattern of surface warming. Given zonal mean patterns of radiative forcing, radiative feedbacks, and ocean heat uptake, the MEBM accurately predicts zonal mean warming as simulated by general circulation models under increased CO2. Over a wide range of latitudes, the MEBM captures approximately 90% of the variance in zonal mean warming across the general circulation models, with approximately 70% of the variance attributable to differences in radiative feedbacks alone. Partitioning the radiative feedbacks into individual components shows that the majority of the uncertainty in the meridional pattern of warming arises from uncertainty in cloud feedbacks. Isolating feedback uncertainty within specific regions demonstrates that tropical feedback uncertainty leads to surface warming uncertainty that is global and nearly uniform with latitude, whereas polar feedback uncertainty leads to surface warming uncertainty that is largely confined to the poles.
Analysis of the Transcriptome of the Infective Stage of the Beet Cyst Nematode, H. schachtii

The beet cyst nematode, Heterodera schachtii, is a major root pest that significantly impacts the yield of sugar beet, brassicas and related species. There has been limited molecular characterisation of this important plant pathogen: to identify target genes for its control the transcriptome of the pre-parasitic J2 stage of H. schachtii was sequenced using Roche GS FLX. Ninety seven percent of reads (i.e., 387,668) with an average PHRED score > 22 were assembled with CAP3 and CLC Genomics Workbench into 37,345 and 47,263 contigs, respectively. The transcripts were annotated by comparing with gene and genomic sequences of other nematodes and annotated proteins on public databases. The annotated transcripts were much more similar to sequences of Heterodera glycines than to those of Globodera pallida and root knot nematodes (Meloidogyne spp.). Analysis of these transcripts showed that a subset of 2,918 transcripts was common to free-living and plant parasitic nematodes suggesting that this subset is involved in general nematode metabolism and development. A set of 148 contigs and 183 singletons encoding putative homologues of effectors previously characterised for plant parasitic nematodes were also identified: these are known to be important for parasitism of host plants during migration through tissues or feeding from cells or are thought to be involved in evasion or modulation of host defences. In addition, the presence of sequences from a nematode virus is suggested. The sequencing and annotation of this transcriptome significantly adds to the genetic data available for H. schachtii, and identifies genes primed to undertake required roles in the critical pre-parasitic and early post-parasitic J2 stages. These data provide new information for identifying potential gene targets for future protection of susceptible crops against H. schachtii.
Links Optimization for Resource-Constrained Project Scheduling

An optimizing mathematical model with the objective function of minimizing the total number of resource links is established. Improved table dispatching method and continuous adjustment method in closed circuit are proposed to solve the model, by which the optimal solution can be gotten. Critical sequences in the project scheduling can be identified by the float computing like CPM model on the basis of the optimal solution.
Accuracy-based measures provide a better measure of sequence learning than reaction time-based measures

The Serial Reaction Time Task (SRTT) was designed to measure motor sequence learning and is widely used in many fields in cognitive science and neuroscience. However, the common performance measures derived from SRTT—reaction time (RT) difference scores—may not provide valid measures of sequence learning. This is because RT-difference scores may be subject to floor effects and otherwise not sufficiently reflective of learning. A ratio RT measure might minimize floor effects. Furthermore, measures derived from predictive accuracy may provide a better assessment of sequence learning. Accordingly, we developed a Predictive Sequence Learning Task (PSLT) in which performance can be assessed via both RT and predictive accuracy. We compared performance of N = 99 adults on SRTT and PSLT in a within-subjects design and also measured fluid abilities. The RT-difference scores on both tasks were generally not related to fluid abilities, replicating previous findings. In contrast, a ratio RT measure on SRTT and PSLT and accuracy measures on PSLT were related to fluid abilities. The accuracy measures also indicated an age-related decline in performance on PSLT. The current patterns of results were thus inconsistent across different measures on the same tasks, and we demonstrate that this discrepancy is potentially due to floor effects on the RT difference scores. This may limit the potential of SRTT to measure sequence learning and we argue that PSLT accuracy measures could provide a more accurate reflection of learning ability.
A Study of Android Application Security

The fluidity of application markets complicate smartphone security. Although recent efforts have shed light on particular security issues, there remains little insight into broader security characteristics of smartphone applications. This paper seeks to better understand smartphone application security by studying 1,100 popular free Android applications. We introduce the ded decompiler, which recovers Android application source code directly from its installation image. We design and execute a horizontal study of smartphone applications based on static analysis of 21 million lines of recovered code. Our analysis uncovered pervasive use/misuse of personal/ phone identifiers, and deep penetration of advertising and analytics networks. However, we did not find evidence of malware or exploitable vulnerabilities in the studied applications. We conclude by considering the implications of these preliminary findings and offer directions for future analysis.
Deferred-Acceptance Auctions for Multiple Levels of Service

Deferred-acceptance (DA) auctions} are mechanisms that are based on backward-greedy algorithms and possess a number of remarkable incentive properties, including implementation as an obviously-strategyproof ascending auction. All existing work on DA auctions considers only binary single-parameter problems, where each bidder either ``wins'' or ``loses. '' This paper generalizes the DA auction framework to non-binary settings, and applies this generalized framework to obtain approximately welfare-maximizing DA auctions for a number of basic mechanism design problems: multiunit auctions, problems with polymatroid constraints or multiple knapsack constraints, and the problem of scheduling jobs to minimize their total weighted completion time. Our results require the design of novel backward-greedy algorithms with good approximation guarantees.
Color QR Codes: Increased Capacity Via Per-Channel Data Encoding and Interference Cancellation

Monochrome 2-D barcodes have recently become extremely popular in mobile imaging applications. To accommodate higher data rates, we present a methodology for extending these barcodes to color. We use independent per channel data encoding in cyan, magenta, and yellow print colorant channels and decode the information in the complementary red, green, and blue channels used in capture, effectively increasing the data rate by a factor of three. To overcome unavoidable inter-channel interference, our framework utilizesadaptive thresholding and model-based interference cancellation at the decoder which are facilitated by an intelligent barcode design that allows estimation of parameters required for thresholding and cancellation. We present the framework by constructing and evaluating the performance for a color version of the QR code, the most commonly deployed monochrome barcode in mobile applications. Experimental results demonstrate that the framework is effective and allows recovery of embedded data with low bit error rates, which can be readily handled by the builtin error correction withinthe QRcode standard.
Postsynaptic Targeting of Alternative Postsynaptic Density-95 Isoforms by Distinct Mechanisms

Members of the postsynaptic density-95 (PSD95)/synapse-associated protein-90 (SAP90) family of scaffolding proteins contain a common set of modular protein interaction motifs including PDZ (postsynaptic density-95/Discs large/zona occludens-1), Src homology 3, and guanylate kinase domains, which regulate signaling and plasticity at excitatory synapses. We report that N-terminal alternative splicing of PSD95 generates an isoform, PSD95β that contains an additional “L27” motif, which is also present in SAP97. Using yeast two hybrid and coimmunoprecipitation assays, we demonstrate that this N-terminal L27 domain of PSD-95β, binds to an L27 domain in the membrane-associated guanylate kinase calcium/calmodulin-dependent serine kinase, and to Hrs, an endosomal ATPase that regulates vesicular trafficking. By transfecting heterologous cells and hippocampal neurons, we find that interactions with the L27 domain regulate synaptic clustering of PSD95β. Disrupting Hrs-regulated early endosomal sorting in hippocampal neurons selectively blocks synaptic clustering of PSD95β but does not interfere with trafficking of the palmitoylated isoform, PSD95α. These studies identify molecular and functional heterogeneity in synaptic PSD95 complexes and reveal critical roles for L27 domain interactions and Hrs regulated vesicular trafficking in postsynaptic protein clustering.
Variable Preconditioning of Krylov Subspace Methods for Hierarchical Matrices With Adaptive Cross Approximation

This paper discusses Krylov subspace methods to solve a linear system whose coefficient matrix is represented by a hierarchical matrix. We propose a preconditioning technique using a part of the original hierarchical matrix to accelerate the convergence of the Krylov subspace methods. The proposed preconditioning technique is based on the assumption that the submatrices on the original hierarchical matrix are approximated using the adaptive cross approximation or variants thereof. The performance of Krylov subspace methods with the proposed preconditioning technique is examined through numerical experiments on an electrostatic field analysis.
Application and Research on the Clustering Method in the Flow Transfer of Power Network

Flow transfer is one of main causes of cascading failures. It is important to identify the initial fault line which has serious impacts on the power network due to flow transfer. The authors propose a method which is based on Fuzzy C-mean (FCM) algorithm to divide the initial failures which has different impacts on the power network due to flow transfer. The method provides an analytical measure to divide the different effects of different initial failures and try to find weaknesses in the power network. The method combines structure and operating characteristics of the power network and proposes an elaborate structure of the data samples, therefore, the clustering analysis is more comprehensive and an example in IEEE14 system proves that the method is reasonable.