Miracle-dz/UniFAR-FTUs huggingface dataset:
Association of common variations of the E-cadherin with endometriosis

Abstract Endometriosis is a polygenic and multifactorial disease. E-cadherin (CDH1) gene encodes an epithelial cell–cell adhesion glycoprotein that modulates a wide variety of processes, including cell polarization, migration and cancer metastasis. Decreased expression of CDH1 in epithelial cells in peritoneal endometriosis has been reported in advanced stages of endometriotic lesions. We investigated the CDH1 −160C/A and +54C/T variations with susceptibility to endometriosis in an Iranian population. In this case-control study, 149 patients with endometriosis (stages I–IV) and 151 healthy women as controls were included. Genotyping was performed using PCR-RFLP method. A p value of <0.05 was considered statistically significant. The CDH1 + 54TT genotype was significantly lower (p = 0.012; OR = 0.30, 95% CI: 0.12–0.77) in the patients (11.6%) than the control group (26.7%). The CDH1 + 54T allele was significantly lower (p = 0.001; OR = 0.55, 95% CI: 0.38–0.77) in the cases (35.7%) compared with the control group (50.3%). No association was found between CDH1 − 160C/A polymorphism and endometriosis. The CDH1 +54C/T was associated with susceptibility to endometriosis in Iranian population, and +54T allele may have a protective role in progression of endometriosis. Chinese abstract 子宫内膜异位症是一种多基因、多因素的疾病。 钙黏蛋白(CDH1)基因编码一种上皮细胞间的粘着糖蛋白，该粘着糖蛋白调节包括细胞极化、迁移及癌症转移在内的多种进程。 腹膜型子宫内膜异位的上皮细胞CDH1基因的表达下调已经在子宫内膜异位症的晚期阶段病变报道过。 我们在一个伊朗人群中研究了CDH1 -160C/A和+54C/T变异对于子宫内膜异位症的易感性。 这个病例对照研究对象包括149名子宫内膜异位症（分期I-IV）患者和151名作为对照的健康女性。 通过限制性片段长度多态性分析技术（PCR-RFLP）进行基因分型。 P<0.05被认为有统计学意义。 子宫内膜异位症患者(11.6%)的CDH1 + 54TT基因型与正常对照组(26.7%)相比显著减少(p=0.012；OR=0.30，95% CI：0.12–0.77)。 与对照组(50.3%)相比，病例组(35.7%)的CDH1 + 54T的等位基因明显减少（p=0.001；OR=0.55，95% CI：0.38–0.77) 。 尚未发现 CDH1的-160C/A多态性和子宫内膜异位症之间的相关性。 而在伊朗群体中 CDH1 +54C/T与子宫内膜异位症的发病相关。 同时+54T的等位基因可能在子宫内膜异位症的发展进程中起到保护作用。
Membrane Estrogen Receptor Engagement Activates Endothelial Nitric Oxide Synthase via the PI3-Kinase–Akt Pathway in Human Endothelial Cells

17&bgr;-Estradiol (E2) is a rapid activator of endothelial nitric oxide synthase (eNOS). The product of this activation event, NO, is a fundamental determinant of cardiovascular homeostasis. We previously demonstrated that E2-stimulated endothelial NO release can occur without an increase in cytosolic Ca2+. Here we demonstrate for the first time, to our knowledge, that E2 rapidly induces phosphorylation and activation of eNOS through the phosphatidylinositol 3 (PI3)-kinase–Akt pathway. E2 treatment (10 ng/mL) of the human endothelial cell line, EA.hy926, resulted in increased NO production, which was abrogated by the PI3-kinase inhibitor, LY294002, and the estrogen receptor antagonist ICI 182,780. E2 stimulated rapid Akt phosphorylation on serine 473. As has been shown for vascular endothelial growth factor, eNOS is an E2-activated Akt substrate, demonstrated by rapid eNOS phosphorylation on serine 1177, a critical residue for eNOS activation and enhanced sensitivity to resting cellular Ca2+ levels. Adenoviral-mediated EA.hy926 transduction confirmed functional involvement of Akt, because a kinase-deficient, dominant-negative Akt abolished E2-stimulated NO release. The membrane-impermeant E2BSA conjugate, shown to bind endothelial cell membrane sites, also induced rapid Akt and consequent eNOS phosphorylation. Thus, engagement of membrane estrogen receptors results in rapid endothelial NO release through a PI3-kinase–Akt-dependent pathway. This explains, in part, the reduced requirement for cytosolic Ca2+ fluxes and describes an important pathway relevant to cardiovascular pathophysiology.
Epigenetic control of the variable expression of a Plasmodium falciparum receptor protein for erythrocyte invasion

Plasmodium falciparum can invade erythrocytes by redundant receptors, some of which have variable expression. A P. falciparum clone Dd2 requiring erythrocyte sialic acid for invasion can be switched to a sialic acid-independent progeny clone Dd2NM by growing the Dd2 clone with neuraminidase-treated erythrocytes. The RH4 gene is transcriptionally up-regulated in Dd2NM compared to Dd2, despite the absence of DNA changes in and around the gene. We determined the epigenetic modifications around the transcription start site (TSS) at the time of expression of RH4 in Dd2NM (44 h) and at an earlier time when RH4 is not expressed (24 h). At 44 h, the occupancy of the +1 nucleosome site downstream of the TSS of the active RH4 gene in Dd2NM was markedly reduced compared to Dd2; no difference was observed at 24 h. At 44 h, histone modifications associated with up-regulation were positively correlated to the active RH4 gene of Dd2NM compared to Dd2; no differences were observed at 24 h. Histone H3K9 trimethylation (a marker for silencing) was higher in Dd2 than Dd2NM along the 5′-UTRs of the RH4 gene at both 44 and 24 h. Our data indicate that the failure of Dd2 to express the sialic acid-independent invasion receptor gene RH4 is associated with the epigenetic silencing mark H3K9 trimethylation present throughout the cycle.
Exoenzyme T Plays a Pivotal Role in the IFN-γ Production after Pseudomonas Challenge in IL-12 Primed Natural Killer Cells

Pseudomonas aeruginosa (PA) expresses the type III secretion system (T3SS) and effector exoenzymes that interfere with intracellular pathways. Natural killer (NK) cells play a key role in antibacterial immunity and their activation is highly dependent on IL-12 produced by myeloid cells. We studied PA and NK cell interactions and the role of IL-12 using human peripheral blood mononuclear cells, sorted human NK cells, and a human NK cell line (NK92). We used a wild-type (WT) strain of PA (PAO1) or isogenic PA-deleted strains to delineate the role of T3SS and exoenzymes. Our hypotheses were tested in vivo in a PA-pneumonia mouse model. Human NK cells or NK92 cell line produced low levels of IFN-γ in response to PA without IL-12 stimulation, whereas PA significantly increased IFN-γ after IL-12 priming. The modulation of IFN-γ production by PA required bacteria-to-cell contact. Among T3SS effectors, exoenzyme T (ExoT) upregulates IFN-γ production and control ERK activation. In vivo, ExoT also increases IFN-γ levels and the percentage of IFN-γ+ NK cells in lungs during PA pneumonia, confirming in vitro data. In conclusion, our results suggest that T3SS could modulate the production of IFN-γ by NK cells after PA infection through ERK activation.
Clinical Utility of Machine-Learning Approaches in Schizophrenia: Improving Diagnostic Confidence for Translational Neuroimaging

Machine-learning approaches are becoming commonplace in the neuroimaging literature as potential diagnostic and prognostic tools for the study of clinical populations. However, very few studies provide clinically informative measures to aid in decision-making and resource allocation. Head-to-head comparison of neuroimaging-based multivariate classifiers is an essential first step to promote translation of these tools to clinical practice. We systematically evaluated the classifier performance using back-to-back structural MRI in two field strengths (3- and 7-T) to discriminate patients with schizophrenia (n = 19) from healthy controls (n = 20). Gray matter (GM) and white matter images were used as inputs into a support vector machine to classify patients and control subjects. Seven Tesla classifiers outperformed the 3-T classifiers with accuracy reaching as high as 77% for the 7-T GM classifier compared to 66.6% for the 3-T GM classifier. Furthermore, diagnostic odds ratio (a measure that is not affected by variations in sample characteristics) and number needed to predict (a measure based on Bayesian certainty of a test result) indicated superior performance of the 7-T classifiers, whereby for each correct diagnosis made, the number of patients that need to be examined using the 7-T GM classifier was one less than the number that need to be examined if a different classifier was used. Using a hypothetical example, we highlight how these findings could have significant implications for clinical decision-making. We encourage the reporting of measures proposed here in future studies utilizing machine-learning approaches. This will not only promote the search for an optimum diagnostic tool but also aid in the translation of neuroimaging to clinical use.
Stented pulmonary valve allografts as tricuspid valve substitutes in sheep

In sheep, stented pulmonary semilunar valves have been allografted as tricuspid valve substitutes and their biological behaviour has been followed postoperatively. Whereas there was initial pleasing function with normal cusp competence, by day 102 the cusps had retracted to partial incompetence. This process of valve decline was accentuated by day 150, and by day 241 was complete. Histological studies at day 150 showed cusp foreshortening, with scant nuclei and collagen looser than normal. These findings suggested that the mechanism causing the valve decline was a host to foreign body reaction rather than the usual histological pattern of graft rejection.
Using Dynamic Symbolic Execution to Generate Inputs in Search-Based GUI Testing

Search-based testing has been successfully applied to generate complex sequences of events for graphical user interfaces (GUIs), but typically relies on simple heuristics or random values for data widgets like text boxes. This may greatly reduce the effectiveness of test generation for applications which expect specific input values to be entered in their GUI by users. Generating such specific input values is one of the virtues of dynamic symbolic execution (DSE), but DSE is less suitable to generate sequences of events. Therefore, this paper describes a hybrid approach that uses search-based testing to generate sequences of events, and DSE to build input data for text boxes. This is achieved by replacing standard widgets in a system under test with symbolic ones, allowing us to execute GUIs symbolically. In this paper, we demonstrate an extension of the search-based GUI testing tool EXSYST, which uses DSE to successfully increase the obtained code coverage on two case study applications.
Postmodernism And Social Inquiry

Literature dealing with postmodernism - or with the tension between modernity and postmodernity - has been confined primarily within the domains of philosophy, literature, and the arts. Integrating philosophy and the humanities with sociological theory and research methods, this pioneering volume is one of the first books to address the relevance of postmodernism to the social sciences and to explore the application of postmodern thinking to the study of society. Postmodernism and Social Inquiry will inform sociologists, other social scientists and anyone interested in cultural studies or in other major issues and themes in postmodern inquiry. Written in an accessible, jargon-free style, it is an excellent introduction for advanced undergraduates and graduate students in the social sciences, and for nonacademics seeking an overview of the field.
Inhibition of ultraviolet B–induced c‐fos gene expression and p38 mitogen‐activated protein kinase activation by (‐)‐epigallocatechin gallate in a human keratinocyte cell line

(‐)‐Epigallocatechin gallate (EGCG), the major polyphenol isolated from green tea, is an active chemoprevention agent against cancer. However, the molecular mechanisms that underlie the inhibitory effects of EGCG are not well understood. In this study, we tested the effects of EGCG on ultraviolet (UV) B radiation–induced c‐fos gene expression in a human keratinocyte cell line, HaCaT. EGCG inhibited UVB‐induced steady‐state message and transcriptional activation of the c‐fos gene in a dose‐dependent manner. Western analyses further indicated that EGCG had an inhibitory effect on UVB‐induced accumulation of the c‐fos protein within the same dose range. To further examine the mechanism by which EGCG inhibits UVB‐induced c‐fos expression, we tested the effect of EGCG on upstream activators of the c‐fos gene. We found that EGCG significantly inhibited activation of p38 mitogen‐activated protein kinase but not c‐jun NH2‐terminal kinase or extracellular signal‐regulated protein kinase activation. Our previous studies have indicated that UVB‐induced c‐fos expression may play a key role in UVB‐induced activation of the activator protein‐1 transcription factor and EGCG‐inhibited, UVB‐induced activation of AP‐1 in HaCaT cells. Because AP‐1 is important for tumor promotion and c‐fos is a major component of AP‐1, the inhibitory effects of EGCG on c‐fos expression may further explain the anti–tumor‐promoting effects of EGCG. Mol. Carcinog. 24:79–84, 1999. © 1999 Wiley‐Liss, Inc.
Understanding News Story Chains using Information Retrieval and Network Clustering Techniques

ABSTRACT Content analysis of news stories is a cornerstone of the communication studies field. However, much research is conducted at the level of individual news articles, despite the fact that news events are frequently presented as “stories” by news outlets: chains of connected articles offering follow up reporting as new facts emerge or covering the same event from different angles. These stories are theoretically highly important; they also create measurement issues for general quantitative studies of news output. Yet, thus far, the field has lacked an efficient method for detecting groups of articles which form stories in a way that enables their analysis. In this work, we present a novel, automated method for identifying news stories from within a corpus of articles, which makes use of techniques drawn from the fields of information retrieval and network analysis. We demonstrate the application of the method to a corpus of almost 40,000 news articles, and show that it can effectively identify valid story chains within the corpus. We use the results to make observations about the prevalence and dynamics of stories within the UK news media, showing that more than 50% of news production takes place within the form of story chains.
Rotation Method for Reconstructing Process and Field from Imperfect Data

Reconstruction of processes and fields from noisy data is to solve a set of linear algebraic equations. Three factors affect the accuracy of reconstruction: (a) a large condition number of the coefficient matrix, (b) high noise-to-signal ratio in the source term, and (c) no a priori knowledge of noise statistics. To improve reconstruction accuracy, the set of linear algebraic equations is transformed into a new set with minimum condition number and noise-to-signal ratio using the rotation matrix. The procedure does not require any knowledge of low-order statistics of noises. Several examples including highly distorted Lorenz attractor illustrate the benefit of using this procedure.
Diagnosing a Failed Proof in Fault-Tolerance: A Disproving Challenge Problem

This paper proposes a challenge problem in disproving. We describe a fault-tolerant distributed protocol designed at NASA for use in a fly-by-wire system for next-generation commercial aircraft. An early design of the protocol contains a subtle bug that is highly unlikely to be caught in fault injection testing. We describe a failed proof of the protocol's correctness in a mechanical theorem prover (PVS) with a complex unfinished proof conjecture. We use a model checking suite (SAL) to generate a concrete counterexample to the unproven conjecture to demonstrate the existence of a bug. However, we argue that the effort required in our approach is too high and propose what conditions a better solution would satisfy. We carefully describe the protocol and bug to provide a challenging but feasible case study for disproving research.
A case study on privacy information protection in campus

Privacy protection currently circulating in global IT industries could potentially cause the next wave in information security. However, currently still lack of success story among different industries. We aimed to develop an influenza solution and assessed its effectiveness to help school planned to build up their own system. We brainstormed from among experts from the school administration, law enforcement departments and layers, and IT specialists, because lacked of successful story; the opinions from experts were helpful when blinded in founding the directions. We built a prototype with applications used in campus and took the PDCA to defined flows and procedures based on the suggestions from experts followed by penetration testing to test the result. This research aimed to find out what, why and how of relation between school and privacy protection in digital times. We used Delphi to brainstorming the outcome was the requirement and success factors on how to build up a privacy information management system in campus. And followed by a series of processes and procedures to construct the system. The results were statistic ratio from AHP and workflows with procedures to be consider when we built the privacy protection system in our case study. Our findings highlight the potential of a well design system combine with thoughtful administration can manage privacy information effectiveness.
Divided Majority and Information Aggregation: Theory and Experiment

We propose a theory-based experimental approach to compare the properties of approval voting (AV) with thoseof plurality. This comparison is motivated by the theoretical prediction that, in our aggregate uncertainty setup,AV should produce close to first-best outcomes,while pluralitywill not. The experiment shows, first, thatwelfaregains are substantial. Second, both aggregate and individual responses are in line with theoretical predictions,and thus with strategic voting. Finally, subjects' behavior under AV highlights the need to study equilibria inasymmetric strategies.
Audio in Image Steganography based on Wavelet Transform

Security of data is very important in data communication. Everyday a lot of information is transferred form one user to another on internet and so the possibility of data theft also increases. Steganography provides a solution for the security of information during data transmission. Steganography is the science which makes the valuable information invisible to prevent it from unauthorized user. In this paper an audio message has been embedded in an image using the LSB (Least Significant Bit) technique and the wavelet transform. To hide a speech in an image is challenging as size of speech is larger than size of image. Number of bits in 1kb of speech is almost equal to an image. This paper describes how maximum speech can be embed in an image.
Strong Photonic Localizations Generated in Single-Optical-Waveguide Ring

In this paper, an extreme simple single-optical-waveguide ring (SOWR) is designed to generate strong photonic localizations by considering the similarities between electrons in electronic mesoscopic networks and photons in optical waveguide networks (OWNs). This interesting structure is designed based on the single-electronic-mesoscopic ring that can produce huge electronic persistent currents. We obtain the fitting formulas of the intensity, site number, and site positions for the maximal photonic localization in a SOWR. These interesting SOWRs may provide attractive applications like multichannel high-efficiency energy storages, high power super luminescent light emitting diodes, optical switches, and other correlative all-optical devices. Moreover, the approach of referencing single-electronic-mesoscopic ring to design SOWR may offer a new way to devise optical structures being capable of producing strong photonic localizations and may also deepen people's knowledge on the correlation between OWN and the electronic mesoscopic network.
Allocating bandwidth for bursty connections

In this paper, we undertake the first study of statistical multiplexing from the perspective of approximation algorithms. The basic issue underlying statistical multiplexing is the following: in high-speed networks, individual connections (i.e., communication sessions) are very bursty, with transmission rates that vary greatly over time. As such, the problem of packing multiple connections together on a link becomes more subtle than in the case when each connection is assumed to have a fixed demand. We consider one of the most commonly studied models in this domain: that of two communicating nodes connected by a set of parallel edges, where the rate of each connection between them is a random variable. We consider three related problems: (1) stochastic load balancing, (2) stochastic bin-packing, and (3) stochastic knapsack. In the first problem the number of links is given and we want to minimize the expected value of the maximum load. In the other two problems the link capacity and an allowed overflow probability p are given, and the objective is to assign connections to links, so that the probability that the load of a link exceeds the link capacity is at most p. In binpacking we need to assign each connection to a link using as few links as possible. In the knapsack problem each connection has a value, and we have only one link. The problem is to accept as many connections as possible. For the stochastic load balancing problem we give an O(1)-approximation algorithm for arbitrary random variables. For the other two problems we have algorithms restricted to on-off sources (the most common special case studied in the statistical multiplexing literature), with a somewhat weaker range of performance guarantees. A standard approach that has emerged for dealing with probabilistic resource requirements is the notion of effective bandwidth—this is a means of associating a fixed demand with a bursty connection that “represents” its distribution as closely as possible. Our approximation algorithms make use of the standard definition of effective bandwidth and also a new one that we introduce; the performance guarantees are based on new results showing that a combination of these measures can be used to provide bounds on the optimal solution.
Combining the Finite Element Method with Structural Connectome-based Analysis for Modeling Neurotrauma: Connectome Neurotrauma Mechanics

This article presents the integration of brain injury biomechanics and graph theoretical analysis of neuronal connections, or connectomics, to form a neurocomputational model that captures spatiotemporal characteristics of trauma. We relate localized mechanical brain damage predicted from biofidelic finite element simulations of the human head subjected to impact with degradation in the structural connectome for a single individual. The finite element model incorporates various length scales into the full head simulations by including anisotropic constitutive laws informed by diffusion tensor imaging. Coupling between the finite element analysis and network-based tools is established through experimentally-based cellular injury thresholds for white matter regions. Once edges are degraded, graph theoretical measures are computed on the “damaged” network. For a frontal impact, the simulations predict that the temporal and occipital regions undergo the most axonal strain and strain rate at short times (less than 24 hrs), which leads to cellular death initiation, which results in damage that shows dependence on angle of impact and underlying microstructure of brain tissue. The monotonic cellular death relationships predict a spatiotemporal change of structural damage. Interestingly, at 96 hrs post-impact, computations predict no network nodes were completely disconnected from the network, despite significant damage to network edges. At early times () network measures of global and local efficiency were degraded little; however, as time increased to 96 hrs the network properties were significantly reduced. In the future, this computational framework could help inform functional networks from physics-based structural brain biomechanics to obtain not only a biomechanics-based understanding of injury, but also neurophysiological insight.