Miracle-dz/UniFAR-FTUs huggingface dataset:
Serum Interleukin-18 and Its Gene Haplotypes Profile as Predictors in Patients with Diabetic Nephropathy

BACKGROUND: Diabetic nephropathy (DN) is known as an acute microvascular complexity as a subsequence progression in diabetes mellitus type 1 and 2. Many evidence pointed that the proinflammatory cytokine Interleukin (IL)-18 might be involved in the pathogenesis of DN. AIM: The current study aimed to evaluate the association of serum IL-18 and its promoter gene polymorphisms with diabetic nephropathy. METHODS: This study included 62 diabetic nephropathy patients (DN group) compared to 52 diabetes mellitus patients (DM group). The two groups were subjected to anthropometry assessment, molecular studies including SNP genotyping by RFLP and finally statistical analysis. RESULTS: The assessment of the serum IL-18 level and the frequencies of its allele and haplotype: -137G/C, -607C/A and -656G/T among the DN and DM subjects revealed that -137G allele has significant variation between DN and DM subjects (about 80.8%, P = 0.05) but, no significant variation in -607 or -656 alleles IL-18 gene promoter. CONCLUSION: These data confirm the impact of high serum IL-18 and the haplotype of the polymorphism located in the promoter region of the IL-18 gene with the DN.
81 Nonenzymatic recombination of RNA: detection of novel sequences by next-generation sequencing

Implementation of the fluorescent proteins has made labeling proteins and DNA in live cells a routine procedure. At the same time labeling RNA in vivo is still a challenge. Most methods for labeling RNA make use of RNA aptamers attached to RNA. These aptamers are then labeled with a cognate RNA-binding protein that is fused with the fluorescent protein. Several years ago we modified this aptamer-based approach by introducing protein complementation (PC). In this approach the fluorescent protein is split and non-fluorescent until it is bound to RNA. Application of PC allowed to reduce the fluorescent background and thus to increase sensitivity of RNA detection (Valencia-Burton et al., 2007, 2009). To overcome another important limitation of the aptamer-based RNA labelingthe necessity to modify RNA by aptamer taggingwe combined protein complementation with the split aptamer approach (Toran et al., 2014, see Fig). In this method the cells are programmed to express two RNA probes that contain split aptamer sequences flanked with the anti-sense arms. Both RNA probes are expressed within one transcript. In the presence of the target RNA the RNA probes bind to the target via the anti-sense sequences which brings together the fragments of the split aptamer. The aptamer re-assembles and binds two split proteins which trigger protein complementation. In the course of this study we uncovered a mechanism of RNP complex formation that resulted in very high sensitivity of RNA detection. Our experiments revealed specific localization of an endogenous bacterial mRNA expressed on a physiological level. This work is the first example of the RNA-templated reassembly of split aptamers in vivo, which expands the set of available tools for the RNA-dependent circuit engineering. This research has been supported by the NSF Award 1050609.
Working Paper Series

This paper examines the roles of bank capital regulation and monetary policy in mitigating procyclicality and promoting macroeconomic and nancial stability. The analysis is based on a dynamic stochastic model with imperfect credit markets. Macroeconomic ( nancial) stability is de ned in terms of the volatility of nominal income (real house prices). Numerical experiments show that even if monetary policy can react strongly to in ation deviations from target, combining a credit-augmented interest rate rule and a Basel III-type countercyclical capital regulatory rule may be optimal for promoting overall economic stability. The greater the degree of interest rate smoothing, and the stronger the policymaker’s concern with macroeconomic stability, the larger is the sensitivity of the regulatory rule to credit growth gaps. JEL Classi cation Numbers: E44, E51, F41. Professor, School of Social Sciences, University of Manchester, United Kingdom, and co-Director, Centre for Growth and Business Cycle Research; Economist, Research Department, Central Bank of Turkey; Deputy Governor, Central Bank of Brazil. We would like to thank Otaviano Canuto, participants at the ECB workshop on The Bank Lending Channel in the Euro Area: New Models and Empirical Analysis (Frankfurt, June 24-25), and particularly our discussant, Javier Suarez, as well as participants at seminars at the European University Institute and the University of Manchester, for helpful comments on a previous draft. Financial support from the World Bank is gratefully acknowledged. A more detailed version of this paper, containing Appendices A, B, and C is available upon request. The views expressed in this paper are our own.
Caveolin 1 Is Overexpressed and Amplified in a Subset of Basal-like and Metaplastic Breast Carcinomas: A Morphologic, Ultrastructural, Immunohistochemical, and In situ Hybridization Analysis

Purpose: The distribution and significance of caveolin 1 (CAV1) expression in different breast cell types and role in breast carcinogenesis remain poorly understood. Both tumor-suppressive and oncogenic roles have been proposed for this protein. The aims of this study were to characterize the distribution of CAV1 in normal breast, benign breast lesions, breast cancer precursors, and metaplastic breast carcinomas; to assess the prognostic significance of CAV1 expression in invasive breast carcinomas; and to define whether CAV1 gene amplification is the underlying genetic mechanism driving CAV1 overexpression in breast carcinomas. Experimental Design: CAV1 distribution in frozen and paraffin-embedded whole tissue sections of normal breast was evaluated using immunohistochemistry, immunofluorescence, and immunoelectron microscopy. CAV1 expression was immunohistochemically analyzed in benign lesions, breast cancer precursors, and metaplastic breast carcinomas and in a cohort of 245 invasive breast carcinomas from patients treated with surgery followed by anthracycline-based chemotherapy. In 25 cases, CAV1 gene amplification was assessed by chromogenic in situ hybridization. Results: In normal breast, CAV1 was expressed in myoepithelial cells, endothelial cells, and a subset of fibroblasts. Luminal epithelial cells showed negligible staining. CAV1 was expressed in 90% of 39 metaplastic breast carcinomas and in 9.4% of 245 invasive breast cancers. In the later cohort, CAV1 expression was significantly associated with ‘basal-like’ immunophenotype and with shorter disease-free and overall survival on univariate analysis. CAV1 gene amplification was found in 13% of cases with strong CAV1 expression. Conclusions: The concurrent CAV1 amplification and overexpression call into question its tumor-suppressive effects in basal-like breast carcinomas.
Syntax-aware Neural Machine Translation Using CCG

Neural machine translation (NMT) models are able to partially learn syntactic information from sequential lexical information. Still, some complex syntactic phenomena such as prepositional phrase attachment are poorly modeled. This work aims to answer two questions: 1) Does explicitly modeling source or target language syntax help NMT? 2) Is tight integration of words and syntax better than multitask training? We introduce syntactic information in the form of CCG supertags either in the source as an extra feature in the embedding, or in the target, by interleaving the target supertags with the word sequence. Our results on WMT data show that explicitly modeling syntax improves machine translation quality for English-German, a high-resource pair, and for English-Romanian, a low-resource pair and also several syntactic phenomena including prepositional phrase attachment. Furthermore, a tight coupling of words and syntax improves translation quality more than multitask training.
Phenotypic characterization of rare interstitial deletion of chromosome 4

Abstract Interstitial deletion of the long arm of chromosome 4 is rare. Patients with interstitial deletion of the long arm of chromosome 4 differ from those with terminal deletions. Phenotypes may be variable, depending upon the specific length and location of the deleted portion. Here, we report on a boy exhibiting most of the congenital malformations encountered in terminal 4q syndrome. The conventional karyotyping and Fluorescence in-situ hybridization revealed a de novo interstitial del (4)(q31q32). The current report is a further document highlighting that deletion of segment q31 could be contributing to the expression of most of the phenotype of 4q deletion syndrome. Using array comparative genome hybridization methodology is recommended for investigating further cases with similar segmental interstitial deletions to support and delineate findings and to define genes implicated in the pathogenesis of the disorder.
Static Detection of Second-Order Vulnerabilities in Web Applications

Web applications evolved in the last decades from simple scripts to multi-functional applications. Such complex web applications are prone to different types of security vulnerabilities that lead to data leakage or a compromise of the underlying web server. So called second-order vulnerabilities occur when an attack payload is first stored by the application on the web server and then later on used in a security-critical operation. In this paper, we introduce the first automated static code analysis approach to detect second-order vulnerabilities and related multi-step exploits in web applications. By analyzing reads and writes to memory locations of the web server, we are able to identify unsanitized data flows by connecting input and output points of data in persistent data stores such as databases or session data. As a result, we identified 159 second-order vulnerabilities in six popular web applications such as the conference management systems HotCRP and Open-Conf. Moreover, the analysis of web applications evaluated in related work revealed that we are able to detect several critical vulnerabilities previously missed.
Stent-Based Delivery of Tissue Inhibitor of Metalloproteinase-3 Adenovirus Inhibits Neointimal Formation in Porcine Coronary Arteries

Background—Stent-based antiproliferative therapy appears to decrease in-stent restenosis. However, alternative approaches might produce equivalent efficacy with better long-term safety. In previous work, an adenovirus capable of expressing the tissue inhibitor of metalloproteinase-3 (RAdTIMP-3) inhibited neointima formation in cell cultures and porcine saphenous vein grafts. RAdTIMP-3 decreased smooth muscle cell migration, stabilized the extracellular matrix, and uniquely promoted apoptosis. The current study developed eluting stent technology to deliver RAdTIMP-3 during stenting of pig coronary arteries. Methods and Results—Binding of virus to and elution from stents and transduction of pig coronary arteries were confirmed using &bgr;-galactosidase as a reporter gene in vitro and in vivo. Deployment of RAdTIMP-3–coated stents increased apoptosis and reduced neointimal cell density, but did not increase inflammation or proliferation compared with &bgr;-galactosidase–expressing adenovirus (RAdlacZ). Neointimal area after 28 days was significantly reduced to 1.27±0.19 mm2 with RAdTIMP-3 versus 2.61±0.31 mm2 with RAdlacZ stents (P<0.001) and 2.12±0.20 mm2 with bare stents (P<0.005). Conclusions—Our results demonstrate for the first time to our knowledge the feasibility of adenovirus-coated stent technology and highlight the potential of TIMP-3 to produce significant inhibition of in-stent neointima formation.
The Elasticity of Taxable Income: Estimates and Flat Tax Predictions using the Hungarian Tax Changes in 2005

Many Central and Eastern European countries are adopting flat tax schemes in order to boost their economies and tax revenues. Though there are signs that some countries do manage to improve on both fronts, it is in general hard to distinguish the behavioral response to tax changes from the effect of increased tax enforcement. This paper addresses this gap by estimating the elasticity of taxable income in Hungary, one of the outliers in terms of not having a flat tax scheme. We analyze taxpayer behavior using a medium-scale tax reform episode in 2005, which changed marginal and average tax rates but kept enforcement constant. We employ a Tax and Financial Control Administration (APEH) panel dataset between 2004 and 2005 with roughly 215,000 taxpayers. Our results suggest a relatively small but highly significant tax price elasticity of about 0.06 for the population earning above the minimum wage (around 70% of all taxpayers). This number increases to around 0.3 when we focus on the upper 20% of the income distribution, with some income groups exhibiting even higher elasticities (0.45). We first demonstrate that such an elasticity substantially modifies the response of government revenues to the 2004-2005 tax changes, and then quantify the impact of a hypothetical flat income tax scheme. Our calculations indicate that though there is room for a parallel improvement of budget revenues and after-tax income, those gains are modest (2% and 1.4%, respectively). Moreover, such a reform involves important adverse changes in income inequality, and its burden falls mostly on lower-middle income taxpayers.
On Dinur’s proof of the PCP theorem

Probabilistically checkable proofs are proofs that can checked probabilistically by reading very few bits of the proof. In the early 1990’s, it was shown that proofs could be transformed into probabilistically checkable ones with only a modest increase in their size. The initial transformations, though elementary, were a little too complex. A recent work due to Irit Dinur gives a dramatically simple (and radically new) construction of probabilistically checkable proofs. This article explains the notion of a probabilistically checkable proof, presents the formal definition and then introduces the reader to Dinur’s work along with some of the context.
Serologic Testing for Human Granulocytic Ehrlichiosis at a National Referral Center

ABSTRACT An indirect immunofluorescence assay (IFA) was used to identify patients with antibodies reactive to the human granulocytic ehrlichiosis (HGE) agent. Serum samples collected from clinically ill individuals were submitted to the Centers for Disease Control and Prevention by physicians via state health departments from throughout the United States and tested against a panel of ehrlichial and rickettsial pathogens. Antibodies reactive to the HGE agent were detected in 142 (8.9%) of 1,602 individuals tested. There were 19 confirmed and 59 probable (n = 78) cases of HGE as defined by seroconversion or a fourfold or higher titer to the HGE agent than to the Ehrlichia chaffeensis antigens. The average age of patients with HGE was 57 years, and males accounted for 53 (68%) of the patients. Cases of HGE occurred in 21 states; 47 (60%) of the cases occurred in Connecticut (n = 14), New York (n = 18), and Wisconsin (n = 15). Onset of HGE was identified from April through December, with cases peaking in June and July. The earliest confirmed cases of HGE occurred in 1987 in Wisconsin and 1988 in Florida. No fatalities were reported among the 78 patients with confirmed or probable HGE. Reactivity to the HGE agent and to either Coxiella burnetii, Rickettsia rickettsii, or Rickettsia typhi was infrequent; however, 74 (52%) of the 142 individuals who were positive for HGE had at least one serum sample that also reacted to the E. chaffeensis antigen. Thirty-four persons with confirmed or probable human monocytic ehrlichiosis due to E. chaffeensis also had antibodies to the HGE agent in at least one serum sample. The specific etiologic agent for 30 patients was not ascribed because of similarity of titers to both ehrlichial antigens. The use of both antigens may be required to correctly diagnose most cases of human ehrlichiosis, especially in geographic regions where both the HGE agent and E. chaffeensis occur.
Mdx muscle grafts retain the mdx phenotype in normal hosts

Whole muscle grafts were made between mdx and normal mice to investigate whether the mdx myopathic lesion is intrinsic to mdx muscle or is a property of its environment. Grafts were examined between 20 and 101 days. Unequivocal necrotic muscle fibers and/or newly formed basophilic myotubes were noted in 8 of 16 grafts of mdx muscle made in normal hosts but in none of 16 grafts of normal muscle made in mdx hosts. In older grafts, the proportion of centrally nucleated fibers and variability of fiber diameter were both higher in mdx muscle grafted into normal hosts than in normal muscle grafted into either mdx or normal hosts. Analysis of the glucose‐6‐phosphate isomerase (GPI) isoenzyme content of the grafts indicated that the muscle formed was predominantly of donor origin. These findings provide evidence that the mdx lesion is a primary myopathy rather than secondary to an extramuscular primary lesion.
Specialist or Nonspecialist Physical Education Teachers in Ontario Elementary Schools: Examining Differences in Opportunities for Physical Activity

Research supports the position that specialists are the preferred providers of physical education in elementary (primary) school settings. We examined whether specialists delivered more physical education lessons and provided greater opportunities for moderate and vigorous physical activity and whether barriers to curricular and extracurricular physical activity opportunities in Ontario elementary schools differed for specialist and nonspecialist teachers. Using a cross-sectional design, a questionnaire was mailed to key informants in 599 randomly selected elementary schools in Ontario, yielding an 85% response rate. Most physical education in Ontario elementary schools is delivered by nonspecialists (63%). No self-reported differences were found between specialists and generalist teachers in the number of physical education lessons delivered per week, the minutes per physical education class, or in the amount of reported moderate or vigorous physical activity in lessons. Compared with specialists, respondents in schools in which generalist teachers taught PE perceived lack of training as a greater barrier to delivering physical education. Given the importance of subject knowledge in teaching effectively, there is still need to advocate for specialist physical education teaching in elementary schools. However, concerns about teaching specialism may be secondary to broader and more complex factors surrounding the delivery of physical education in elementary schools.
Rat liver injury following normothermic ischemia is prevented by a phosphinic matrix metalloproteinase inhibitor

Hepatic ischemia occurs in liver transplantation, hemodynamic or cardiogenic shock, and liver resection associated with trauma or tumor. Ischemia/reperfusion (I/R) injury results in microcirculation failure followed by apoptosis and necrosis. Matrix metalloproteinases (MMPs) are involved in many physiological and pathological processes, but their expression and function during liver I/R remains poorly documented. In this study, we evaluated the expression of nine MMPs and their natural inhibitors, tissue inhibitors of MMPs (TIMPs), in a rat model of liver I/R. Analysis of MMP and TIMP expression show that although most of these genes are not constitutively expressed in the normal liver, they are induced in a specific time‐dependent manner following I/R. Stromelysin‐1, gelatinase B, and collagenase‐3 are induced during the early phase of acute liver injury associated with inflammation and increased necrosis/apoptosis, whereas gelatinase A, membrane type‐MMP, stromelysin‐3, metalloelastase, TIMP‐1, and TIMP‐2 are essentially detectable during the recovery phase of liver injury corresponding to hepatocyte regeneration. This observation suggested that MMPs and TIMPs could play both deleterious and beneficial roles following I/R. We thus tested the effect of a specific phosphinic MMP inhibitor on acute liver I/R injury. Inhibition of MMP activity was shown to significantly decrease liver injury in ischemic/reperfused liver tissue as assessed by histological studies and serum hepatic enzyme levels. We therefore propose that MMP inhibitors may be of clinical relevance in liver‐associated ischemic diseases or after liver transplantation.
Testing Guilt Aversion with an Exogenous Shift in Beliefs

We conduct a laboratory experiment to test whether subjects tend to meet the expectations of others (the guilt aversion hypothesis). The specificity of our approach is that second-order beliefs are manipulated exogenously just by changing the parameters of the experimental game. In particular, we consider a simple communication game where the sender is perfectly informed about his material benefit from lying to the receiver. At the same time, the receiver knows only the ex-ante distribution of the sender's material incentives. By changing this distribution between the experimental treatments, we achieve an exogenous variation in the receiver's payoff expectations (and hence in the corresponding sender's second-order beliefs) while keeping the sender's actual material incentives fixed. The results show that the rate of lying is significantly lower when the receiver is supposed to have higher payoff expectations, however only in the case when the monetary incentives for lying are fixed at a moderate level.
Incremental tensor analysis: Theory and applications

How do we find patterns in author-keyword associations, evolving over time? Or in data cubes (tensors), with product-branchcustomer sales information? And more generally, how to summarize high-order data cubes (tensors)? How to incrementally update these patterns over time? Matrix decompositions, like principal component analysis (PCA) and variants, are invaluable tools for mining, dimensionality reduction, feature selection, rule identification in numerous settings like streaming data, text, graphs, social networks, and many more settings. However, they have only two orders (i.e., matrices, like author and keyword in the previous example). We propose to envision such higher-order data as tensors, and tap the vast literature on the topic. However, these methods do not necessarily scale up, let alone operate on semi-infinite streams. Thus, we introduce a general framework, incremental tensor analysis (ITA), which efficiently computes a compact summary for high-order and high-dimensional data, and also reveals the hidden correlations. Three variants of ITA are presented: (1) dynamic tensor analysis (DTA); (2) streaming tensor analysis (STA); and (3) window-based tensor analysis (WTA). In paricular, we explore several fundamental design trade-offs such as space efficiency, computational cost, approximation accuracy, time dependency, and model complexity. We implement all our methods and apply them in several real settings, such as network anomaly detection, multiway latent semantic indexing on citation networks, and correlation study on sensor measurements. Our empirical studies show that the proposed methods are fast and accurate and that they find interesting patterns and outliers on the real datasets.