Miracle-dz/UniFAR-FTUs huggingface dataset:
MicroRNA-21 Knockout Improve the Survival Rate in DSS Induced Fatal Colitis through Protecting against Inflammation and Tissue Injury

Background MicroRNA-21 (miR-21) is overexpressed in most inflammatory diseases, but its physiological role in gut inflammation and tissue injury is poorly understood. The goal of this work is to understand the role of miR-21 in colitis and damage progression of intestine in a genetically modified murine model. Methods Experimental colitis was induced in miR-21 KO and wild-type (WT) mice by 3.5% dextran sulphate sodium (DSS) administration for 7 days. Disease activity index(DAI), blood parameters, intestinal permeability, histopathologic injury, cytokine and chemokine production, and epithelial cells apoptosis were examined in colons of miR-21 KO and WT mice. Results miR-21 was overexpressed in intestine of inflammatory bowel diseases (IBD) and acute intestinal obstruction (AIO) patients when compared with normal intestinal tissues. Likewise, miR-21 was up-regulated in colon of IL-10 KO mice when compared with control mice. WT mice rapidly lost weight and were moribund 5 days after treatment with 3.5% DSS, while miR-21 KO mice survived for at least 6 days. Elevated leukocytes and more severe histopathology were observed in WT mice when compared with miR-21 KO mice. Elevated levels of TNF-α and macrophage inflammatory protein-2(MIP-2) in colon culture supernatants from WT mice exhibited significant higher than miR-21 KO mice. Furthermore, CD3 and CD68 positive cells, intestinal permeability and apoptosis of epithelial cells were significantly increased in WT mice when compared with miR-21 KO mice. Finally, we found that miR-21 regulated the intestinal barrier function through modulating the expression of RhoB and CDC42. Conclusion Our results suggest that miR-21 is overexpressed in intestinal inflammation and tissue injury, while knockout of miR-21 in mice improve the survival rate in DSS-induced fatal colitis through protecting against inflammation and tissue injury. Therefore, attenuated expression of miR-21 in gut may prevent the onset or progression of inflammatory bowel disease in patients.
Effective Network Management via S ystem-Wide Coordination and Optimization

As networked systems grow and traffic patterns evolve, management applications are increasing in complexity and functionality. To address the requirements of these management applications, equipment vendors and administrators today depend on incremental solutions that increase the complexity of network elements and deployment costs for operators. Despite this increased complexity and cost, the incremental nature of these solutions still leaves a significant gap between the policy objectives of system administrators and today’s mechanisms. These challenges arise in several application contexts in different networking domains: ISPs, enterprise settings, and data centers. Much of this disconnect arises from the narrow device-centric view of current solutions. Such piecemeal solutions are inefficient: network elements duplicate tasks and some locations become overloaded. Worse still, administrators struggle to retrofit their high-level goals within device-centric configurations. This dissertation argues for a clean-slate system-wide approach for resource management in large-scale networked systems based on three highlevel principles: (1) systematic selection and placement of device-level primitives, (2) lightweight coordination mechanisms that enable different network elements to effectively complement one another, and (3) practical optimization models that capture operating constraints and policy objectives. This dissertation demonstrates the benefits of this system-wide approach in three application contexts: (1) meeting fine-grained coverage and accuracy requirements in traffic monitoring, (2) implementing a redundancy elimination service to improve network performance, and (3) managing the deployment of intrusion detection and prevention systems.
A SOM and Bayesian Network Architecture for Alert Filtering in Network Intrusion Detection Systems

With the ever growing deployment of networks and the Internet, the importance of network security has increased. Recently, however, systems that detect intrusions, which are important in security countermeasures, have been unable to provide proper analysis or an effective defense mechanism. Instead, they have overwhelmed human operators with a large volume of intrusion detection alerts. This paper presents a new approach for handling intrusion detection alarms more efficiently. We propose here an architecture for automated alarm filtering based on classical method of clustering (self-organizing maps) coupled with probabilistic graphical model (Bayesian belief networks) for determining if the network is really attacked
Perceived Indoor Environment and Occupants’ Comfort in European “Modern” Office Buildings: The OFFICAIR Study

Indoor environmental conditions (thermal, noise, light, and indoor air quality) may affect workers’ comfort, and consequently their health and well-being, as well as their productivity. This study aimed to assess the relations between perceived indoor environment and occupants’ comfort, and to examine the modifying effects of both personal and building characteristics. Within the framework of the European project OFFICAIR, a questionnaire survey was administered to 7441 workers in 167 “modern” office buildings in eight European countries (Finland, France, Greece, Hungary, Italy, The Netherlands, Portugal, and Spain). Occupants assessed indoor environmental quality (IEQ) using both crude IEQ items (satisfaction with thermal comfort, noise, light, and indoor air quality), and detailed items related to indoor environmental parameters (e.g., too hot/cold temperature, humid/dry air, noise inside/outside, natural/artificial light, odor) of their office environment. Ordinal logistic regression analyses were performed to assess the relations between perceived IEQ and occupants’ comfort. The highest association with occupants’ overall comfort was found for “noise”, followed by “air quality”, “light” and “thermal” satisfaction. Analysis of detailed parameters revealed that “noise inside the buildings” was highly associated with occupants’ overall comfort. “Layout of the offices” was the next parameter highly associated with overall comfort. The relations between IEQ and comfort differed by personal characteristics (gender, age, and the Effort Reward Imbalance index), and building characteristics (office type and building’s location). Workplace design should take into account both occupant and the building characteristics in order to provide healthier and more comfortable conditions to their occupants.
Multi-stage fusion of local and global features based classification for traffic sign recognition

The automatic traffic sign detection and recognition (TSDR) provide an additional level of driver assistance, leading to increase passengers, road users and vehicles safety. As part of Advanced Driving Assistance Systems (ADAS), traffic sign recognition (TSR) has drawn considerable research attention in recent years due to its challenging nature as a computer vision problem. It is usually tackled in three stages: detection, feature extraction and classification. This paper focuses on the second stage of the process, namely traffic sign feature extraction and proposes to fuse two discriminative and complementary feature sets. In this approach, Discrete Cosine Transform (DCT) is used to extract global features of traffic sign while Local Binary Patterns (LBP) is used to extract local descriptors. The classification of these features is performed using the Support Vector Machine (SVM). The proposed fusion approach is validated on the German Traffic Sign Recognition Benchmark Dataset (GTSRD) and has been found to be more efficient than a recognition system which uses only one feature, trained individually.
A technique for interferometric synthetic aperture sonar image processing.

Interferometric Synthetic Aperture Sonar provides a means of obtaining high resolution three-dimensional images of objects on the sea floor. This paper describes a technique for forming images using interferometric sonar data. The technique is novel in the way it combines image co-registration and height estimation. Results of applying the technique to real sonar data are given.
Interest Rates and Output in the Long-Run

In this paper we argue that both statistics and economic theory-based evidence largely indicate the absence of long run relationships between the real output and the most relevant monetary indicator for the U.K. and the U.S, short term interest rates. These findings are not only a full sample result, but also valid in most of the sub-samples throughout the second half of the 20th century and are robust to the inclusion of possible omitted real variables. JEL Classification: E3, E4, E5
Study of modifiable risk factors for asthma exacerbations: virus infection and allergen exposure increase the risk of asthma hospital admissions in children

Background: Asthma exacerbation is the most common cause of hospital admission in children. A study was undertaken to investigate the importance of allergen exposure in sensitised individuals in combination with viral infections and other potentially modifiable risk factors precipitating asthma hospital admission in children. Methods: Eighty four children aged 3–17 years admitted to hospital over a 1 year period with an acute asthma exacerbation (AA) were matched for age and sex with two control groups: stable asthmatics (SA) and children admitted to hospital with non-respiratory conditions (IC). Risk factors were assessed by questionnaires and determination of allergen sensitisation, home allergen exposure, pollen exposure, and respiratory virus infection. Results: Several non-modifiable factors (atopy, duration of asthma) were associated with increased risk. Among the modifiable factors, pet ownership, housing characteristics, and parental smoking did not differ between the groups. Regular inhaled corticosteroid treatment was significantly less common in the AA group than in the SA group (OR 0.2, 95% CI 0.1 to 0.6; p = 0.002). A significantly higher proportion of the AA group were virus infected (44%) and sensitised and highly exposed to sensitising allergen (76%) compared with the SA (18% and 48%) and IC groups (17% and 28%; both p<0.001). In a multiple conditional logistic regression (AA v SA), allergen sensitisation and exposure or virus detection alone were no longer independently associated with hospital admission. However, the combination of virus detection and sensitisation with high allergen exposure substantially increased the risk of admission to hospital (OR 19.4, 95% CI 3.7 to 101.5, p<0.001). Conclusions: Natural virus infection and real life allergen exposure in allergic asthmatic children increase the risk of hospital admission. Strategies for preventing exacerbations will need to address these factors.
Low cost robotic endoscope design considerations

An endoscopic robot capable of assisting medical professionals in the public health sector by providing imaging and biopsy functionalities during Gastrointestinal Tract (GIT) procedures at a reduced cost, was to be designed. The endoscope was designed using soft robotic technology and to use a novel approach to provide robust and precise control over the robot. The design is separated into functional sections: the head module, bending module, body module, the hydraulic system and control network. Material selection was based on suitability for use in the GIT and its ability to withstand medical cleaning. The results of computational analysis and simulation illustrated the robotic endoscope can be actuated utilising a bending module comprising of variably pressurised chambers and this actuation can be accurately controlled and allows system disturbances to being effectively rejected. The proposed design was evaluated against current endoscopes and indicated improvements in precision control of the motion of the endoscope and the cost of production, and the use of the endoscopes in a South African context.
Analysis of Beta-Cell Gene Expression Reveals Inflammatory Signaling and Evidence of Dedifferentiation following Human Islet Isolation and Culture

The stresses encountered during islet isolation and culture may have deleterious effects on beta-cell physiology. However, the biological response of human islet cells to isolation remains poorly characterized. A better understanding of the network of signaling pathways induced by islet isolation and culturing may lead to strategies aimed at improving islet graft survival and function. Laser capture microdissection (LCM) was used to extract beta-cell RNA from 1) intact pancreatic islets, 2) freshly isolated islets, 3) islets cultured for 3 days, and changes in gene expression were examined by microarray analysis. We identified a strong inflammatory response induced by islet isolation that continues during in-vitro culture manifested by upregulation of several cytokines and cytokine-receptors. The most highly upregulated gene, interleukin-8 (IL-8), was induced by 3.6-fold following islet isolation and 56-fold after 3 days in culture. Immunofluorescence studies showed that the majority of IL-8 was produced by beta-cells themselves. We also observed that several pancreas-specific transcription factors were down-regulated in cultured islets. Concordantly, several pancreatic progenitor cell-specific transcription factors like SOX4, SOX9, and ID2 were upregulated in cultured islets, suggesting progressive transformation of mature beta-cell phenotype toward an immature endocrine cell phenotype. Our findings suggest islet isolation and culture induces an inflammatory response and loss of the mature endocrine cell phenotype. A better understanding of the signals required to maintain a mature beta-cell phenotype may help improve the efficacy of islet transplantation.
Vaccine-Induced Immunity in Baboons by Using DNA and Replication-Incompetent Adenovirus Type 5 Vectors Expressing a Human Immunodeficiency Virus Type 1 gag Gene

ABSTRACT The cellular immunogenicity of formulated plasmid DNA and replication-defective human adenovirus serotype 5 (Ad5) vaccine vectors expressing a codon-optimized human immunodeficiency virus type 1 gag gene was examined in baboons. The Ad5 vaccine was capable of inducing consistently strong, long-lived CD8+-biased T-cell responses and in vitro cytotoxic activities. The DNA vaccine-elicited immune responses were weaker than those elicited by the Ad5 vaccine and highly variable; formulation with chemical adjuvants led to moderate increases in the levels of Gag-specific T cells. Increasing the DNA-primed responses with booster doses of either Ad5 or modified vaccinia virus Ankara vaccines suggests a difference in the relative levels of cytotoxic and helper responses. The implications of these results are discussed.
BP-Miner: Mining Paired Functions from the Binary Code of Drivers for Error Handling

Kernel extension functions are provided as interfaces for drivers to manage devices and resources, and there are many implicit rules about their usages. One of the most important rules is that many functions should be called in pairs. That is to say, when an error occurs in a function, the driver should call related functions to handle it and release the acquired resources before returning, and we name these functions between normal execution paths and error handling paths as paired functions. However, many developers are unaware of them, which causes lots of bugs. Therefore, it is highly significant to automatically extract paired functions and detect violations for drivers. This paper proposes an efficient tool named BP-Miner, which can extract paired functions from binary code of driver modules and detect violations for error handling in drivers with extracted paired functions. BP-Miner constructs control flow graph (CFG) based on basic blocks of binary code, and locates potential execution paths to extract paired functions. We have evaluated BP-Miner with Linux drivers 2.6. 38 and 3.13. 0-rc7. 76 bugs are reported by BP-Miner in 2.6. 38 which have been fixed in the current latest version 3.13. 0-rc7. BP-Miner spends about 90 minutes handling 3653 module files for 3.13. 0-rc7, and 859 violations have been detected with 1167 extracted paired functions. As it works on the binary code, it can be utilized to check close-source drivers.
An Adaptive Agent for Web Exploration Based on Concept Hierarchies

In this paper we present the design of a client-side agent, named ARCH, for assisting users in one of the most difficult information retrieval tasks, i.e., that of formulating an effective search query. In contrast to traditional methods based on relevance feedback, ARCH assists users in query modification prior to the search task. The initial user query is (semi-)automatically modified based on the user's interaction with an embedded, but modular, concept hierarchy. This allows for the generation of richer queries than is possible, for example, based on simple query expansion according to lexical variants such as synonyms. In addition, ARCH passively learns a user profile by observing the user's past browsing behavior. The profiles are used to provide additional context to the user's information need represented by the initial query.
Structure-Performance Relation in Nepalese Banking Industry

This paper aims at testing the structure-performance hypotheses in the context of Nepalese banking industry for the period of 2001-2009 under the Berger and Hannan (1993) empirical framework. The empirical results suggest that traditional structure-conduct-performance hypothesis and quit life hypothesis are at work in explaining concentration-profitability relation and there are weak supports for efficiency structure hypotheses. The results of this study hold significant policy and managerial implications.
Pricing structured equity products on GPUs

Pricing and risk analysis for today's structured equity products is computationally more and more demanding and time consuming. GPUs offer the possibility to significantly increase computing performance even at reduced costs. We applied this technology to replace a large amount of our CPU based computing grid by hybrid GPU/CPU pricing engines. One GPU based pricing engine with two Tesla C1060 replaced 140 CPU cores in performing Monte Carlo based simulation of our productive structured equity portfolio with the local and stochastic volatility model.
A correction for endogeneity in choice models with psychological constructs

This research aims at integrating two methods mitigating parameter biases resulting from the omission of unobserved factors of decisions in discrete choice models. The first method is to estimate an integrated choice and latent variable model (Walker and Ben-Akiva, 2002, Walker, 2001), where a latent factor captures an unobserved qualitative attribute (e.g. the comfort of a transport mode). Omitting this attribute can lead to an inconsistent estimate of the parameters relative to economic factors (e.g. the travel time), and consequently to inconsistent willingness to pay indicators. The second method uses the multiple indicator solution (MIS) to introduce a factor of correction in the choice model, in order to obtain consistent estimates of the economic factors (Guevara and Polanco, 2013).
Linear types for packet processing (extended version)

We present PacLang: an imperative, concurrent, linearly-typed language designed for expressing packet processing applications. PacLang’s linear type system ensures that no packet is referenced by more than one thread, but allows multiple references to a packet within a thread . We argue (i) that this property greatly simplifies compilation of high-level programs to the distributed memory architectures of modern Network Processors; and (ii) that PacLang’s type system captures that style in which imperative packet processing programs are already written. Claim (ii) is justified by means of a case-study: we describe a PacLang implementation of the IPv4 unicast packet forwarding algorithm. PacLang is formalised by means of an operational semantics and a Unique Ownership theorem formalises its correctness with respect to the type system.
Efficient evaluation of reverberant sound fields

An image method due to Allen and Berkley (1979) is often used to simulate the effect of reverberation in rooms. This method is relatively expensive computationally. We present a fast method for conducting such simulations using multipole expansions. For M real and image sources and N evaluation points, while the image method requires O(MN) operations, our method achieves the calculations in O(M + N) operations, resulting in a substantial speedup. Applications of our technique are also expected in simulation of virtual audio.
Population Genomic Analysis of Ancient and Modern Genomes Yields New Insights into the Genetic Ancestry of the Tyrolean Iceman and the Genetic Structure of Europe

Genome sequencing of the 5,300-year-old mummy of the Tyrolean Iceman, found in 1991 on a glacier near the border of Italy and Austria, has yielded new insights into his origin and relationship to modern European populations. A key finding of that study was an apparent recent common ancestry with individuals from Sardinia, based largely on the Y chromosome haplogroup and common autosomal SNP variation. Here, we compiled and analyzed genomic datasets from both modern and ancient Europeans, including genome sequence data from over 400 Sardinians and two ancient Thracians from Bulgaria, to investigate this result in greater detail and determine its implications for the genetic structure of Neolithic Europe. Using whole-genome sequencing data, we confirm that the Iceman is, indeed, most closely related to Sardinians. Furthermore, we show that this relationship extends to other individuals from cultural contexts associated with the spread of agriculture during the Neolithic transition, in contrast to individuals from a hunter-gatherer context. We hypothesize that this genetic affinity of ancient samples from different parts of Europe with Sardinians represents a common genetic component that was geographically widespread across Europe during the Neolithic, likely related to migrations and population expansions associated with the spread of agriculture.
Identifying Changed Source Code Lines from Version Repositories

Observing the evolution of software systems at different levels of granularity has been a key issue for a number of studies, aiming at predicting defects or at studying certain phenomena, such as the presence of clones or of crosscutting concerns. Versioning systems such as CVS and SVN, however, only provide information about lines added or deleted by a contributor: any change is shown as a sequence of additions and deletions. This provides an erroneous estimate of the amount of code changed. This paper shows how the evolution of changes at source code line level can be inferred from CVS repositories, by combining information retrieval techniques and the Levenshtein edit distance. The application of the proposed approach to the ArgoUML case study indicates a high precision and recall.
Economics and Finance

IN an address on “Finance and the War” given to members of the Parliamentary Labour Party at the House of Commons on November 9, which has now been published by the Economic Reform Club and Institute, Prof. F. Soddy stresses the importance of distinguishing between genuine and fictitious credit if we wish to put an end to recurring economic booms and slumps and periodic world wars primarily of economic or monetary origin. We live in a world of potential abundance beyond our unscientific ancestors' powers of foreseeing, but that abundance cannot be realized until we clearly distinguish between the creation and the acquisition of wealth. All genuine money reformers are unanimous in demanding that money should not be put into circulation as a debt arbitrarily terminable, and most, if not all, that it should be paid into circulation by the nation for full value received by the nation.