Miracle-dz/UniFAR-FTUs huggingface dataset:
Partial characterization of 2-β-mercaptoethanol-soluble surface-associated antigens of Onchocerca volvulus

Antigens were extracted from the epicuticle/cuticle of intact female Onchocerca volvulus using 2% 2-β-mercaptoethanol and 1% SDS. In Western blot analysis a human infection serum selected for its high antibody titre against whole worm homogenates did not recognize any component solubilized by 1% SDS. However, the same serum did bind at least 7 antigens among the material extracted with 2-β-mercaptoethanol. These antigens have apparent molecular weights (Mr) of: 15 000, 18 000, 28 000, 78 000, 98 000, 120 000 and 200 000. In ELISA using this preparation as target antigen, 151 out of 153 human infection sera gave positive results. An Onchocerca-specific IgG1 monoclonal antibody, designated Cam1, recognized the 28 000 Mr antigen, which is the most prominent antigen detected by Western blot analysis using human infection sera. In ELISA, using material affinity-purified with Cam1 as target antigen, 149 out of 153 human infection sera gave a positive IgG response. From a cDNA library three expressing clones were isolated with a rabbit serum raised against 2-β-mercaptoethanol solubilized material. One of these clones was recognized by the monoclonal antibody Cam1.
Aalborg Universitet CBRecSys 2015 . New Trends on Content-Based Recommender Systems

Nowadays, most information filtering systems provide recommendations by either building a model of the users’ past behavior, referred to as collaborative filtering, or by identifying items with similar properties, referred to as content-based recommendation. In this presentation, I will present various use cases and scenarios where recommendations are provided based on a preceding content analysis. The use cases will illustrate both strengths and weaknesses of content-based recommendation. Permission to make digital or hard copies of all or part of this work for personal or classroom use is granted without fee provided that copies are not made or distributed for profit or commercial advantage and that copies bear this notice and the full citation on the first page. To copy otherwise, to republish, to post on servers or to redistribute to lists, requires prior specific permission and/or a fee. CBRecSys 2015, September 20, 2015, Vienna, Austria. Copyright 2015 by the author(s).
Anatomy of Mdm2 and Mdm4 in evolution

Abstract Mouse double minute (Mdm) genes span an evolutionary timeframe from the ancient eukaryotic placozoa Trichoplax adhaerens to Homo sapiens, implying a significant and possibly conserved cellular role throughout history. Maintenance of DNA integrity and response to DNA damage involve many key regulatory pathways, including precise control over the tumour suppressor protein p53. In most vertebrates, degradation of p53 through proteasomal targeting is primarily mediated by heterodimers of Mdm2 and the Mdm2-related protein Mdm4 (also known as MdmX). Both Mdm2 and Mdm4 have p53-binding regions, acidic domains, zinc fingers, and C-terminal RING domains that are conserved throughout evolution. Vertebrates typically have both Mdm2 and Mdm4 genes, while analyses of sequenced genomes of invertebrate species have identified single Mdm genes, suggesting that a duplication event occurred prior to emergence of jawless vertebrates about 550–440 million years ago. The functional relationship between Mdm and p53 in T. adhaerens, an organism that has existed for 1 billion years, implies that these two proteins have evolved together to maintain a conserved and regulated function.
End-to-End Navigation in Unknown Environments using Neural Networks

We investigate how a neural network can learn perception actions loops for navigation in unknown environments. Specifically, we consider how to learn to navigate in environments populated with cul-de-sacs that represent convex local minima that the robot could fall into instead of finding a set of feasible actions that take it to the goal. Traditional methods rely on maintaining a global map to solve the problem of over coming a long cul-de-sac. However, due to errors induced from local and global drift, it is highly challenging to maintain such a map for long periods of time. One way to mitigate this problem is by using learning techniques that do not rely on hand engineered map representations and instead output appropriate control policies directly from their sensory input. We first demonstrate that such a problem cannot be solved directly by deep reinforcement learning due to the sparse reward structure of the environment. Further, we demonstrate that deep supervised learning also cannot be used directly to solve this problem. We then investigate network models that offer a combination of reinforcement learning and supervised learning and highlight the significance of adding fully differentiable memory units to such networks. We evaluate our networks on their ability to generalize to new environments and show that adding memory to such networks offers huge jumps in performance
Stack Overflow Considered Harmful? The Impact of Copy&Paste on Android Application Security

Online programming discussion platforms such as Stack Overflow serve as a rich source of information for software developers. Available information include vibrant discussions and oftentimes ready-to-use code snippets. Previous research identified Stack Overflow as one of the most important information sources developers rely on. Anecdotes report that software developers copy and paste code snippets from those information sources for convenience reasons. Such behavior results in a constant flow of community-provided code snippets into production software. To date, the impact of this behaviour on code security is unknown. We answer this highly important question by quantifying the proliferation of security-related code snippets from Stack Overflow in Android applications available on Google Play. Access to the rich source of information available on Stack Overflow including ready-to-use code snippets provides huge benefits for software developers. However, when it comes to code security there are some caveats to bear in mind: Due to the complex nature of code security, it is very difficult to provide ready-to-use and secure solutions for every problem. Hence, integrating a security-related code snippet from Stack Overflow into production software requires caution and expertise. Unsurprisingly, we observed insecure code snippets being copied into Android applications millions of users install from Google Play every day. To quantitatively evaluate the extent of this observation, we scanned Stack Overflow for code snippets and evaluated their security score using a stochastic gradient descent classifier. In order to identify code reuse in Android applications, we applied state-of-the-art static analysis. Our results are alarming: 15.4% of the 1.3 million Android applications we analyzed, contained security-related code snippets from Stack Overflow. Out of these 97.9% contain at least one insecure code snippet.
Obstacle detection, avoidance and anti collision for MEREDITH AUV

This paper describes the design and implementation of an obstacle detection, obstacle avoidance and anti-collision system using a COTS multi-beam forward looking sonar. The purpose is to equip our in-house built MEREDITH autonomous underwater vehicle the capability to navigate around obstacles that arise in its programmed path. This is important for operating near the littorals, where potential hazards are prevalent. For such a system, the ability to identify unknown obstacles and discards false returns and noise is an important issue and extremely challenging. The crux of the problem is to correctly pick-up potential obstacles from the sonar image. To address this problem, image processing technique is employed to extract potential obstacles from the sonar image. This is follow by the employment of a real-time multi-frame filter to confirm the presence of obstacles. Subsequently, confirmed obstacles are put in a 2D grid map, which serves as a workspace representation for MEREDITH to perform real-time path planning. Simulation studies and sea trials were conducted to verify the implementation.
Cytoskeletal F-actin, not the circumferential coil of microtubules, regulates platelet dense-body granule secretion

Cytoskeletal F-actin assembly and microtubule reorganization are principal cellular events responsible for activation-induced platelet shape change; however, their roles in regulating platelet secretion have remained controversial. Herein, label-free microelectrochemistry techniques and pharmacological approaches are used to probe the role of F-actin and the microtubule in platelet dense-body secretion. Altered microtubule integrity via exposure to paclitaxel or vincristine had no effect on serotonin release in platelet suspensions. Disruption of F-actin by cytochalasin D (CytoD) or latrunculin A (LatA) substantially enhanced the rate of serotonin release, while inhibition of the F-actin-dependent platelet motor protein myosin IIA by blebbistatin had no effect. CytoD-treated platelets also showed enhanced serotonin quantal secretion rate. These results clearly indicate that F-actin, but not the microtubule, regulates platelet dense-body secretion and does so by serving as a physical barrier. This study also demonstrates the promise of microelectrochemistry for giving important insight into platelet quantal secretion mechanisms in future studies.
The Distribution of Intervals Between Visits as a Basis for Assessing and Regulating Physician Services in Nursing Homes

We propose a new indicator of responsiveness of physician care in nursing homes: the distribution of intervals between physician visits. Current reimbursement and certification practices work to contain costs and assure minimum quality by influencing the intervals between visits. Data from a comparative study of 2 systems of medical care in nursing homes reveal marked differences in the interval distributions of the 2 systems. The system operating under current reimbursement procedures had interval distributions more concentrated around the minimum reimbursable interval. We interpret this concentration as a sign that the reimbursement procedure makes care less responsive to randomly occurring acute episodes by discouraging brief intervals. The interval distributions also document the impact of Medicaid certification standards on longer intervals. A mathematical model of intervals between visits is developed and used to estimate the interval distribution which would obtain in the absence of current reimbursement and certification procedures. This model also describes the distribution of intervals between physician (and dentist) services to noninstitutionalized individuals. These results suggest that such a model might be used in a system of “stochastic regulation” of physician services which would allow physicians greater freedom to respond to patient needs while still permitting public payors to oversee service provision.
The L2/HNK‐1 Carbohydrate Epitope is Involved in the Preferential Outgrowth of Motor Neurons on Ventral Roots and Motor Nerves

Based on the observation that in adult mice the carbohydrate epitope L2/HNK‐1 is detectable on Schwann cells in ventral spinal roots, but only scarcely in dorsal roots (Martini et al., Dev. Biol., 129, 330–338, 1988), the possibility was investigated that the carbohydrate is involved in the outgrowth of regenerating motor neuron axons on peripheral nerve substrates expressing the epitope. To monitor whether the L2 carbohydrate remains present during the time periods in which regenerating axons penetrate the denervated distal nerve stumps, the expression of L2 in motor and sensory branches of the femoral nerve was investigated in normal animals and after a crush lesion. During the first two postoperative weeks, L2 immunoreactivity remained high in the myelinating Schwann cells of the motor branch, whereas L2 immunoreactivity was virtually absent in the sensory branch. In a first experimental approach, cryosections of ventral and dorsal spinal roots and of motor and sensory nerves of adult rats and mice were used as substrates for neurite outgrowth. Neurites of motor neurons from chicken embryos were ∼35% longer after 30 h of maintenance on ventral roots than on dorsal roots. Neurites from sensory neurons had the same length on dorsal as on ventral motors and were as long as neurites from motor neurons grown on dorsal roots. L2 antibodies reduced neurite outgrowth of motor neurons on ventral roots but not on dorsal roots. Neurite outgrowth of sensory neurons on both roots was not altered by the antibodies. Neurite outgrowth of motor neurons on a mixture of the extracellular matrix glycoprotein laminin and the L2 carbohydrate‐carrying glycolipid was significantly higher than on the laminin substrate mixture with GD1b ganglioside or sulphatide. L2 antibodies reduced neurite outgrowth of motor neurons by 50% on the L2 glycolipid, but not on GD1b or sulphatide. These observations indicate that the L2 carbohydrate promotes neurite outgrowth of motor neurons in vitro and may thus contribute to the preferential reinnervation of motor nerves by regenerating motor axons in vivo.
Aerosols

We and others have recently reported that prions can be transmitted to mice via aerosols. These reports spurred a lively public discussion on the possible public-health threats represented by prion-containing aerosols. Here we offer our view on the context in which these findings should be placed. On the one hand, the fact that nebulized prions can transmit disease cannot be taken to signify that prions are airborne under natural circumstances. On the other hand, it appears important to underscore the fact that aerosols can originate very easily in a broad variety of experimental and natural environmental conditions. Aerosols are a virtually unavoidable consequence of the handling of fluids; complete prevention of the generation of aerosols is very difficult. While prions have never been found to be transmissible via aerosols under natural conditions, it appears prudent to strive to minimize exposure to potentially prion-infected aerosols whenever the latter may arise – for example in scientific and diagnostic laboratories handling brain matter, cerebrospinal fluids, and other potentially contaminated materials, as well as abattoirs. Equally important is that prion biosafety training be focused on the control of, and protection from, prion-infected aerosols.
Improved H2/H∞ Control Design for Time Delay Systems: Synthesis and Analysis

This paper presents an unified approach to design suboptimal H2/H∞ controllers for different sorts of time delay systems (TDSs). The system stability is ensured by using a Lyapunov-Krasovski (LK) approach, and it is theoretically demonstrated that the method outperforms H2/H∞ designs in the literature. The improvement comes neither from new LK functionals nor from mathematical manipulations, but from the method to solve the H2 problem. The result can be easily inherited by others authors by combining it with their LK functionals and bounding techniques. The paper ends with some numerical examples to compare the proposed technique and other well-referenced designs.
Simultaneous and sensitive measurement of anabasine, nicotine, and nicotine metabolites in human urine by liquid chromatography-tandem mass spectrometry.

BACKGROUND Determination of nicotine metabolism/pharmacokinetics provides a useful tool for estimating uptake of nicotine and tobacco-related toxicants, for understanding the pharmacologic effects of nicotine and nicotine addiction, and for optimizing nicotine dependency treatment. METHODS We developed a sensitive method for analysis of nicotine and five major nicotine metabolites, including cotinine, trans-3'-hydroxycotinine, nicotine-N'-oxide, cotinine-N-oxide, and nornicotine, in human urine by liquid chromatography coupled with a TSQ Quantum triple quadrupole tandem mass spectrometer (LC/MS/MS). Urine samples to which deuterium-labeled internal standards had been added were extracted with a simple solid-phase extraction procedure. Anabasine, a minor tobacco alkaloid, was also included. RESULTS The quantification limits of the method were 0.1-0.2 microg/L, except for nicotine (1 microg/L). Cotinine-N-oxide, trans-3'-hydroxycotinine, nicotine, and anabasine in urine were almost completely recovered by the solid-phase extraction, whereas the mean extraction recoveries of nicotine-N'-oxide, cotinine, and nornicotine were 51.4%, 78.6%, and 78.8%, respectively. This procedure provided a linearity of three to four orders of magnitude for the target analytes: 0.2-400 microg/L for nicotine-N'-oxide, cotinine-N-oxide, and anabasine; 0.2-4000 microg/L for cotinine, nornicotine, and trans-3'-hydroxycotinine; and 1.0-4000 microg/L for nicotine. The overall interday method imprecision and recovery were 2.5-18% and 92-109%, respectively. CONCLUSIONS This sensitive LC/MS/MS procedure can be used to determine nicotine metabolism profiles of smokers, people during nicotine replacement therapy, and passively exposed nonsmokers. This method avoids the need for a time-consuming and labor-intensive sample enrichment step and thus allows for high-throughput sample preparation and automation.
Etiology and Treatment of Overactive Bladder in Women

Overactive bladder (OAB) is a condition that affects millions of women in the United States (US). Although the etiology is largely unknown, risk factors include Caucasian race, insulin-dependent diabetes mellitus, and history of depression. Patients present with urgency with or without urinary incontinence and often have urinary frequency and nocturia. Most patients can be evaluated in the office setting utilizing simple testing. Current treatments consist of behavioral/lifestyle modification, usually in combination with antimuscarinic drug therapy. Improvements in the adverse effect profiles of antimuscarinic drugs have positively impacted quality of life. When appropriately evaluated, most patients presenting to primary care providers can be effectively treated.
Molecular weight determination of high molecular mass (glyco)proteins using CGE‐on‐a‐chip, planar SDS‐PAGE and MALDI‐TOF‐MS

The molecular weights (MW) of seven (glyco)proteins, of which five were plasma‐derived, with MWs higher than 200 kDa were determined with three techniques: CGE‐on‐a‐chip, SDS‐PAGE and MALDI‐TOF‐MS. While the analysis of medium to high MW proteins with SDS‐PAGE was an already well‐established technique, the usefulness of MALDI‐TOF‐MS for the exact MW determination of high mass proteins was only partly described in literature so far. CGE‐on‐a‐chip is the newest of all three applied techniques and was so far not applicable. Therefore, it was not evaluated for high MW (glyco)proteins. All proteins were analyzed under nonreducing as well as reducing conditions. In this work, it was demonstrated that all three described techniques were capable of determining the MW of all high molecular weight (glyco)proteins. The noncommercial CGE‐on‐a‐chip assay allowed for the first time the electrophoretic separation of proteins in the MW range from 14 to 1000 kDa. MW assignment was limited to 500 kDa in the case of SDS‐PAGE and 660 kDa in the case of the high MW CGE‐on‐a‐chip assay. With the proper matrix and sample preparation, analysis with a standard MALDI‐TOF‐MS provided accurate MWs for all high MW proteins up to 1 MDa.
Acid resistance in enteric bacteria

Shigella species require a uniquely small inoculum for causing dysentery. One explanation for the low infective dose is that Shigella species are better able to survive the acidic conditions encountered in the stomach than are other enteric pathogens. We have tested Shigella species, Escherichia coli, and Salmonella species for the ability to survive at pH 2.5 for at least 2 h. Most isolates of Shigella and E. coli survived this treatment, whereas none of the Salmonella isolates were able to do so. The ability of Shigella species to survive at low pHs does not require the presence of the large virulence plasmid or growth at 37 degrees C but is strikingly dependent on growth phase. We have also found that Shigella isolates exposed to acid lose the ability to invade epithelial cells.
Design of a Privacy-Preserving Decentralized File Storage with Financial Incentives

Surveys indicate that users are often afraid to entrust data to cloud storage providers, because these do not offer sufficient privacy. On the other hand, peer-2-peer–based privacy-preserving storage systems like Freenet suffer from a lack of contribution and storage capacity, since there is basically no incentive to contribute own storage capacity to other participants in the network. We address these contradicting requirements by a design which combines a distributed storage with a privacy-preserving blockchain-based payment system to create incentives for participation while maintaining user privacy. By following a Privacy-by-Design strategy integrating privacy throughout the whole system life cycle, we show that it is possible to achieve levels of privacy comparable to state-of-the-art distributed storage technologies, despite integrating a payment mechanism. Our results show that it is possible to combine storage contracts and payments in a privacy-preserving way. Further, our system design may serve as an inspiration for future similar architectures.
Measuring Social Sustainability with the Developed MCSA Model: Güzelyurt Case

The aim of the study is to develop a sample scale to measure social sustainability in an urban context. Social sustainability is an important component of sustainable development and it gained importance in the 1990s with awareness of the rising welfare of the society. The definitions, criteria, and the measurement system of social sustainability are still vague. In this context, this article bridges the gap in measuring social sustainability in an urban context and it proposes a model called Measurement of the City from Social Aspects (MCSA). The developed model was applied to the city of Güzelyurt, which has continuously experienced immigration from past to present. Quantitative research method was used in the research and the data was collected through interviews and a questionnaire survey, conducted with 400 local residents. The proposed model was tested in terms of model fit using confirmatory factor analysis. Also, the construct validity and discriminant validity of the model were tested. Research results indicate that the developed MCSA model works and it is suitable to be applied to other cities for measuring their social sustainability. Thus, the problems in the social aspects of the cities could be revealed and solutions could be generated to ensure the social sustainability of the cities.