Miracle-dz/UniFAR-FTUs huggingface dataset:
Trophic polymorphism in introduced bluegill in Japan

We demonstrate that bluegill (Lepomis macrochirus) introduced from their native North American source to Lake Biwa in Japan showed considerable trophic and morphological variations (morphs). Three morphs were found for larger bluegills, specialized in three distinct resources (i.e. plankton, benthic invertebrates and aquatic plant), and two morphs were found for smaller bluegills, specialized in two slightly different prey taxa (i.e. calanoid and cyclopoid plankton). These morphs, especially for the large size class, can be distinguished primarily by differences in midbody length and depth. The dietary specialization and morphological differentiation among individuals were considered to be a result of different requirements for efficient resource utilization, which is a unique example of trophic polymorphism occurring in an introduced fish species in a species-rich fish community.
Objective voice and speech analysis of persons with chronic hoarseness by prosodic analysis of speech samples

Automatic voice assessment is often performed using sustained vowels. In contrast, speech analysis of read-out texts can be applied to voice and speech assessment. Automatic speech recognition and prosodic analysis were used to find regression formulae between automatic and perceptual assessment of four voice and four speech criteria. The regression was trained with 21 men and 62 women (average age 49.2 years) and tested with another set of 24 men and 49 women (48.3 years), all suffering from chronic hoarseness. They read the text ‘Der Nordwind und die Sonne’ (‘The North Wind and the Sun’). Five voice and speech therapists evaluated the data on 5-point Likert scales. Ten prosodic and recognition accuracy measures (features) were identified which describe all the examined criteria. Inter-rater correlation within the expert group was between r = 0.63 for the criterion ‘match of breath and sense units’ and r = 0.87 for the overall voice quality. Human–machine correlation was between r = 0.40 for the match of breath and sense units and r = 0.82 for intelligibility. The perceptual ratings of different criteria were highly correlated with each other. Likewise, the feature sets modeling the criteria were very similar. The automatic method is suitable for assessing chronic hoarseness in general and for subgroups of functional and organic dysphonia. In its current version, it is almost as reliable as a randomly picked rater from a group of voice and speech therapists.
Methodologies to Develop Quantitative Risk Evaluation Metrics

goal of this work is to advance a new methodology to measure a severity cost for each host using the Common Vulnerability Scoring System (CVSS) based on base, temporal and environmental metrics by combining related sub-scores to produce a unique severity cost by modeling the problem"s parameters in to a mathematical framework. We build our own CVSS Calculator using our equations to simplify the calculations of the vulnerabilities scores and to benchmark with other models. We design and develop a new approach to represent the cost assigned to each host by dividing the scores of the vulnerabilities to two main levels of privileges, user and root, and we classify these levels into operational levels to identify and calculate the severity cost of multi steps vulnerabilities. Finally we implement our framework on a simple network, using Nessus scanner as tool to discover known vulnerabilities and to implement the results to build and represent our cost centric attack graph.
Performance Analysis of a Chaos-Based Multi-User Communication System Implemented in DSP Technology

This paper presents the implementation of a multi-user chaos-based communication system in DSP. The system is based on the chaotic phase shift keying (CPSK) digital modulation scheme, where chaotic signals are used as the spreading sequences of a CDMA system. Using chaotic signals offers the advantages of increased security and higher system capacity compared with conventional sequences. The aim of this hardware implementation was to enable a comparison against analytical performance results for CPSK. The transceiver prototype was implemented on a 32-bit floating-point TigerSHARC DSP. Its bit error rate (BER) characteristics were measured in the presence of additive white Gaussian noise. The prototype achieves excellent BER performance, matching that of theoretical CPSK. The effects of the limited number precision of the hardware platform are thus negligible. However, due to the limited concurrency of DSP, the multi-user system only supports low data rates.
An Efficient Delegation and Transfer of Ownership Protocol for RFID tags

RFID technology raises many privacy concerns among which the potential tracking of an RFID tag bearer and the possibility of collecting information about him. As RFID tags may often change hands, it is also necessary to guarantee the privacy of a new tag owner. In this paper, we introduce a new protocol based on pseudonyms that solves these privacy issues while enabling tag identification without the need of a continuous connectivity between reading devices (readers) and a centralised online database.
Control of translational activation by PIM kinase in activated B-cell diffuse large B-cell lymphoma confers sensitivity to inhibition by PIM447

The PIM family kinases promote growth and survival of tumor cells and are expressed in a wide variety of human cancers. Their potential as therapeutic targets, however, is complicated by overlapping activities with multiple other pathways and remains poorly defined in most clinical scenarios. Here we explore activity of the new pan-PIM inhibitor PIM447 in a variety of lymphoid-derived tumors. We find strong activity in cell lines derived from the activated B-cell subtype of diffuse large B-cell lymphoma (ABC-DLBCL). Sensitive lines show lost activation of the mTORC1 signaling complex and subsequent lost activation of cap-dependent protein translation. In addition, we characterize recurrent PIM1 protein-coding mutations found in DLBCL clinical samples and find most preserve the wild-type protein's ability to protect cells from apoptosis but do not bypass activity of PIM447. Pan-PIM inhibition therefore may have an important role to play in the therapy of selected ABC-DLBCL cases.
Evaluation of thin film coatings for erosive–corrosive wear prevention in die casting dies

AbstractDie casting dies are exposed to an extreme erosive–corrosive environment during a typical die casting operation using aluminium alloys. The erosive actions are primarily due to the high velocity injection of the liquid melt through narrow gates. This molten spray of liquid droplets attacks surfaces in front of the gates and normal to the flow front and is called ‘washout’ by die casters. The corrosive action on the other hand is governed by the solubility of the die material (often H13) in the molten aluminium alloy and is controlled by the composition of the cast metal and the die steel, and causes ‘soldering’ in die casting. To protect die surfaces from these erosive–corrosive actions, surface treatments and thin film ceramic coatings applied by PVD and CVD techniques have been evaluated using both laboratory tests and production evaluation. This paper provides details of the coating candidates, the tests, and the analysis of coating failure. It presents the results of these tests and explains t.
Effective Stimuli for Constructing Reliable Neuron Models

The rich dynamical nature of neurons poses major conceptual and technical challenges for unraveling their nonlinear membrane properties. Traditionally, various current waveforms have been injected at the soma to probe neuron dynamics, but the rationale for selecting specific stimuli has never been rigorously justified. The present experimental and theoretical study proposes a novel framework, inspired by learning theory, for objectively selecting the stimuli that best unravel the neuron's dynamics. The efficacy of stimuli is assessed in terms of their ability to constrain the parameter space of biophysically detailed conductance-based models that faithfully replicate the neuron's dynamics as attested by their ability to generalize well to the neuron's response to novel experimental stimuli. We used this framework to evaluate a variety of stimuli in different types of cortical neurons, ages and animals. Despite their simplicity, a set of stimuli consisting of step and ramp current pulses outperforms synaptic-like noisy stimuli in revealing the dynamics of these neurons. The general framework that we propose paves a new way for defining, evaluating and standardizing effective electrical probing of neurons and will thus lay the foundation for a much deeper understanding of the electrical nature of these highly sophisticated and non-linear devices and of the neuronal networks that they compose.
Natural Bactericidal Antibodies: Observations on the Bactericidal Mechanism of Normal Serum

1. An analytical study has been made of the mechanism of natural bactericidal action by the serum of various animals (ox, sheep, horse, rabbit, guinea-pig, rat, man) towards certain organisms (B. typhosus, B. dysenteriae Shiga, B. proteus, V. cholerae) exhibiting the maximum reactivity to this effect. 2. Serum-complement has no bactericidal action per se, and an antibodylike agent invariably acts as an intermediary agent, “sensitising” the particular organism to the action of the complement and capable of being “absorbed” by it from serum at 0° C. 3. This sensitising agent is stable at 55° C. but labile at 60°–65° C. In this respect it resembles natural haemolysins and agglutinins, but contrasts with the more stable immune antibodies and the more labile natural complement-fixing antibodies (for bacterial antigens). It is resident mainly in the carbonic-acid-insoluble fraction of the serum. It is present in the serum of young animals before certain other natural antibodies have developed. 4. Absorption tests demonstrate the high degree of specificity of these natural bactericidal antibodies for particular bacteria. 5. A non-specific extracellular substance occurs in bacterial cultures which may neutralise or inhibit these antibodies, and interfere with their sensitising action even at 0° C. 6. This substance is liberated in large amount in cultures heated at high temperatures (120° C). It can be removed by repeated washing of growths in saline solution. It may inactivate a bactericidal antibody in heated serum, though not in fresh unheated serum, and may inactivate a particular antibody in the serum of one animal species but not in another. Strains of bacteria vary in their production of this substance. 7. The observations submitted in this paper, correlated with previous studies of natural antibodies by the authors and others, indicate that immune antibodies have their precursors specifically differentiated in the serum of normal animals and that, in general, immune antibodies are not substances formed de novo.
Direct writing of chitosan scaffolds using a robotic system

Purpose – This paper aims to present a novel rapid prototyping (RP) fabrication methods and preliminary characterization for chitosan scaffolds. Design – A desktop rapid prototyping robot dispensing (RPBOD) system has been developed to fabricate scaffolds for tissue engineering (TE) applications. The system is a computer-controlled four-axis machine with a multiple-dispenser head. Neutralization of the acetic acid by the sodium hydroxide results in a precipitate to form a gel-like chitosan strand. The scaffold properties were characterized by scanning electron microscopy, porosity calculation and compression test. An example of fabrication of a freeform hydrogel scaffold is demonstrated. The required geometric data for the freeform scaffold were obtained from CT-scan images and the dispensing path control data were converted form its volume model. The applications of the scaffolds are discussed based on its potential for TE. Findings – It is shown that the RPBOD system can be interfaced with imaging techniques and computational modeling to produce scaffolds which can be customized in overall size and shape allowing tissue-engineered grafts to be tailored to specific applications or even for individual patients. Research limitations/implications – Important challenges for further research are the incorporation of growth factors, as well as cell seeding into the 3D dispensing plotting materials. Improvements regarding the mechanical properties of the scaffolds are also necessary. Originality/value – One of the important aspects of TE is the design scaffolds. For customized TE, it is essential to be able to fabricate 3D scaffolds of various geometric shapes, in order to repair tissue defects. RP or solid free-form fabrication techniques hold great promise for designing 3D customized scaffolds; yet traditional cell-seeding techniques may not provide enough cell mass for larger constructs. This paper presents a novel attempt to fabricate 3D scaffolds, using hydrogels which in the future can be combined with cells.
The Pseudomonas aeruginosa flagellum confers resistance to pulmonary surfactant protein‐A by impacting the production of exoproteases through quorum‐sensing

Surfactant protein‐A (SP‐A) is an important antimicrobial protein that opsonizes and permeabilizes membranes of microbial pathogens in mammalian lungs. Previously, we have shown that Pseudomonas aeruginosa flagellum‐deficient mutants are preferentially cleared in the lungs of wild‐type mice by SP‐A‐mediated membrane permeabilization, and not by opsonization. In this study, we report a flagellum‐mediated mechanism of P. aeruginosa resistance to SP‐A. We discovered that flagellum‐deficient (ΔfliC) bacteria are unable to produce adequate amounts of exoproteases to degrade SP‐A in vitro and in vivo, leading to its preferential clearance in the lungs of SP‐A+/+ mice. In addition, ΔfliC bacteria failed to degrade another important lung antimicrobial protein lysozyme. Detailed analyses showed that ΔfliC bacteria are unable to upregulate the transcription of lasI and rhlI genes, impairing the production of homoserine lactones necessary for quorum‐sensing, an important virulence process that regulates the production of multiple exoproteases. Thus, reduced ability of ΔfliC bacteria to quorum‐sense attenuates production of exoproteases and limits degradation of SP‐A, thereby conferring susceptibility to this major pulmonary host defence protein.
A Systematic Solution to the (De-)Composition Problem in General Game Playing

General game players can drastically reduce the cost of search if they are able to solve smaller subproblems individually and synthesise the resulting solutions. To provide a systematic solution to this (de-)composition problem, we start off with generalising the standard decomposition problem in planning by allowing the composition of individual solutions to be further constrained by domain-dependent requirements of the global planning problem. We solve this generalised problem based on a systematic analysis of composition operators for transition systems, and we demonstrate how this solution can be further generalised to general game playing.
Investigating the role of laccase and laccase mediator systems to improve the saccharification of biomass for bioethanol production

As global energy demands increase, there is a requirement to decrease our dependency on fossil fuels due to their finite supply and negative environmental impacts. Alternative sources of energy are required that offer sustainability, reduced cost and environmental benefits. Second generation biofuels remove the ? food vs fuel? drawback of the first generation. They utilise lignocellulosic biomass, providing cheap and abundant starting materials for energy production. The major biotechnological challenge associated with lignocellulosic processing is the natural recalcitrance of the substrate to sugar conversion (saccharification). This recalcitrance is largely associated with lignin, an aromatic heteropolymer that encases cellulose. To improve bioethanol yields, there is a need for cost effective and environmentally friendly pretreatment methods that can remove lignin.An enzymatic pretreatment strategy was investigated using laccase from the fungus Trametes versicolor (TvL). Expansion of the laccase substrate range towards non-phenolic substrates was explored by screening of a panel of synthetic and naturally derived phenolic compounds as potential redox mediators with laccase. Both groups enabled decolourisation of the recalcitrant dye (RB-5) to varying degrees, which laccase alone was unable to achieve. In the case veratryl alcohol, a lignin model substrate, synthetic compounds 1-HBT, ABTS and violuric acid proved effective laccase mediators. On this basis, TvL with 1-HBT was selected as the most successful laccase mediator system (LMS) and was further explored as a biomass pretreatment method.The effects of LMS treatments towards the saccharification of acid hydrolysed wheat straw were extensively investigated. Optimisation revealed that when both TvL and a TvL LMS of synthetic origin (1-HBT, violuric acid) were applied, saccharification was improved. The observed increase in glucose release was only detected when a second lignin removing technique was applied in succession. Both alkaline-peroxide and organosolv extractions were successfully used to demonstrate the role of laccase/LMS in saccharification improvement, with improvements reaching up to 44.6%. The effect was further demonstrated with additional substrates (corn and sorghum stover) and additional laccases (Pleurotus ostreatus, Agaricus bisporus and Rhus vernicifera). Further studies using ? -O-4 structures, py-GC/MS and FTIR analyses provide further information on the structural actions of an LMS towards lignin, including strong evidence for C? -C? cleavage and C? hydroxyl oxidation mechanisms.
A New Mobile Platform (RHyMo) for Smooth Movement on Rugged Terrain

This paper suggests a new performance metric for a mobile platform called as a posture variation index (PVI) to evaluate the smoothness of its movement, which is an important factor to predict undesired oscillations or shocks on a mobile platform while traveling on rugged terrain. The PVI consists of the height and pitch angle variations of center of mass of a mobile platform. By using the PVI, the movements of well-known mobile platforms are systematically analyzed. In order to ensure smooth movement as well as high terrainability on rugged terrain, a new mobile platform (RHyMo) is constructed on the basis of the kinematic and quasi-static analyses. The extensive experiments are carried out by using the RHyMo and the Rocker-Bogie platform on the artificial rugged terrain, which verify that in comparison with the Rocker-Bogie platform, the average and maximum height variations of RHyMo are reduced by 12.72% and 5.96%, respectively. Moreover, the average and maximum pitch angle variations of RHyMo are significantly reduced by 65.87% and 60.53%, respectively. The terrainability of RHyMo against a high step and steep stairs is improved with the help of the track mechanism installed in the front linkage.
QDIME: QoS-Aware Dynamic Binary Instrumentation

Software systems with quality of service (QoS), such as database management systems and web servers, are ubiquitous. Such systems must meet strict performance requirements. Instrumentation is a useful technique for the analysis and debugging of QoS systems. Dynamic binary instrumentation (DBI) extracts runtime information to comprehend system's behavior and detect performance bottlenecks. However, existing DBI tools are intrusive; adding unacceptable delay to the program execution. Such delay alters the performance requirements and degrades the overall quality and the user experience of the system. Moreover, the delay may change the system behavior, thus, producing misleading run-time information.This paper presents QDIME, a QoS-aware dynamic binary instrumentation technique that respects system's performance requirements. QDIME takes a user-defined QoS threshold as an input and periodically gathers QoS feedback from the system under analysis to decide its instrumentation budget.We implemented QDIME on top of PIN, a popular DBI framework. We evaluated QDIME with Gzip, MySQL server, Apache HTTP server, and Redis. The experiments show that QDIME respects the user-defined QoS threshold and, thus, improves the performance of the monitored application by manifolds. QDIME is able to provide up to 100% instrumentation coverage with an average of 92% when compared to PIN. Moreover, QDIME reduces the slow-down factor of the instrumented application by 1.41, 5.67, and 10.26 folds for Sys-trace, Call-trace, and Branch-profile respectively. A release of QDIME is available for download at https://github.com/pansy-arafa/qdime.
Dexter: an open source framework for entity linking

We introduce Dexter, an open source framework for entity linking. The entity linking task aims at identifying all the small text fragments in a document referring to an entity contained in a given knowledge base, e.g., Wikipedia. The annotation is usually organized in three tasks. Given an input document the first task consists in discovering the fragments that could refer to an entity. Since a mention could refer to multiple entities, it is necessary to perform a disambiguation step, where the correct entity is selected among the candidates. Finally, discovered entities are ranked by some measure of relevance. Many entity linking algorithms have been proposed, but unfortunately only a few authors have released the source code or some APIs. As a result, evaluating today the performance of a method on a single subtask, or comparing different techniques is difficult. In this work we present a new open framework, called Dexter, which implements some popular algorithms and provides all the tools needed to develop any entity linking technique. We believe that a shared framework is fundamental to perform fair comparisons and improve the state of the art.
Reducing bubbles in friction lap welded joint of magnesium alloy and polyamide

The direct joining between AZ31B Mg alloy and MC Nylon 6 using friction lap welding (FLW) was performed over a wide range of welding parameters to clarify the effect of welding parameters on bubble formation for the purpose of obtaining high strength hybrid joints without bubbles. The volume of bubbles in the FLW joints was influenced by the amount of gases generated due to the pyrolysis of Nylon 6 and the amount of gases squeezed out of the joints during welding. An appropriate increase in welding speed, tool rotation rate and plunge depth can reduce the volume of bubbles. Strong FLW joint with area fraction of bubbles <8% was obtained after welding process optimisation.