Miracle-dz/UniFAR-FTUs huggingface dataset:
Discovery of Single Nucleotide Polymorphisms and Mutations by Pyrosequencing

Comparative genomics, analyzing variation among individual genomes, is an area of intense investigation. DNA sequencing is usually employed to look for polymorphisms and mutations. Pyrosequencing, a real-time DNA sequencing method, is emerging as a popular platform for comparative genomics. Here we review the use of this technology for mutation scanning, polymorphism discovery and chemical haplotyping. We describe the methodology and accuracy of this technique and discuss how to reduce the cost for large-scale analysis.
Adaptive Human-Robot Interaction System using Interactive EC

We created a human-robot communication system that can adapt to user preferences that can easily change through communication. Even if any learning algorithms are used, evaluating the human-robot interaction is indispensable and difficult. To solve this problem, we installed a machine learning algorithm called interactive evolutionary computation (IEC) into a communication robot named WAMOEBA-3. IEC is a kind of evolutionary computation like a genetic algorithm. With IEC, the fitness function is performed by each user. We carried out experiments on the communication learning system using an advanced IEC system named HMHE. Before the experiments, we did not tell the subjects anything about the robot, so the interaction differed among the experimental subjects. We could observe mutual adaptation, because some subjects noticed the robot's functions and changed their interaction. From the results, we confirmed that, in spite of the changes of the preferences, the system can adapt to the interaction of multiple users
Promiscuous Expression of H2B-GFP Transgene in Hematopoietic Stem Cells

Background The study of adult stem cells relies on the ability to isolate them using complex combinations of markers for flow cytometry. A recent study has used a tetracycline-regulatable H2B-GFP transgenic mouse model analogous to BrdU pulse-chase methods to fluorescently label quiescent skin stem cells in vivo. In this study, we sought to use these mice to fluorescently label hematopoietic stem cells to study niche interactions. Methods and Findings We crossed the H2B-GFP mice to mice carrying a tetracycline-regulated transactivator protein. When these mice were administered doxycycline, we observed a gradual decrease in total bone marrow GFP+ cells over 12 weeks but the hematopoietic stem cell population remained largely GFP+ (>85%). In histological bone sections, the long-term GFP label-retaining cells tended to concentrate at the endosteal surface and competitive transplantation assays showed that the majority of hematopoietic stem cell activity was contained in the GFP+ cell fraction. However, in response to stimulation with 5-fluorouracil, the hematopoietic stem cells of the crossed mice still retained a high level of GFP expression when it was anticipated the label should be lost when the cells divide. Upon further review, it was determined that the founder H2B-GFP mice showed spurious expression of the transgene at high levels in the hematopoietic stem cell population, thus the observed response of hematopoietic stem cells in the double transgenic mice to doxycycline was due to aberrant expression of the transgene and not the correct tetracycline-regulatable system. Conclusions We observed promiscuous expression of the H2B-GFP transgene in the hematopoietic stem cell compartment of the bone marrow. This leaky expression prohibits the use of this model to study hematopoietic stem cells in vivo and careful characterization for each organ must be done if this transgenic system is to be used to isolate other prospective tissue stem cells.
Eliciting expert judgement 2 ACERA Project 0611 Eliciting Expert Judgments Report # 1 : Literature Review

Expert judgements are routine in biosecurity risk analysis. This report reviews methods for eliciting probabilities, quantities, and conceptual models. It defines ‘expert’ status, reviews the literature on biases and heuristics in expert judgements and outlines methods for detecting and eliciting values, attitudes and motivations. The report describes direct and indirect techniques for eliciting point estimates and uncertainties for quantities, frequencies and probabilities, and for eliciting the structure of conceptual models. It evaluates the use of language-based risk categories and describes methods to detect and adjust for bias and variability in expert judgements. Feedback and training are likely to make useful additions to elicitation protocols. Few of the formal techniques for elicitation, calibration or verification have been evaluated in conditions typical of biosecurity risk analysis, creating an opportunity to test the most promising of them.
“If you hit me again, I'll hit you back:” Conflict management strategies of individuals experiencing aggression during conflicts

In interpersonal relationships characterized by aggression, the negotiation of conflict is especially significant. The present study examined the conflict management strategies used by 31 individuals who had experienced verbal and/or physical aggression during conflicts with their partners. Sillars’ (1986) conflict tactics coding system was used as a framework to analyze 960 pages of transcribed data. The results of this deductive content analysis indicated that the participants reported using primarily Distributive conflict strategies. Analytic induction was also used to interpret nonverbal forms of conflict management, revealing three common tactics: crying, nonverbal avoidance, and aggression. Implications for using these conflict strategies in interpersonal relationships characterized by aggression are discussed.
A Tool for Mining Patterns based on Data Structure

The primary goal of a software developer is to produce and deliver high quality software systems which are produced at low cost and high productivity. In order to produce such software systems, programmers generally reuse existing libraries rather than developing the source code from scratch. However, while reusing a library, developers face many problems such as lack of knowledge about program interfaces and lack of time because of which effective test inputs cannot be generated during white box testing. The first two problems reduce software productivity whereas the latter affects software testing. To resolve these problems, we propose a tool named DSP (Data Structure Patterns). The tool will help users to search the relevant code, analyze it to find the most appropriate data structures and then mine the relevant patterns from the data structures and finally recommend the most suited pattern for use.
Comparison of Heuristics for Scheduling Independent Tasks on Heterogeneous Distributed Environments

Scheduling is one of the core steps to efficientlyexploit the capabilities of heterogeneous distributedcomputing systems and is an NP-complete problem.Therefore using meta-heuristic algorithms is asuitable approach in order to cope with its difficulty.In meta-heuristic algorithms, generating individualsin the initial step has an important effect on theconvergence behavior of the algorithm and finalsolutions. Using some heuristics for generating one ormore near-optimal individuals in the initial step canimprove the final solutions obtained by meta-heuristicalgorithms. Different criteria can be used forevaluating the efficiency of scheduling algorithms, themost important of which are makespan and flowtime.In this paper we propose an efficient heuristic methodand then we will compare with five popular heuristicsfor minimizing makespan and flowtime inheterogeneous distributed computing systems.
ARMlock: Hardware-based Fault Isolation for ARM

Software fault isolation (SFI) is an effective mechanism to confine untrusted modules inside isolated domains to protect their host applications. Since its debut, researchers have proposed different SFI systems for many purposes such as safe execution of untrusted native browser plugins. However, most of these systems focus on the x86 architecture. Inrecent years, ARM has become the dominant architecture for mobile devices and gains in popularity in data centers.Hence there is a compellingneed for an efficient SFI system for the ARM architecture. Unfortunately, existing systems either have prohibitively high performance overhead or place various limitations on the memory layout and instructions of untrusted modules. In this paper, we propose ARMlock, a hardware-based fault isolation for ARM. It uniquely leverages the memory domain support in ARM processors to create multiple sandboxes. Memory accesses by the untrusted module (including read, write, and execution) are strictly confined by the hardware,and instructions running inside the sandbox execute at the same speed as those outside it. ARMlock imposes virtually no structural constraints on untrusted modules. For example, they can use self-modifying code, receive exceptions, and make system calls. Moreover, system calls can be interposed by ARMlock to enforce the policies set by the host. We have implemented a prototype of ARMlock for Linux that supports the popular ARMv6 and ARMv7 sub-architecture. Our security assessment and performance measurement show that ARMlock is practical, effective, and efficient.
The Relationship Between Extracellular Free-Water and Gray Matter Volume in Retired Professional Football Players With History of Mild Repetitive Head Injuries

The goal of this work was to investigate whether there was a relationship present between extracellular free water and gray matter volumes in the brains of retired professional football players. A study done by Maier-Hein et al. was able to establish the relationship in a population of participants that presented clinical symptoms of Alzheimer’s Disease. Due to the multiple similarities between Chronic Traumatic Encephalopathy (CTE) and Alzheimer’s Disease, the relationship mentioned above was examined in this study using a population of retired professional football players at high risk for CTE. Changes in the white matter microstructure as well as general volumetric changes were observed by using MRI techniques. We did not find a correlation between gray matter volume and extracellular water in the players, suggesting that despite the similarities between CTE and Alzheimer’s Disease there are also distinct differences between the diseases. Multiple brain regions were found to be different between control and player groups providing evidence for brain alterations in retired football players. The regions that were statistically different in CTE compared with controls were then correlated against one another, and it was determined that multiple regions within the brain functioned as a network in its alterations. Lastly, it was shown that diffusivities of the white matter tracts correlated with volumes of the gray matter suggesting an interaction between white a gray matter in the brains of retired football players.
LANES: an inter-domain data-oriented routing architecture

Data-oriented networking has attracted research recently, but the efficiency of the state-of-the-art solutions can still be improved. Our work towards this goal is set in a clean-slate architecture consisting of modular rendezvous, routing, and forwarding functions. In this paper we present the interdomain routing layer and its interplay with the other components of the system. The proposed system is built around two types of nodes: forwarding nodes and branching nodes. The forwarding nodes are optimized for throughput with no per-subscription state and no need to change passing packets, while branching nodes contain a large memory for caching and can make complex routing decisions. The amount of storage space and bandwidth can be independently scaled to suit the needs of each network. In the background, topology nodes perform load-balancing and configure routes in each domain using a two-dimensional addressing mechanism. The paths taken by packets adapt to the number of active subscribers to keep the amount of in-network state and latency low. A new data-oriented congestion control scheme is introduced, which takes into account the use of storage resources on-path and is fair to multicast flows.
Warped discs and the directional stability of jets in active galactic nuclei

Warped accretion discs in active galactic nuclei (AGN) exert a torque on the black hole that tends to align the rotation axis with the angular momentum of the outer disc. We compute the magnitude of this torque by solving numerically for the steady-state shape of the warped disc, and verify that the analytic solution of Scheuer & Feiler provides an excellent approximation. We generalize these results for discs with strong warps and arbitrary surface density profiles, and calculate the time-scale over which the black hole becomes aligned with the angular momentum in the outer disc. For massive black holes and accretion rates of the order of the Eddington limit, the alignment time-scale is always short (≲106 yr), so that jets accelerated from the inner disc region provide a prompt tracer of the angular momentum of gas at large radii in the disc. Longer time-scales are predicted for low-luminosity systems, depending on the degree of anisotropy in the hydrodynamic response of the disc to shear and warp, and for the final decay of modest warps at large radii in the disc that are potentially observable via very-long-baseline interferometry (VLBI). We discuss the implications of this for the inferred accretion history of those AGN with jet directions that appear to be stable over long time-scales. The large energy deposition rate at modest disc radii during rapid realignment episodes should make such objects transiently bright at optical and infrared wavelengths.
Fuzzy logic inspired bearing fault-model membership estimation

In rotary machines bearings are a primary cause of failure. In order to estimate the time before failure to provide information for timely bearing replacement strategies, condition-based machine health monitoring techniques are employed. This paper discusses a model for estimating the severity of bearing faults that can be used for residual bearing life estimation by processing the vibration signal. The proposed technique used in this model examines the spectral content of vibration signals across frequency bins and then fits Gaussian distributions to each frequency bin. With the use of these Gaussian models and training set examples with different fault severity levels, characteristic membership functions are constructed. This enables estimation of the severity levels of the bearing faults through a fuzzy-logic inspired process, whereby the severity level corresponds to the maximum of the set of corresponding membership functions. Thus based on discrete fault severity levels, trained Gaussian fittings of spectral bins and characteristic fault membership functions are capable to estimate the fault severity on a continuous scale.
Event detection: BJTU-SED at Trecvid 2011

: In trecvid 2011, our team takes part in 2 event detection competition including pointing and cell to ear. We build two systems to recognize these events separately. For pointing, we extract texture and silhouette to recognize this action. And for cell to ear, we use orientation of optical flow and SVM classifier to finish this work.
Scalable community detection from networks by computing edge betweenness on MapReduce

Community detection from social network data gains much attention from academia and industry since it has many real-world applications. The Girvan-Newman (GN) algorithm is a divisive hierarchical clustering algorithm for community detection, which is regarded as one of the most popular algorithms. It exploits the concept of edge betweenness to divide a network into multiple communities. Though it is being widely used, it has limitations in supporting large-scale networks since it needs to calculate the shortest path between every pair of nodes in a network. In this paper, we develop a parallel version of the GN algorithm to support large-scale networks. To this end, we propose a new algorithm, which we call Shortest Path Betweenness MapReduce Algorithm (SPB-MRA), that utilizes the MapReduce model. This algorithm consists of four major stages, and all operations are executed in parallel. In addition, we suggest an approximation technique to further speed up community detection processes. We implemented SPB-MRA on Hadoop, which is the most popular open-source platform for MapReduce, and then conducted performance tests for SPB-MRA on Amazon EC2 instances. The results showed that elapsed time decreases almost linearly as the number of reducers increases and the approximation technique introduces negligible errors.
Microwave Filters Using Quarter-Wave Couplings

This paper presents a method of designing bandpass and band-rejection microwave filters by appropriately transforming lumped-element filters. Such microwave filters are realized physically as chains of resonant elements (either cavities or irises), coupled by quarter-wave sections of line. A structure of this type has a number of practical advantages over other types of filter structures, such as a chain of directly coupled cavities, because it permits the construction of the resonant elements as separate units, and yields more liberal tolerances on the dimensions of the coupling irises. A comparison is made of the theoretical and measured characteristics of an experimental four-cavity filter.
Laser only feature based multi robot SLAM

This paper presents multi-robot simultaneous localization and mapping (SLAM) framework for a team of robots with unknown initial poses. The proposed solution is using feature based Rao-Blackwellised particle filter (RBPF) SLAM for each robot working in an unknown environment equipped only with 2D range sensor and communication module. To represent the environment in compact form, line and corner features (or point features) are used. By sharing and comparing distinct feature based maps of each robot, a global map with known poses is formed without any physical meeting among the robots. This approach can easily applicable to the distributed or centralized robotic systems with ease of data handling and reduced computational cost.
The generation of representations of word meanings from dictionaries

This paper describes the generation of iconic and categorical representations of word meaning, in propositional form, from the WordNet lexical database. These are derived from the list of synonyms, the descriptive gloss, and from the hypernym and meronym relations of each WordNet word sense. We demonstrate that these representations promote identification and discrimination, these being suggested qualities of representations of meaning, and finally suggest that these representations have further applications in language engineering.
Analysis of design meetings for understanding software architecture decisions

Software architecture teams use verbal and graphical contributions to evaluate and select alternative design decisions. Usually the rationale behind these decisions is not recorded in the architecture document itself, and many contributions and rationale are lost to future reviewers and builders. This article describes Design Verbal Interventions Analysis (DVIA), which applies verbal protocol analysis to transcribed meetings logs to classify verbal interventions as either issue, orientation, mandatory orientation, request for clarification, explanation, disagreement, constraint, assessment, choice, or assumption. The approach is illustrated with a case study using transcribed meetings from undergraduate student teams designing a command-and-control center for a pan-Andean spatial project. The study shows that much of the interaction supports coevolution of problem understanding and solution framing, with designers engaged in simultaneous resolution of several design issues, following a cyclical structure. This strategy will allow to retrieve software architecture decisions from architecture team meetings.
Wireless reconfigurable modules for robotic endoluminal surgery

In this paper, a reconfigurable modular robotic system is proposed to augment the dexterity of endoluminal interventions in the gastrointestinal tract. In the proposed system, miniaturized robotic modules are ingested and assembled in the stomach cavity. The assembled robot can change its configuration according to the target location, thus enabling complicated surgical tasks. The robotic assembly, the robotic configuration and the surgical tasks are controlled via wireless bidirectional communication. Based on this concept, early prototypes of the robotic modules were designed and fabricated. The developed module has 2DOF (±90° of bending and 360° of rotation), measures 15.4 mm in diameter and 36.5 mm in length. It weighs 5.6 g and contains a Li-Po battery, two brushless DC motors, and a custom-made control board capable of wireless communication. The performance of the bending and rotational motion was evaluated and the future work has been discussed.
Aβ Deposition Is Associated with Neuropil Changes, but not with Overt Neuronal Loss in the Human Amyloid Precursor Protein V717F (PDAPP) Transgenic Mouse

The PDAPP transgenic mouse overexpresses human amyloid precursor protein V717F (PDAPP minigene) and develops age-related cerebral amyloid-β protein (Aβ) deposits similar to senile plaques in Alzheimer’s disease. We find age-related cortical and limbic Aβ deposition that begins at 8 months and progresses to cover 20–50% of the neuropil in cingulate cortex, entorhinal cortex, and hippocampus of 18-month-old heterozygotic animals. The regional patterns of transgene expression and amyloid deposition suggest that Aβ deposits occur at the terminals of overexpressing neurons. Amyloid deposition is associated with dystrophic neurites and extensive gliosis. However, stereological analysis shows that there is no overt neuronal loss in entorhinal cortex, CA1 hippocampal subfield, or cingulate cortex through 18 months of age. In addition, there is no apparent loss of mRNA encoding neuronal synaptic, cytoskeletal, or metabolic proteins. Thus, widespread Aβ deposition in 18-month-old heterozygotic mice produces neuritic alterations and gliosis without widespread neuronal death.