Miracle-dz/UniFAR-FTUs huggingface dataset:
Parallel and memory-e cient reads indexing for genome assembly

As genomes, transcriptomes and meta-genomes are being sequenced at a faster pace than ever, there is a pressing need for e cient genome assembly methods. Two practical issues in assembly are heavy memory usage and long execution time during the read indexing phase. In this article, a parallel and memory-e cient method is proposed for reads indexing prior to assembly. Speci cally, a hash-based structure that stores a reduced amount of read information is designed. Erroneous entries are ltered on the y during index construction. A prototype implementation has been designed and applied to actual Illumina short reads. Benchmark evaluation shows that this indexing method requires signi cantly less memory than those from popular assemblers.
PrPl: a decentralized social networking infrastructure

This paper presents PrPl, a decentralized infrastructure that lets users participate in online social networking without loss of data ownership. PrPl, short for private-public, has a person-centric architecture--each individual uses a Personal-Cloud Butler service that provides a safe haven for one's personal digital assets and supports sharing with fine-grain access control. A user can choose to run the Butler on a home server, or use a paid or ad-supported vendor of his choice. Each Butler provides a federation of data storage; it keeps a semantic index to data that can reside, possibly encrypted, in other storage services. It uses the standard, decentralized OpenID management system, so users can use their established personas in accessing the data. One pre-requisite to the success of a platform is the availability of applications, which means that ease of application development is essential. We have developed a language called SociaLite, based on Datalog, that allows developers to use a simple declarative database query to access the large collection of private data served up by the Butlers in our social circle running under different administrative domains. We have developed a prototype of the PrPl infrastructure and implemented a number of simple social applications on the system. We found that the applications can be written in a small number of lines of code using SociaLite. Preliminary experimental results suggest that it is viable to enable sharing of private social data between close friends with a decentralized architecture.
Baryon- and Lepton-Nonconserving Processes

( ~Present address: Fermi National Accelerator Laboratory, P. O. Box 500, Batavia, Ill. 60510. T. Appelguist and J. Carazzone, Phys. Rev. D 11, 2856 (1975). E. G. , J. Collins, F. Wilczek, and A. Zee, Phys. Rev. D 18, 242 (1978); D. Toussaint, Phys. Rev. D 18, 1626 (1978}. Yoichi Kazama and York-Peng Yao, to be published. C. Callan, Phys. Hev. D 2, 1541 (1970); K. Symanzik, Commun. Math. Phys. 18, 227 (1970). W. Zimmermann, in Lectures on Elementary Particles and Quantum Field Theory, edited by S. Deser et al. (MIT Press, Cambridge, Mass. , 1971), Vol. I, p. 897. S. L. Adler and W. A. Bardeen, Phys. Rev. D 4, S045 (1971). ~C. K. Lee, Ph.D. thesis, Stanford University, 1975 (unpublished) . The corresponding operators are
Control design to achieve dynamic walking on a bipedal robot with compliance

We propose a control framework for dynamic bipedal locomotion with compliant joints. A novel 3D dynamic walking is achieved by utilizing natural dynamics of the system. It is done by 1) driving robot joints directly with the posture-based state machine and 2) controlling tendon-driven compliant actuators. To enlarge gait's basin attraction for stable walking, we also adaptively plan step-to-step motion and compensate stance/swing motion. Final joint input is described by a superposition of state machine control torques and compensation torques of balancers. Various walking styles are easily generated by composing straight and turning gait-primitives and such walking is effectively able to adapt on various environments. Our proposed method is applied to a torque controlled robot platform, Roboray. Experimental results show that gaits are able to traverse inclined and rough terrains with bounded variations, and the result gaits are human-like comparing the conventional knee bent walkers.
Real-time object detection and Tracking using color feature and motion

This paper, introduces a technique for automating the methodology of detecting and tracking objects utilizing color feature and motion. Video Tracking is the methodology of finding a moving object over the long distance using a camera. The main aim of video tracking is to relate target objects in consecutive video frames. The relationship can be especially troublesome when the objects are moving speedy with respect to the frame rate. An interchange situation that grows the unpredictability of the issue is the time when the tracking object changes orientation after eventually. For these circumstances video tracking frameworks typically utilize a movement model which depicts how the image of the target may change for distinctive conceivable movements of the object. In this paper an algorithm is developed to track the real-time moving objects in different frames of a video using color feature and motion.
Ds Requirement Analysis

By considering the problems to be solved from a software engineering point of view, we will not only consider the feasibility provided by the mechanisms embedded in the platform we are defining, but also the economic1 aspects. This last point burns down to: how easy will it be to implement, deploy and manage complex distributed services in the application domains we are considering, i.e. firewall based security assessment, video on demand services, business process modeling and transactional workflow system applied to business to business electronic commerce, by using the mechanisms, methodologies and tools providing support to the approach(s) defined within C 3 DS.
The effects of trauma on cognitive behaviour therapy for depression and alcohol misuse

Posttraumatic stress disorder (PTSD) has been found to commonly co-occur with depression and alcohol use problems (including alcohol use disorders). PTSD when present with depression and/or alcohol use problems has also been found to exacerbate the comorbid symptoms. Despite the high comorbidity with (and the impact of) PTSD on depression and alcohol use problems, people presenting to services for treatment for depression and/or alcohol use tend not to be screened or treated for PTSD. Therefore, it is unknown what the effects of having PTSD on CBT treatment for depression and/or alcohol use problems are. Therefore, this thesis identifies and discusses prevalence rates of trauma exposure and PTSD in community and treatment seeking populations for depression and alcohol misuse. The impact of experiencing different traumatic event types on posttraumatic stress symptoms (PTSS), depression, and alcohol misuse are also explored. The effects of also having PTSD and/or experiencing particular traumatic event types on cognitive behaviour therapy (CBT) for depression and/or alcohol use disorders (AUD) is further explored. Finally, assessment and treatment recommendations (that are based on the findings of this thesis) for PTSD comorbidity in non-PTSD treatment settings, are proposed. Chapter 1 provides a literature review on the prevalence of traumatic event exposure, and rates of PTSD, major depressive disorder (MDD), and AUD in community and clinical populations. Diagnostic criteria for PTSD, depression, and AUD are reviewed, along with models of how these disorders develop and are maintained. The issue of PTSD comorbidity is discussed, with a focus on the current comorbidity perspective to expand from a dual diagnosis (i.e., PTSDMDD and PTSD-AUD) to a multiple comorbidity framework (such as PTSDMDD-AUD). CBT therapies are identified as an evidence-based treatment for PTSD, depression, and substance/alcohol use as a single disorder. Emerging
Hypothesis-driven accent discrimination

Native and non-native use of language differs, depending on the proficiency of the speaker, in clear and quantifiable ways. It has been shown that customizing the acoustic and language models of a natural language understanding system can significantly improve handling of non-native input; in order to make such a switch, however, the nativeness status of the user must be known. In this paper, we show how the recognition hypothesis can be used to predict with very high accuracy whether the speaker is native. Effectiveness of both word-based and phone-based classification are evaluated, and a discussion of the primary discriminative features is presented. In an LVCSR system in which users are both native and non-native, we have achieved a 15.6% relative decrease in word error rate by integrating this classification method with speech recognition.
Role of the parCBA Operon of the Broad-Host-Range Plasmid RK2 in Stable Plasmid Maintenance

ABSTRACT The par region of the stably maintained broad-host-range plasmid RK2 is organized as two divergent operons,parCBA and parDE, and a cis-acting site. parDE encodes a postsegregational killing system, andparCBA encodes a resolvase (ParA), a nuclease (ParB), and a protein of unknown function (ParC). The present study was undertaken to further delineate the role of the parCBA region in the stable maintenance of RK2 by first introducing precise deletions in the three genes and then assessing the abilities of the different constructs to stabilize RK2 in three strains of Escherichia coli and two strains of Pseudomonas aeruginosa. The intact parCBA operon was effective in stabilizing a conjugation-defective RK2 derivative in E. coli MC1061K and RR1 but was relatively ineffective in E. coli MV10Δlac. In the two strains in which the parCBA operon was effective, deletions in parB, parC, or bothparB and parC caused an approximately twofold reduction in the stabilizing ability of the operon, while a deletion in the parA gene resulted in a much greater loss ofparCBA activity. For P. aeruginosaPAO1161Rifr, the parCBA operon provided little if any plasmid stability, but for P. aeruginosaPAC452Rifr, the RK2 plasmid was stabilized to a substantial extent by parCBA. With this latter strain, parAand res alone were sufficient for stabilization. Thecer resolvase system of plasmid ColE1 and theloxP/Cre system of plasmid P1 were tested in comparison with the parCBA operon. We found that, not unlike what was previously observed with MC1061K, cer failed to stabilize the RK2 plasmid with par deletions in strain MV10Δlac, but this multimer resolution system was effective in stabilizing the plasmid in strain RR1. The loxP/Cre system, on the other hand, was very effective in stabilizing the plasmid in all threeE. coli strains. These observations indicate that theparA gene, along with its res site, exhibits a significant level of plasmid stabilization in the absence of theparC and parB genes but that in at least oneE. coli strain, all three genes are required for maximum stabilization. It cannot be determined from these results whether or not the stabilization effects seen with parCBA or thecer and loxP/Cre systems are strictly due to a reduction in the level of RK2 dimers and an increase in the number of plasmid monomer units or if these systems play a role in a more complex process of plasmid stabilization that requires as an essential step the resolution of plasmid dimers.
Supervised Clustering and Fuzzy Decision Tree Induction for the Identification of Compact Classifiers

Fuzzy decision tree induction algorithms require the fuzzy quantization of the input variables. This paper demonstrates that supervised fuzzy clustering combined with similarity-based rule-simplification algorithms is an effective tool to obtain the fuzzy quantization of the input variables, so the synergistic combination of supervised fuzzy clustering and fuzzy decision tree induction can be effectively used to build compact and accurate fuzzy classifiers. Fuzzy Decision Trees, Fuzzy Clustering, Input Quantization, Fuzzy Classifier
The optimal test PID control for CVT control system

To increase control precision and improve dynamic characteristic of Continuously Variable Transmission Control system, a method of processing data called Optimal test that usually adopted in chemical experiment is applied. After parameters are ensured, the Critical gain KV of the open-loop system is determined by the Stability, then the factors are determined and the orthogonal table is constituted to try out. In the end, the dynamic characteristics of the system are simulated by SIMULINK software. Thus the optimum PID parameters can be achieved. Through the method above, we can avoid a lot of complex trials which determine PID parameters and get better control effect. It is shown by simulation that the PID rectification for CVT control system using Optimal test increases fairly control precision, rapidity of step response and make the quality of the control system best.
Collecting Coupons on Trees, and the Analysis of Random Walks

We consider the cover time E>sub /sub sub /sub sub /sub sub /sub sub /sub 2n^2. This improves the leadingconstant in previously known upper bounds. \endlistWe also provide upper bouhnds on E^+_uG, the expected timeto cover G and return to u
An efficient service discovery protocol for 6LoWPANs

In the ubiquitous computing era, devices and services are everywhere. To make use of the existing capabilities, a proficient service announcement and discovery protocol is needed. In this paper, we propose an efficient protocol to announce and discover services in IP-based ubiquitous sensor networks; a promising technology to make real the revelation of ubiquity. The proposed protocol adopts a fully distributed approach using an adaptive pull-push model to ensure optimal acquisition times, low energy consumption, and low generated overhead with timely reaction to topology changes. The proposed protocol achieves this by using context-awareness information, delivered by a trickle algorithm. The protocol is implemented in Contiki and evaluated in the Cooja simulator. Obtained results prove the protocol capabilities to realize optimal acquisition times with a minimal cost in terms of energy and generated overhead, making it suitable for mobile networks.
Cellular Signaling Pathway Alterations and Potential Targeted Therapies for Medullary Thyroid Carcinoma

Parafollicular C-cell-derived medullary thyroid cancer (MTC) comprises 3% to 4% of all thyroid cancers. While cytotoxic treatments have been shown to have limited efficacy, targeted molecular therapies that inhibit rearranged during transfection (RET) and other tyrosine kinase receptors that are mainly involved in angiogenesis have shown great promise in the treatment of metastatic or locally advanced MTC. Multi-tyrosine kinase inhibitors such as vandetanib, which is already approved for the treatment of progressive MTC, and cabozantinib have shown distinct advantages with regard to rates of disease response and control. However, these types of tyrosine kinase inhibitor compounds are able to concurrently block several types of targets, which limits the understanding of RET as a specific target. Moreover, important resistances to tyrosine kinase inhibitors can occur, which limit the long-term efficacy of these treatments. Deregulated cellular signaling pathways and genetic alterations in MTC, particularly the activation of the RAS/mammalian target of rapamycin (mTOR) cascades and RET crosstalk signaling, are now emerging as novel and potentially promising therapeutic treatments for aggressive MTC.
GeoloGIS-BH: An Information System for Using the Built Heritage for Geological Teaching

There are examples of using stones of the cultural heritage for teaching purposes. Information systems have found several potential uses in the promotion and preservation of cultural heritage. In this paper is considered the conceptual framework of an information system concerning features of geological interest (FGI) in the built heritage (without any consideration in terms of its software implementation). This FGI concept is used here in a very wide sense to encompass characteristics of geological materials that can be recognized with the naked eye and analogies of geological processes in the built environment. Two perspectives are considered for information organization: occurrences of FGIs in the built heritage (more suitable for Earth Sciences teaching) and FGIs as components of built heritage elements (more suitable for humanities teaching). The main issue that arises from the ensuing discussion was found to be the findability of a given FGI, depending on its visual contrast and the characteristics of the built heritage element. It is argued that, in this way, geological concepts can contribute to the promotion and conservation of the built heritage.
Cation selectivity of and cation binding to the cGMP-dependent channel in bovine rod outer segment membranes

The properties of the cGMP-dependent channel present in membrane vesicles prepared from intact isolated bovine rod outer segments (ROS) were investigated with the optical probe neutral red. The binding of neutral red is sensitive to transport of cations across vesicular membranes by the effect of the translocated cations on the surface potential at the intravesicular membrane/water interface (Schnetkamp, P. P. M. J. Membr. Biol. 88: 249-262). Only 20-25% of ROS membrane vesicles exhibited cGMP-dependent cation fluxes. The cGMP-dependent channel in bovine ROS carried currents of alkali and earth alkali cations, but not of organic cations such as choline and tetramethylammonium; little discrimination among alkali cations (K greater than Na = Li greater than Cs) or among earth alkali cations (Ca greater than Mn greater than Sr greater than Ba = Mg) was observed. The cation dependence of cGMP-induced cation fluxes could be reasonably well described by a Michaelis-Menten equation with a dissociation constant for alkali cations of about 100 mM, and a dissociation constant for Ca2+ of 2 mM. cGMP-induced Na+ fluxes were blocked by Mg2+, but not by Ca2+, when the cations were applied to the cytoplasmic side of the channel. cGMP-dependent cation fluxes showed a sigmoidal dependence on the cGMP concentration with a Hill coefficient of 2.1 and a dissociation constant for cGMP of 92 microM. cGMP-induced cation fluxes showed two pharmacologically distinct components; one component was blocked by both tetracaine and L-cis diltiazem, whereas the other component was only blocked by tetracaine.
Echocontrast-enhanced ultrasound of extracranial internal carotid artery high-grade stenosis and occlusion.

BACKGROUND AND PURPOSE Proper assessment of extracranial internal carotid artery high-grade stenosis and occlusion by extracranial color-coded duplex sonography (ECCD) is occasionally made difficult by shadowing, an unfavorable insonation angle, low flow velocity or volume, or a deep insonation depth. In these cases, echocontrast could be helpful to quantify the degree of stenosis and to diagnose occlusion. METHODS We investigated 17 arteries with poor precontrast investigation conditions and suspected high-grade stenosis or occlusion by contrast-enhanced ECCD. RESULTS Compared with the precontrast scans, echocontrast allowed for significantly more segments to be evaluated by pulsed Doppler sonography (P<0.001) and for longer lumen segments to be displayed on color mode (P<0.001). Because it was now possible to place the sample volume right into the jet of the stenosis, the maximal flow velocity registered increased in all patients with stenosis. CONCLUSIONS Echocontrast-enhanced ECCD of the carotid arteries is helpful for stenosis classification in a small group of preselected patients with poor original examination conditions.
Protocol/Mechanism Design for Cooperation/Competition

Developing interaction rules/protocols among multiple agents is one of the central research topics in multi-agent systems. For cooperative agents, we need to develop protocols so that agents can achieve some common goal if they follow the protocol. Also, for competitive/selfish agents, we need to design mechanisms/protocols so that some socially desirable outcome can be achieved, even if agents act selfishly. This article presents a brief overview of the authorýs works on this topic over the last five years.
A data type for discretized time representation in DEVS

This paper addresses the problems related to data types used for time representation in DEVS, a formalism for the specification and simulation of discrete-event systems. When evaluating a DEVS simulation model into an actual computer simulation program, a data type is required to hold the virtual time of the simulation and the time elapsed in the model of the simulated system. We review the commonly data types used, and discuss the problems that each of them induce. In the case of floating point we show how, under certain conditions, the simulation can break causality relations, treat simultaneous events as non simultaneous or treat non simultaneous events as simultaneous. In the case of integers using fixed unit we list a number of problems arising when composing models operating at different timescales. In the case of structures that combine several fields, we show that, at the cost of a lower performance, most of the previous problems can be avoided, although not totally. Finally, we describe an alternative representation data type we developed to cope with the data type problems.
Randomized allocation processes

We investigate various randomized processes allocating balls into bins that arise in applications in dynamic resource allocation and on-line load balancing. We consider the scenario when m balls arriving sequentially are to be allocated into n bins on-line and without using a global controller. Traditionally, the main aim of allocation processes is to place the balls into bins to minimize the maximum load in bins. However in many applications it is equally important to minimize the number of trails performed by the balls (the allocation time). We study adaptive allocation schemes that achieve optimal tradeoffs between the maximum load, the maximum allocation time, and the average allocation time. We investigate allocation processes that may reallocate the balls. We provide a tight analysis of the maximum load of processes that during placing a new ball may reassign the balls in up to d randomly chosen bins. We study infinite processes, in which in each step a random ball is removed and a new ball is placed according to some scheduling rule. We present a novel approach that establishes a tight estimation of the time needed for the infinite process to be in the state near to its equilibrium. Finally, we provide a tight analysis of the maximum load of the off-line process in which each ball may be placed into one of d randomly chosen bins. We apply this result to competitive analysis of on-line load balancing processes.