Miracle-dz/UniFAR-FTUs huggingface dataset:
Mäntylä Bad Smells in Software – a Taxonomy and an Empirical Study

In this work, the bad code smells are studied empirically and their relationship to source code metrics is evaluated. This work also presents an initial taxonomy for the bad code smell, which improves their understandability and feasibility The bad code smells, presented by Martin Fowler and Kent Beck, are dissatisfactory structures in the source code of software that decrease software quality by making it less maintainable. The maintainability of software is important, because it is one of the factors affecting the cost of the future development activities. The literature study looks at the concept of software maintainability, discusses how software maintainability can be measured, and provides motivation and migration techniques to achieve more maintainable software. Based on the literature study, this work proposes a taxonomy for the bad code smells and evaluates the measurability of each bad code smell with source code metrics. A survey is used to collect the developers' opinions on the existence of bad code smells in particular software modules. The results of this survey show that the developers' opinions on a particular smell in a particular software module are not very uniform. The survey also provides more support to the theoretical taxonomy by showing that there are many strong correlations within the taxonomy's categories. This study also compares the results of the smell survey to the source code metrics collected with automatic tools. The results show that developers' evaluations of the bad code smells do not correlate with the actual source code metrics. This means that the smell evaluations from developers are not very reliable and that there is a need for automatic smell measurement.
The Role of Protein Interactions in Mediating Essentiality and Synthetic Lethality

Genes are characterized as essential if their knockout is associated with a lethal phenotype, and these “essential genes” play a central role in biological function. In addition, some genes are only essential when deleted in pairs, a phenomenon known as synthetic lethality. Here we consider genes displaying synthetic lethality as “essential pairs” of genes, and analyze the properties of yeast essential genes and synthetic lethal pairs together. As gene duplication initially produces an identical pair or sets of genes, it is often invoked as an explanation for synthetic lethality. However, we find that duplication explains only a minority of cases of synthetic lethality. Similarly, disruption of metabolic pathways leads to relatively few examples of synthetic lethality. By contrast, the vast majority of synthetic lethal gene pairs code for proteins with related functions that share interaction partners. We also find that essential genes and synthetic lethal pairs cluster in the protein-protein interaction network. These results suggest that synthetic lethality is strongly dependent on the formation of protein-protein interactions. Compensation by duplicates does not usually occur mainly because the genes involved are recent duplicates, but is more commonly due to functional similarity that permits preservation of essential protein complexes. This unified view, combining genes that are individually essential with those that form essential pairs, suggests that essentiality is a feature of physical interactions between proteins protein-protein interactions, rather than being inherent in gene and protein products themselves.
Quanti fi cation of microscopic diffusion anisotropy disentangles effects of orientation dispersion from microstructure : Applications in healthy volunteers and in brain tumors

(2015). Quantification of microscopic diffusion anisotropy disentangles effects of orientation dispersion from microstructure: Applications in healthy volunteers and in brain tumors. NeuroImage, 104, 241-252. General rights Copyright and moral rights for the publications made accessible in the public portal are retained by the authors and/or other copyright owners and it is a condition of accessing publications that users recognise and abide by the legal requirements associated with these rights. • Users may download and print one copy of any publication from the public portal for the purpose of private study or research. • You may not further distribute the material or use it for any profit-making activity or commercial gain • You may freely distribute the URL identifying the publication in the public portal ? Take down policy If you believe that this document breaches copyright please contact us providing details, and we will remove access to the work immediately and investigate your claim. a b s t r a c t a r t i c l e i n f o Keywords: Diffusion weighted imaging Microscopic anisotropy Microscopic fractional anisotropy Order parameter Magic angle spinning of the q-vector The anisotropy of water diffusion in brain tissue is affected by both disease and development. This change can be detected using diffusion MRI and is often quantified by the fractional anisotropy (FA) derived from diffusion ten-sor imaging (DTI). Although FA is sensitive to anisotropic cell structures, such as axons, it is also sensitive to their orientation dispersion. This is a major limitation to the use of FA as a biomarker for " tissue integrity " , especially in regions of complex microarchitecture. In this work, we seek to circumvent this limitation by disentangling the effects of microscopic diffusion anisotropy from the orientation dispersion. The microscopic fractional anisotropy (μFA) and the order parameter (OP) were calculated from the contrast between signal prepared with directional and isotropic diffusion encoding, where the latter was achieved by magic angle spinning of the q-vector (qMAS). These parameters were quantified in healthy volunteers and in two patients ; one patient with meningioma and one with glioblastoma. Finally, we used simulations to elucidate the relation between FA and μFA in various micro-architectures. Generally, μFA was high in the white matter and low in the gray matter. In the white matter, the largest differences between μFA and FA were found in crossing white matter and in interfaces between …
The behavior of model probability in multiple model algorithms

The behavior of the model probability is closely related to the performance of multiple model algorithm. A clear view about the behavior of model probability will benefit the performance analysis and the model set design for multiple model algorithm. We investigate the behavior of the model probability of multiple model algorithm for parameter estimation and filtering. It turns out that the Kullback-Leibler information between the true model and the model in the model set plays an important role to determine the evolution of model probability. Most importantly, we draw a connection between multiple model algorithm and the comparison of multiple estimation algorithms through the view of multiple hypotheses. The behavior of the model probability suggests a feasible way to combine multiple algorithms to obtain a new method of better performance. An illustrative example is also presented.
Kinematic optimisation of the gantry-tau parallel kinematic manipulator with respect to its workspace

The Gantry-Tau is a recently developed parallel kinematic manipulator (PKM). Since the actuators are stationary it possesses the following characteristics: high speed, high acceleration, small moving mass and high static and dynamic accuracy. Since all link forces in the structure are axial, high stiffness can also be achieved. One of the main advantages of the Gantry-Tau machine is a large workspace area in comparison with traditional parallel machines. However, parameters of the machine, such as link lengths and dimension of support frames, can be difficult to design manually. In this paper we present a method to optimise such parameters to achieve the largest possible workspace. The problem is solved by using a non-linear optimization routine and imposing the parameterization on the midpoints of three spheres generated by the parallel links that intersect at the tool center point (TCP).
Privacy protection of textual medical documents

With the adoption of ITs, a large amount patient-related documents is compiled by healthcare organisations. Quite often, this data is needed to be released to third parties for research or business purposes. The inherent sensitivity of patient's information has brought to the definition of legislations to protect the privacy of individuals. To meet with these legislations, redaction or sanitization of patient-related documents is needed before their release. This is usually done manually, which is costly and time-consuming, or by means of ad-hoc solutions that just protect structured types of sensitive information (e.g. social security numbers), or that are based on removing sensitive terms, which hampers the utility of the output. In this paper, we propose an automatic sanitization method for textual medical documents that is able to protect sensitive terms and those that are semantically related, while retaining the utility of the output as much as possible. Different to redaction schemas, which are based on term removal, our method improves the utility of the protected output by replacing sensitive terms with appropriate generalisations retrieved from medical and general-purpose knowledge bases. Experiments conducted on highly sensitive documents and in coherency with current regulations on healthcare data privacy show promising results in terms of output's privacy and utility.
Spatial Perspective and Coordinate Systems in Autoscopy: A Case Report of a “Fantome de Profil” in Occipital Brain Damage

Autoscopic phenomena refer to complex experiences involving the illusory reduplication of one's own body. Here we report the third long-lasting case of autoscopy in a patient with right occipital lesion. Instead of the commonly reported frontal mirror view (fantôme spéculaire), the patient saw her head and upper trunk laterally in side view (fantôme de profil). We found that the visual appearance and completeness of the autoscopic image could be selectively modulated by active and passive movements, without being influenced by imagining the same movements or by tactile and auditory stimulation. Eyes closure did not disrupt either the perception of the autoscopic body or the effects of the motor stimulation. Moreover, the visual body reduplication was coded neither in purely eye-centered nor in head-centered frames of reference, suggesting the involvement of egocentric coordinate systems (eyes and head centered). A follow-up examination highlighted the stability of the visual characteristics of the body reduplication and its shift induced by displacement of both head and eyes. These findings support the view that autoscopic phenomena have a multisensory motor origin and proprioceptive signals may play an important role in modulating the illusory visual reduplication of the patient's own body, most likely via cross-modal modulation of extrastriate areas involved in body and face perception.
IBM Research Report An ECO Algorithm for Resolving OPC and Crosstalk Violations

In the deep submicron manufacturing (DSM) era, lithography/yield and noise are critical issues to be considered. Optical Proximity Correction (OPC) is becoming a key compensate technique for the light diffraction effect in lithography. Both OPC effect and the capacitive crosstalk on some wire segments can only be analyzed post routing in late design stage or post-silicon stepping design change. ECO (Engineering Change Orders) is used in late design stage to ﬁx violations that exceed the given OPC and crosstalk thresholds derived from analysis. These violations must be corrected in order to guarantee performance and yield. In this paper, we propose the ﬁrst ECO routing algorithm which eliminates both OPC and crosstalk violations for wires. At the same time, the ECO routing obeys the given constraints so as to keep the new routing solution close to the existing one to preserve design timing and layout convergence.
Schwarz-Christoffel mapping in the computer era.

Thanks to powerful algorithms and computers, Schwarz{ Christooel mapping is a practical reality. With the ability to compute have come new mathematical ideas. The state of the art is surveyed. 1. Introduction. In the past twenty years, because of new algorithms and new computers, Schwarz{Christooel conformal mapping of polygons has matured to a technology that can be used at the touch of a button. Many authors have con-The principal SC software tools are the Fortran package SCPACK 15] and its more capable Matlab successor , the Schwarz{Christooel Toolbox 3]. It is now a routine matter to compute an SC map involving a dozen vertices to ten digits of accuracy in a few seconds on a workstation. With the power to compute has come the ability to explore. The obvious kind of problem|\here is a polygon; map it onto a disk or a half-plane"|is rarely what one encounters in practice. Instead it is variations on the idea of SC mapping that arise. In this article, after brieey mentioning the algorithmic developments that have made SC mapping possible, we describe four of these variations: oblique derivative problems on polygons; ideal free-streamline ows; the CRDT (cross-ratio Delaunay triangulation) algorithm; and Green's functions for symmetric multiply connected domains.
A switched reluctance machine for high-torque low-speed applications

This paper presents a first overview of an unconventional switched-reluctance rotating machine conceived to provide high specific torque in low-speed applications by leveraging on the magnetic gearing effect while featuring a simple, modular, highly symmetrical structure that should permit to limit manufacturing costs. After recalling the main proposals found in the literature for similar targets, the first application considered for the machine is briefly described. The proposed structure is then introduced and briefly analyzed, highlighting the main features and issues related to manufacturing, performance and control. A few results coming from 3-D FEM analysis of the machine are finally reported and briefly commented
The benefits of community participation in rural healthservice development: where is the evidence?

The term ‘community participation’ is commonly understood as the collective involvement of local people in assessing their needs and organising strategies to meet those needs. The importance of community participation in rural health service development is uncontested. The rural health policy framework Healthy Horizons Outlook includes the principle, ‘participation by individuals, communities and special groups in determining their health priorities should be pursued as a basis for successful programs and services to maintain and improve their health’. The document also states that ‘social capability and the physical capacity to plan and implement local programs are required for communities to improve and maintain their health’
Future trends for wireless communication frontends in nanometer CMOS

CMOS technology is evolving deeper and deeper into the nanometer era, with designs now being done in 90nm and even 65nm. This makes the integration of entire systems possible, many of which are mixed-signal in nature, including analog and/or RF parts. The advancement in CMOS technology offers many opportunities for new telecom applications, such as 4G software-defined radios and wireless sensor networks. This invited paper first describes basic architectural concepts for 4G radio frontends. This is then illustrated with circuit solutions for a fully reconfigurable 4G A/D converter. Also low-power wireless sensor networks offer large opportunities for ubiquitous sensing and ambient intelligence, opening up applications such as improved human health care and comfort in the future. Designing these wireless circuits in nanometer CMOS technologies with increasing technology tolerances, reducing supply voltages and worsening signal integrity conditions are key challenges that designers face and that require new design tools to address these problems. Some examples are presented in this paper.
PPTLens: Create Digital Objects with Sketch Images

In this work, we introduce the PPTLens system to convert sketch images captured by smart phones to digital flowcharts in PowerPoint. Different from existing sketch recognition system, which is based on hand-drawn strokes, PPTLens enables users to use sketch images as inputs directly. It's more challenging since strokes extracted from sketch images might not only be very messy, but also without temporal information of the drawings. To implement the 'Image to Object' (I2O) scenario, we propose a novel sketch image recognition framework, including an effective stroke extraction strategy and a novel offline sketch parsing algorithm. By enabling sketch images as inputs, our system makes flowchart/diagram production much more convenient and easier.
Length bias and search limitations in cartesian genetic programming

In this paper we examine how Cartesian Genetic Programming's (CGP's) method for encoding directed acyclic graphs (DAGs) and its mutation operator bias the effective length of individuals as well as the distribution of inactive nodes in the genome. We investigate these biases experimentally using two CGP variants as comparisons: Reorder, a method for shuffling node ordering without effecting individual evaluation, and DAG, a method for removing the concept of node position. Experiments were performed on four problems tailored to highlight potential search limitations, with further testing on the 3-bit multiplier problem. Unlike previous work, our experiments show that CGP has an innate parsimony pressure that makes it very difficult to evolve individuals with a high percentage of active nodes. This bias is particularly prevalent as the length of an individual increases. Furthermore, these problems are compounded by CGP's positional biases which can make some problems effectively unsolvable. Both Reorder and DAG appear to avoid these problems and outperform Normal CGP on preliminary benchmark testing. Finally, these new techniques require more reasonable genome sizes than those suggested in current CGP, with some evidence that solutions are also more terse.
Evolutionary Strata on the X Chromosomes of the Dioecious Plant Silene latifolia: Evidence From New Sex-Linked Genes

Despite its recent evolutionary origin, the sex chromosome system of the plant Silene latifolia shows signs of progressive suppression of recombination having created evolutionary strata of different X–Y divergence on sex chromosomes. However, even after 8 years of effort, this result is based on analyses of five sex-linked gene sequences, and the maximum divergence (and thus the age of this plant's sex chromosome system) has remained uncertain. More genes are therefore needed. Here, by segregation analysis of intron size variants (ISVS) and single nucleotide polymorphisms (SNPs), we identify three new Y-linked genes, one being duplicated on the Y chromosome, and test for evolutionary strata. All the new genes have homologs on the X and Y chromosomes. Synonymous divergence estimated between the X and Y homolog pairs is within the range of those already reported. Genetic mapping of the new X-linked loci shows that the map is the same in all three families that have been studied so far and that X–Y divergence increases with genetic distance from the pseudoautosomal region. We can now conclude that the divergence value is saturated, confirming the cessation of X–Y recombination in the evolution of the sex chromosomes at ∼10–20 MYA.
An Improved Genetic Algorithm for Dual-Resource Constrained Flexible Job Shop Scheduling

In this paper, a dual-resource constrained job shop scheduling problem was studied. According to the information processing mechanism of an immune system in biotic science, a new immune Genetic Algorithm for flexible job shop scheduling through combining immune algorithm with genetic algorithm was proposed. The algorithm can effectively avoid the premature convergence problem caused by the high selective pressure. Moreover, it improves the ability of searching an optimum solution and increases the convergent speed. The operation-based encoding and an active schedule decoding method were employed, and several kinds of crossover operations were adopted in order to keep individual diversity and to improve the level of adaptability of the individual diversity in the population. This new algorithm reasonably assigns the resources of machines and workers to jobs and achieves optimum on some performance. Compared with the solutions suggested by other researchers, the simulations show that the developed algorithm can search for better solution on make-span and that it is available and efficient.
Resource Allocation for Session-Based Two-Dimensional Service Differentiation on e-Commerce Servers

A scalable e-commerce server should be able to provide different levels of quality of service (QoS) to different types of requests based on clients' navigation patterns and the server capacity. E-commerce workloads are composed of sessions. In this paper, we propose a session-based two-dimensional (2D) service differentiation model for online transactions: intersession and intrasession. The intersession model aims to provide different levels of QoS to sessions from different customer classes, and the intrasession model aims to provide different levels of QoS to requests in different states of a session. A primary performance metric of online transactions is slowdown. It measures the waiting time of a request relative to its service time. We present a processing rate allocation scheme for 2D proportional slowdown differentiation. We then introduce service slowdown as a systemwide QoS metric of an e-commerce server. It is defined as the weighted sum of request slowdown in different sessions and in different session states. We formulate the problem of 2D service differentiation as an optimization of processing rate allocation with the objective of minimizing the service slowdown of the server. We prove that the derived rate allocation scheme based on the optimization guarantees client requests' slowdown to be square-root proportional to their prespecified differentiation weights in both intersession and intrasession dimensions. We evaluate this square-root proportional rate allocation scheme and a proportional rate allocation scheme via extensive simulations. Results validate that both schemes can achieve predictable, controllable, and fair 2D service differentiation on e-commerce servers. The square-root proportional rate allocation scheme provides 2D service differentiation at a minimum cost of service slowdown