Miracle-dz/UniFAR-FTUs huggingface dataset:
Comparative Analysis of Teleost Genome Sequences Reveals an Ancient Intron Size Expansion in the Zebrafish Lineage

We have developed a bioinformatics pipeline for the comparative evolutionary analysis of Ensembl genomes and have used it to analyze the introns of the five available teleost fish genomes. We show our pipeline to be a powerful tool for revealing variation between genomes that may otherwise be overlooked with simple summary statistics. We identify that the zebrafish, Danio rerio, has an unusual distribution of intron sizes, with a greater number of larger introns in general and a notable peak in the frequency of introns of approximately 500 to 2,000 bp compared with the monotonically decreasing frequency distributions of the other fish. We determine that 47% of D. rerio introns are composed of repetitive sequences, although the remainder, over 331 Mb, is not. Because repetitive elements may be the origin of the majority of all noncoding DNA, it is likely that the remaining D. rerio intronic sequence has an ancient repetitive origin and has since accumulated so many mutations that it can no longer be recognized as such. To study such an ancient expansion of repeats in the Danio, lineage will require further comparative analysis of fish genomes incorporating a broader distribution of teleost lineages.
Turkish version of Facebook Jealousy Questionnaire: reliability and validity studies on university students -

Objective: The aim of the present study was to develop and assess validity and reliability of the Turkish version of the Facebook Jealousy Questionnaire. Methods: A Turkish version of the Facebook Jealousy Questionnaire was translated to Turkish from English, and then translated back to English. The sample consisted of 307 students from two different universities in Ankara. In order to determine criterion validity of the scale, its correlation with the Turkish version of Romantic Jealousy Scale’s subscale ‘triggers of jealousy’ was used. Results: For determining the reliability and validity of the scale, internal consistency (Cronbach’s alpha), test-retest and corrected item-total correlations, criterion validity were used. Gender, age and some relational differences such as relational satisfaction and attractiveness of the partner were examined. There were only a significant negative correlation between age and Facebook jealousy score. Conclusions: This study supports the one-factor model of the Facebook Jealousy Questionnaire indicated by the original study. Findings demonstrate that the Turkish version of the Facebook Jealousy Questionnaire is a highly reliable and valid instrument to measure Facebook jealousy.
Putting patient-reported outcomes on the ‘Big Data Road Map’

The term ‘big data’ is used to describe large, complex datasets and the associated advances in technology and analytics. Within healthcare, this covers many different types of data including, for example: routinely collected clinic data in electronic health records; healthcare claims data, genomics data; public data releases, such as aggregated population health data or clinical trials results; data from automated sensors and smart devices; and information from healthcare forums and social media. In late 2013, the Association of the British Pharmaceutical Industry published its ‘Big data road map’, which sets out an action plan to direct progress in the use of big data over the next four years. The road map highlights the need to increase awareness and understanding of big data, build capability and capacity, create sustainable data ecosystems and accelerate high-value opportunities. These suggestions do not just apply to pharma, however, but also to healthcare more generally as clinicians, patients and policy-makers look to take advantage of the potential benefits of big data. There is, however, a risk that patient-reported outcome (PRO) data may be underrepresented in the big data ‘revolution’. PRO data are important in providing patients’ perspective on their own health. However, in contrast to countries such as the US and Netherlands, PROs are not routinely collected in UK clinical settings (other than for a small number of procedures, via the NHS PROMs programme). If this situation is not addressed, we risk continuing our overreliance on routinely collected clinical indicators to provide evidence for health policy: a potential backwards step in the move towards patient-centred care.
Bootstrapping pairs in Distance-Based Regression

Distance-based regression is a prediction method consisting of two steps: from distances between observations we obtain latent variables which, in turn, are the regressors in an ordinary least squares linear model. Distances are computed from actually observed predictors by means of a suitable dissimilarity function. Being in general nonlinearly related with the response their selection by the usual F tests is unavailable. In this paper we propose a solution to this predictor selection problem, by defining generalized test statistics and adapting a non-parametric bootstrap method to estimate their p-values. We include a numerical example with automobile insurance data.
1 Morphotropic Phase Boundary in Ferroelectric Materials

Certain solid solutions of perovskite-type ferroelectrics show excellent properties such as giant dielectric response and high electromechanical coupling constant in the vicinity of the morphotropic phase boundary (MPB). These materials are of importance to applications such as electrostrictive actuators and sensors, because of the large dielectric and piezoelectric constants (Jaffe et al., 1971; Sawaguchi, 1953; Kuwata et al., 1982; Newnham, 1997). The term “morphotropic” was originally used to refer to refer to phase transitions due to changes in composition (Ahart et al., 2008). Nowadays, the term ‘morphotropic phase boundaries’ (MPB) is used to refer to the phase transition between the tetragonal and the rhombohedral ferroelectric phases as a result of varying the composition or as a result of mechanical pressure (Jaffe et al., 1954; Yamashita, 1994; Yamamoto & Ohashi, 1994; Cao & Cross, 1993; Amin et al., 1986; Ahart et al., 2008). In the vicinity of the MPB, the crystal structure changes abruptly and the dielectric properties in ferroelectric (FE) materials and the electromechanical properties in piezoelectric materials become maximum. The common ferroelectric materials used for MPB applications is usually complexstructured solid solutions such as lead zirconate titanate PbZr1−xTixO3 (PZT) and Lead Magnesium niobate-lead titanate (1-x)PbMg1/3Nb2/3O3-xPbTiO3), shortly known as PMNPT. For example, PZT is a perovskite ferroelectrics which has a MPB between the tetragonal and rhombohedral FE phases in the temperature-composition phase diagram. However, these materials are complex-structured and require a complicated and costly process to prepare its solid solutions. Furthermore, the study of the microscopic origin of its properties is very complicated. Recently, scientists started to pay attention to the MPB in simple-structured pure compound ferroelectric materials such as ferroelectric oxides. For example, a recent experimental study on lead titanate proved that PbTiO3 can display a large MPB under pressure (Ahart et al., 2008). These experimental results even showed richer phase diagrams than those predicted by first-principle calculations. Therefore, it is of particular importance to study the
Audio Quality Improvement of Vehicular Hands-Free Communication Using Variable Step-Size Affine-Projection Algorithm

For a vehicular hands-free communication system, the sound quality of communication is usually degraded by noise which is known to be detrimental to system performance. In this paper, a novel adaptive filtering algorithm and an integrated system for acoustic echo and noise cancellation are presented. The proposed system includes adaptive noise cancellation, line enhancer, and echo cancellation which are based on a variable step-size affine-projection algorithm (VSS APA). The proposed VSS APA filtering algorithm is a combination of a variable step-size least-mean-square (VSS LMS) and an affine-projection algorithm (APA). The matrix of the APA allows more accurate, thorough input data and transforms the data into the structure of orthogonality, thus making the estimate of the weight vector faster and more accurate. To understand and verify the effectiveness of the proposed system, performance evaluation and comparison were conducted to compare the proposed algorithm and various traditional adaptive filtering algorithms in this application. The results demonstrated that the VSS APA has an effective performance and convergence in sound quality improvement of hands-free communication systems.
Formalization of UML Statechart Models Using Concurrent Regular Expressions

The Unified Modeling Language (UML) is widely used in the software development process for specification of system based on the object-oriented paradigm. Thought the current version of UML is semi-formal, it is difficult to determine whether the model is consistent, unambiguous, or complete. This paper proposes the transformation rules for formalizing UML statechart diagrams. The target language for the transformation is Concurrent Regular Expressions (CREs) which are extensions of regular expression. The transformation result will be represented in mathematical form and suitable for applying verification. We also show that this formalization can be used to check the simple inconsistency of the system.
Intracellular cleavage and ligation of hepatitis delta virus genomic RNA: regulation of ribozyme activity by cis-acting sequences and host factors

During replication, a ribozyme within the genomic RNA of hepatitis delta virus cleaves multimeric precursors to release a unit-length linear intermediate. Intramolecular ligation of this intermediate produces the circular genomic RNA. Although one copy of the ribozyme is reconstituted by such ligation, it does not subsequently cleave and destroy the circular conformation. We have identified cis-acting attenuator sequences that prevent self-cleavage of the circular product by base pairing with and inactivating the ribozyme. Furthermore, we have shown that during the initial processing of the multimeric precursor RNA, host-specific factors activate the ribozyme by preventing its association with the attenuator sequences. Thus, we demonstrate a novel switching mechanism that regulates ribozyme activity inside the cell.
Gastric Varices Secondary to Splenic Vein Occlusion due to Pancreatic Diseases

Gastric varices that arise secondary to splenic vein occlusion can result in hypersplenism or gastrointestinal hemorrhaging. This article review gastric varices secondary to splenic vein occlusion due to pancreatic diseases with regard to causes of the condition, as well as diagnostic and therapeutic approaches. Diagnosis of gastric varices is made following esophago-gastro-duodenoscopy, and splenic vein occlusions are diagnosed from enhanced computed tomographic scans in almost all cases. Specific findings of gastric varices secondary to splenic vein occlusion are based on endoscopic ultrasonographic color flow images of gastric variceal flow that clearly depicted round cardiac and fundal regions at the center, with varices expanding to the curvatura ventriculi major of the gastric body. Several treatment options for gastric variceal bleeding secondary to splenic vein occlusion have been proposed. Splenectomy, which decompresses the short gastric vein by cutting off inflow, has generally been considered the best treatment of choice in such condition. Endoscopic injection sclerotherapy using cyanoacrylate, is useful in the treatment of bleeding gastric varices due to splenic vein occlusion. As patients with splenic vein occlusion have normal portal pressure and normal hepatic function, portal systemic shunting is not indicated. Splenic arterial embolization, which reduces blood flow through the splenic parenchyma, is another effective method of controlling bleeding from gastric varices secondary to splenic vein occlusion. Treatment of gastric varices secondary to splenic vein occlusion is directed to the underlying pancreatic diseases.
Reflecting on the Purpose of the PhD Oral Examination

Details of a survey which examines the views of doctoral candidates at the University of Auckland, New Zealand, on the purpose of the oral examination or viva voce for the Ph.D. and the feedback in the examination process are presented. The continuing questions on whether the Ph.D. oral examination in New Zealand universities are aimed at the clarification and authentication of the thesis or at producing a researcher with appropriate training are discussed.
On Household Wealth Trends in Sweden Over the 1990s

Influenced by a major tax reform in the beginning of the 1990s and by the exceptional boom in the stock market at the end of this decade the level as well as the inequality of the wealth of Swedish households have increased. The large baby-boom cohorts of the 1940s have been successful in accumulating wealth and they also have large claims on the public pension system. The implicit wealth in the form of these claims dominates private wealth in most Swedish households, and in this paper it is argued that private life-cycle savings have been small in Sweden. Most of these savings have been done though the public pension systems. However, concern about the future viability of the pension systems has probably increased private life-cycle savings in the 1990s.
Affective computing using clustering method for mapping human's emotion

In this study, we proposed a method which could be used for mapping people's emotion state on the two-dimensional arousal-valence model of effect. The final target of our research is to apply this kind of emotional recognition system to robots or some assistant apparatus which service activities of daily living (ADL). Since in our previous studies, we have finished the work of recognizing people's emotion state on the dimension of arousal by evaluating subjects' heartbeat and LF/HF, which is calculated from the frequency domain analysis of HRV, as the second step's work, we focused on how to recognize people's emotion state on valence dimension. To be specific, we used some kinds of normative affective stimuluses to elicit subjects' emotional change, then collected multiple physiological data during this emotional stimulation process. Finally, as for data analyzing, we didn't use the supervised learning method, like SVM, but made a new attempt to apply the unsupervised clustering method to sample data, dividing the data set into several natural clusters by analyzing the physiological features we abstracted. The calculated results of our experiment have verified the feasibility of mapping human's emotion state on the two-dimensional arousal-valence model of effect at a quadrant level.
A Dominating Sets and Target Radius Based Localized Activity Scheduling and Minimum Energy Broadcast Protocol for Ad Hoc and Sensor Networks.

Several localized broadcasting protocols for ad hoc and sensor networks were proposed recently, with the goal of minimizing the energy consumption, while still guaranteeing a total coverage of the network. Also, several activity scheduling protocols were proposed, which select nodes in a connected dominating set to be active, with the rest of nodes left in sleep mode for energy savings. This article is the first to consider both problems as a single combined one, in which a localized protocol is proposed as a solution. First, each node considers only neighbors whose distance is no greater than the target radius (which depends on the power consumption model used), and neighbors in a localized connected topological structure such as RNG or LMST. Then, a connected dominating set is constructed using this subgraph. Next, nodes not selected for the set are sent to sleep mode (they periodically wake up for sending and receiving messages from associated closest dominating set nodes). Nodes in selected dominating set remain active and apply neighbor elimination based broadcasting (reduced to a subset of dominant neighbors with the help of the RNG or LMST), with transmission range adjusted to their furthest neighbor (in the considered subgraph) not covered by other transmissions. The algorithm has been implemented and compared with a centralized (BIP) and target radius based minimum energy broadcasting (TR-LBOP) protocol (which do not place any node to sleep mode). It is shown that our algorithm requires similar amount of energy for broadcasting as TR-LBOP, but in addition also has energy savings coming from sleep mode status of significant number of nodes. Moreover, our protocol offers the advantage of a smaller latency, since fewer nodes participate in the broadcast.
A systematic survey of CMM experience and results

The capability maturity model (CMM) for software has become very influential as a basis for software process improvement (SPI). Most of the evidence to date showing the results of these efforts has consisted of case studies. We present a systematic survey of organizations that have undertaken CMM-based SPI to get more representative results. We found evidence that process maturity is in fact associated with better organizational performance, and that software process appraisals are viewed, in retrospect, as extremely valuable and accurate guides for the improvement effort. The path was not always smooth, however, and efforts generally took longer and cost more than expected. A number of factors that distinguished highly successful from unsuccessful efforts are identified. Most of these factors are under management control, suggesting that a number of specific management decisions are likely to have a major impact on the success of the effort.
On the design of MLC-LDPC-OFDM in DRM MF and HF channels

Orthogonal Frequency Division Multiplexing (OFDM), aided by proper channel coding schemes, can realize very dependable transmission in fading channels. For the purpose of improving the performance of the OFDM based DRM digital AM broadcasting in MF and HF channels, this paper designs MLC-LDPC-OFDM transmission scheme that is suitable for MF and HF channels. The equivalent channel capacities of MLC-LDPC-OFDM with two different decoding strategies, namely IMSD and PDL, are analyzed, basing on which this paper redesigns the code rates of MLC. In addition, the calculation of likelihood ratio in LDPC decoding is modified according to channel models. The simulation results show that the proposed schemes have better performance than the existing ones in MF and HF channels.
An adaptive coevolutionary Differential Evolution algorithm for large-scale optimization

In this paper, we propose a new algorithm, named JACC-G, for large scale optimization problems. The motivation is to improve our previous work on grouping and adaptive weighting based cooperative coevolution algorithm, DECC-G [1], which uses random grouping strategy to divide the objective vector into subcomponents, and solve each of them in a cyclical fashion. The adaptive weighting mechanism is used to adjust all the subcomponents together at the end of each cycle. In the new JACC-G algorithm: (1) A most recent and efficient Differential Evolution (DE) variant, JADE [2], is employed as the subcomponent optimizer to seek for a better performance; (2) The adaptive weighting is time-consuming and expected to work only in the first few cycles, so a detection module is added to prevent applying it arbitrarily; (3) JADE is also used to optimize the weight vector in adaptive weighting process instead of using a basic DE in previous DECC-G. The efficacy of the proposed JACC-G algorithm is evaluated on two sets of widely used benchmark functions up to 1000 dimensions.
Beyond Inference in Perception

The controversy over inference in perception turns on the nature of the processes that intervene between the stimulus and the perceptual experience or percept. Should the processes be viewed as something like inference and computation, or should they be viewed as psychologically primitive mechanisms whose workings are best accounted for at a neurological or physiological level? It is argued that the view that computational and inference-like processes play a role in perceptual processes should be adopted.
Specific Class II Histocompatibility Gene Polymorphism in BB Rats

The BB rat spontaneously develops insulin-dependent diabetes mellitus of autoimmune etiology. From breeding studies, one of the genes necessary for the development of diabetes in these animals is linked to RT1, the rat major histocompatibility complex. To better define the BB rat's RT1-linked diabetogenic gene (RT1-DM), we have used restriction endonucleases BamH1 and EcoR1 in conjunction with an I-A alpha (class II mouse major histocompatibility complex) gene probe to study RT1 class II gene polymorphisms among diabetes-prone BB rats and the related non-diabetes-prone BBN rats. Both BB and BBN rats are indistinguishable RT1U by serologie methods. Four polymorphic chromosome types (la, lb, Ha, and lib) were recognized among the control BBN rats. In contrast, all BB rats were homozygous (IIa/IIa). From the multiple breeding programs involved, we hypothesize that the BB rat's RT1-linked diabetogenic gene is linked to an I-A alpha-defined gene of the type Ha chromosome. The ability to split the RT1U of BB rats will provide a powerful tool to localize and characterize RT1-DM.
Adopting Systems Development Methods: An Exploratory Study

Abstract:A general opinion is that systems personnel are unlikely adopters of new systems development methods. Thirty-five systems persons from eleven organizations who attended a seminar/workshop on a requirements defining method were surveyed three months after the seminar to determine whether they used the method and factors influencing usage. Factors about the potential adoptee, the current tasks assigned, and the organization and its existing methods were considered as predictors of usage. The study found adopters to be younger, to have spent less time in their organization and in systems work, not to have a current method that they would have to give up, to perceive themselves to be risk takers, and to be more optimistic about their ability to use the method and have it fit in their organization.