Miracle-dz/UniFAR-FTUs huggingface dataset:
Novel ENU-Induced Mutation in Tbx6 Causes Dominant Spondylocostal Dysostosis-Like Vertebral Malformations in the Rat

Congenital vertebral malformations caused by embryonic segmentation defects are relatively common in humans and domestic animals. Although reverse genetics approaches in mice have provided information on the molecular mechanisms of embryonic somite segmentation, hypothesis-driven approaches cannot adequately reflect human dysmorphology within the population. In a N-ethyl-N-nitrosourea (ENU) mutagenesis project in Kyoto, the Oune mutant rat strain was isolated due to a short and kinked caudal vertebra phenotype. Skeletal staining of heterozygous rats showed partial loss of the cervical vertebrae as well as hemivertebrae and fused vertebral blocks in lumbar and sacral vertebrae. In homozygous embryos, severe displacement of the whole vertebrae was observed. The Oune locus was genetically mapped to rat chromosome 1 using 202 backcross animals and 50 genome-wide microsatellite markers. Subsequently, a miss-sense mutation in the Tbx6 gene was identified in the critical region. Although the mutation is located within the T-box domain near a predicted dimmer-interface, in vitro experiments revealed that the Tbx6 variant retains normal DNA binding ability and translational efficiency. However, the variant has decreased transcriptional activation potential in response to Notch-mediated signaling. Recently, it was reported that a dominant type of familial spondylocostal dysostosis is caused by a stoploss mutation in TBX6. Thus, we propose that partial dysfunction of Tbx6 leads to similar congenital vertebral malformations in both humans and rats. The Oune strain could be a unique animal model for dominant spondylocostal dysostosis and is useful for molecular dissection of the pathology of congenital vertebral malformations in humans.
ASPECTS REGARDING SYNTHESIS AND APPLICATIONS OF ZnO NANOMATERIALS

Zinc oxide (ZnO) is a promising material which gained increasing interest in recent years owing to its preparation methods and remarkable performances. The paper presents the most common techniques for the synthesis of ZnO nanoparticles, such as mechanochemical process, precipitation, sol-gel method, solvothermal and hydrothermal processes. Due to their optical, mechanical, chemical and electrical properties, ZnO offers the possibility to be used in different technological domains, as well as the future outlooks for application of these materials.
Design considerations and performance evaluation of hybrid DC circuit breakers for HVDC grids

This paper presents a performance evaluation in terms of applicability, response times, energy dissipation, passive components and power semiconductors requirements of the four most promising hybrid DC circuit breaker concepts for HVDC grids. Specific design guidelines for all of the hybrid DC circuit breakers are also shown. The evaluation of the hybrid DC circuit breakers has been performed using PLECS.
A regression model for estimating DNA copy number applied to capture sequencing data

MOTIVATION Target enrichment, also referred to as DNA capture, provides an effective way to focus sequencing efforts on a genomic region of interest. Capture data are typically used to detect single-nucleotide variants. It can also be used to detect copy number alterations, which is particularly useful in the context of cancer, where such changes occur frequently. In copy number analysis, it is a common practice to determine log-ratios between test and control samples, but this approach results in a loss of information as it disregards the total coverage or intensity at a locus. RESULTS We modeled the coverage or intensity of the test sample as a linear function of the control sample. This regression approach is able to deal with regions that are completely deleted, which are problematic for methods that use log-ratios. To demonstrate the utility of our approach, we used capture data to determine copy number for a set of 600 genes in a panel of nine breast cancer cell lines. We found high concordance between our results and those generated using a single-nucleotide polymorphsim genotyping platform. When we compared our results with other log-ratio-based methods, including ExomeCNV, we found that our approach produced better overall correlation with SNP data. AVAILABILITY The algorithm is implemented in C and R and the code can be downloaded from http://bioinformatics.nki.nl/ocs/ CONTACT l.wessels@nki.nl SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
Identification and Characterization of a Hemolysin Gene Cluster in Vibrio anguillarum

ABSTRACT Vibrio anguillarum is a causative agent of vibriosis in fish. Hemolytic activity has been suggested as a virulence factor by contributing to hemorrhagic septicemia and diarrhea. In order to identify and characterize the hemolysin genes and examine the role of hemolytic activity in virulence, a mini-Tn10Kan mutagenesis clone bank of V. anguillarum was screened. While no hemolysin-negative strains were observed, several mutants with two- to threefold-increased hemolytic activity were found. The region containing the insertion mutation was cloned, sequenced, and found to contain the V. anguillarum hemolysin (vah1) and two other open reading frames, coding for a putative lactonizing lipase (llpA) and a putative phospholipase (plp). The mini-Tn10Kan was inserted into plp. Site-directed mutagenesis of each gene revealed that mutations in vah1 and llpA did not affect hemolytic activity, but insertions into plp caused a two- to threefold increase in hemolysis. Double mutations in plp and either vah1 or llpA resulted in wild-type hemolytic activity. Complementation of plp restored hemolytic activity to wild-type levels. Spectrophotometric determination of hemolysin specific activity revealed that activity on a per cell basis peaked during the first 2 h of growth in LB20. Real-time quantitative reverse transcriptase PCR used to quantitate transcription of the hemolysin genes plp and vah1 in V. anguillarum wild-type strains M93Sm and NB10 revealed that transcription of plp and vah1 peaked at 2 h of growth in LB20. Additionally, expression of vah1 measured in the plp mutant strain, JL01, during the first 2 h of growth was >8 times higher than that in M93Sm. Mutations in plp and llpA did not affect virulence of V. anguillarum. The mutation in vah1 attenuated V. anguillarum virulence in fish. These data show that several genes are responsible for hemolytic activity in V. anguillarum. At least three genes (plp, llpA, and vah1) are responsible for one hemolytic activity. The data also suggest that plp acts as a negative regulator of vah1 and llpA.
How to Optimally allocate your budget of attention in social networks

We consider the performance of information propagation through social networks in a scenario where each user has a budget of attention, that is, a constraint on the frequency with which he pulls content from neighbors. In this context we ask the question “when users make selfish decisions on how to allocate their limited access frequency among neighbors, does information propagate efficiently? ” For the metric of average propagation delay, we provide characterizations of the optimal social cost and the social cost under selfish user optimizations for various topologies of interest. Three situations may arise: well-connected topologies where delay is small even under selfish optimization; tree-like topologies where selfish optimization performs poorly while optimal social cost is low; and “stretched” topologies where even optimal social cost is high. We propose a mechanism for incentivizing users to modify their selfish behaviour, and observe its efficiency in the family of tree-like topologies mentioned above.
Study on Bio-inspired TNP Implementation Structure of BMNSM

Based on BMNSM (bio-inspired multidimensional network security model), this paper briefly states "three-net paralleling (TNP)" mode and proves its state attribute. Because the implementation structure of TNP decides the exertion of each performance of BMNSM, this paper analyses three types of implementation structures - elementary structure (implementation structure of traditional network security), evolutive structure and advanced structure and concludes that the advanced structure owns excellent performances comparing to other implantation structures by quantificational compare
Pattern Ambiguities for Pure Context{free Grammars Pattern Ambiguities for Pure Context{free Grammars Pattern Ambiguities for Pure Context{free Grammars

We consider here some special forms of ambiguity for pure context-free grammars, namely pattern avoiding ambiguity, pattern preserving ambiguity, pattern ambiguity, and grammar avoiding ambiguity. The rst two properties are undecidable for arbitrary pure context-free grammars, and in a particular but general enough case we can eeectively decide whether or not a pure context-free grammar is pattern preserving ambiguous.
Time transformations, intraday data and volatility models

In this paper, we focus on the trade and quote data for the IBM stock traded at the NYSE.We present two different frameworks for analyzing this dataset. First, using regularly sampled observations, we characterize the intraday volatility of the mid-point of the bid-ask quotes by estimating GARCH and EGARCH models, with intraday seasonalitybeing accounted for. We also highlight the impact of characteristics of the trade process (traded volume, number of trades and average volume per trade) on the volatility specifications. Secondly, we deal directly with the irregularly spaced data. We review two time transformations that allowa thinning of the original dataset such that new durations are defined. The newly defined price and volume durations are characterized and the performance of the Log-ACD model for modelling these durations is assessed. Moreover, price durations allowan easy computation of intraday volatility and this method compares favorablyto ARCH estimations.
Theoretical Study of Structure and Energetics of Gold Clusters with the EAM Method

Abstract Using the embedded-atom method as developed by Voter and Chen in combination with the variable metric/quasi-Newton and our own Aufbau/Abbau methods, we have identified the three most stable isomers of AuN clusters with N up to 150. For the first time clusters with tetrahedral symmetry are found to form the ground states of Au17 and Au34. The Au54icosahedron without a central atom and the Au146decahedron are found to be particularly stable, whereas the highly symmetric second and third Mackay icosahedra that could have been obtained for N = 55 and 147, respectively, do not correspond to the particularly stable structures. The three lowest-lying isomers of Au55 and Au147 are low-symmetrical structures. Various structural and energetic properties are analysed, such as stability function, occurrence of magic-sized clusters, construction of icosahedral and fcc shells, and cluster growth.
Self-Efficacy and IPS: An Empirical Study.

The fact that some learners learn language more successfully than others who are at the same level of aptitude and capabilities is inevitable. To understand why, the researcher has focused her attention on individual differences among learners. The ones that have been taken into account in this study are namely called selfefficacy and identity processing styles and the relationship between them in EFL learners. In addition, the difference between the identity processing styles among male and female participants is investigated. A group of 20 MA students from the Ontario College of Teachers, Canada participated in the study. Quantitative data were collected through two questionnaires namely the Revised Identity Style Inventory (ISI-4) which was developed by Berzonsky et al. (2011) and a general self-efficacy scale. Getting benefit of SPSS, the researcher first coded and then analyzed the data were coded. In order to determine the relationship between Canadian EFL learners’ identity style and self-efficacy, the Spearman’s rank order correlation formula was used. Secondly, to show the existence of a significant difference between the identity processing styles of male and female participants of the study, the Mann-Whitney U test was run. Statistical analyses indicated that there was a meaningful relationship between self-efficacy and identity processing styles among Canadian EFL learners and no difference was seen between the identity processing styles of both groups of male and female participants of the study.
Requirements engineering in a model-based methodology for embedded automotive software

This paper resumes the requirements engineering in a model-based methodology for embedded automotive software. The methodology relies on two standard languages: EAST-ADL for automotive architecture description and SysML for systems modeling. The requirements engineering in the methodology describes phases of elicitation, modeling, traceability, verification and validation. It is illustrated by applying on a case study - the knock controller - a part of the engine management system.
Students with autism transitioning from primary to secondary schools: parents’ perspectives and experiences

ABSTRACT The transition from primary to high school can be a challenging process for students with autism spectrum disorder (ASD). During this time, research-based practices like home–school collaboration are crucial in facilitating a smoother transition. However, existing research indicates that the transition from primary to high school is a period of anxiety and reduced support for students with ASD and their families. This article describes the experiences of parents of students with ASD in regard to this transition and home–school collaboration. Semi-structured interviews were carried out with 15 parents of children with ASD who attended mainstream government high schools in metropolitan Sydney. Through content analysis, parents were found to have received varying levels of transition support. Their experiences of home–school collaboration were, however, generally positive. Overall, it is recommended that parents’ knowledge of their children with ASD should be prioritised and utilised in transition planning. Findings also suggest that a greater implementation of practices including mandated transition planning and home–school collaboration in schools would contribute to more authentic inclusion of students with ASD.
5 Summary and Discussion

Jet streaks and their associated divergence and vertical motion patterns feature prominently in synoptic literature and, as discussed in the Introduction, numerous conceptual models have been formulated that relate such patterns to jet streaks. Moreover, the divergence and vertical motion elds historically have been considered to be of fundamental importance to the existence and behaviour of jet streaks. by observations shown in Fig. 5, suggests that the rotational component of the ageostrophic wind associated with jet streaks is considerably larger than the divergent component, implying that nondivergent barotropic dynamics may play a signiicant role in jet-streak behaviour. This apparent paradox raises issues that do not appear to have been addressed previously in relation to the fundamental dynamics of jet streaks, such as which processes dominate in governing the structure, motion and evolution of these features. The aim of this thesis, then, is to ooer a preliminary investigation into the dynamics of tropopause-based jet streaks using idealised barotropic models (nondivergent barotropic and shallow-water) on f-and-planes. Motivated by the apparently prevalent association of jet streaks in the atmosphere with mesoscale coherent vortices that often occur as a dipole pair (e.g., Fig. 4), we have examined the possibility that the theory of vortex dipoles may give insight into the structure, motion and evolution of jet streaks. Of particular interest throughout the course of this investigation has been the extent to which nondivergent barotropic dynamics provide a satisfactory explanation of jet-streak behaviour, or if divergent ageostrophic circulations indeed are necessary at leading order; this question has been examined through the use of comparison simulations with the respective models. It is shown in Chapter 2 that numerical solutions in both models of arbitrary dipolar elliptical vortices (DEVs) in isolation exhibit structure similar to the observed jet streak shown in Figs. 4 and 5. In particular, associated with the DEV is a localised maximum in uid speed and an ageostrophic ow that is directed
Path-Source Oriented Session Identification Based on Linked Referrers and Log Indexing

Summary Web usage mining has been widely adopted in various fields such as optimizing site structure, user-behavior analysis, personalized web services and system performance tuning. Although much research has been done against web log mining algorithms and log preprocessing techniques, the study of efficient retrieval of the structured contents for web log mining is seldom reported. In this paper, we first show that people are much more interested in discovering user navigation based on various path-sources. Then, we present a novel session identification algorithm Referrer Link based on discovering linked referrers to serve source-oriented path mining. Next, an efficient web log indexing and path extracting technique is introduced to provide structured web log data for general purpose log mining. The experimental results has shown that the accuracy of the mining results conducted against the sessions discovered by the proposed Referrer Link algorithm is 10% higher in average compared with Time-out approach.
Funcionamiento ejecutivo y rendimiento matemático: un estudio longitudinal.

This longitudinal study aimed to analyze the predictive power of the executive functions of inhibition and working memory (WM) assessed at Kindergarten (T1) on the formal and informal aspects of the mathematical performance in 2nd grade of Primary School (T2). The initial sample consisted of 209 preschool children of 5-6 years old. The 86.12% of this sample was re-evaluated in the T2 (7-8 years). In the T1 six neuropsychological tasks related to the executive functions of inhibition and verbal and visuospatial WM were administered. In T2, the test TEMA-3 (Ginsburg & Baroody, 2003) was used to assess different aspects of math performance. The results showed that 5 of the 6 tasks applied in kindergarten are able to predict later math achievement, with a special weight of the verbal WM function. The implications of these findings for research and practice are discussed.
Claudin Proteins in Ovarian Cancer

Members of the claudin family of tight junction proteins have been found altered in several malignancies, including ovarian cancer. Because claudin-3 and -4 are elevated in the vast majority of ovarian tumors, they may represent useful biomarkers for detection and prognosis, as well as ideal targets for therapy using the Clostridium perfringens enterotoxin.
-The spouses' perspective

4 LIST OF ORIGINAL PAPERS 5 LIST OF ABBREVIATIONS AND DEFINITIONS 6 INTRODUCTION 7 BACKGROUND 8 Incidence 8 Riks-Stroke 8 The stroke patient 9 Informal caregivers 10 Transition from hospital to home 10 Preparation and information 10 Discharge 12 Resources in the community 12 Consequences of caregiving 13 Family in a social context 14 Models of family caregiving 14 Gender aspects of informal caregiving 14 Changing roles 15 Quality of Life 15 Life situation 15 Coping as informal caregivers 16 Existing instruments for assessing the caregivers’ situation 17 Supportive nursing interventions 18 Identifying caregivers in need of support 19 AIMS 20 METHODS AND MATERIALS 21 Design 21 Sample and data collection 21 Instruments and questionnaires 21 Quality of Life and Economic Situation 22 Life Situation Among Spouses After the Stroke Event 22 Well-being questionnaire short form 22 Health state from the Euro-QoL 5D 23 Sense of Coherence 23 The Interview Schedule for Social Interaction 23 The Comprehensive Psychopathological Rating Scale Self Affective 23 Barthel Index 24 Nursing support and education programme for spouses of stroke patients 24 ANALYSES 25 Analyses Paper I 26 Analyses Paper II 26 Analyses Paper III 27 Analyses Paper IV 27
Effective Verification of Weak Diagnosability

Abstract The diagnosability problem can be stated as follows: does a given labeled Discrete Event System allow for an outside observer to determine the occurrence of the “invisible” fault, no later than a bounded number of events after that unobservable occurrence, and based on the partial observation of the behaviour? When this problem is investigated in the context of concurrent systems, partial order semantics induces a separation between classical or strong diagnosability on the one hand, and weak diagnosability on the other hand. The present paper presents the first solution for checking weak diagnosability, via a verifier construction.
The importance of adopting a package-aware chip design flow

In this paper, we discuss about the short- and long-term implications of ignoring the relationship between the chip, package and PCB during I/O planning and how these issues manifest themselves as we move toward 65 and 45nm technology. It also introduces a whole new approach to chip/package I/O planning and optimization. This new approach simultaneously synthesizes the entire interconnect from the I/O driver to the package ball and establishes an interconnect plan that is optimized for both chip and package
Fusion fingerprint minutiae matching system for personal identification

Fingerprint is most popular biometric because it can easily used and its features are highly reliable. Many fingerprint matching algorithm have been reported in literatures and in all most algorithms minutiae matching is used. In this paper modified fusion algorithm is proposed. It uses one technique of structure with Delaunay triangle's based, formed by minutiae, and for matched candidate triangle local ridge texture information is extracted using Local Binary Pattern (LBP). Here triangle matching score is given a full weightage and minutiae matching score is given weightage as per requirement. The experimental results show that proposed algorithm is effective and reliable. Algorithm is tested on a DB1 Database of FVC 2004 competition.
Value Distributions of Exponential Sums From Perfect Nonlinear Functions and Their Applications

In this paper we present a unified way to determine the values and their multiplicities of the exponential sums Sigma<sub>xisinF(q)</sub>zeta<sub>p</sub> <sup>Tr(af(x)+bx)</sup>(a,bisinF<sub>q</sub>,q=p<sup>m</sup>,pges3) for all perfect nonlinear functions f which is a Dembowski-Ostrom polynomial or p = 3,f=<sup>x(3(k)+1)/2</sup> where k is odd and (k,m)=1. As applications, we determine (1) the correlation distribution of the m-sequence {a<sub>lambda</sub>=Tr(gamma<sup>lambda</sup>)}(lambda=0,1,.) and the sequence {b<sub>lambda</sub>=Tr(f(gamma<sup>lambda</sup>))}(lambda=0,1,.) over F<sub>p</sub> where gamma is a primitive element of F<sub>q</sub> and (2) the weight distributions of the linear codes over F<sub>p</sub> defined by f.