Miracle-dz/UniFAR-FTUs huggingface dataset:
Large and small splice variants of collagen XII: differential expression and ligand binding

Collagen XII has a short collagenous tail and a very large, three-armed NC3 domains consisting primarily of fibronectin type III repeats. Differential splicing within this domain gives rise to a large (320 kD) and a small (220 kD) subunit; the large but not the small can carry glycosaminoglycan. To investigate whether collagen XII variants have distinct expression patterns and functions, we generated antibody and cDNA probes specific for the alternatively spliced domain. We report here that the large variant has a more restricted expression in embryonic tissue than the small. For example, whereas the small variant is widespread in the dermis, the large is limited to the base of feather buds. Distinct proportions of mRNA for the two variants were detected depending on the tissue. Monoclonal antibodies allowed us to separate collagen XII variants, and to show that homo- and heterotrimers exist. Collagen XII variants differ in ligand binding. Small subunits interact weakly with heparin via their COOH-terminal domain. Large subunits have additional, stronger heparin-binding site(s) in their NH2-terminal extra domain. In vivo, both large and small collagen XII are associated with interstitial collagen. Here we show biochemically and ultrastructurally that collagen XII can be incorporated into collagen I fibrils when it is present during, but not after, fibril formation. Removal of the collagenous domain of collagen XII reduces its coprecipitation with collagen I. Our results indicate that collagen XII is specifically associated with fibrillar collagen, and that the large variant has binding sites for extracellular ligands not present in the small variant.
Post-Glacial Spatial Dynamics in a Rainforest Biodiversity Hot Spot

Here we investigate the interaction between ecology and climate concerning the distribution of rainforest species differentially distributed along altitudinal gradients of eastern Australia. The potential distributions of the two species closely associated with different rainforest types were modelled to infer the potential contribution of post-glacial warming on spatial distribution and altitudinal range shift. Nothofagus moorei is an integral element of cool temperate rainforest, including cloud forests at high elevation. This distinct climatic envelope is at increased risk with future global warming. Elaeocarpus grandis on the other hand is a lowland species and typical element of subtropical rainforest occupying a climatic envelope that may shift upwards into areas currently occupied by N. moorei. Climate envelope models were used to infer range shift differences between the two species in the past (21 thousand years ago), current and future (2050) scenarios, and to provide a framework to explain observed genetic diversity/structure of both species. The models suggest continuing contraction of the highland cool temperate climatic envelope and expansion of the lowland warm subtropical envelope, with both showing a core average increase in elevation in response to post-glacial warming. Spatial and altitudinal overlap between the species climatic envelopes was at a maximum during the last glacial maximum and is predicted to be a minimum at 2050.
"Lifelike" behavior of communication robots based on developmental psychology findings

Researchers in developmental psychology have reported various findings about animate-inanimate distinctions, especially the decision criteria of human infants categorizing animate existence, such as distinguishing animals and humans from the inanimate. The purpose of our research is to develop animate or "lifelike" behavior for humanoid robots based on such categorizing, which would be expected to potentially make human-robot interaction more natural. Our approach is unique because we focus on the robot's mechanism and behavior design using environmental sensors. Consequently, we use a motion capturing system, which enables us to leapfrog technological developments for the robots' sensing abilities. The robot that we have developed reacts to human behavior, and it is implemented in order to satisfy the features of animate existence according to developmental psychology. Two experiments were conducted to verify its effects. The results of the first experiment verified the effectiveness of lifelike behavior and also showed that random behavior, which partly satisfies the features of animate existence, received a halfway evaluation for lifelikeness. The second experiment demonstrated the effectiveness of the developed robot for investigating the effect of a robot's cognitive ability for human-robot interaction
RAPA: reliability-aware priority arbitration strategy for network on chip

Reliability issue, especially from transient errors due to scaling IC technology, low voltage supply, high frequency and heavy thermal effects, particles emission etc, has become a challenge for NoC design. Focus on this problem, an effective Reliability-Aware Arbitration Strategy simplified as RAPA, is proposed in this paper to decide which flits should be prioritized in the network transmission for higher application-level reliability. Different from pervious performance-oriented arbitration strategies, it includes the application-level reliability requirement to determine the reliability priority ranking. Flits patching mechanism is also used for avoiding starvation. The evaluation metric is redefined to emphasizing application-level reliability. Finally, we verify the reliability based prioritization policy on cycle accurate platform. And the simulation results show that the averaged successful delivery rate is upgraded from three nine of round robin (RR), old age based arbitration(OA) to five nine of our method RAPA. Especially, 67.15%, 41.83% reliability improvement in rest unreliable space on average are obtained over typical RR policy and OA based arbitration policy respectively with guaranteed performance.
Optimal Monetary Policy under Heterogeneous Banks

We introduce the heterogeneous stickinesses in loan interest rate adjustments, which are supported by empirical analyses in developed countries, into the standard New Keynesian model with bank sector. The welfare analysis reveals that the central bank should care about the interest rate di¤erence, i.e. credit spread, between heterogeneous loan interest rates and the rst di¤erences of each loan interest rate. We show that the central bank should negatively respond to the credit spread shock between heterogeneous loan interest rates, i.e. idiosyncratic shock in the nancial market. There the heterogeneity in staggeredness of loan interest rates rather than the credit spread is quantitatively so important to implement the optimal monetary policy when stickinesses of loan interest rates are high. Finally, we show that the central bank puts its priority to the loan interest rate with more stickiness rather than a weighted average of heterogeneous loan interest rate to achieve the optimal monetary policy when the market share of loans is not so di¤erent. But, as the share of the sticky loan decreases, the central bank should pay attention to both sticky and less sticky loans. We thank Toni Braun, Simon Gilchrist, Francois Gourio, Humio Hayashi, Eric Leeper, Masao Ogaki, Wako Watanabe, and Mike Woodford for insightful comments, suggestions and encouragements. We also thank the seminer participants at Tokyo University for their comments. The views expressed in this paper are those of the authors and do not necessarily reect the o¢ cial views of the Bank of Japan. yE-mail: nao.sudou@boj.or. jp zE-mail: yuuki.teranishi@boj.or. jp
The New Modelica MultiBody Library

A new Modelica library for the modeling and simulation of 3-dimensional mechanical systems has been developed. It will be freely available in the Modelica standard library. Furthermore, the Dymola simulation environment has been considerably enhanced to support the needed features. The MultiBody library is first presented from a user’s point of view. Furthermore, all essential details of the implementation are described. The library includes features that are usually not available in other multi-body software, such as analytic handling of a large class of kinematical loops, or the arbitrary connection feature of objects. For example, series connection of 3D line force components is possible.
Towards Aspectual i*

The i* framework is a very popular approach in the Requirements Engineering community. However, crosscutting concerns are not handled explicitly in i*, compromising the modularity and consequently the complexity and evolution of such models. To deal with the complexity of i* models, the use of structuring mechanisms has been investigated. Moreover, the i* framework has been extended to incorporate the principles of aspect orientation, aiming at handling explicitly crosscutting concerns in i* models. Some metrics have been created to evaluate the understandability of requirements modeled using both the i* framework and the aspectual i*.
Social, Economic and Health Impacts of WaveLength's Work with Loneliness and Isolation

This report presents the findings of qualitative research into the social, economic and health impacts of WaveLength’s work on loneliness and social isolation. WaveLength is a charitable organisation which provides access to media technology for people who are lonely or socially isolated and living in poverty. This research was an exploratory qualitative study using semi-structured interviews. The overarching aim of the research was to understand the ways and means through which media technology (radio, TV and tablets) contributes to reducing loneliness and social isolation among vulnerable groups. The research sought to understand what difference the technologies provided by WaveLength make in different domains of people’s lives, including emotional, social, economic and health.
Moving In, Staying In, Falling Out: Employment Transitions of Disabled People

Responsibility for any remaining errors is, of course, mine alone, and the views expressed in this paper are not necessarily those of the Joseph Rowntree Foundation. ABSTRACT The low rate of employment among disabled people in Britain has often been observed, but is not well understood. This paper examines the dynamics of disabled people's employment, with a view to reaching a better understanding of the processes which underlie the cross-sectional picture. The analysis uses data from the first seven waves of the British Household Panel Survey and focuses on three transitions: movements into work, employment retention for new entrants, and loss of employment after becoming disabled in work. Comparisons are made with the non-disabled population, with and without controls for age, educational qualifications and occupational background. Where possible, types and severities of impairment are differentiated. The results show disabled people out of work are one-sixth as likely as non-disabled people to move into work during the course of a year. Those that do so are more likely to enter manual occupations and work in smaller workplaces. One-third of new entrants are out of work again by the following year, compared to one-fifth of non-disabled entrants. Among individuals who become disabled while in work, 1 in 5 leave employment within the following year. Controls for personal characteristics reduce but do not eliminate the differentials. The paper concludes that there are three distinct sources of labour-market disadvantage for disabled people: firstly, there are impairment-specific barriers; secondly, disabled people are more likely to have characteristics associated with general labour market disadvantage, such as low qualifications; and thirdly, in some cases the difference between advantage and disadvantage-for example between manual and non-manual occupations-is sharper for disabled than non-disabled people. Each of these sources of disadvantage will need to be tackled if labour market opportunities are to be equalised.
Dual-colour imaging of RNAs using quencher- and fluorophore-binding aptamers

In order to gain deeper insight into the functions and dynamics of RNA in cells, the development of methods for imaging multiple RNAs simultaneously is of paramount importance. Here, we describe a modular approach to image RNA in living cells using an RNA aptamer that binds to dinitroaniline, an efficient general contact quencher. Dinitroaniline quenches the fluorescence of different fluorophores when directly conjugated to them via ethylene glycol linkers by forming a non-fluorescent intramolecular complex. Since the binding of the RNA aptamer to the quencher destroys the fluorophore-quencher complex, fluorescence increases dramatically upon binding. Using this principle, a series of fluorophores were turned into fluorescent turn-on probes by conjugating them to dinitroaniline. These probes ranged from fluorescein-dinitroaniline (green) to TexasRed-dinitroaniline (red) spanning across the visible spectrum. The dinitroaniline-binding aptamer (DNB) was generated by in vitro selection, and was found to bind all probes, leading to fluorescence increase in vitro and in living cells. When expressed in E. coli, the DNB aptamer could be labelled and visualized with different-coloured fluorophores and therefore it can be used as a genetically encoded tag to image target RNAs. Furthermore, combining contact-quenched fluorogenic probes with orthogonal DNB (the quencher-binding RNA aptamer) and SRB-2 aptamers (a fluorophore-binding RNA aptamer) allowed dual-colour imaging of two different fluorescence-enhancing RNA tags in living cells, opening new avenues for studying RNA co-localization and trafficking.
A study on an approach for analysing test basis using I/O test data patterns

For software testing, it is important to derive test cases without lacking or duplication before test execution. Test basis to be analysed in test development process for black box testing is a functional specification. And it is less analysed under consistency rules. As a result, this has the potential to cause the lacking or duplication of test cases. This paper proposes an approach for analysing test basis focusing on data I/O in test execution to achieve analysing test basis can be more comprehensive. Moreover, in order to demonstrate this approach, an experiment is performed comparing with test cases in a real project.
Near-isometric linear embeddings of manifolds

We propose a new method for linear dimensionality reduction of manifold-modeled data. Given a training set X of Q points belonging to a manifold M ⊂ ℝ<sup>N</sup>, we construct a linear operator P : ℝ<sup>N</sup> → ℝ<sup>M</sup> that approximately preserves the norms of all (<sub>2</sub><sup>Q</sup>) pairwise difference vectors (or secants) of X. We design the matrix P via a trace-norm minimization that can be efficiently solved as a semi-definite program (SDP). When X comprises a sufficiently dense sampling of M, we prove that the optimal matrix P preserves all pairs of secants over M. We numerically demonstrate the considerable gains using our SDP-based approach over existing linear dimensionality reduction methods, such as principal components analysis (PCA) and random projections.
Default probabilities of European sovereign debt: market-based estimates

For a number of EMU member Governments, prices of their (mainly) DM-denominated debt are compared with otherwise identical debt issued by the German Government, so as to extract implied risk-neutral default probabilities. In most cases, the probabilities are small, though in the case of Italy they average over 4% even under the most conservative assumptions.
High and low dose radiation effects on mammary adenocarcinoma cells – an epigenetic connection

The successful treatment of cancer, including breast cancer, depends largely on radiation therapy and proper diagnostics. The effect of ionizing radiation on cells and tissues depends on the radiation dose and energy level, but there is insufficient evidence concerning how tumor cells respond to the low and high doses of radiation that are often used in medical diagnostic and treatment modalities. The purpose of this study was to investigate radiation-induced gene expression changes in the MCF-7 breast adenocarcinoma cell line. Using microarray technology tools, we were able to screen the differential gene expressions profiles between various radiation doses applied to MCF-7 cells. Here, we report the substantial alteration in the expression level of genes after high-dose treatment. In contrast, no dramatic gene expression alterations were noticed after the application of low and medium doses of radiation. In response to a high radiation dose, MCF-7 cells exhibited down-regulation of biological pathways such as cell cycle, DNA replication, and DNA repair and activation of the p53 pathway. Similar dose-dependent responses were seen on the epigenetic level, which was tested by a microRNA expression analysis. MicroRNA analysis showed dose-dependent radiation-induced microRNA expression alterations that were associated with cell cycle arrest and cell death. An increased rate of apoptosis was determined by an Annexin V assay. The results of this study showed that high doses of radiation affect gene expression genetically and epigenetically, leading to alterations in cell cycle, DNA replication, and apoptosis.
Alterations in cerebral blood flow and cerebrovascular reactivity during 14 days at 5050 m

Brain blood flow increases during the first week of living at high altitude. We do not understand completely what causes the increase or how the factors that regulate brain blood flow are affected by the high‐altitude environment. Our results show that the balance of oxygen (O2) and carbon dioxide (CO2) pressures in arterial blood explains 40% of the change in brain blood flow upon arrival at high altitude (5050 m). We also show that blood vessels in the brain respond to increases and decreases in CO2 differently at high altitude compared to sea level, and that this can affect breathing responses as well. These results help us to better understand the regulation of brain blood flow at high altitude and are also relevant to diseases that are accompanied by reductions in the pressure of oxygen in the blood.
“There is Space, and There are Limits”: The Challenge of Teaching Controversial Topics in an Illiberal Democracy

Background/Context Research indicates that across democratic societies, teachers face numerous intellectual and emotional challenges when handling controversial topics in the classroom. Less attention, however, has been paid to how teachers’ willingness to teach controversial topics intersects with political and other societal factors in different sociopolitical milieu and, in particular, in an authoritarian–democratic and culturally diverse state like Singapore. Focus of Study This study focused on constraints to the teaching of controversial topics relating to diversity and the manner in which teachers navigated their personal beliefs amidst the evolving contours of public and official discourses in Singapore. By attending to the intersections of teachers’ beliefs, state policies, and other sociopolitical factors, we aimed to inform scholarship on the teaching of controversial topics and illuminate states’ powers to demarcate the discursive spaces of teachers. Research Design The study adhered to the qualitative case study design. We collected data from interviews that featured various elicitation tasks to describe 35 social studies teachers’ perceptions and practice of controversial issues discussions relating to topics of diversity. Additionally, we drew on policy and curricular documents to portray the evolving contours of public discourse in Singapore. Findings/Results The findings highlight how the participants, influenced largely by state policies, differentiated between topics that were controversial-appropriate and controversial-taboo. In spite of the numerous legal constraints limiting the nature of public discussion of race and politics, the majority of the teachers regarded these topics as controversial-appropriate. There was, conversely, a consensus among the participants that topics related to sexual orientation were controversial-taboo even though there were no similar laws constraining public discussion of this issue. Conclusions/Recommendations This study challenges conventional assumptions about the impact of state-imposed constraints and controls on the teaching of controversial topics in schools. Under some circumstances, state controls and constraints can result in teachers having more freedom to discuss controversial topics because of the clearly demarcated political and social boundaries. However, if the state's position is ambiguous, this may result in a Kafkaesque situation in which teachers become even more conservative in their curriculum decision making due to a heightened sense of uncertainty and insecurity. Ultimately, the study brings to light the nuanced ways that state control and censorship influence the spaces and limits of issues-centered discussion, and underlines the need for research that attends to various social forces that frame the teaching of controversial topics in different democratic settings.
Minimal molecular surfaces and their applications

This article presents a novel concept, the minimal molecular surface (MMS), for the theoretical modeling of biomolecules. The MMS can be viewed as a result of the surface free energy minimization when an apolar molecule, such as protein, DNA or RNA is immersed in a polar solvent. Based on the theory of differential geometry, the MMS is created via the mean curvature minimization of molecular hypersurface functions. A detailed numerical algorithm is presented for the practical generation of MMSs. Extensive numerical experiments, including those with internal and open cavities, are carried out to demonstrated the proposed concept and algorithms. The proposed MMS is typically free of geometric singularities. Application of the MMS to the electrostatic analysis is considered for a set of twenty six proteins. © 2007 Wiley Periodicals, Inc. J Comput Chem, 2008
The radii of M-dwarfs in the young open cluster NGC 2516

Using a novel technique, which combines previously determined rotation periods with new spectroscopic determinations of projected rotation velocity, we have determined radii for fast-rotating, low-mass (0.2–0.7 M⊙) M-dwarfs in the young, solar-metallicity open cluster, NGC 2516. The mean radii are larger than model predictions at a given absolute I or K magnitude and also larger than the measured radii of magnetically inactive M-dwarfs; the difference increases from a few per cent to 50 per cent for the lowest luminosity stars in our sample. We show that a simple two-temperature starspot model is broadly capable of explaining these observations, but requires spot coverage fractions of about 50 per cent in rapidly rotating M-dwarfs.
Lip reading using fuzzy logic network with memory

This paper proposes a new approach for lip reading. Most existing systems for lip reading utilize a kind of neural network or hidden Markov models as classifiers. We propose a new approach where fuzzy combinational networks with fuzzy flip-flop memories are combined into one network. Our model introduces a hierarchical structure of this network, where single layers are contextually dependent. Experiments with fuzzy flip-flop network propose a new approach in the process of automatic lip-reading system where time dependence in inputs series is modeled with memories. Such approach provides possibilities for continuous speech recognition.