Miracle-dz/UniFAR-FTUs huggingface dataset:
MtbHLH1, a bHLH transcription factor involved in Medicago truncatula nodule vascular patterning and nodule to plant metabolic exchanges

This study aimed at defining the role of a basic helix–loop–helix (bHLH) transcription factor gene from Medicago truncatula, MtbHLH1, whose expression is upregulated during the development of root nodules produced upon infection by rhizobia bacteria. We used MtbHLH1 promoter::GUS fusions and quantitative reverse-transcription polymerase chain reaction analyses to finely characterize the MtbHLH1 expression pattern. We altered MtbHLH1 function by expressing a dominantly repressed construct (CRES-T approach) and looked for possible MtbHLH1 target genes by transcriptomics. We found that MtbHLH1 is expressed in nodule primordia cells derived from pericycle divisions, in nodule vascular bundles (VBs) and in uninfected cells of the nitrogen (N) fixation zone. MtbHLH1 is also expressed in root tips, lateral root primordia cells and root VBs, and induced upon auxin treatment. Altering MtbHLH1 function led to an unusual phenotype, with a modified patterning of nodule VB development and a reduced growth of aerial parts of the plant, even though the nodules were able to fix atmospheric N. Several putative MtbHLH1 regulated genes were identified, including an asparagine synthase and a LOB (lateral organ boundary) transcription factor. Our results suggest that the MtbHLH1 gene is involved in the control of nodule vasculature patterning and nutrient exchanges between nodules and roots.
Applications and Graphics for Propensity Score Analysis* Applications and Graphics for Propensity Score Analysis Applications and Graphics for Propensity Score Analysis

Methods for propensity score analysis (PSA) originated with Rosenbaum and Rubin (1983), as vehicles to sharpen and clarify treatment group comparisons in observational studies. Although highly recommended by many statisticians, and applied often in medical sciences, PSA has seen relatively few applications in the social and behavioral sciences. This paper aims to facilitate sound PSA applications in psychological and other social sciences, and to emphasize the role visualization can play in such contexts. Numerous references to the expanding PSA literature are also provided.
On Non-Standard Models of Peano Arithmetic and Tennenbaum's Theorem

Throughout the course of mathematical history, generalizations of previously understood concepts and structures have led to the fruitful development of the hierarchy of number systems, non-euclidean geometry, and many other epochal phases in mathematical progress. In the study of formalized theories of arithmetic, it is only natural to consider the extension from the standard model of Peano arithmetic, $\langle \mathbb{N},+,\times,\leq,0,1 \rangle$, to non-standard models of arithmetic. The existence of non-standard models of Peano arithmetic provided motivation in the early $20^{th}$ century for a variety of questions in model theory regarding the classification of models up to isomorphism and the properties that non-standard models of Peano arithmetic have. This paper presents these questions and the necessary results to prove Tennenbaum's Theorem, which draws an explicit line between the properties of standard and non-standard models; namely, that no countable non-standard model of Peano arithmetic is recursive. These model-theoretic results have contributed to the foundational framework within which research programs developed by Skolem, Rosser, Tarski, Mostowski and others have flourished. While such foundational topics were crucial to active fields of research during the middle of the $20^{th}$ century, numerous open questions about models of arithmetic, and model theory in general, still remain pertinent to the realm of $21^{st}$ century mathematical discourse.
Formal specification of usability measures in model-driven development of context-sensitive user interfaces

Developing usability studies to evaluate user interfaces (UIs) is a task requiring a wide variety of skills. In this paper we propose conceptual architecture for design and integration of usability tests in model-driven development of context-sensitive user interfaces. Upon the extended model for development of context-sensitive user interfaces, we introduce a generic framework that developers can use to design usability tests. This is enabled by using common vocabulary for description of usability test models and human models. Basic principles of the proposed approach are given in brief. As an example, we give formal model of human working memory that can be used in design of various cognitive load metrics.
AIAA 2001-2645 Numerical Simulations of the Lagrangian Averaged Navier-Stokes ( LANS-oc ) Equations for Forced Homogeneous Isotropic Turbulence

The modeling capabilities of the Lagrangian Averaged Navier-Stokes-a equations (LANS-a) is investigated in statistically stationary three-dimensional homogeneous and isotropic turbulence. The predictive abilities of the LANS-a equations are analyzed by comparison with DNS data. Two different forcing techniques were implemented to model the energetics of the energy containing scales. The resolved flow is examined by comparison of the energy spectra of the LANS-a and the DNS computations; furthermore, the correlation between the vorticity and the eigenvectors of the rate of the resolved strain tensor is studied. We find that the LANS-a equations captures the gross features of the flow while the wave activity below a given scale a is filtered by the nonlinear dispersion.
A survey on security patterns

Security has become an important topic for many software systems. Security patterns are reusable solutions to security problems. Although many security patterns and techniques for using them have been proposed, it is still difficult to adapt security patterns to each phase of software development. This paper provides a survey of approaches to security patterns. As a result of classifying these approaches, a direction for the integration and future research topics is illustrated.
Covariant BRST Quantization of Closed String in PP-Wave Background

We canonically quantize closed string theory in the pp-wave background with a non-zero flux of the three-form field strength by using the covariant BRST operator formalism. In this canonical quantization, we completely construct new covariant free-mode representations, where it is particularly important to note the commutation relations of the zero mode of the spacetime light-cone string coordinate X− with other modes. All covariant string coordinates are composed of the free modes. Moreover, by applying these covariant string coordinates to the energy momentum tensor, we calculate the anomaly in the Virasoro algebra and determine the dimension of spacetime and the ordering constant from the nilpotency condition of the BRST charge in the pp-wave background. ∗) e-mail: yoichizaki@stu.rikkyo. ne.jp ∗∗) e-mail: yahiko@rikkyo.ac. jp 1 §
Performance modeling of overlapping IBSSs in the IEEE 802.11 DCF mode

In this paper, we extend a saturation throughput model for the IEEE 802.11 DCF MAC protocol to the case of multiple overlapping IBSSs (independent basic service sets) sharing the same frequency of operation. This analytical model is a necessary step to the performance modeling of multi-hop ad hoc networks on top of 802.11 platforms
Utility-Consistent Discrete-Continuous Choices in Soil Conservation

A utility-consistent model of participation and participation intensity choices for a voluntary soil conservation program is developed. A modified form of Roy's Identity is used to derive a two-equation system that links the discrete, dichotomous choice (participation) and the continuous choice (intensity) to the same utility function. The model corrects for selectivity bias that arises in single-equation approaches. An application to a filter strip program in two counties in Illinois and Michigan demonstrates that different factors affect responses to the program across the sample regions. Estimated willingness-to-accept payments for participation in the program suggest policy impacts are not uniform across locations.
A new species of taipan (Elapidae: Oxyuranus) from central Australia

Snakes in the Australo-Papuan elapid genus Oxyuranus are considered to be the most venomous species in the world. A recent expedition to the central ranges of Western Australia discovered a third species, which is described here from the only known specimen. Molecular genetic analyses using mitochondrial nucleotide sequences places the new species as the sister lineage of the two described Oxyuranus species, with all three species united by a long branch that also separates them from the nearest of the brown snakes species (Pseudonaja) to which the taipans are close relatives. Morphologically, the new species shares with the other Oxyuranus an undivided anal scale, high midbody scale row (21) and ventral scale (250) counts, but differs in having a single primary temporal scale and fewer lower labials (six). Maximum body size and venom potency are unknown. The discovery of a third species of taipan in the remote central ranges of Australia underlines the paucity of collecting from this region.
A Multilevel Gamma-Clustering Layout Algorithm for Visualization of Biological Networks

Visualization of large complex networks has become an indispensable part of systems biology, where organisms need to be considered as one complex system. The visualization of the corresponding network is challenging due to the size and density of edges. In many cases, the use of standard visualization algorithms can lead to high running times and poorly readable visualizations due to many edge crossings. We suggest an approach that analyzes the structure of the graph first and then generates a new graph which contains specific semantic symbols for regular substructures like dense clusters. We propose a multilevel gamma-clustering layout visualization algorithm (MLGA) which proceeds in three subsequent steps: (i) a multilevel γ-clustering is used to identify the structure of the underlying network, (ii) the network is transformed to a tree, and (iii) finally, the resulting tree which shows the network structure is drawn using a variation of a force-directed algorithm. The algorithm has a potential to visualize very large networks because it uses modern clustering heuristics which are optimized for large graphs. Moreover, most of the edges are removed from the visual representation which allows keeping the overview over complex graphs with dense subgraphs.
Identifying Water Security Issues at the Local Level

Abstract Water security has been traditionally thought to be an issue for developing countries. In the United States, the Clean Water Act has made water quality and watershed management increasingly relevant to community decision makers. However, the extent to which local stakeholders perceive and understand water scarcity and quality constraints in the United States remains uncertain. The reported research uses a series of focus groups to evaluate their efficacy and for learning from local beneficiaries about local water security concerns for mid-Michigan's Red Cedar River. In Michigan, it appears that the water security issue is water quality. The findings show that focus groups are effective data collection tools and that Michigan stakeholders recognize water security problems, causes, and potential solutions.
Retention and Accelerated Vesting Preliminary ! Pls Do Not Circulate !

The introduction of SFAS 123R provides a useful experimental setting to study whether firms grant stock options broadly as a way of retaining employees (Oyer, 2004). We show that under the hypothesis that firms grant options to retain employees, the cost/benefit calculation regarding accelerated vesting is a function of the employee’s (random, as of the option grant date) interim outside option, and the firm’s (random, as of the option grant date) stock return. Under the retention hypothesis, we therefore should have predictable variation in firms’ accelerated vesting choices, as function of these random variable. Experimental settings such as this are rare in the large empirical literature on employee stock options. Our empirical analysis offers little support for the retention hypothesis. We do not find that accelerated vesting choices are related to industry stock returns or local employment in the manner predicted by the theory. ∗Hayes: David Eccles School of Business, University of Utah. rachel.hayes@utah.edu. Schaefer: David Eccles School of Business and Institute for Public and International Affairs, University of Utah. scott.schaefer@utah.edu. We thank Jack Ciesielski at R.G. Associates, Inc. for providing data on accelerated vestings and workshop participants at Emory University, University of Oregon, and Duke University for helpful comments. We thank Dongyoung Lee and Mingming Qiu for research assistance, and our colleague Brian Cadman for some data and programs.
Modeling the circulation of the intermediate layer in the Sea of Okhotsk

Recently, the Sea of Okhotsk has been recognized as a primary iron source region to the northwestern Pacific (Nishioka et al., 2007). Cold and dense water, which is referred to as Dense Shelf Water (DSW), is formed as a result of brine rejection from sea ice on the northwestern shelf in the Sea of Okhotsk. Iron, together with other chemical particles, is considered to be incorporated into DSW through, for example, tidal mixing (Nakatsuka et al., 2004). DSW, including iron, is transported southward by the East Sakhalin Current in the intermediate layer off Sakhalin, and flows out into the Pacific through the Kuril straits. Thus iron is supplied to the northwestern Pacific.
Overview of the NTCIR-9 INTENT Task

This is an overview of the NTCIR-9 INTENT task, which comprises the Subtopic Mining and the Document Ranking subtasks. The INTENT task attracted participating teams from seven different countries/regions – 16 teams for Subtopic Mining and 8 teams for Document Ranking. The Subtopic Mining subtask received 42 Chinese runs and 14 Japanese runs; the Document Ranking subtask received 24 Chinese runs and 18 Japanese runs. We describe the subtasks, data and evaluation methods, and then report on the results.
Personality and Social Psycholog Y Bulletin Halliday, Graham / " If I Get Locked Up, I Get Locked up " " If I Get Locked Up, I Get Locked up " : Secondary Control and Adjustment among Juvenile Offenders

This study examined relations between two types of control (primary and secondary) and the psychological and community adjustment of adolescent offenders. Prior to release from confinement , 279 male adolescent offenders were interviewed about their control beliefs and a number of adjustment variables, including emotional/behavior problems, feelings of despair, expectations to avoid recontact with the law, and recognition of costs for reoffending. In addition, probation officers were interviewed regarding the participants' adjustment to the community 8 weeks following their release and official records were searched for a 6-month period to determine the nature and timing of any reincarcerations. Secondary control was significantly associated with maladjustment for all psychological and behavioral outcomes. When predicting reincarceration, this relationship was qualified by a significant interaction with primary control, such that those who recidivated the soonest had high levels of both primary and secondary control. These data suggest that secondary control beliefs may be maladaptive among adolescent offenders, particularly when perceived primary control is high. People who feel that they have control over stressful events experience better adjustment. This relationship has been demonstrated in numerous contexts, including coping with chronic illness (e.g. establishing new friendships in unfamiliar settings (e.g., Lopez & Little, 1996). Indeed, a common theme underlying most theories of control is that when people believe that they have control over outcomes, they initiate activity , exert effort, and persist in the face of failure or other setbacks. In contrast, individuals who appraise their outcomes as largely uncontrollable tend to withdraw or otherwise become passive, depressed, and pessimistic. Because stressful events differ in the degree to which they are modifiable by instrumental activity, refinements to theories of control have attempted to explain how individuals successfully adapt in circumstances where their opportunities to influence outcomes are limited. Relevant to this analysis is a distinction between primary and secondary control introduced by Rothbaum, Weisz, and Snyder (1982). Primary control refers to attempts to change one's outcomes (e.g., " I can control how much danger I will face in my neighborhood "). It focuses on attempts to alter the environment to fit with the self. The control literature has traditionally emphasized this form of efficacious behavior. Secondary control is the sense of control derived from accepting or adjusting to existing realities (e.g., " Living with danger is just the way it is in my neighborhood "). It is concerned with attempts to change the self or …
A NEW VIEW OF THE SUPER STAR CLUSTERS IN THE LOW-METALLICITY GALAXY SBS 0335-052

We present a study of the individual super star clusters (SSCs) in the low-metallicity galaxy SBS 0335-052 using new near-infrared (near-IR) and archival optical Hubble Space Telescope observations. The physical properties of the SSCs are derived from fitting model spectral energy distributions (SEDs) to the optical photometry, as well as from the Hα and Paα nebular emission lines. Among the clusters, we find a significant age spread that is correlated with position in the galaxy, suggesting that successive cluster formation occurred in SBS 0335-052 triggered by a large-scale disturbance traveling through the galaxy at a speed of ∼35 km s−1. The SSCs exhibit I-band (∼0.8 μm) and near-IR (∼1.6–2.1 μm) excesses with respect to model SEDs that are fit to the optical data. We hypothesize that the I-band excess is dominated by a photoluminescent process known as Extended Red Emission; however, this mechanism cannot account for the excesses observed at longer near-IR wavelengths. From the cluster SEDs and colors, we find that the primary origin of the near-IR excess observed in the youngest SSCs (≲3 Myr) is hot dust emission, while evolved red supergiants dominate the near-IR light in the older (≳7 Myr) clusters. We also find evidence for a porous and clumpy interstellar medium surrounding the youngest, embedded SSCs: the ionized gas emission underpredicts the expected ionizing luminosities from the optical stellar continuum, suggesting that ionizing photons leak out of the immediate vicinity of the clusters before ionizing hydrogen. The corrected, intrinsic ionizing luminosities of the two SSCs younger than ∼3 Myr are each ∼5 × 1052s−1, which is equivalent to each cluster hosting ∼5000 O7.5 V stars. The inferred masses of these SSCs are ∼106 M☉.
Independent Distractor Frequency and Age-of-Acquisition Effects in Picture–Word Interference: fMRI Evidence for Post-lexical and Lexical Accounts according to Distractor Type

In two fMRI experiments, participants named pictures with superimposed distractors that were high or low in frequency or varied in terms of age of acquisition. Pictures superimposed with low-frequency words were named more slowly than those superimposed with high-frequency words, and late-acquired words interfered with picture naming to a greater extent than early-acquired words. The distractor frequency effect (Experiment 1) was associated with increased activity in left premotor and posterior superior temporal cortices, consistent with the operation of an articulatory response buffer and verbal self-monitoring system. Conversely, the distractor age-of-acquisition effect (Experiment 2) was associated with increased activity in the left middle and posterior middle temporal cortex, consistent with the operation of lexical level processes such as lemma and phonological word form retrieval. The spatially dissociated patterns of activity across the two experiments indicate that distractor effects in picture–word interference may occur at lexical or postlexical levels of processing in speech production.
Institutional Assets and Competitive Advantages of French over U.S. Cinema, 1895-1914

This paper examines the influence of the complex interactions of the institutional environment, governance structures, and strategic assets on the creation and maintenance of the competitive advantages of leading firms. It introduces an original theoretical model combining the two complementary approaches of the new institutional economics (institutional environment and institutions of governance) with the resource-based view (strategic asset endowment of firms). This model is then used to investigate why French cinema gained and reinforced an initial competitive advantage over its U.S. counterpart from 1895 to 1914. Our findings show that a more favorable institutional environment explains the initial French advantage from 1895 to 1907. A culture of mutual forbearance between members of the elite combined with low levels of patent protection influenced the leading French cinema companies to concentrate on the creation of strategic assets such as supplies and studio facilities. Inside an environment of fierce competition and strong patent protection, U.S. cinema companies developed legal assets for patent wars on equipment. More economizing governance choices and contractual innovations by French firms at home and abroad reinforced the French advantage between 1908 and 1914. U.S. firms developed institutional assets to negotiate and enforce private cartels to the detriment of distribution assets. Later, U.S. antitrust law and conflicts of interests between cartel members influenced the emergence of independent U.S. firms with a strategic focus on cinema production and distribution assets. Ultimately, U.S. formal institutions reduced the transaction costs of local printed-film producers and provided more socially efficient forms of regulation than private cartel arrangements.
A pilot study of comparison gesture analysis in motion driven video games

This study investigates whether there are significant differences in the gestures made by gamers and non-gamers whilst playing commercial games that employ gesture inputs. Specifically, the study focuses on testing a prototype of multimodal capture tool that we used to obtain real-time audio, video and skeletal gesture data. Additionally, we developed an experimental design framework for the acquisition of spatio-temporal gesture data and analysed the vector magnitude of a gesture to compare the relative displacement of each participant whilst playing a game.
Devising the Future of the Models@run.time Workshop

The 9th edition of the workshop Models@run.time was held at the 17th International Conference on Model Driven Engineering Languages and Systems (MODELS). The workshop took place in the city of Valencia, Spain, on the 30th of September 2014. The workshop was organised by Sebastian Götz, Nelly Bencomo and Robert France. Despite the high number of concurrent workshops, it was attended by 27 people as it is still one of the most popular workshops in MODELS. The major focus of this year's edition of the workshop was to identify future directions for the workshop, which currently faces a matured community. Hence, in this report we first present a synopsis of the workshop sessions, which included a separate session on introducing the current body of knowledge of models@run.time. Moreover, we show and discuss a survey on new topics of interest we conducted with the workshop participants and program committee. In addition, to further explore the evolution and effects of the workshop and research area models@run.time, we have conducted an interview of three young researchers who work in the area of models@run.time. They tell us about how models@run.time has influenced their own research and how they envision the evolution of the topic.