Miracle-dz/UniFAR-FTUs huggingface dataset:
Gene Trap Lines Define Domains of Gene Regulation in Arabidopsis Petals and Stamensw⃞

To identify genes involved in Arabidopsis thaliana petal and stamen organogenesis, we used a gene trap approach to examine the patterns of reporter expression at each stage of flower development of 1765 gene trap lines. In 80 lines, the reporter gene showed petal- and/or stamen-specific expression or lack of expression, or expression in distinct patterns within the petals and/or the stamens, including distinct suborgan domains of expression, such as tissue-specific lines marking epidermis and vasculature, as well as lines demarcating the proximodistal or abaxial/adaxial axes of the organs. Interestingly, reporter gene expression was typically restricted along the proximodistal axis of petals and stamens, indicating the importance of this developmental axis in patterning of gene expression domains in these organs. We identified novel domains of gene expression along the axis marking the midregion of the petals and apical and basal parts of the anthers. Most of the genes tagged in these 80 lines were identified, and their possible functions in petal and/or stamen differentiation are discussed. We also scored the floral phenotypes of the 1765 gene trap lines and recovered two mutants affecting previously uncharacterized genes. In addition to revealing common domains of gene expression, the gene trap lines reported here provide both useful markers and valuable starting points for reverse genetic analyses of the differentiation pathways in petal and stamen development.
Live ultrasound volume reconstruction using scout scanning

Ultrasound-guided interventions often necessitate scanning of deep-seated anatomical structures that may be hard to visualize. Visualization can be improved using reconstructed 3D ultrasound volumes. High-resolution 3D reconstruction of a large area during clinical interventions is challenging if the region of interest is unknown. We propose a two-stage scanning method allowing the user to perform quick low-resolution scouting followed by high-resolution live volume reconstruction. Scout scanning is accomplished by stacking 2D tracked ultrasound images into a low-resolution volume. Then, within a region of interest defined in the scout scan, live volume reconstruction can be performed by continuous scanning until sufficient image density is achieved. We implemented the workflow as a module of the open-source 3D Slicer application, within the SlicerIGT extension and building on the PLUS toolkit. Scout scanning is performed in a few seconds using 3 mm spacing to allow region of interest definition. Live reconstruction parameters are set to provide good image quality (0.5 mm spacing, hole filling enabled) and feedback is given during live scanning by regularly updated display of the reconstructed volume. Use of scout scanning may allow the physician to identify anatomical structures. Subsequent live volume reconstruction in a region of interest may assist in procedures such as targeting needle interventions or estimating brain shift during surgery.
Sequence analysis Evolutionary simulations to detect functional lineage-speciﬁc genes

Motivation: Supporting the functionality of recent duplicate gene copies is usually difficult, owing to high sequence similarity between duplicate counterparts and shallow phylogenies, which hamper both the statistical and experimental inference. Results: Wedevelopedanintegratedevolutionaryapproachtoidentify functional duplicate gene copies and other lineage-specific genes. By repeatedly simulating neutral evolution, our method estimates the probabilitythatanORFwasselectivelyconservedandisthereforelikely to represent a bona fide coding region. In parallel, our method tests whether the accumulation of non-synonymous substitutions reveals signatures of selective constraint. We show that our approach has high power to identify functional lineage-specific genes using simulated and real data. For example, a coding region of average length ( (cid:1) 1400 bp), restricted to hominoids, can be predicted to be functional in (cid:1) 94–100% of cases. Notably, the method may support functionality for instances where classical selection tests based on the ratio of non-synonymous to synonymous substitutions fail to reveal signatures of selection. Our method is available as an automated tool, ReEVOLVER, which will also be useful to systematically detect functional lineage-specific genes of closely related species on a large scale. Availability: ReEVOLVER is available at http://www.unil. ch/cig/
On religion and public policy: Does Catholicism make a difference?

Abstract. This paper suggests that differences in religious adherence and/or in degrees of secularization between advanced nations may be as relevant to understanding cross-national variance in a wide range of public policy outcomes as the impact of socio-economic and political factors. The prima facie evidence for such a thesis is demonstrated in areas as diverse as welfare expenditure, family policy and labour market policy outcomes, and is shown to have a particular salience wherever gender-related outcomes are at issue. On the basis of this evidence, it is suggested that, in policy outcome terms at least, it is possible to identify a distinctive Catholic family of nations consisting of a grouping of core Western European and Southern European countries.
Workplace smoking ban policy and smoking behavior.

OBJECTIVES To evaluate the impact of the workplace smoking ban in South Korea, where the male smoking rate is high (57%), on smoking behavior and secondhand smoke exposure. METHODS A workplace smoking ban legislation implemented in April 2003 requires offices, meeting rooms, and lobbies located in larger than 3,000 square meter buildings (or 2,000 square meter multipurpose buildings) should be smoke free. A representative cross-sectional survey, the third wave (2005) of health supplements in the National Health Nutrition Survey of South Korea, was used to measure the impact of the 2003 workplace smoking ban implementation on smoking behavior. It contained 3,122 observations of adults 20 to 65 years old (excluding self-employed and non-working populations). A multivariate statistical model was used. The self-reported workplace smoking ban policy (full workplace ban, partial workplace ban, and no workplace ban) was used as the key measure. RESULTS A full workplace smoking ban reduced the current smoking rate by 6.4 percentage points among all workers and also decreased the average daily consumption among smokers by 3.7 cigarettes relative to no smoking ban. Secondhand smoke showed a dramatic decrease of 86 percent (= -1.74/2.03)from the sample mean for full workplace ban. However, public anti-smoking campaign did not show any significant impact on smoking behavior. CONCLUSIONS The full workplace ban policy is effective in South Korea. Male group showed bigger impact of smoking ban policy than female group. The public antismoking campaign did not show any effectiveness.
A Novel Objects of Interest Extraction Approach Using Attention-Driven Model for Content-Based Image Retrieval

Visual attention plays a vital role for humans to understand a scene by intuitively emphasizing some focused objects, and recent work in the computational model of visual attention has demonstrated that a purely bottom-up approach to identify salient regions within an image can be successfully applied to diverse and practical problems. Being aware of this, we propose a new approach of extracting objects of interest (OOIs) using attention-driven model. In this approach, images are coarsely segmented into regions using EM (Expectation-Maximization) algorithm, and then we use the modified Itti-Koch model (M-Itti-Koch) of visual attention to find salient peaks, if these peaks overlap with regions generated by EM algorithm, we proceed to extract attentive object around those points. Experiment results demonstrate that the proposed approach gives good performance, as compared with the current peer method in the literature.
Calmodulin UAS‐constructs and the in vivo roles of calmodulin: Analysis of a muscle‐specific phenotype

The vast range of intracellular processes that are regulated by Ca 2 (cid:1) ﬂuxes has only recently begun to be appreciated. The Ca 2 (cid:1) -binding protein calmodulin (CaM) is recognized as a central player in Ca 2 (cid:1) signaling, although its precise roles, particularly in developmental processes, are largely undeﬁned. CaM is a dumbbell-shaped molecule, with terminal globular domains each containing a pair of “EF-hand” type Ca 2 (cid:1) binding sites (Nelson and Chazin, 1998). The conformational changes associated with Ca 2 (cid:1) binding allow CaM to interact with different targets in its Ca 2 (cid:1) -free (apo-) and Ca 2 (cid:1) -bound (holo-) forms and thus to execute its role as a Ca 2 (cid:1) sensor (Zhang et al. , 1995). Although the N-and C-terminal domains of CaM are very similar, the C-terminal binding sites (3 and
Reasons for sequence preferences

Much research shows that when it comes to preferences over sequences of money, such as a monthly paycheck, people do not always maximize present value. Rather, they often choose the lower-valued of a pair of sequences, especially when it has attractive properties such as an increasing trend. To unearth the reasons for sequence preferences we conducted a verbal-protocol analysis of choices between money sequences, including lifetime and one-year earnings and one-year lottery winnings, as well as lifetime health sequences. Participants thought aloud while choosing between visual representations of sequences. Their verbalizations contained reference to a wide range of previously hypothesized, as well as new, reasons for choice. These reasons were also correlated in sensible ways with the choices made. There was some evidence of solid economic reasoning (which we called maximization), although this was largely restricted to choices for one-year earnings. More commonly, respondents did not distinguish between earnings and consumption, and thought about money as if they would automatically spend it at the rate it was received. This meant the most frequently given reason was what we called appropriateness—how well the money received at a given point matched the desired consumption at that point. Other common explanations include the expectedness of a sequence (we argue this is mediated by appropriateness), the way that parts of the sequence constitute reference points for other parts, and the ease with which incoming money can be managed (convenience). Copyright © 2002 John Wiley & Sons, Ltd.
A Gap Year for Institutional Theory: Integrating the Study of Institutional Work and Participatory Action Research

Institutional theory has energized a large and vibrant academic community, but it is largely unknown to managers and inconsequential with respect to the management of organizations. This is despite what the authors believe is an immense potential practical contribution. In this article, the authors suggest that institutional theory needs a gap year—a period in which core frameworks and insights from an institutional perspective are brought into contact with complex social problems. The authors focus on the study of institutional work and argue that an extended encounter with the world of participatory action research could lead to new answers to key questions and energize the development of institutional theory as both an academic and a practical project.
Estimation of motion and position of a rigid object using a sequence of images (tridimensional Kalman filter approach)

The purpose of this paper is to show the application of Kalman Filter theory to the problem of extracting the motion parameters from a sequence of images of a rigid body which is moving in a tridimensional space. The objective is to apply the Kalman Filter equations to the system of a moving object using the state variable approach. The system is described by a set of equations that specify the position and orientation of the body in space and how these coordinates are changing in time. The images provide the necessary data to drive the algorithm of the Kalman Filter. Some feature points are extracted from the images, and their positions in the image coordinate system are used to update the
THE DEVELOPMENT OF THEORY OF MIND ABILITY IN AUTISTIC CHILDREN

This study looks into the Theory of Mind (ToM) development of autistic children in Macau. Wellman and Liu’s (2004) Theory of Mind Tasks is used to examine the development of ToM ability among autistic children, and to compare it with that of Down’s syndrome and normal children. The sample includes 16 autistic, 12 Down’s syndrome and 104 normal children, a total of 132. Two sub-samples are drawn, which aim to compare autistic children with the other two groups of a similar age and verbal age in terms of PPVT score. The psychometric properties of Wellman’s scale are investigated in detail. As the sample of autistic children is relatively small, both parametric and non-parametric statistical procedures are used. Results showed that the ToM ability of autistic children was significantly lower than that of Down’s syndrome or normal children of a similar age and verbal age. But their ToM ability does not vanish, which leads to the conjecture that they can be gradually developed. Though Pearson correlations are non-significant, the effect sizes of ToM ability against age and verbal age are respectively medium and large in the case of autistic children, whose development is at least five years later than normal. There are potential correlations between ToM ability with verbal age.
Spike-Threshold Adaptation Predicted by Membrane Potential Dynamics In Vivo

Neurons encode information in sequences of spikes, which are triggered when their membrane potential crosses a threshold. In vivo, the spiking threshold displays large variability suggesting that threshold dynamics have a profound influence on how the combined input of a neuron is encoded in the spiking. Threshold variability could be explained by adaptation to the membrane potential. However, it could also be the case that most threshold variability reflects noise and processes other than threshold adaptation. Here, we investigated threshold variation in auditory neurons responses recorded in vivo in barn owls. We found that spike threshold is quantitatively predicted by a model in which the threshold adapts, tracking the membrane potential at a short timescale. As a result, in these neurons, slow voltage fluctuations do not contribute to spiking because they are filtered by threshold adaptation. More importantly, these neurons can only respond to input spikes arriving together on a millisecond timescale. These results demonstrate that fast adaptation to the membrane potential captures spike threshold variability in vivo.
VARiD: A variation detection framework for color-space and letter-space platforms

Motivation: High-throughput sequencing (HTS) technologies are transforming the study of genomic variation. The various HTS technologies have different sequencing biases and error rates, and while most HTS technologies sequence the residues of the genome directly, generating base calls for each position, the Applied Biosystem's SOLiD platform generates dibase-coded (color space) sequences. While combining data from the various platforms should increase the accuracy of variation detection, to date there are only a few tools that can identify variants from color space data, and none that can analyze color space and regular (letter space) data together. Results: We present VARiD—a probabilistic method for variation detection from both letter- and color-space reads simultaneously. VARiD is based on a hidden Markov model and uses the forward-backward algorithm to accurately identify heterozygous, homozygous and tri-allelic SNPs, as well as micro-indels. Our analysis shows that VARiD performs better than the AB SOLiD toolset at detecting variants from color-space data alone, and improves the calls dramatically when letter- and color-space reads are combined. Availability: The toolset is freely available at http://compbio.cs. utoronto.ca/varid Contact: varid@cs.toronto. edu
Managing Community Controversy in Suburban Wildlife Management: Adopting Practices that Address Value Differences

Wildlife managers in the United States are devoting greater attention to wildlife in suburban areas, where wildlife in close proximity to people pose problems. Local community leaders and residents often demand to be involved with management decision-making. Wildlife managers attempt to facilitate development of community-derived management objectives and implement management actions tailored to local needs and circumstances. Promoting collaborative solutions in such a complex decision-making environment has several challenges: (1) individuals and groups involved in wildlife issues have markedly different attitudes and values regarding wildlife and its management, (2) participants in decision-making approach the process with differing expectations as to how they will be involved, and (3) the technical and social complexity of these issues demand the knowledge, experience, and skills of multiple players. These challenges for community-based wildlife management in suburban areas need not be viewed as insurmountable obstacles. The authors conducted 12 case studies of community-based collaborative deer management in the eastern United States to examine these challenges more fully. The results suggest that learning and capacity are two important components of effective collaborative, community-based deer management. Funding for this work was provided by the Northeast Wildlife Damage Management Research and Outreach Cooperative, the New York State Department of Environmental Conservation (New York Federal Aid in Wildlife Restoration Grant WE-173-G Subgrant 146-R), the Cornell University Agricultural Experiment Station, the University of Massachusetts Agricultural Experiment Station, and the Doris Duke Charitable Foundation.
NK Cells Contribute to the Control of Trypanosoma cruzi Infection by Killing Free Parasites by Perforin-Independent Mechanisms

ABSTRACT The protozoan parasite Trypanosoma cruzi circulates in the blood as trypomastigotes and invades a variety of cells to multiply intracellularly as amastigotes. The acute phase leads to an immune response that restricts the proliferation of the parasite. However, parasites are able to persist in different tissues, which causes the pathology of Chagas' disease. Natural killer (NK) cells play an important role in innate resistance to a variety of pathogens. In the present study we analyzed whether NK cells participated in the control of experimental T. cruzi infection. NK cells were depleted from C57BL/6 mice by antiasialo antibodies. This treatment caused an increased parasitemia during the acute phase, but tissue parasite burdens were not significantly altered according to quantitative real-time PCR. Our results demonstrated that NK cells were activated during the initial phase of a T. cruzi infection and exhibited a contact-dependent antiparasitic activity against extracellular parasites that was independent from perforin. Thus, NK cells limit the propagation of the parasite by acting on circulating T. cruzi trypomastigotes.
Distributed iterative processing for interference channels with receiver cooperation

We propose a method for the design and evaluation of distributed iterative algorithms for receiver cooperation in interference-limited wireless systems. Our approach views the processing within and collaboration between receivers as the solution to an inference problem in the probabilistic model of the whole system. The probabilistic model is formulated to explicitly incorporate the receivers' ability to share information of a predefined type. We employ a recently proposed unified message-passing tool to infer the variables of interest in the factor graph representation of the probabilistic model. The exchange of information between receivers arises in the form of passing messages along some specific edges of the factor graph; the rate of updating and passing these messages determines the amount of communication overhead associated with cooperation. Simulation results illustrate the high performance of the proposed algorithm even with a low number of message exchanges between receivers.
A software-based root-of-trust primitive on multicore platforms

Software-based root-of-trust has been proposed to overcome the disadvantage of hardware-based root-of-trust, which is the high cost in deployment and upgrade (when vulnerabilities are discovered). However, prior research on software-based root-of-trust only focuses on uniprocessor platforms. The essential security properties of such software-based root-of-trust, as analyzed and demonstrated in our paper, can be violated on multicore platforms. Since multicore processors are becoming increasingly popular, it is imperative to explore the feasibility of software-based root-of-trust on them. In this paper, we analyze the challenges of designing software-based root-of-trust on multicore platforms and present two practical attacks that utilize the parallel computing capability to break the existing schemes. We then propose a timing-based primitive, called MT-SRoT, as the first step towards software-based root-of-trust on multicore platforms. MT-SRoT is able to ensure untam-pered execution of a critical security task, such as remote software attestation, on homogeneous shared-memory multicore platforms without the support of tamper-resistant hardware. We implement MT-SRoT and show its effectiveness on both Intel dual-core and quad-core processors.
Applications of Advances in Neuroscience to Assessment of Brain Injury

Abstract The application of neuroscience advances to brain injury is addressed in the context of our studies of the role of the corpus callosum in the interhemispheric transfer of auditory and tactile information. The outcome of these studies, which were conducted over a period of 30 years in normal individuals as well as those with congenital and acquired lesions of the corpus callosum, have since been confirmed and extended by modern brain imaging techniques. These techniques nevertheless continue to rely on the use of sensitive, specific, valid and reliable behavioural testing paradigms.
Differences among western European countries in anticoagulation management of atrial fibrillation

Summary Due to improved implementation of guidelines, new scoring approaches to improve risk categorisation, and introduction of novel oral anticoagulants, medical management of patients with atrial fibrillation (AF) is continuously improving. The PREFER in AF registry enrolled 7,243 consecutive patients with ECG-confirmed AF in seven European countries in 2012–2013 (mean age: 71.5 ± 10.7 years; 60.1% males; mean CHA2DS 2 -VASc score: 3.4). While patient characteristics were generally homogeneous across countries, anticoagulation management showed important differences: the proportion of patients taking vitamin K antagonists (VKAs) varied between 86.0% (in France) and 71.4% (in Italy). Warfarin was used predominantly in the UK and Italy (74.9% and 62.0%, respectively), phenprocoumon in Germany (74.1%), acenocoumarol in Spain (67.3%), and fluindione in France (61.8 %). The major sites for international normalised ratio (INR) measurements were biology laboratories in France anticoagulation clinics in Italy, Spain, and the UK, and physicians’ offices or self-measurement in Germany. Temporary VKA discontinuation and bridging with other anticoagulants was frequent (at least once in the previous 12 months for 22.9% of the patients, on average; ranging from 29.7% in Germany to 14.9% in the UK). Time in therapeutic range (TTR), defined as at least two of the last three available INR values between 2.0–3.0 prior to enrolment, ranged from 70.3% in Spain to 81.4% in Germany. TTR was constantly overestimated by physicians. While the type and half-lives of VKA as well as the mode of INR surveillance differed, overall quality of anticoagulation management by TTR was relatively homogenous in AF patients across countries.