Miracle-dz/UniFAR-FTUs huggingface dataset:
Gene Classification Based on Amino Acid Motifs and Residues: The DLX (distal-less) Test Case

Background Comparative studies using hundreds of sequences can give a detailed picture of the evolution of a given gene family. Nevertheless, retrieving only the sequences of interest from public databases can be difficult, in particular, when working with highly divergent sequences. The difficulty increases substantially when one wants to include in the study sequences from many (or less well studied) species whose genomes are non-annotated or incompletely annotated. Methodology/Principal Findings In this work we evaluate the usefulness of different approaches of gene retrieval and classification, using the distal-less (DLX) gene family as a test case. Furthermore, we evaluate whether the use of a large number of gene sequences from a wide range of animal species, the use of multiple alternative alignments, and the use of amino acids aligned with high confidence only, is enough to recover the accepted DLX evolutionary history. Conclusions/Significance The canonical DLX homeobox gene sequence here derived, together with the characteristic amino acid variants here identified in the DLX homeodomain region, can be used to retrieve and classify DLX genes in a simple and efficient way. A program is made available that allows the easy retrieval of synteny information that can be used to classify gene sequences. Maximum likelihood trees using hundreds of sequences can be used for gene identification. Nevertheless, for the DLX case, the proposed DLX evolutionary is not recovered even when multiple alignment algorithms are used.
Cell-to-Cell and Long-Distance Trafficking of the Green Fluorescent Protein in the Phloem and Symplastic Unloading of the Protein into Sink Tissues

Macromolecular trafficking within the sieve element–companion cell complex, phloem unloading, and post-phloem transport were studied using the jellyfish green fluorescent protein (GFP). The GFP gene was expressed in Arabidopsis and tobacco under the control of the AtSUC2 promoter. In wild-type Arabidopsis plants, this promoter regulates expression of the companion cell–specific AtSUC2 sucrose–H+ symporter gene. Analyses of the AtSUC2 promoter–GFP plants demonstrated that the 27-kD GFP protein can traffic through plasmodesmata from companion cells into sieve elements and migrate within the phloem. With the stream of assimilates, the GFP is partitioned between different sinks, such as petals, root tips, anthers, funiculi, or young rosette leaves. Eventually, the GFP can be unloaded symplastically from the phloem into sink tissues, such as the seed coat, the anther connective tissue, cells of the root tip, and sink leaf mesophyll cells. In all of these tissues, the GFP can traffic cell to cell by symplastic post-phloem transport. The presented data show that plasmodesmata of the sieve element–companion cell complex, as well as plasmodesmata into and within the analyzed sinks, allow trafficking of the 27-kD nonphloem GFP protein. The data also show that the size exclusion limit of plasmodesmata can change during organ development. The results are also discussed in terms of the phloem mobility of assimilates and of small, low molecular weight companion cell proteins.
Collaborative knowledge-making in the everyday practice of youth suicide prevention education

The development and implementation of a new school‐based suicide prevention education programme in one secondary school in Vancouver, British Columbia, recently provided us with an opportunity to conduct an in‐depth, qualitative case study. The purpose of our study was to deepen our understanding of how school‐based suicide prevention education programmes like this one get planned and enacted in particular, local settings. We argue that the narrow range of methodologies that have traditionally been deployed to study school‐based youth suicide prevention education programmes have hindered our ability to see the complexities and potentialities of this work. Through the presentation of a sub‐set of findings, we aim to show the possibilities for fresh thinking and contextualized understandings that a qualitative case study, informed by a constructionist methodology, invites.
An Investigation into Sharing Metadata: "I'm not thinking what you are thinking"

A small collection of metadata concepts has been jointly negotiated among a group of specialists to be relevant for classifying data used in their field. A series of comparisons are made to test levels of agreement between individuals when these concepts are used to tag data items. Inter-coder agreement measures are presented for a range of data sets and individuals with varying relationships to the data sets. The implications of the results for the use of metadata as a supporting mechanism for knowledge sharing are discussed.
Degree of Swelling of the Medial Rectus Muscle on CT Images to Differentiate Old From New Medial Orbital Wall Fracture

Abstract The aims of this study were to compare the degree of swelling of the medial rectus muscle (MR) in a recent fracture group, an old fracture group, and a normal group and to use this to differentiate old medial orbital wall fracture from recent fracture. We made measurements of the computed tomography images of 43 patients with a recent medial orbital wall fracture (the recent fracture group), 46 patients with depression of the medial wall and who were without a recent trauma history (the old fracture group), and 86 patients who were without any facial injury (the normal group). On the axial view, the width of the MR was measured bilaterally, and the width ratio to the contralateral side was calculated. On the coronal view, the height of the MR was measured bilaterally, and the height ratio to the contralateral side was calculated. The width-to-height ratio was also measured on the involved side. The width ratio of the recent fracture group was 1.42 ± 0.31, and it was significantly higher than that of the old fracture group (1.25 ± 0.15) or the normal group (1.00 ± 0.09). The width ratio of the old fracture group was also significantly higher than that of the normal group. The height ratio of the normal group (1.00 ± 0.04) was significantly higher than that of the recent fracture group (0.91 ± 0.15) or the old fracture group (0.86 ± 0.07). The height ratio of the recent fracture group was also significantly higher than that of the old fracture group (P = 0.043). The width-height ratio of the recent fracture group (0.63 ± 0.23) was significantly higher than that of the old fracture group (0.55 ± 0.09) or the normal group (0.37 ± 0.05). The height-to-width ratio of the old fracture group was also significantly higher than that of the normal group. We think the width ratio of the MR of the injured side to the MR of the contralateral side can be the better parameter to differentiate a recent fracture from an old fracture.
Blood Pressure Effects of Yoga, Alone or in Combination With Lifestyle Measures: Results of the Lifestyle Modification and Blood Pressure Study (LIMBS)

The authors conducted a study to assess the effects of yoga on blood pressure (BP). Patients were randomized to yoga (Blood Pressure Education Program [BPEP]), or a combined program (COMBO). Ambulatory BP was measured at baseline and at 12 and 24 weeks. Data are presented for all enrolled patients (n=137) and for completers only (n=90). Systolic BP (SBP) and diastolic BP (DBP) were significantly decreased within all groups at 12 and 24 weeks (P<.001) for enrolled patients and completers. SBP was significantly reduced in the yoga and COMBO groups as compared with the BPEP group at 12 weeks in all enrolled and completers. SBP differences were no longer significant at 24 weeks between groups in all enrolled patients; however, there was a greater reduction in SBP at 24 weeks in completers favoring BPEP over yoga. No differences in DBP between groups or in BP between the yoga and COMBO groups were present. The authors did not observe an additive benefit from combining yoga with BPEP measures. Reasons for this are unclear at this time. BP lowering with yoga, however, was similar to that achieved with lifestyle measures.
Interactive presentation: A process splitting transformation for Kahn process networks

In this paper we present a process splitting transformation for Kahn process networks. Running applications written in this parallel program specification on a multiprocessor architecture does not guarantee that the runtime requirements are met. Therefore, it may be necessary to further analyze and optimize Kahn process networks. In this paper, we will present a four-step transformation that results in a functionally equivalent process network, but with a changed and optimized network structure. The class of networks that can be handled is not restricted to static networks. The novelty of this approach is that it can also handle processes with dynamic program statements. We will illustrate the transformation prototyped in GCC for a JPEG decoder, showing a 21% performance improvements.
Frontiers in Computational Neuroscience Materials and Methods Measures of Correlation

In particular, count correlations computed for time bins larger than the intrinsic temporal scale of correlations can vanish for some functional forms of input correlations. These potential ambiguities were not reported in previous studies of leaky integrate and fi re models which focused on the analytically accessible choice of white noise input currents (de la Rocha et al., 2007; Shea-Brown et al., 2008). The paper is organized as follows: we fi rst introduce several common spike count measures (Section " Materials and Methods ") and the statistical framework (Section " Results "). Then we study the zero time lag correlations (Section " Spike Correlations with Zero Time Lag ") and the infl uence of the temporal structure of input correlations on measures of spike correlations (Section " Temporal Scale of Spike Correlations "). We show that spike count correlations can vanish despite the presence of input cross correlations (Section " Vanishing Count Covariance in the Presence of Cross Correlations "). Finally, we discuss potential consequences of our fi ndings for the design of population models and the experimentally measured spike correlations. The spike train s i (t) of a neuron i is completely described by the sequence of spike times t i. This description is often simplifi ed using discrete bins of size T (Figure 1). To describe pairwise spike correlations , several competing measures are used (Perkel et al.
Scene independent real-time indirect illumination

A novel method for real-time simulation of indirect illumination is presented in this paper. The method, which we call direct radiance mapping (DRM), is based on basal radiance calculations and does not impose any restrictions on scene geometry or dynamics. This makes the method tractable for real-time rendering of arbitrary dynamic environments and for interactive preview of feature animations. Through DRM we simulate two diffuse reflections of light, but can also, in combination with traditional real-time methods for specular reflections, simulate more complex light paths. DRM is a GPU-based method, which can draw further advantages from upcoming GPU functionalities. The method has been tested for moderately sized scenes with close to real-time frame rates and it scales with interactive frame rates for more complex scenes.
The Understanding of Teaching in Children with Autism Spectrum Disorder

Current interventions to improve the social, academic, and behavioral skills in children with Autism Spectrum Disorders (ASD) all require teaching activities. A central component of being able to engage in and benefit from teaching activities is the ability to recognize and understand when and how teaching occurs. The emergence of an understanding of teaching as a means by which we acquire knowledge from others is a key feature of socio-cognitive development. However, it is not known whether children with ASD develop the ability to understand the fundamental concept of teaching. Understanding what children with ASD know about the concept of teaching is important in order to optimize interventions that incorporate teaching as a method of learning. This dissertation examines the understanding of teaching in children with ASD compared to typically developing children. Specifically, we investigate the two defining features of an understanding of teaching: 1) that teaching requires a knowledge difference between teacher and learner, and 2) that teaching is an intentional activity. We use a cross-sectional design to assess whether the understanding of these two components is intact or impaired in high functioning children with ASD compared to typical children individually matched on verbal ability. This study also investigates the interrelations among the understanding of teaching, theory of mind acquisition, and concurrent understanding of intention in others in this population. Our results indicate that the understanding of the two core components that underlie the concept of teaching is impaired in high functioning children with ASD, compared to matched controls. The role that intention and theory of mind play in the understanding of teaching in high functioning children with ASD is also discussed. This work has broad implications for improving teaching and teaching-based interventions for children with ASD Degree Type Dissertation Degree Name Doctor of Philosophy (PhD) Graduate Group Education First Advisor Douglas A. Frye
Translational Paradigms in Cerebrovascular Gene Transfer

Gene transfer involves the use of an engineered biologic vehicle known as a vector to introduce a gene encoding a protein of interest into a particular tissue. In diseases with known defects at a genetic level, gene transfer offers a potential means of restoring a normal molecular environment via vector-mediated entry (transduction) and expression of genes encoding potentially therapeutic proteins selectively in diseased tissues. The technology of gene transfer therefore underlies the concept of gene therapy and falls under the umbrella of the current genomics revolution. Particularly since 1995, numerous attempts have been made to introduce genes into intracranial blood vessels to demonstrate and characterize viable transduction. More recently, in attempting to translate cerebrovascular gene transfer technology closer to the clinical arena, successful transductions of normal human cerebral arteries ex vivo and diseased animal cerebral arteries in vivo have been reported using vasomodulatory vectors. Considering the emerging importance of gene-based strategies for the treatment of the spectrum of human disease, the goals of the present report are to overview the fundamentals of gene transfer and review experimental studies germane to the clinical translation of a technology that can facilitate genetic modification of cerebral blood vessels.
Animal-Vehicle Collision Mitigation System for Automated Vehicles

Detecting large animals on roadways using automated systems such as robots or vehicles is a vital task. This can be achieved using conventional tools such as ultrasonic sensors, or with innovative technology based on smart cameras. In this paper, we investigate a vision-based solution. We begin the paper by performing a comparative study between three detectors: 1) Haar-AdaBoost; 2) histogram of oriented gradient (HOG)-AdaBoost; and 3) local binary pattern (LBP)-AdaBoost, which were initially developed to detect humans and their faces. These detectors are implemented, evaluated, and compared to each other in terms of accuracy and processing time. Based on our evaluation and comparison results, we design a two-stage architecture which outperforms the aforementioned detectors. The proposed architecture detects candidate regions of interest using LBP-AdaBoost in the first stage, which offers robustness to false positives in real-time conditions. The second stage is based on support vector machine classifiers that were trained using HOG features. The training data are generated from our novel dataset called large animal dataset, which contains common and thermographic images of large road-animals. We emphasize that no such public dataset currently exists.
Symbolic Communication in Multidisciplinary Cooperations

With the advent of strategic science, multidisciplinary and cross-institutional research is more and more becoming the rule. The problems encountered by such multidisciplinary research and development cooperations are highly varied. They derive from multiple differences in the backgrounds of the participants and are often perceived as cultural gaps that need to be bridged for cooperation. The main argument of the article is that multidisciplinary collaborations have mechanisms at their disposal to cooperate despite multiple problems counteracting such a cooperation. Since symbolic communication is the primary medium of articulation across sites, this article focuses on how symbolic communication enables cooperation across sites without a deep comprehension of each other's work. Multidisciplinary cooperations start out with few shared symbolic resources, but as the cooperation continues, they may develop communicative boundarytranscending objects such as active and passive dictionaries and hybrid repertoires.
On the Transfer Properties of the “Generalized Sub-Optimal” Second-Order Sliding Mode Control Algorithm

A class of second order sliding mode control systems is studied in terms of its transfer properties, which allows for investigating the system response to an external signal representing either a disturbance, which the system is supposed to reject, or the reference input, which the system is supposed to track. An approach based on the locus of a perturbed relay system (LPRS) is developed making reference to linear plant/actuator/sensor dynamics and to the ldquogeneralized sub-optimalrdquo second-order sliding mode control algorithm in the closed loop. A thoroughly discussed example shows the feasibility of the presented procedure and confirms the theoretical results.
Garbage Cans, New Institutionalism, and the Study of Politics

Bendor, Moe, and Shotts want to rescue some of the ideas of the garbage can model and the new institutionalism. Their rescue program, however, is alien to the spirit of not only our work but also some recent developments that may promise a climate of dialogue between different approaches in political science. Bendor, Moe, and Shotts place themselves closer to a tradition of unproductive tribal warfare than to more recent attempts to explore the limits of and the alternatives to (means-end) rational interpretations of political actors, institutions, and change. By building on a narrow concept of what is valuable political science, they cut themselves off from key issues that have occupied political scientists for centuries.
Field-Evolved Resistance to Bt Maize by Western Corn Rootworm

Background Crops engineered to produce insecticidal toxins derived from the bacterium Bacillus thuringiensis (Bt) are planted on millions of hectares annually, reducing the use of conventional insecticides and suppressing pests. However, the evolution of resistance could cut short these benefits. A primary pest targeted by Bt maize in the United States is the western corn rootworm Diabrotica virgifera virgifera (Coleoptera: Chrysomelidae). Methodology/Principal Findings We report that fields identified by farmers as having severe rootworm feeding injury to Bt maize contained populations of western corn rootworm that displayed significantly higher survival on Cry3Bb1 maize in laboratory bioassays than did western corn rootworm from fields not associated with such feeding injury. In all cases, fields experiencing severe rootworm feeding contained Cry3Bb1 maize. Interviews with farmers indicated that Cry3Bb1 maize had been grown in those fields for at least three consecutive years. There was a significant positive correlation between the number of years Cry3Bb1 maize had been grown in a field and the survival of rootworm populations on Cry3Bb1 maize in bioassays. However, there was no significant correlation among populations for survival on Cry34/35Ab1 maize and Cry3Bb1 maize, suggesting a lack of cross resistance between these Bt toxins. Conclusions/Significance This is the first report of field-evolved resistance to a Bt toxin by the western corn rootworm and by any species of Coleoptera. Insufficient planting of refuges and non-recessive inheritance of resistance may have contributed to resistance. These results suggest that improvements in resistance management and a more integrated approach to the use of Bt crops may be necessary.
Idiosyncratic Weighting of Trait Information in Impression Formation

An analysis is offered of the role of unequal weighting in the averaging model of information integration. A distinction is made between unequal weighting at the normative level (which has been referred to as "differential weighting") and unequal weighting at the level of the individual subject (which we refer to as "idiosyncratic weighting"). Two studies are reported that examine the prevalence of idiosyncratic weighting in the trait-judgment impression formation task. Whereas most past research on the question of unequal weighting in this task involved averaging responses across both subjects and stimulus replications, the present studies were analyzed at the level of an individual subject's repeated responses to separate stimulus replications. Clear evidence of idiosyncratic weighting was obtained from about 50% of the 120 subjects; only 20% of the subjects indicated absolutely no tendency toward unequal weighting. There was no evidence that idiosyncratic weighting was restricted to just a subset of stimuli, since all of the 20 stimulus replications showed idiosyncratic weighting effects. In contrast to previous findings, negative traits did not always receive more weight than positive traits. In more than 20% of the instances of unequal weighting, the more positive trait was accorded a higher weight.
Dependent Dirichlet Priors and Optimal Linear Estimators for Belief Net Parameters

A Bayesian belief network is a model of a joint distribution over a finite set of variables, with a DAG structure representing immediate dependencies among the variables. For each node, a table of parameters (CP-table) represents local conditional probabilities, with rows indexed by conditioning events (assignments to parents). CP-table rows are usually modeled as independent random vectors, each assigned a Dirichlet prior distribution. The assumption that rows are independent permits a relatively simple analysis but may not reflect actual prior opinion about the parameters. Rows representing similar conditioning events often have similar conditional probabilities. This paper introduces a more flexible family of "dependent Dirichlet" prior distributions, where rows are not necessarily independent. Simple methods are developed to approximate the Bayes estimators of CP-table parameters with optimal linear estimators; i.e., linear combinations of sample proportions and prior means. This approach yields more efficient estimators by sharing information among rows. Improvements in efficiency can be substantial when a CP-table has many rows and samples sizes are small.