Miracle-dz/UniFAR-FTUs huggingface dataset:
A Population Genetic Approach to Mapping Neurological Disorder Genes Using Deep Resequencing

Deep resequencing of functional regions in human genomes is key to identifying potentially causal rare variants for complex disorders. Here, we present the results from a large-sample resequencing (n = 285 patients) study of candidate genes coupled with population genetics and statistical methods to identify rare variants associated with Autism Spectrum Disorder and Schizophrenia. Three genes, MAP1A, GRIN2B, and CACNA1F, were consistently identified by different methods as having significant excess of rare missense mutations in either one or both disease cohorts. In a broader context, we also found that the overall site frequency spectrum of variation in these cases is best explained by population models of both selection and complex demography rather than neutral models or models accounting for complex demography alone. Mutations in the three disease-associated genes explained much of the difference in the overall site frequency spectrum among the cases versus controls. This study demonstrates that genes associated with complex disorders can be mapped using resequencing and analytical methods with sample sizes far smaller than those required by genome-wide association studies. Additionally, our findings support the hypothesis that rare mutations account for a proportion of the phenotypic variance of these complex disorders.
Kinetoplastid Specific RNA-Protein Interactions in Trypanosoma cruzi Ribosome Biogenesis

RNA binding proteins (RBP) play essential roles in the highly conserved and coordinated process of ribosome biogenesis. Our laboratory has previously characterized two essential and abundant RBPs, P34 and P37, in Trypanosoma brucei which are required for several critical steps in ribosome biogenesis. The genes for these proteins have only been identified in kinetoplastid organisms but not in the host genome. We have identified a homolog of the TbP34 and TbP37 in a T. cruzi strain (termed TcP37/NRBD). Although the N-terminal APK-rich domain and RNA recognition motifs are conserved, the C-terminal region which contains putative nuclear and nucleolar localization signals in TbP34 and TbP37 is almost entirely missing from TcP37/NRBD. We have shown that TcP37/NRBD is expressed in T. cruzi epimastigotes at the level of mature mRNA and protein. Despite the loss of the C-terminal domain, TcP37/NRBD is present in the nucleus, including the nucleolus, and the cytoplasm. TcP37/NRBD interacts directly with Tc 5S rRNA, but does not associate with polyadenylated RNA. TcP37/NRBD also associates in vivo and in vitro with large ribosomal protein TcL5 and, unlike the case of T. brucei, this association is strongly enhanced by the presence of 5S rRNA, suggesting that the loss of the C-terminal domain of TcP37/NRBD may alter the interactions within the complex. These results indicate that the unique preribosomal complex comprised of L5, 5S rRNA, and the trypanosome-specific TcP37/NRBD or TbP34 and TbP37 is functionally conserved in trypanosomes despite the differences in the C-termini of the trypanosome-specific protein components.
Understanding The Importance Of Intermediate Representations In Engineering Problem Solving

This paper describes an emerging theory on the role that representations play in engineering problem solving. Modern cognitive psychology has shown that not only do problem solvers use different representations to store information and ideas, the representation itself influences the problem-solvers’ solution approach. I extend this notion to the engineering domain, and illustrate it with an example from programmable logic controller (PLC) programming. These ideas have important implications for how educators can help students develop effective problem-solving skills.
Voting power in the European Union Star Game

The complexity of a computational problem is the order of computational resources which are necessary and su±cient to solve the problem. The algorithm complexity is the cost of a particular algorithm. We say that a problem has polynomial complexity if its computational complexity is a polynomial in the measure of input size. We introduce a new algorithmic procedure for computing the Myerson value of star-restricted games and we show that there exist problems with polynomial algorithm complexity. Moreover, we present a notebook of the system Mathematica that will be used for computing the Myerson value of the voting power in the European Union Star Game. 1 Voting power In general, it is di±cult to de ̄ne the idea of power, but for the special case of voting power there are mathematical power indices that have been used. The ̄rst such power index was proposed by Shapley and Shubik [15] who apply the Shapley value [14] to the case of simple games. Another concept for measuring voting power was introduced by Banzhaf [1], a lawyer, whose work has appeared mainly in law journals, and whose index has been used in arguments in various legal proceedings. A simple game is a function v : 2N ! f0; 1g ; such that v (N) = 1 and v is nondecreasing, i.e. v(S) · v(T ) whenever S μ T μ N: A coalition is winning if v(S) = 1; and losing if v(S) = 0. The collection of all winning coalitions is denoted by W: We introduce a class of games called weighted voting games. The symbol [q; w1; : : : ; wn] will be used, where the quota q and the weights w1; : : : ; wn are positive integers with 0 < q · Pn i=1 wi: Here there are n players, wi is the number of votes of player i, and q is the quota needed for a coalition to win. Then, the above symbol represents the simple game v : 2N ! f0; 1g de ̄ned for all S μ N by v(S) = 1⁄2 1 if w(S) ̧ q; 0 if w(S) < q; where w(S) = P i2S wi: ¤http://www.esi2. us.es/~mbilbao/ E-mail: mbilbao@cica.es
Causal Discovery from Changes

We propose a new method of discovering causal structures, based on the detection of local, spontaneous changes in the underlying data-generating model. We analyze the classes of structures that axe equivalent relative to a stream of distributions produced by local changes, and devise algorithms that output graphical representations of these equivalence classes. We present experimental results, using simulated data, and examine the errors associated with detection of changes and recovery of structures.
Plasma membrane protein sorting in polarized epithelial cells

PATIAL asymmetry is fundamental to the structure and function ofmost eukaryotic cells. A basic aspect of this polarity is that the cell's plasma membrane is divided into discrete domains. Examples include the membranes of axons and dendrites in neurons, the growing bud and mating projection in the yeast Saccharomyces cerevisiae, and lamel-lipodia in fibroblasts. However, the best-studied type of polarity is found in epithelia, which is the most common type of tissue in animals 56). In simple epithelia the cells form a monolayer where one surface of the cell-the apical-faces the outside world or a topologically equivalent space, such as the lumen of the intestines. This is separated by tight junctions from the basolateral surface, which con-tacts adjacent cells and the underlying connective tissue.
Rotational studies in the Orion Nebula Cluster: from solar mass stars to brown dwarfs

Rotational studies at a variety of ages and masses are important for constraining the angular momentum evolution of young stellar objects (YSO). Of particular interest are the very low mass (VLM) stars and brown dwarfs (BDs), because of the significant lack of known rotational periods in that mass range. We provide for the first time information on rotational periods for a large sample of young VLM stars and BDs. This extensive rotational period study in the 1 Myr old Orion Nebula Cluster (ONC) is based on a deep photometric monitoring campaign using the Wide Field Imager (WFI) camera on the ESO/MPG 2.2m telescope on La Silla, Chile. Accurate I-band photometry of 2908 stars was obtained, extending three magnitudes deeper than previous studies in the ONC. We found 487 periodic variables with estimated masses between 0.5 Msun and 0.015 Msun, 124 of which are BD candidates. This is by far the most extensive and complete rotational period data set for young VLM stars and BDs. In addition, 808 objects show non-periodic brightness variations. We study the dependence of the period distribution on mass and variability level and compare this with known higher mass objects in the ONC (Herbst et al. 2002) and with the 2 Myr old cluster NGC 2264 (Lamm et al., 2004). We find that substellar objects rotate on average faster than the VLM stars. Our rotational data also suggest a dependence of the rotational periods on position within the field, which can be explained by a possible age spread in the ONC. In addition, periodic variables with larger peak-to-peak amplitudes rotate on average slower than those with small peak-to-peak amplitude variations, which can possibly be explained by different magnetic field topologies.
Joint box-constraint and deregularization in multiuser detection

Multiuser detection can be described as a quadratic optimization problem with binary constraint. Many techniques are available to find approximate solution to this problem. These techniques can be characterized in terms of complexity and detection performance. The “efficient frontier” of known techniques include the decision-feedback (DF), branch-and-bound (BB) and probabilistic data association (PDA) detectors. We propose a novel iterative multiuser detection technique based on joint deregularized and box-constrained solution to quadratic optimization with iterations similar to that used in the nonstationary Tikhonov iterated algorithm. The deregularization maximizes the energy of the solution; this is opposite to the Tikhonov regularization where the energy is minimized. However, combined with box-constraints, the deregularization forces the solution to be close to the binary set. Our development improves the “efficient frontier” in multiuser detection, which is illustrated by simulation results.
Early Signs of Success: A Case Study in the Organizational Transformation of a Community College.

This paper is a study of the organizational changes that were implemented at Nova Scotia Community College (NSCC) (Canada) over a 3-year period beginning in 1998. NSCC consists of 13 campuses enrolling 7,000 students in a range of postsecondary certificate and diploma programs, as well as about 500 students in adult learning programs. The College's institutional changes were instigated by NSCC's new president who implemented "Strategic Directions," which includes a strategic plan, mission and vision statements, and articulation of organizational values, all of which were approved by NSCC's Board of Governors. The study argues that employee job satisfaction is a key indicator of positive organizational transformation. An institution-wide survey of employee job satisfaction was conducted in 1999 and again in the spring of 2001. In both instances, at least 86% of faculty and staff participated. There was a 13% increase in the level of satisfaction regarding treatment of employees, a 19% increase in satisfaction with organizational leadership, and a 10% increase in satisfaction with opportunities for advancement. The president devised the strategic planning process as a collaboration between administration, faculty, students, the board, and staff members. This paper details the reorganization process. Appended are the mission statement, an organizational chart, and a strategic plan overview. (Contains 27 references.) (NB) Reproductions supplied by EDRS are the best that can be made from the original document. JA Early Signs of Success A Case Study in the Organizational Transformation of a Community College By Suzanne Drapeau, BSc, BPR, MBA Manager of Institutional Research and Analysis Nova Scotia Community College Halifax, Canada U.S. DEPARTMENT OF EDUCATION Office of Educational Research and Improvement EDUCATIONAL RESOURCES INFORMATION CENTER (ERIC) 2This document has been reproduced as received from the person or organization originating it. Minor changes have been made to improve reproduction quality. Presented at the Association for Institutional Research, Points of view or opinions stated in this document do not necessarily represent International Forum official OERI position or policy. Toronto May, 2002 PERMISSION TO REPRODUCE AND DISSEMINATE THIS MATERIAL HAS BEEN GRANTED BY
Object-Orientation by Immersion

The author describes an approach to teaching object-oriented programming, analysis and design that is being used in a department at the Faculty of Arts, grounding the students’ learning process in a setting outside the traditional computer science curriculum. This involves using a broad approach to programming and systems development, supporting the students’ learning with a scaffolding of different techniques. The author wishes to show that advances in teaching object orientation isn’t necesarily restricted to the realm of computer science.
Mathematical model of a human leg: The switched linear system approach

This article presents a novel approach to modelling of the human leg with the use of linear switched systems. Second order differential equations forming a two-segments leg model moving in a vertical plane are shown. State space linear equations describing given model are derived. A linear switched system for such model is presented, where the switching function is modelled as state-dependent. Based on this approach a linear system is presented, which is composed of four subsystems between which switching occurs depending on two state variables. These variables represent angular displacements. As a consequence, a state space division is shown together with a linear system describing human leg in this setting. Finally, a set of simulations presents differences between standard linear modelling approach and a switched linear system approach.
Oxygen trends in the Galactic thin and thick disks

We present oxygen abundances for 72 F and G dwarf stars in the solar neighbourhood. Using the kinematics of the stars we divide them into two sub-samples with space velocities that are typical for the thick and thin disks, respectively. The metallicities of the stars range from (Fe/H) 0: 9t o+0:4 and we use the derived oxygen abundances of the stars to: (1) perform ad ierential study of the oxygen trends in the thin and the thick disk; (2) to follow the trend of oxygen in the thin disk to the highest metallicities. We analyze the forbidden oxygen lines at 6300 A and 6363 A as well as the (NLTE aicted) triplet lines around 7774 A. For the forbidden line at 6300 A we have spectra of very high S=N (>400) and resolution (R& 215 000). This has enabled a very accurate modeling of the oxygen line and the blending Ni lines. The high internal accuracy in our determination of the oxygen abundances from this line is reflected in the very tight trends we find for oxygen relative to iron. From these abundances we are able to draw the following major conclusions: (i) That the (O/Fe) trend at super-solar (Fe/H) continues downward which is in concordance with models of Galactic chemical evolution. This is not seen in previous studies as it has not been possible to take the blending Ni lines in the forbidden oxygen line at 6300 A properly into account; (ii) That the oxygen trends in the thin and the thick disks are distinctly dierent. This confirms and extends previous studies of the other -elements; (iii) That oxygen does not follow Mg at super-solar metallicities; (iv) We also provide an empirical NLTE correction for the infrared Oi triplet that could be used for dwarf star spectra with a S=N such that only the triplet lines can be analyzed well, e.g. stars at large distances; (v) Finally, we find that Gratton et al. (1999) overestimate the NLTE corrections for the permitted oxygen triplet lines at7774 A for the parameter space that our stars span.
High performance distributed Denial-of-Service resilient web cluster architecture

Though the WWW has come a long way since when it was monikered the World Wide Wait, it is still not reliable during heavy workload conditions. Overloads due to sudden arrival of users (flash crowds) is known to exponentially increase download times. More recently, online banks and portals have been the target of Distributed Denial-of-Service (DDoS) attacks, which send a deluge of requests and drive away the legitimate users. These overloads pose a new set of challenges towards efficient operation at enterprises that host web content which this dissertation addresses by combining knowledge of the network as well as server performance. In particular, this dissertation proposes a web hosting architecture consisting of a grid of clusters, to provide high-performance in the presence of standard overload conditions as well as resilience during attacks. The architecture's high-performance component is provided by a server selection framework which selects the "best server" to serve a request as well as allows for an efficient multiplexing of resources across the entire cluster grid. Traditional approaches assume that minimizing network hop count minimizes client latency. In contrast, the proposed mechanism for server selection collects fine-grained server load and network latency measurements and forwards requests to the server that minimizes the total of estimated network and server delays. The architecture's DDoS- resilience is provided via a combination of anomaly detection and scheduling based mitigation of DDoS attacks. In contrast to prior work, the suspicion mechanism assigns a continuous valued vs. binary suspicion measure to each client session, and the scheduler utilizes these values to determine if and when to schedule a session's requests. Via a combination of analytical modeling and testbed experiments over an online bookstore implementation, the performance benefits achieved by the proposed cluster architecture are justified.
Effects of Dietary Linseed Oil and Propionate Precursors on Ruminal Microbial Community, Composition, and Diversity in Yanbian Yellow Cattle

The rumen microbial ecosystem is a complex system where rumen fermentation processes involve interactions among microorganisms. There are important relationships between diet and the ruminal bacterial composition. Thus, we investigated the ruminal fermentation characteristics and compared ruminal bacterial communities using tag amplicon pyrosequencing analysis in Yanbian yellow steers, which were fed linseed oil (LO) and propionate precursors. We used eight ruminally cannulated Yanbian yellow steers (510 ± 5.8 kg) in a replicated 4 × 4 Latin square design with four dietary treatments. Steers were fed a basal diet that comprised 80% concentrate and 20% rice straw (DM basis, CON). The CON diet was supplemented with LO at 4%. The LO diet was also supplemented with 2% dl-malate or 2% fumarate as ruminal precursors of propionate. Dietary supplementation with LO and propionate precursors increased ruminal pH, total volatile fatty acid concentrations, and the molar proportion of propionate. The most abundant bacterial operational taxonomic units in the rumen were related to dietary treatments. Bacteroidetes dominated the ruminal bacterial community and the genus Prevotella was highly represented when steers were fed LO plus propionate precursors. However, with the CON and LO diet plus malate or fumarate, Firmicutes was the most abundant phylum and the genus Ruminococcus was predominant. In summary, supplementing the diets of ruminants with a moderate level of LO plus propionate precursors modified the ruminal fermentation pattern. The most positive responses to LO and propionate precursors supplementation were in the phyla Bacteriodetes and Firmicutes, and in the genus Ruminococcus and Prevotella. Thus, diets containing LO plus malate or fumarate have significant effects on the composition of the rumen microbial community.
Applications of Artificial Intelligence in Safe Human–Robot Interactions

The integration of industrial robots into the human workspace presents a set of unique challenges. This paper introduces a new sensory system for modeling, tracking, and predicting human motions within a robot workspace. A reactive control scheme to modify a robot's operations for accommodating the presence of the human within the robot workspace is also presented. To this end, a special class of artificial neural networks, namely, self-organizing maps (SOMs), is employed for obtaining a superquadric-based model of the human. The SOM network receives information of the human's footprints from the sensory system and infers necessary data for rendering the human model. The model is then used in order to assess the danger of the robot operations based on the measured as well as predicted human motions. This is followed by the introduction of a new reactive control scheme that results in the least interferences between the human and robot operations. The approach enables the robot to foresee an upcoming danger and take preventive actions before the danger becomes imminent. Simulation and experimental results are presented in order to validate the effectiveness of the proposed method.
Vole Problems, Management Options, and Research Needs in the United States

Voles (Microtus spp.) are ubiquitous to the northern hemisphere. Numerous species occur in North America and several species cause significant damage of various types: food crops, livestock forage production (e.g., alfalfa), nursery trees, reforestation, orchards, rangeland forage, and damage to lawns, golf courses and ground cover. Much research has been conducted with voles and a number of management options have been developed, including habitat manipulation, rodenticides, traps, repellents, barriers, supplemental feeding, and increased natural predation. However, significant damage still occurs because voles are not easily managed. Voles are small and secretive, prolific, active year-round, able to exploit refugia, and cyclic with periodic irruptions. Currently there are no permanent solutions to managing voles, so long-term monitoring and management of populations is required. We review what is known about voles, the types and extent of damage they cause, advantages and disadvantages of management methods, and some research needs. Research needs include the development of effective repellents, effective rodenticide baiting strategies that minimize nontarget hazards, and cost-effective methods to protect the root systems of woody plants.
Agility for underwater floating manipulation: Task & subsystem priority based control strategy

The need for actual autonomy in underwater robotic systems is rapidly increasing. Many challenging issues derive from such a trend, one in all the requirement of coordinately controlling the motion of an underwater floating I-AUV endowing a robotic arm, to accomplish complex manipulation tasks. This work is aimed to present a strategy based on the prioritization of tasks of equality and inequality type, once combined with Dynamic Programming techniques, for coordinately controlling the motion of such I-AUV. A general algorithmic framework is developed and simulative results supporting its resulting effectiveness are presented.