Miracle-dz/UniFAR-FTUs huggingface dataset:
Spatial and Topological Organization of DNA Chains Induced by Gene Co-localization

Transcriptional activity has been shown to relate to the organization of chromosomes in the eukaryotic nucleus and in the bacterial nucleoid. In particular, highly transcribed genes, RNA polymerases and transcription factors gather into discrete spatial foci called transcription factories. However, the mechanisms underlying the formation of these foci and the resulting topological order of the chromosome remain to be elucidated. Here we consider a thermodynamic framework based on a worm-like chain model of chromosomes where sparse designated sites along the DNA are able to interact whenever they are spatially close by. This is motivated by recurrent evidence that there exist physical interactions between genes that operate together. Three important results come out of this simple framework. First, the resulting formation of transcription foci can be viewed as a micro-phase separation of the interacting sites from the rest of the DNA. In this respect, a thermodynamic analysis suggests transcription factors to be appropriate candidates for mediating the physical interactions between genes. Next, numerical simulations of the polymer reveal a rich variety of phases that are associated with different topological orderings, each providing a way to increase the local concentrations of the interacting sites. Finally, the numerical results show that both one-dimensional clustering and periodic location of the binding sites along the DNA, which have been observed in several organisms, make the spatial co-localization of multiple families of genes particularly efficient.
Extracting Professional Preferences of Users from Natural Language Essays

This paper presents an unsupervised sentiment analysis approach for extracting professional preferences of users from natural language essays in a career recommendation scenario. Our system first extracts terms facilitating career recommendation such as objects, activities, hobbies, and places from the essays. Then, it applies a lexicon-based sentiment analysis approach to assign polarities representing user preferences.
The Adaptive Significance of Sexual Conditioning: Pavlovian Control of Sperm Release

Male quail received Pavlovian conditioning trials that consisted of placement in a distinctive experimental chamber (the conditioned stimulus) paired with the opportunity to copulate with a female (the unconditioned stimulus). For control subjects, exposures to the conditioned and unconditioned stimuli were unpaired. After four and six trials, each subject was placed in the experimental chamber with a probe stimulus that included some of the visual cues of a female's head and neck. Pavlovian conditioning increased how much time subjects spent near the probe stimulus. Conditioned subjects also released greater volumes of semen and greater numbers of spermatozoa than the control subjects. Significant differences were not obtained in serum testosterone levels or in other measures of sperm quality. These results demonstrate that sexual Pavlovian conditioning can affect reflexes involved in sperm release and thereby modulate reproductive fitness.
Recovery and potential utility of YACs as circular YACs/BACs.

A method has been established to convert pYAC4-based linear yeast artificial chromosomes (YACs) into circular chromosomes that can also be propagated in Escherichia coli cells as bacterial artificial chromosomes (BACs). The circularization is based on use of a vector that contains a yeast dominant selectable marker (G418R), a BAC cassette and short targeting sequences adjacent to the edges of the insert in the pYAC4 vector. When it is introduced into yeast, the vector recombines with the YAC target sequences to form a circular molecule, retaining the insert but discarding most of the sequences of the YAC telomeric arms. YACs up to 670 kb can be efficiently circularized using this vector. Re-isolation of megabase-size YAC inserts as a set of overlapping circular YAC/BACs, based on the use of an Alu-containing targeting vector, is also described. We have shown that circular DNA molecules up to 250 kb can be efficiently and accurately transferred into E.coli cells by electroporation. Larger circular DNAs cannot be moved into bacterial cells, but can be purified away from linear yeast chromosomes. We propose that the described system for generation of circular YAC derivatives can facilitate sequencing as well as functional analysis of genomic regions.
The puppeteer display: attracting and actively shaping the audience with an interactive public banner display

We present a wide interactive banner display installed at a city sidewalk and the findings from two long-term field studies investigating the opportunities of public displays to actively shape the audience. In order to improve parallel usage and dissolve crowds, our wide display subtly directs individual users by visual stimuli and manipulates the audience like a puppeteer, thus reversing the notion of adaptive content being implicitly manipulated by the users. We first investigated visual signifiers which attract initial users approaching sideways, and then others, which actively influence user positions and regulate audience constellations. We found that dynamic visual stimuli such as frames and ellipses are effective (1) to direct users in front of the display, (2) to distribute multiple users along the display, (3) static frames are more effective than moving or interactive ones, and (4) these visual stimuli also work indirectly by inducing social pressure among users.
Role Negotiations in a Temporary Organization: Making Sense During Role Development in an Educational Theater Production

Negotiating the performance of an individual’s role is an essential part of the assimilation process. Role negotiations consist of a two-part process: (a) negotiating a particular organizational role to perform and (b) negotiating that role’s performance once it is assumed. Whereas previous research has failed to explore how these two processes interact,this participant-observation study used sensemaking to examine the communication individuals used both to negotiate a specific role in a temporary organization, an educational theater production, and then to negotiate that role’s performance. The temporary organization provided a unique opportunity to observe both processes from beginning to end and allowed for examination of specific communication behaviors individuals used to make sense during both negotiations. The results provide insight into the relationship between negotiating a specific role and negotiating that role’s performance as well as extending the understanding of sensemaking.
Contour‐based polygonal ambient occlusion using a single‐depth texture

We present a novel approximation of a global illumination technique called contour‐based polygonal ambient occlusion, an approach that darkens by only using a depth texture as screen‐space ambient occlusion without additional information such as a normal buffer. We introduce a discrete level structure to calculate the amount of occlusion by using the contour level, an integer value derived from the depth difference of neighboring texels. We use the uniform sampling to define the positions of the neighboring texels in the depth texture. Our method does not depend on geometric complexity because our method works in screen space and works well for both static and dynamic scenes without any precomputation. Copyright © 2013 John Wiley & Sons, Ltd.
The Role of Macros in Tractable Planning

This paper presents several new tractability results for planning based on macros. We describe an algorithm that optimally solves planning problems in a class that we call inverted tree reducible, and is provably tractable for several subclasses of this class. By using macros to store partial plans that recur frequently in the solution, the algorithm is polynomial in time and space even for exponentially long plans. We generalize the inverted tree reducible class in several ways and describe modifications of the algorithm to deal with these new classes. Theoretical results are validated in experiments.
TCP with adaptive pacing for multihop wireless networks

In this paper, we introduce a novel congestion control algorithm for TCP over multihop IEEE 802.11 wireless networks implementing rate-based scheduling of transmissions within the TCP congestion window. We show how a TCP sender can adapt its transmission rate close to the optimum using an estimate of the current 4-hop propagation delay and the coefficient of variation of recently measured round-trip times. The novel TCP variant is denoted as TCP with Adaptive Pacing (TCP-AP). Opposed to previous proposals for improving TCP over multihop IEEE 802.11 networks, TCP-AP retains the end-to-end semantics of TCP and does neither rely on modifications on the routing or the link layer nor requires cross-layer information from intermediate nodes along the path. A comprehensive simulation study using ns-2 shows that TCP-AP achieves up to 84% more goodput than TCP NewReno, provides excellent fairness in almost all scenarios, and is highly responsive to changing traffic conditions.
Multiresolution Analysis on Irregular Surface Meshes

Wavelet-based methods have proven their efficiency for visualization at different levels of detail, progressive transmission, and compression of large data sets. The required core of all wavelet-based methods is a hierarchy of meshes that satisfies subdivision-connectivity. This hierarchy has to be the result of a subdivision process starting from a base mesh. Examples include quadtree uniform 2D meshes, octree uniform 3D meshes, or 4-to-1 split triangular meshes. In particular, the necessity of subdivision-connectivity prevents the application of wavelet-based methods on irregular triangular meshes. In this paper, a "wavelet-like" decomposition is introduced that works on piecewise constant data sets over irregular triangular surface meshes. The decomposition/reconstruction algorithms are based on an extension of wavelet-theory allowing hierarchical meshes without property. Among others, this approach has the following features: it allows exact reconstruction of the data set, even for nonregular triangulations, and it extends previous results on Haar-wavelets over 4-to-1 split triangulations.
Using multiple hash functions to improve IP lookups

High performance Internet routers require a mechanism for very efficient IP address lookups. Some techniques used to this end, such as binary search on levels, need to construct quickly a good hash table for the appropriate IP prefixes. We describe an approach for obtaining good hash tables based on using multiple hashes of each input key (which is an IP address). The methods we describe are fast, simple, scalable, parallelizable, and flexible. In particular, in instances where the goal is to have one hash bucket fit into a cache line, using multiple hashes proves extremely suitable. We provide a general analysis of this hashing technique and specifically discuss its application to binary search on levels.
Model predictive control for linear parameter varying systems using parameter dependent Lyapunov function

In this paper, we propose a method for synthesizing a model predictive control (MPC) law for linear parameter varying (LPV) systems. The proposed MPC algorithm is reduced to the optimization problem with linear matrix inequality (LMI) constraints that are derived by using the parameter dependent Lyapunov function (PDLF). The proposed control law achieves less conservative results as compared with the existing method. A numerical example is provided to illustrate effectiveness of the proposed method.
Achieving Proportional Representation in Conference Programs

We study the optimization problem of designing theprogram of a conference with parallel sessions, so that the intended participants are as happy as possible from the talks they can attend. Interestingly,this can be thought of as a two-dimensional ex-tension of a scheme proposed by Chamberlin and Courant [1983] for achieving proportional representation in multi-winner elections. We show that different variations of the problem are computa-ionally hard by exploiting relations of the problem with well-known hard graph problems. On the positive side, we present polynomial-time algorithms that compute conference programs that have a social utility that is provably close to the optimal one (within constant factors). Our algorithms are either combinatorial or based on linear programming and randomized rounding.
Routing and spectrum assignment problem in three-C-aware dynamic flexible optical networks

In order to meet various bandwidth requirements, such as sub-wavelength and super-wavelength, and overcome the power consumption bottleneck, dynamic flexible optical networks have become the middle term solution of all optical networks instead of optical packet switching (OPS) networks. Different from routing and wavelength assignment (RWA) in WDM networks, routing and spectrum assignment (RSA) in dynamic flexible optical networks faces more constraints, which are summarized as three-C constraints, i.e. Continuity, Consistency, and re-Configurability. Routing and spectrum assignment problem in three-C-aware dynamic flexible optical networks is mainly investigated in the paper.
A logic for strategic reasoning

Rational strategic reasoning is the process whereby an agent reasons about the best strategy to adopt in a given multi-agent scenario, taking into account the likely behaviour of other participants in the scenario, and, in particular, how the agent's choice of strategy will affect the choices of others. We present CATL, a logic that is intended to facilitate such reasoning. CATL is an extension of Alternating-time Temporal Logic (ATL), which supports reasoning about the abilities of agents and their coalitions in game-like multi-agent systems. CATL extends ATL with a ternary counterfactual commitment operator of the form Ci(σ, φ), with the intended reading "if it were the case that agent i committed to strategy σ, then φ". By using this operator in combination with the ability operators of ATL, it is possible to reason about the implications of different possible choices by agents. We illustrate the approach by showing how CATL may be used to express properties of games such as Nash equilibrium and Pareto efficiency. We also show that the model checking problem for CATL is tractable, and hence that efficient implementations of strategic reasoners based on CATL are feasible.
Optimizing time allocation for network defence

The presence of unpatched, exploitable vulnerabilities in software is a prerequisite for many forms of cyberattack. Because of the almost inevitable discovery of a vulnerability and creation of an exploit for all types of software, multiple layers of security are usually used to protect vital systems from compromise. Accordingly, attackers seeking to access protected systems must circumvent all of these layers. Resource- and budget-constrained defenders must choose when to execute actions such as patching, monitoring and cleaning infected systems in order to best protect their networks. Similarly, attackers must also decide when to attempt to penetrate a system and which exploit to use when doing so. We present an approach to modelling computer networks and vulnerabilities that can be used to find the optimal allocation of time to different system defence tasks. The vulnerabilities, state of the system and actions by the attacker and defender are used to build partially observable stochastic games. These games capture the uncertainty about the current state of the system and the uncertainty about the future. The solution to these games is a policy, which indicates the optimal actions to take for a given belief about the current state of the system. We demonstrate this approach using several different network configurations and types of player. We consider a trade-off for the system administrator, where they must allocate their time to performing either security-related tasks or performing other required non-security tasks. The results presented highlight that, with the requirement for other tasks to be performed, following the optimal policy means spending time on only the most essential security-related tasks, while the majority of time is spent on non-security tasks.
Common-Sense Knowledge of Space: Learning from Experience

The TOUR model is a computational model of human commonsense Knowledge of large-scale space. It shows how observations are assimilated into a description, from multiple perspectives, of the spatial environment. In this paper we propose a representation for sensory events at a level suited to this investigation, and an inference strategy by which these sensory events are assimilated into descriptions of spatial structure. We also discuss the states of partial Knowledge that occur during the learning process, and show that the representation exhibits graceful degradation of performance under resource limitations.
TargetFinder and Annotator : a Simple Approach for Finding Full-length Target cDNAs and for Annotating EST Sequences

In a large scale EST (expressed sequence tag) or cDNA sequencing project, it is often desirable to know whether the ESTs identify genes of interest and whether the cloned cDNAs include intact coding regions (are of full-length). In this work, we present two Perl tools, TargetFinder and Annotator. TargetFinder automates the identification of full-length cDNAs from assembled EST sequences including singletons and contigs. Annotator is used to annotate ESTs and their assembled sequences by assigning a provisional function to each sequence and predicting whether or not they include intact coding regions. The programs use the output of BLASTX to predict the correct reading frame, search for a putative start codon, and predict whether a query sequence includes an intact ORF. In addition the programs also predict whether the sequence of the coding region of a cDNA clone or a contig is complete. Using our own Aspergillus niger EST data, TargetFinder rapidly and accurately found full-length target genes within a large set of assembled ESTs and Annotator functionally annotated the ESTs and their assembled sequences.
Science Teachers’ Assessment and Grading Practices in Swedish Upper Secondary Schools

This study examines science teachers’ assessment and grading practices as well as student participation in the assessment process in the upper secondary school. The teachers were asked about how and when they assess students and what was crucial when grading students. We asked when they considered students to have developed the following knowledge criteria: aptitude for critical thinking, analytical and practical skills and how they assessed students regarding these skills. We report overall evidence-based assessment practices from the teachers’ comments in face-to-face interviews. Teachers’ comments are closely aligned and associated with long-established beliefs. The assessment and grading practices were found to be at odds with modern perspectives of assessment as well as its role in learning.
Interspecies chimeric sperm lysins identify regions mediating species-specific recognition of the abalone egg vitelline envelope.

Abalone sperm lysin is a nonenzymatic, 16-kDa protein that creates a hole in the egg vitelline envelope (VE) through which the sperm swims to fuse with the egg. The dissolution of isolated VE by lysin is species specific. Interspecies comparisons show that the most divergent region of lysin is the N-terminal segment of residues 1-12 which is always species-unique. The C-terminus and three internal segments are moderately variable between species, but not species unique. Analysis of nucleotide substitutions shows that lysin evolves rapidly by positive Darwinian selection, suggesting that there is adaptive value in altering its amino acid sequence. The results reported here, in which segments of lysin were exchanged between two species, prove by direct experimentation that the interspecies variable termini play major roles in the species-specific recognition between sperm lysin and the egg VE.
Systematic Dissection of the Sequence Determinants of Gene 3’ End Mediated Expression Control

The 3’end genomic region encodes a wide range of regulatory process including mRNA stability, 3’ end processing and translation. Here, we systematically investigate the sequence determinants of 3’ end mediated expression control by measuring the effect of 13,000 designed 3’ end sequence variants on constitutive expression levels in yeast. By including a high resolution scanning mutagenesis of more than 200 native 3’ end sequences in this designed set, we found that most mutations had only a mild effect on expression, and that the vast majority (~90%) of strongly effecting mutations localized to a single positive TA-rich element, similar to a previously described 3’ end processing efficiency element, and resulted in up to ten-fold decrease in expression. Measurements of 3’ UTR lengths revealed that these mutations result in mRNAs with aberrantly long 3’UTRs, confirming the role for this element in 3’ end processing. Interestingly, we found that other sequence elements that were previously described in the literature to be part of the polyadenylation signal had a minor effect on expression. We further characterize the sequence specificities of the TA-rich element using additional synthetic 3’ end sequences and show that its activity is sensitive to single base pair mutations and strongly depends on the A/T content of the surrounding sequences. Finally, using a computational model, we show that the strength of this element in native 3’ end sequences can explain some of their measured expression variability (R = 0.41). Together, our results emphasize the importance of efficient 3’ end processing for endogenous protein levels and contribute to an improved understanding of the sequence elements involved in this process.
Cartesian Impedance Control of a UAV with a Robotic Arm

Abstract The dynamic model of a UAV with an attached robotic arm is derived in a symbolic matrix form through the Euler-Lagrangian formalism. A Cartesian impedance control, which provides a dynamic relationship between external generalized forces acting on the structure and the system motion, is then designed. The hovering control of a quadrotor, equipped with a 3-DOF robotic arm and subject to contact forces and external disturbances, is tested in a simulated case study.
Robust Control Synthesis Techniques for Multirate and Multisensing Track-Following Servo Systems in Hard Disk Drives

This paper proposes controller design methods, specially for track-following control of the magnetic read/write head in a hard disk drive (HDD). The servo system to be considered is a general dual-stage multisensing system, which encompasses most of the track-following configurations encountered in the HDD industry, including the traditional single-stage system. For the general system, a robust track-following problem is formulated as a time-varying version of the robust H 2 synthesis problem. Both dynamic and real parametric uncertainties, which are typical model uncertainties in track-following control, are taken into account in the formulation. Three optimal robust controller design techniques with different robustness guarantees are applied to solve the synthesis problem. These are mixed H 2 /H ∞ , mixed H 2 /μ, and robust H 2 syntheses. Advantages and disadvantages of each method are presented. Multirate control, which is inherent to control problems in HDDs, is obtained by reducing multirate problems into linear time-invariant ones, for which there are many useful theories and algorithms available. Most of the techniques proposed in this paper heavily rely on efficient numerical tools for solving linear matrix inequalities.