Miracle-dz/UniFAR-FTUs huggingface dataset:
Towards direct head navigation for robot-guided Transcranial Magnetic Stimulation using 3D laserscans: Idea, setup and feasibility

Direct tracking is more robust than tracking that is based on additional markers. 3D laser scans can be used for direct tracking because they result in a 3D data set of surface points of the scanned object. For head-navigated robotized systems, it is crucial to know where the patient's head is positioned relatively to the robot. We present a novel method to use a 3D laserscanner for direct head navigation in the robotized TMS system that places a coil on the patient's head using an industrial robot. First experimental results showed a translational error < 2mm in the robot hand-eye-calibration with the laserscanner. The rotational error was 0.75° and the scaling error < 0.001. Furthermore, we found that the error of a scanned head to a reference head image was < 0.2mm using ICP. These results have shown that a direct head navigation is feasible for the robotized TMS system. Additional effort has to be made in future systems to speed up the compution time for real time capability.
ATPG Using Fast Justification and Propagation on the Implication Graph

Automatic Test Pattern Generation (ATPG) primarily has to solve three fundamental Boolean problems: justification, propagation, and implication. In the past, various data structures (e.g. netlists, CNFs, decision diagrams) have been used to tackle these problems w ith none of them being specifically optimized for all these tasks. Tha t is why we propose fast and optimized algorithms for justification, propagation, and implication that are part of a versatile and efficie nt SAT based implication engine[1]. It inherits the advantages of structural as well as SAT based techniques as it includes all topological and fu ctional information into a single graph model of the CNF, calledimplication graph (IG) [1]. The multitude of heuristics developed for structural techniques can directly be transfered to the IG. As the compl ex functional operations of justification, propagation, and impli cat on reduce to simple graph algorithms they are easily extended to make u se of bitparallel techniques resulting in a high efficiency. This pap er introduces new methods for fast IG based justification and propagation t hat are included into the implication engine of [1]. Using these algor ithms our tool TIP outperforms the state-of-the-art in structural and SAT bas ed ATPG. Since the IG is automatically generated for an arbitra ry logic and the presented algorithms for justification and implicat ion remain applicable independent of the chosen logic, ATPG for variou s fault models can easily be built on top of the same engine. Tools for pathdelay, gate delay, and stuck-at fault models have already be en d veloped.
Arian: A General Architecture for Advisable Agents

One of the most important issues in multi-agent systems is communication. The agents with more comprehensi ve information (which can be a human observer) advise other age nts by sending messages. Similar agents may also communicate to transfer their experience. These messages are called advic e. In this paper a general method, which is applicable for all agen t architectures will be proposed for integrating advice. In this method advice is modeled by a case in a case-based reasoning system. It is the duty of the advice receiver to der ive a case from each advice message. Each case is composed of a problem, which is circumstances that the advice will be usedand a solution, which is the solution of the advice to that problem. In this paper a 2-layered architecture for refining the agent architecture and internal algorithms with the help of advice will be presented. Two main components of this system is a CBR which refines the parameters and the other is a translator, which translates messages to standard cases. An implemented exam ple is presented to show how this proposed method works.
Floral Induction in Arabidopsis by FLOWERING LOCUS T Requires Direct Repression of BLADE-ON-PETIOLE Genes by the Homeodomain Protein PENNYWISE1[OPEN]

Direct repression of lateral organ boundary genes in the shoot meristem is required for flowering induction. Flowers form on the flanks of the shoot apical meristem (SAM) in response to environmental and endogenous cues. In Arabidopsis (Arabidopsis thaliana), the photoperiodic pathway acts through FLOWERING LOCUS T (FT) to promote floral induction in response to day length. A complex between FT and the basic leucine-zipper transcription factor FD is proposed to form in the SAM, leading to activation of APETALA1 and LEAFY and thereby promoting floral meristem identity. We identified mutations that suppress FT function and recovered a new allele of the homeodomain transcription factor PENNYWISE (PNY). Genetic and molecular analyses showed that ectopic expression of BLADE-ON-PETIOLE1 (BOP1) and BOP2, which encode transcriptional coactivators, in the SAM during vegetative development, confers the late flowering of pny mutants. In wild-type plants, BOP1 and BOP2 are expressed in lateral organs close to boundaries of the SAM, whereas in pny mutants, their expression occurs in the SAM. This ectopic expression lowers FD mRNA levels, reducing responsiveness to FT and impairing activation of APETALA1 and LEAFY. We show that PNY binds to the promoters of BOP1 and BOP2, repressing their transcription. These results demonstrate a direct role for PNY in defining the spatial expression patterns of boundary genes and the significance of this process for floral induction by FT.
Three-Dimensional Ankle Moments and Nonlinear Summation of Rat Triceps Surae Muscles

The Achilles tendon and epimuscular connective tissues mechanically link the triceps surae muscles. These pathways may cause joint moments exerted by each muscle individually not to sum linearly, both in magnitude and direction. The aims were (i) to assess effects of sagittal plane ankle angle (varied between 150° and 70°) on isometric ankle moments, in both magnitude and direction, exerted by active rat triceps surae muscles, (ii) to assess ankle moment summation between those muscles for a range of ankle angles and (iii) to assess effects of sagittal plane ankle angle and muscle activation on Achilles tendon length. At each ankle angle, soleus (SO) and gastrocnemius (GA) muscles were first excited separately to assess ankle-angle moment characteristics and subsequently both muscles were excited simultaneously to investigate moment summation. The magnitude of ankle moment exerted by SO and GA, the SO direction in the transverse and sagittal planes, and the GA direction in the transverse plane were significantly affected by ankle angle. SO moment direction in the frontal and sagittal planes were significantly different from that of GA. Nonlinear magnitude summation varied between 0.6±2.9% and −3.6±2.9%, while the nonlinear direction summation varied between 0.3±0.4° and −0.4±0.7° in the transverse plane, between 0.5±0.4° and 0.1±0.4° in the frontal plane, and between 3.0±7.9° and 0.3±2.3° in the sagittal plane. Changes in tendon length caused by SO contraction were significantly lower than those during contraction of GA and GA+SO simultaneously. Thus, moments exerted by GA and SO sum nonlinearly both in the magnitude and direction. The limited degree of nonlinear summation may be explained by different mechanisms acting in opposite directions.
Clinical utility and patient adherence with ebastine for allergic rhinitis

Allergic rhinitis (AR) is a high prevalence disease, affecting 10%–20% of the general population. AR is sustained by an IgE-mediated reaction, and by a complex inflammatory network of cells, mediators, and cytokines, becoming chronic when exposure to allergen persists. A Th2-biased immune response is the basis for the allergic inflammation. Histamine plays a relevant role in symptom occurrence. Therefore, antihistamine use represents a cornerstone in AR management. Ebastine, a novel antihistamine, is effective overall in controlling symptoms, and its safety profile is good. Recently, a new formulation has been developed, ie, a fast-dissolving tablet. Several studies have demonstrated its favorable characteristics. In conclusion, ebastine is an effective and well tolerated antihistamine that may be prescribed for the treatment of AR. The fast-dissolving tablet formulation provides a new option which may be particularly convenient for the patient.
Stimulus-Dependent Auditory Tuning Results in Synchronous Population Coding of Vocalizations in the Songbird Midbrain

Physiological studies in vocal animals such as songbirds indicate that vocalizations drive auditory neurons particularly well. But the neural mechanisms whereby vocalizations are encoded differently from other sounds in the auditory system are unknown. We used spectrotemporal receptive fields (STRFs) to study the neural encoding of song versus the encoding of a generic sound, modulation-limited noise, by single neurons and the neuronal population in the zebra finch auditory midbrain. The noise was designed to match song in frequency, spectrotemporal modulation boundaries, and power. STRF calculations were balanced between the two stimulus types by forcing a common stimulus subspace. We found that 91% of midbrain neurons showed significant differences in spectral and temporal tuning properties when birds heard song and when birds heard modulation-limited noise. During the processing of noise, spectrotemporal tuning was highly variable across cells. During song processing, the tuning of individual cells became more similar; frequency tuning bandwidth increased, best temporal modulation frequency increased, and spike timing became more precise. The outcome was a population response to song that encoded rapidly changing sounds with power and precision, resulting in a faithful neural representation of the temporal pattern of a song. Modeling responses to song using the tuning to modulation-limited noise showed that the population response would not encode song as precisely or robustly. We conclude that stimulus-dependent changes in auditory tuning during song processing facilitate the high-fidelity encoding of the temporal pattern of a song.
ACCURACY OF ESTIMATED PHYLOGENIES: EFFECTS OF TREE TOPOLOGY AND EVOLUTIONARY MODEL

A simulation study was carried out to investigate the relative importance of tree topology (both balance and stemminess), evolutionary rates (constant, varying among characters, and varying among lineages), and evolutionary models in determining the accuracy with which phylogenetic trees can be estimated. The three evolutionary context models were phyletic (characters can change at each simulated time step), speciational (changes are possible only at the time of speciation into two daughter lineages), and punctuational (changes occur at the time of speciation but only in one of the daughter lineages). UPGMA clustering and maximum parsimony (“Wagner trees”) methods for estimating phylogenies were compared. All trees were based on eight recent OTUs. The three evolutionary context models were found to have the largest influence on accuracy of estimates by both methods. The next most important effect was that of the stemminess × context interaction. Maximum parsimony and UPGMA performed worst under the punctuational models. Under the phyletic model, trees with high stemminess values could be estimated more accurately and balanced trees were slightly easier to estimate than unbalanced ones. Overall, maximum parsimony yielded more accurate trees than UPGMA—but that was expected for these simulations since many more characters than OTUs were used. Our results suggest that the great majority of estimated phylogenetic trees are likely to be quite inaccurate; they underscore the inappropriateness of characterizing current phylogenetic methods as being for reconstruction rather than for estimation.
The Intracellular Bacteria Chlamydia Hijack Peroxisomes and Utilize Their Enzymatic Capacity to Produce Bacteria-Specific Phospholipids

Chlamydia trachomatis is an obligate intracellular pathogen responsible for loss of eyesight through trachoma and for millions of cases annually of sexually transmitted diseases. The bacteria develop within a membrane-bounded inclusion. They lack enzymes for several biosynthetic pathways, including those to make some phospholipids, and exploit their host to compensate. Three-dimensional fluorescence microscopy demonstrates that small organelles of the host, peroxisomes, are translocated into the Chlamydia inclusion and are found adjacent to the bacteria. In cells deficient for peroxisome biogenesis the bacteria are able to multiply and give rise to infectious progeny, demonstrating that peroxisomes are not essential for bacterial development in vitro. Mass spectrometry-based lipidomics reveal the presence in C. trachomatis of plasmalogens, ether phospholipids whose synthesis begins in peroxisomes and have never been described in aerobic bacteria before. Some of the bacterial plasmalogens are novel structures containing bacteria-specific odd-chain fatty acids; they are not made in uninfected cells nor in peroxisome-deficient cells. Their biosynthesis is thus accomplished by the metabolic collaboration of peroxisomes and bacteria.
Appropriate Item Partition for Improving the Mining Performance

Along with the progress of information techniques and the increase of information need, some databases in the real world grow very quickly and their sizes become very huge. If the FP-Growth procedure is directly executed on these databases to mine association rules, the computer memory may not allow all nodes of a FP-tree generated from a huge database. In this paper, a sophisticated mining approach with a flexible partition of items is proposed to effectively derive association rules under the constraint of memory limitation. The experimental results show that the proposed approach can make the mining process under the memory limitation always feasible.
KeyConcept : Exploiting Hierarchical Relationships for Conceptually Indexed Data by Devanand Rajoo Ravindran

Date Accepted 2 Acknowledgements I'm greatly honored to have worked for Dr. Susan Gauch towards my thesis and for KeyConcept. Many thanks are due to her for having helped me hone my skills in programming and inculcate an interest in research. I would also like to thank the committee members of my thesis, Dr. Jerry James and Dr. Costas Tsatsoulis. I also express my gratitude to Sriram Chadalavada, Juan Madrid and Joana Trajkova for having worked with me in my projects. Without their code, I would not be in a position to have completed my thesis. I'm grateful to all ITTC staff for their timely help in solving any technical problems that I've had. I also thank my roommates and the Adams who make my stay in Lawrence more agreeable. I express my heartfelt gratitude to my parents and brother for having believed in me and helping me in all possible ways to pursue my dreams. 3 Abstract As the number of available Web pages grows, users experience increasing difficulty finding documents relevant to their interests. One of the underlying reasons for this is that most search engines find matches based on keywords, regardless of their meanings. To provide the user with more useful information, we need a system that includes information about the conceptual frame of the queries as well as its keywords. This is the goal of KeyConcept, a search engine that retrieves documents based on a combination of keyword and conceptual matching. This paper describes the system architecture of an enhanced KeyConcept, the training of the classifier for the system, and the results of our experiments evaluating system performance. Experiments that check whether result pruning and retrieval based on the hierarchical structure of the ontology help in improving precision are also described. KeyConcept is shown to significantly improve search result precision through its use of conceptual retrieval. Pruning and Hierarchical Retrieval are also shown to yield better results in most cases.
Injection-site lesion prevalence and potential risk factors in UK beef cattle

Injectable veterinary medicinal products (VMPs) are widely used in cattle in the UK, and in particular vaccines are often used on large numbers of animals in the herd. The formation of injection-site lesions (ISLs) is a risk when using injectable products and has potential consequences for meat quality, animal welfare and beef industry income. This study used carcase observation in four abattoirs in England to determine ISL prevalence in beef cattle. Additionally, a questionnaire survey was used to investigate vaccination technique among UK beef farmers. The ISL prevalence was 4.1 per cent (95 per cent CI 3.4 per cent to 4.9 per cent). A potential difference between sites being used for vaccination and the distribution of ISLs on carcases suggested that factors other than vaccination were contributing to ISL incidence. Questionnaire responses highlighted deficits in good vaccination practices such as using the recommended site of injection and needle hygiene. The role of the veterinarian in knowledge transfer is crucial in providing practical injection advice when prescribing vaccines and other VMPs. This study identified factors to address when aiming to reduce ISL formation in UK beef animals.
Polynomial-time algorithms for minimum energy scheduling

The aim of power management policies is to reduce the amount of energy consumed by computer systems while maintaining a satisfactory level of performance. One common method for saving energy is to simply suspend the system during idle times. No energy is consumed in the suspend mode. However, the process of waking up the system itself requires a certain fixed amount of energy, and thus suspending the system is beneficial only if the idle time is long enough to compensate for this additional energy expenditure. In the specific problem studied in the article, we have a set of jobs with release times and deadlines that need to be executed on a single processor. Preemptions are allowed. The processor requires energy L to be woken up and, when it is on, it uses one unit of energy per one unit of time. It has been an open problem whether a schedule minimizing the overall energy consumption can be computed in polynomial time. We solve this problem in positive, by providing an O(n5)-time algorithm. In addition we provide an O(n4)-time algorithm for computing the minimum energy schedule when all jobs have unit length.
Autonomic Nervous System Pharmacogenomics: A Progress Report

Pharmacogenetics, the inherited basis for interindividual differences in drug response, has rapidly expanded with the advent of new molecular tools and the sequencing of the human genome, yielding pharmacogenomics. We review here recent ideas and findings regarding pharmacogenomics of components of the autonomic nervous system, in particular, neuronal nicotinic acetylcholine receptors, postsynaptic receptors with which the parasympathetic and sympathetic neurotransmitters, acetylcholine (ACh) and norepinephrine, respectively, interact. The receptor subtypes that mediate these responses, M1-3 muscarinic cholinergic receptors (mAChRs), and α1A,B,D-, α2A,B,C-, and β1,2,3-adrenergic receptors (AR), show highly variable expression of genetic variants; variants of mAChRs and α1-ARs are relatively rare, whereas α2-AR and β-AR subtype variants are quite common. The largest amount of data is available regarding variants of the latter ARs and represents efforts to associate certain receptor genotypes, most commonly, single nucleotide polymorphisms, with particular phenotypes (e.g., cardiovascular and metabolic responses). In vitro and in vivo studies have yielded inconsistent results; definitive conclusions are limited. We identify several conceptual and methodological problems with available data: sample size, ethnicity, tissue differences, coding versus noncoding variants, limited studies of haplotypes, and interaction among variants. Thus, although progress has been made in identifying genetic variation that influences drug response for autonomic nervous system components, we are still at the early stages of defining the most critical genetic determinants and their role in human physiology and pharmacology.
Analyzing Sequential User Behavior on the Web

This tutorial aims at outlining fundamental methods for studying categorical sequences on the Web. Categorical sequences can refer to any kind of transitional data between a set of states, for example human navigation (transitions) between Web sites (states). Presented methods focus on sequential pattern mining, modeling and inference aiming at better understanding the production of sequences. A core model utilized in this tutorial is the Markov chain model. We hope that this tutorial raises interest and awareness of the field at hand and provides participants with basic tools for analyzing sequential user behavior on the Web.
Self-calibrating networks-on-chip

Networks-on-chip provide an elegant framework to efficiently reuse predesigned cores. However, reuse of cores is jeopardized by new deep sub-micron noise effects that challenge the reliability of CMOS technology. Moreover, noise margins are further reduced as supply voltages scale down. We advocate that self-calibrating techniques will be needed to maintain an acceptable design trade-off between energy, performance, and reliability. As a result, self-calibrating techniques have to be integrated within networks-on-chip. This paper presents a self-calibrating link and discusses qualitatively the problem of controlling adaptively its voltage and frequency.
Fabricating articulated characters from skinned meshes

Articulated deformable characters are widespread in computer animation. Unfortunately, we lack methods for their automatic fabrication using modern additive manufacturing (AM) technologies. We propose a method that takes a skinned mesh as input, then estimates a fabricatable single-material model that approximates the 3D kinematics of the corresponding virtual articulated character in a piecewise linear manner. We first extract a set of potential joint locations. From this set, together with optional, user-specified range constraints, we then estimate mechanical friction joints that satisfy inter-joint non-penetration and other fabrication constraints. To avoid brittle joint designs, we place joint centers on an approximate medial axis representation of the input geometry, and maximize each joint's minimal cross-sectional area. We provide several demonstrations, manufactured as single, assembled pieces using 3D printers.
Health Inequalities Through the Lens of Health Capital Theory: Issues, Solutions, and Future Directions

We explore what health-capital theory has to offer in terms of informing and directing research into health inequality. We argue that economic theory can help in identifying mechanisms through which specific socioeconomic indicators and health interact. Our reading of the literature, and our own work, leads us to conclude that non-degenerate versions of the Grossman model (1972a;b) and its extensions can explain many salient stylized facts on health inequalities. Yet, further development is required in at least two directions. First, a childhood phase needs to be incorporated, in recognition of the importance of childhood endowments and investments in the determination of later-life socioeconomic and health outcomes. Second, a unified theory of joint investment in skill (or human) capital and in health capital could provide a basis for a theory of the relationship between education and health.