Miracle-dz/UniFAR-FTUs huggingface dataset:
Harmonic analysis for the characterization and correction of geometric distortion in MRI.

PURPOSE Magnetic resonance imaging (MRI) is gaining widespread use in radiation therapy planning, patient setup verification, and real-time guidance of radiation delivery. Successful implementation of these technologies relies on the development of simple and efficient methods to characterize and monitor the geometric distortions arising due to system imperfections and gradient nonlinearities. To this end, the authors present the theory and validation of a novel harmonic approach to the quantification of system-related distortions in MRI. METHODS The theory of spatial encoding in MRI is applied to demonstrate that the 3D distortion vector field (DVF) is given by the solution of a second-order boundary value problem (BVP). This BVP is comprised of Laplace's equation and a limited measurement of the distortion on the boundary of a specified region of interest (ROI). An analytical series expansion solving this BVP within a spherical ROI is obtained, and a statistical uncertainty analysis is performed to determine how random errors in the boundary measurements propagate to the ROI interior. This series expansion is then evaluated to obtain volumetric DVF mappings that are compared to reference data obtained on a 3 T full-body scanner. This validation is performed within two spheres of 20 cm diameter (one centered at the scanner origin and the other offset +3 cm along each of the transverse directions). Initially, a high-order mapping requiring measurements at 5810 boundary points is used. Then, after exploring the impact of the boundary sampling density and the effect of series truncation, a reduced-order mapping requiring measurements at 302 boundary points is evaluated. RESULTS The volumetric DVF mappings obtained from the harmonic analysis are in good agreement with the reference data. Following distortion correction using the high-order mapping, the authors estimate a reduction in the mean distortion magnitude from 0.86 to 0.42 mm and from 0.93 to 0.39 mm within the central and offset ROIs, respectively. In addition, the fraction of points with a distortion magnitude greater than 1 mm is reduced from 35.6% to 2.8% and from 40.4% to 1.5%, respectively. Similarly, following correction using the reduced-order mapping, the mean distortion magnitude reduces to 0.45-0.42 mm within the central and offset ROIs, and the fraction of points with a distortion magnitude greater than 1 mm is reduced to 2.8% and 1.5%, respectively. CONCLUSIONS A novel harmonic approach to the characterization of system-related distortions in MRI is presented. This method permits a complete and accurate mapping of the DVF within a specified ROI using a limited measurement of the distortion on the ROI boundary. This technique eliminates the requirement to exhaustively sample the DVF at a dense 3D array of points, thereby permitting the design of simple, inexpensive phantoms that may incorporate additional modules for auxiliary quality assurance objectives.
TeXshade: shading and labeling of multiple sequence alignments using LaTeX2e

Motivation: Typesetting, shading and labeling of nucleotide and peptide alignments using standard word processing or graphics software is time consuming. Available automatic sequence shading programs usually do not allow manual application of additional shadings or labels. Hence, a flexible alignment shading package was designed for both calculated and manual shading, using the macro language of the scientific typesetting software L AT E X2 e. Results: T E Xshade is the first T E X-based alignment shading software featuring, in addition to standard identity and similarity shading, special modes for the display of functional aspects such as charge, hydropathy or solvent accessibility. A plenitude of commands for manual shading, graphical labels, re-arrangements of the sequence order, numbering, legends etc. is implemented. Further, TEXshade allows the inclusion and display of secondary structure predictions in the DSSP-, STRIDEand PHD-format. Availability: From http:// homepages.uni-tuebingen.de/ beitz/ tse.html (macro package and on-line documentation)
A proposed classification for assessing rupture risk in patients with intracranial arteriovenous malformations

Background: Whether cerebral arteriovenous malformations (AVMs) should be treated remains an ongoing debate. Nevertheless, there is a need for predictive factors that assist in labelling lesions as low or high risk for future rupture. Our aim was to design a new classification that would consider hemodynamic and anatomic factors in the rapid assessment of rupture risk in patients with AVMs. Methods: This was a retrospective study that included 639 patients with ruptured and unruptured AVMs. We proposed a new classification score (1–4 points) for AVM rupture risk using three factors: feeding artery mean velocity (Vm), nidus size, and type of venous drainage. We employed descriptive statistics and logistic regression analysis. Results: A total of 639 patients with cerebral AVMs, 388 (60%) had unruptured AVMs and 251 (40%) had ruptured AVMs. Logistic regression analysis revealed a significant effect of Vm, nidus size, and venous drainage type in accounting for the variability of rupture odds (P = 0.0001, R2 = 0.437) for patients with AVMs. Based in the odds ratios, grades 1 and 2 of the proposed classification were corresponded to low risk of hemorrhage, while grades 3 and 4 were associated with hemorrhage: 1 point OR = (0.107 95% CI; 0.061–0.188), 2 point OR = (0.227 95% CI; 0.153–0.338), 3 point OR = (3.292 95% CI; 2.325–4.661), and 4 point OR = (23.304 95% CI; 11.077–49.027). Conclusion: This classification is useful and easy to use, and it may allow for the individualisation of each cerebral AVM and the assessment of rupture risk based on a model of categorisation.
Evaluation of Two Real Time Low Level Image Processing Architecture

The IMAP-VISION - a SIMD architecture Thc papcr presents a study on the impact of using SIMD (S~ngc Instn~ct~on Multiple Data) techniques and architccturcs in low lcvel image processing. Speedups obtained on a SIMD parallel architecture (IMAP- VISION board) and a single Intel MMX processor computer are presented for different low-level image processing operators. While the IMAP-Vision system performs better bccause of the large number of processing elements, the MMX processor remains a good candidate for low-level image processing.
Methodologies, Models and Algorithms for Patients Rehabilitation

Summary Introduction: This editorial is part of the Focus Theme of Methods of Information in Medicine on “Methodologies, Models and Algorithms for Patients Rehabilitation”. Objective: The objective of this focus theme is to present current solutions by means of technologies and human factors related to the use of Information and Communication Technologies (ICT) for improving patient rehabilitation. Methods: The focus theme examines distinctive measurements of strengthening methodologies, models and algorithms for disabled people in terms of rehabilitation and health care, and to explore the extent to which ICT is a useful tool in this process. Results: The focus theme records a set of solutions for ICT systems developed to improve the rehabilitation process of disabled people and to help them in carrying out their daily life. Conclusions: The development and subsequent setting up of computers for the patients’ rehabilitation process is of continuous interest and growth.
Changing Bee and Hoverfly Pollinator Assemblages along an Urban-Rural Gradient

Background The potential for reduced pollination ecosystem service due to global declines of bees and other pollinators is cause for considerable concern. Habitat degradation, destruction and fragmentation due to agricultural intensification have historically been the main causes of this pollinator decline. However, despite increasing and accelerating levels of global urbanization, very little research has investigated the effects of urbanization on pollinator assemblages. We assessed changes in the diversity, abundance and species composition of bee and hoverfly pollinator assemblages in urban, suburban, and rural sites across a UK city. Methodology/Principal Findings Bees and hoverflies were trapped and netted at 24 sites of similar habitat character (churchyards and cemeteries) that varied in position along a gradient of urbanization. Local habitat quality (altitude, shelter from wind, diversity and abundance of flowers), and the broader-scale degree of urbanization (e.g. percentage of built landscape and gardens within 100 m, 250 m, 500 m, 1 km, and 2.5 km of the site) were assessed for each study site. The diversity and abundance of pollinators were both significantly negatively associated with higher levels of urbanization. Assemblage composition changed along the urbanization gradient with some species positively associated with urban and suburban land-use, but more species negatively so. Pollinator assemblages were positively affected by good site habitat quality, in particular the availability of flowering plants. Conclusions/Significance Our results show that urban areas can support diverse pollinator assemblages, but that this capacity is strongly affected by local habitat quality. Nonetheless, in both urban and suburban areas of the city the assemblages had fewer individuals and lower diversity than similar rural habitats. The unique development histories of different urban areas, and the difficulty of assessing mobile pollinator assemblages in just part of their range, mean that complementary studies in different cities and urban habitats are required to discover if these findings are more widely applicable.
Cooperation in wireless ad hoc networks

In wireless ad hoc networks, nodes communicate with far off destinations using intermediate nodes as relays. Since wireless nodes are energy constrained, it may not be in the best interest of a node to always accept relay requests. On the other hand, if all nodes decide not to expend energy in relaying, then network throughput will drop dramatically. Both these extreme scenarios (complete cooperation and complete noncooperation) are inimical to the interests of a user. In this paper we address the issue of user cooperation in ad hoc networks. We assume that nodes are rational, i.e., their actions are strictly determined by self interest, and that each node is associated with a minimum lifetime constraint. Given these lifetime constraints and the assumption of rational behavior, we are able to determine the optimal throughput that each node should receive. We define this to be the rational Pareto optimal operating point. We then propose a distributed and scalable acceptance algorithm called generous tit-for-tat (GTFT). The acceptance algorithm is used by the nodes to decide whether to accept or reject a relay request. We show that GTFT results in a Nash equilibrium and prove that the system converges to the rational and optimal operating point.
In Vitro Activities of Piperaquine, Lumefantrine, and Dihydroartemisinin in Kenyan Plasmodium falciparum Isolates and Polymorphisms in pfcrt and pfmdr1

ABSTRACT We have analyzed the in vitro chemosensitivity profiles of 115 Kenyan isolates for chloroquine (CQ), piperaquine, lumefantrine (LM), and dihydroartemisinin in association with polymorphisms in pfcrt at codon 76 and pfmdr1 at codon 86, as well as with variations of the copy number of pfmdr1. The median drug concentrations that inhibit 50% of parasite growth (IC50s) were 41 nM (interquartile range [IQR], 18 to 73 nM), 50 nM (IQR, 29 to 96 nM), 32 nM (IQR, 17 to 46 nM), and 2 nM (IQR, 1 to 3 nM) for CQ, LM, piperaquine, and dihydroartemisinin, respectively. The activity of CQ correlated inversely with that of LM (r2 = −0.26; P = 0.02). Interestingly, parasites for which LM IC50s were higher were wild type for pfcrt-76 and pfmdr1-86. All isolates had one pfmdr1 copy. Thus, the decrease in LM activity is associated with the selection of wild-type pfcrt-76 and pfmdr1-86 parasites, a feature that accounts for the inverse relationship between CQ and LM. Therefore, the use of LM-artemether is likely to lead to the selection of more CQ-susceptible parasites.
Coordination of hydraulic manipulators by reinforcement learning

In this paper, a reinforcement learning method is applied to coordinate a pair of horizontal hydraulic actuators engaged in the cooperative positioning of an object. The goal is to enable the actuators to discover how to intelligently select control actions that tend to reduce the interaction forces directed along the axis of motion, while maintaining the desired trajectory. First, a detailed and realistic dynamic model of the entire system is derived. A multi-layer reinforcement learning neural network control architecture is designed next to regulate the interaction force during positioning. To regulate the interaction force, the neural network measures the interaction force and proposes a modification to the a priori prescribed formation constrained position trajectory. Each actuator system is outfitted with such a neural controller so that a decentralized reinforcement learning control system results. Simulations demonstrate the efficacy of the approach towards reducing the interaction forces and minimizing the associated object internal force in a single degree of freedom
Reciprocal Inhibitory Connections Regulate the Spatiotemporal Properties of Intrathalamic Oscillations

Mice with an inactivated GABAA receptor β3 subunit gene have features of Angelman syndrome, including absence-like seizures. This suggests the occurrence of abnormal hypersynchrony in the thalamocortical system. Within the thalamus, the efficacy of inhibitory synapses between thalamic reticular (RE) neurons is selectively compromised, and thalamic oscillations in vitro are prolonged and lack spatial phase gradients (Huntsman et al., 1999). Here we used computational models to examine how intra-RE inhibition regulates intrathalamic oscillations. A major effect is an abbreviation of network responses, which is caused by long-lasting intra-RE inhibition that shunts recurrent excitatory input. In addition, differential activation of RE cells desynchronizes network activity. Near the slice center, where many cells are initially activated, there is a resultant high level of intra-RE inhibition. This leads to RE cell burst truncation in the central region and a gradient in the timing of thalamocortical cell activity similar to that observed in vitro. Although RE cell burst durations were shortened by this mechanism, there was very little effect on the times at which RE cells began to burst. The above results depended on widespread stimuli that activated RE cells in regions larger than the diameter of intra-RE connections. By contrast, more focal stimuli could elicit oscillations that lasted several cycles and remained confined to a small region. These results suggest that intra-RE inhibition restricts intrathalamic activity to particular spatiotemporal patterns to allow focal recurrent activity that may be relevant for normal thalamocortical function while preventing widespread synchronization as occurs in seizures.
Resource Reservation Schemes for IEEE 802.11-Based Wireless Networks: A Survey

IEEE 802.11-based wireless technology is widely applied in many areas, supporting communications where wired devices are not available. However, providing satisfactory QoS is still a challenging topic in 802.11-based wireless networks because of the problems such as error-prone wireless channel condition, power consumption, short of centralised facility, mobility as well as channel contention. For addressing these issues, one feasible solution can be to implement resource reservation for the sessions that require QoS assurances. The responsibility of resource reservation scheme is to make sure that QoS-sensitive sessions get sufficient bandwidth in order to sustain their high performance. Difficulties are already identified for designing resource reservation schemes in both network and MAC layers. However, there is no profound investigation outcome for this kind of QoS mechanism. Therefore, in this paper, we intend to produce a comprehensive survey of resource reservation approaches for IEEE 802.11-based wireless networks. The associated research works are summarised and also classified. Moreover, both the drawbacks and the merits of each kind of resource reservation scheme are highlighted.
A new approach for profit-based unit commitment using Lagrangian relaxation combined with ant colony search algorithm

The past decade has seen a dramatic change in the manner in which the power industry is organized. It has moved from a formerly vertically integrated and highly regulated industry to one that has been horizontally integrated in which the generation, transmission and distribution are unbundled. In the past, utilities had to produce power to satisfy their customers with objective to minimize costs and all demand/reserve were met. However, it is not necessary in a restructured system. Under new structure, generation companies (GENCOs) schedule their generators with objective to maximize their own profit without regard for system social benefit. Power and reserve prices become important factors in decision process. GENCOs' decision to commit generating units is associated with financial risks. This unit commitment has a different objective than that of the traditional unit commitment and is referred to as profit-based unit commitment to emphasize the importance of the profit. This paper presents a hybrid model between Lagrangian relaxation (LR) and Ant Colony search algorithm (ACSA) to solve the profit-based UC problem.
The role of visual culture and literacy: reconciling the dialectic

In this paper I wish to develop an argument that ‘context’ is the crucial feature of any program, this has been evidenced in the success of theme based art theory/history programs and most of the significant curator driven exhibitions (Documenta, Asia Pacific Triennial and the Sydney Biennale). Educators must not assume the validity of their subject but must elaborate an essential purpose and relationship to culture, community and the economy. To this end art educators need to be both proficient in practical production and conceptually articulate with the ability to marry theory and practice together.
TOPICAL REVIEW: Coarse grain models and the computer simulation of soft materials

This article presents a topical review of coarse grain simulation techniques. First, we motivate these techniques with illustrative examples from biology and materials science. Next, approaches in the literature for increasing the efficiency of atomistic simulations are mentioned. Considerations related to a specific coarse grain modelling approach are discussed at length, and the consequences arising from the loss of detail are given. Finally, a large number of results are presented to give the reader a feeling for the types of problem which can be addressed.
Automated 2-D cephalometric analysis of X-ray by image registration approach based on least square approximator

This paper presents a new approach to cephalometric x-ray landmark localization. This approach is based on extracting features from face profile of the lateral skull x-ray. The extracted side profile is then segmented based on knowledge of known local facial structures. Once the face profile is properly segmented, nine perceptually significant landmarks (fiducial points) on the face are registered based on a local maximum curvature computation. These fiducial points are used for point-by-point correspondence to find the transformation coefficients of the control points between two images of a scene. Next, we use the obtained coefficients to find the locations of other landmarks on the target image by mapping the landmarks of the reference image. The algorithm was tested on more than 80 x-ray images to locate 20 landmarks. It was possible to locate the landmarks with accuracy of ±2mm on more 90% of the landmarks.
Secure Guaranteed Computation

We introduce secure guaranteed two-party computation, where parties commit in advance to compute a function over their private inputs, by providing some (validated) compensation, such that if a party fails to provide an appropriate input during protocol execution, then the peer receives the compensation. Enforcement of the guarantees requires a trusted enforcement authority (TEA); however, the protocol protects condentiality even from the TEA. Our secure guaranteed computation protocol is optimistic, i.e., the TEA is involved only if a party fails to participate (correctly). Secure guaranteed computation has direct practical applications, such as sensitive trading of nancial products, and could also be used as a building block to motivate parties to complete protocols, e.g., ensuring unbiased coin tossing. The guarantee process can be either symmetric (both parties provide guarantees) or asymmetric (e.g., only server provides guarantee to client). Symmetric guarantees should also be fair, i.e., one party cannot obtain guarantee of the other party without supplying a guarantee as well. The protocol guaranteeing output, which we present uses in a modular manner a new protocol, that we construct, for optimistic fair secure computation, which may be of independent interest, as it is simpler and more ecient than previously known protocols.
TCDSCSS: Dimensionality Reduction to Evaluate Texts of Varying Lengths - an IR Approach

This paper provides system description of the cross-level semantic similarity task for the SEMEVAL-2014 workshop. Crosslevel semantic similarity measures the degree of relatedness between texts of varying lengths such as Paragraph to Sentence and Sentence to Phrase. Latent Semantic Analysis was used to evaluate the cross-level semantic relatedness between the texts to achieve above baseline scores, tested on the training and test datasets. We also tried using a bag-of-vectors approach to evaluate the semantic relatedness. This bag-of-vectors approach however did not produced encouraging results.
Minimum Exposed Path to the Attack (MEPA) in Mobile Ad Hoc Network (MANET)

Lack of infrastructure, central controlling authority and the properties of wireless links make mobile ad hoc networks (MANETs) vulnerable to attacks. Several protocols have been proposed to make the routing protocols handle attacks in MANETs. These protocols detect the misbehaving nodes and re-route the data packets around them, mostly along the shortest such path. However, no single protocol handles all the attacks. A variant of the problem for routing around misbehaving nodes in ad hoc networks can be stated as: given a set of nodes under the danger of attack, one wishes to determine the path which is farthest from the endangered nodes. The problem does not address the problem of handling attack directly but tries to minimize the impact of attack. The problem also finds its applications in sensor networks. In this paper, we present a simple and efficient algorithm to solve the problem. The algorithm converges in O(d2) time where d is the diameter of the network.