Miracle-dz/UniFAR-FTUs huggingface dataset:
Dynamic Image and Fieldmap Joint Estimation Methods for MRI Using Single-Shot Trajectories.

Dynamic Image and Fieldmap Joint Estimation Methods for MRI Using Single-Shot Trajectories by Antonis Matakos Chair: Jeffrey A. Fessler In susceptibility-weighted MRI, ignoring the magnetic field inhomogeneity can lead to severe reconstruction artifacts. Correcting for the effects of magnetic field inhomogeneity requires accurate fieldmaps. Especially in functional MRI, dynamic updates are desirable, since the fieldmap may change in time. Also, susceptibility effects that induce field inhomogeneity often have non-zero through-plane gradients, which, if uncorrected, can cause signal loss in the reconstructed images. Most image reconstruction methods that compensate for field inhomogeneity, even using dynamic fieldmap updates, ignore through-plane fieldmap gradients. Another major consideration in MR image reconstruction is the trajectory selection, since the quality of the obtained results can greatly depend on the chosen trajectory. Therefore, optimizing the trajectory used for the problem at hand may greatly improve the reconstruction quality. Furthermore, the echo-planar (EPI) trajectories used for fast acquisitions are susceptible to misalignments due to scanner imperfections that lead to ghosting artifacts in the reconstructed images. Finally, standard optimization methods, like CG-based algorithms, may be slow to converge and recently proposed algorithms based on the Augmented Lagrangian (AL) framework have shown the potential to lead to more efficient optimization algorithms, especially in MRI reconstruction problems with non-quadratic regularization. In this work, we propose a computationally efficient, model-based iterative method for joint reconstruction of dynamic images and fieldmaps in single coil and parallel MRI, using single-shot trajectories. We first exploit the fieldmap smoothness to perform joint estimation using less than two full data sets and then we exploit the sensitivity encoding from parallel imaging to reduce the acquisition length and perform joint reconstruction using just one full k-space dataset. Subsequently, we extend the proposed method to account for the through-plane gradients of the field
Delay equations driven by rough paths

In this article, we illustrate the flexibility of the algebraic integration formalism introduced in M. Gubinelli, J. Funct. Anal. 216 , 86-140, 2004, Math. Review 2005k:60169 , by establishing an existence and uniqueness result for delay equations driven by rough paths. We then apply our results to the case where the driving path is a fractional Brownian motion with Hurst parameter $H >1/3$.
An investigation on the biodynamic foundation of a rat tail vibration model

The objectives of this study are to examine the fundamental characteristics of the biodynamic responses of a rat tail to vibration and to compare them with those of human fingers. Vibration transmission through tails exposed to three vibration magnitudes (1 g, 5 g, and 10 g r.m.s.) at six frequencies (32 Hz, 63 Hz, 125 Hz, 160 Hz, 250 Hz, and 500 Hz) was measured using a laser vibrometer. A mechanical-equivalent model of the tail was established on the basis of the transmissibility data, which was used to estimate the biodynamic deformation and vibration power absorption at several representative locations on the tail. They were compared with those derived from a mechanical-equivalent model of human fingers reported in the literature. This study found that, similar to human fingers, the biodynamic responses of the rat tail depends on the vibration magnitude, frequency, and measurement location. With the restraint method used in this study, the natural frequency of the rat tail is in the range 161–368 Hz, which is mostly within the general range of human finger resonant frequencies (100–350 Hz). However, the damping ratios of the rat tail at the unconstrained locations are from 0.094 to 0.394, which are lower than those of human fingers (0.708–0.725). Whereas the biodynamic responses of human fingers at frequencies lower than 100 Hz could be significantly influenced by the biodynamics of the entire hand—arm system, the rat tail biodynamic responses can be considered independent of the rat body in the frequency range used in this study. Based on these findings it is concluded that, although there are some differences between the frequency dependences of the biodynamic responses of the rat tail and human fingers, the rat tail model can provide a practical and reasonable approach to examine the relationships between the biodynamic and biological responses at midrange to high frequencies, and to understand the mechanisms underlying vibration-induced finger disorders.
The Role of Organisational Culture on Knowledge Sharing by Using Knowledge Management Systems in MNCs

Knowledge is important in organisations and knowledge cannot be effective unless they are shared. Therefore, Knowledge Management Systems (KMSs) are used in organisations to share, utilise, and integrate knowledge. Organisational culture (OC) is an important factor and needs to be considered in Knowledge Sharing (KS), although it can foster sharing and collaboration, it must be handled sensitively with respect to the natural resistance of people and the existing culture toward change inside organisations. This paper seeks to explore how organisational culture can facilitate knowledge sharing by using KMSs in MNCs. Based on 42 semi-structured interviews, MNCs are recommended to consider OC as a significant factor that affects KMSs usage and KS. They are also advised to create a favourable environment or OC to enable employees in all branches and at all levels to utilise their knowledge resources by using KMSs in KS which will help managers to identify new ways supporting and facilitating knowledge sharing via using KMSs in MNCs.
Role of Urinary Cytology in Detecting Human Polyoma BK Virus in Kidney Transplant Recipients

Objective: To report data on the evaluation of the efficacy of urine cytology in detecting BK virus (BKV). Material and Methods: Papanicolaou-stained cytospin preparations of randomly collected urine samples from 8 renal transplant (RTR) patients (5 males, 3 females, age: 23–63 years) who previously tested positive for BKV by PCR in urine or blood or both were studied. Urine sediment from 3 of the patients was processed for ultrastructural examination (EM). Renal biopsies before and after BKV detection were also evaluated. Results: The interval between renal transplant and urine cytology ranged between 2 and 5 years. Urine from females was difficult to assess due to vaginal contamination. In 2 of the 5 urine specimens from male recipients BKV-infected decoy cells were identified. Viral particles suggestive of BKV were identified on EM in 2 of the 3 specimens studied. Kidney biopsies showed morphologic features suggestive of BKV infection in 2 cases, 1 each detected on cytology and EM, respectively. Conclusion: Screening for the presence of decoy cells in urine provides a simple sensitive means for the diagnosis of BKV nephropathy in RTR.
The Berlin SPARQL Benchmark

The SPARQL Query Language for RDF and the SPARQL Protocol for RDF are implemented by a growing number of storage systems and are used within enterprise and open Web settings. As SPARQL is taken up by the community, there is a growing need for benchmarks to compare the performance of storage systems that expose SPARQL endpoints via the SPARQL protocol. Such systems include native RDF stores as well as systems that rewrite SPARQL queries to SQL queries against non-RDF relational databases. This article introduces the Berlin SPARQL Benchmark (BSBM) for comparing the performance of native RDF stores with the performance of SPARQL-to-SQL rewriters across architectures. The benchmark is built around an e-commerce use case in which a set of products is offered by different vendors and consumers have posted reviews about products. The benchmark query mix emulates the search and navigation pattern of a consumer looking for a product. The article discusses the design of the BSBM benchmark and presents the results of a benchmark experiment comparing the performance of four popular RDF stores (Sesame, Virtuoso, Jena TDB, and Jena SDB) with the performance of two SPARQL-to-SQL rewriters (D2R Server and Virtuoso RDF Views) as well as the performance of two relational database management systems (MySQL and Virtuoso RDBMS).
A New Group B Adenovirus Receptor Is Expressed at High Levels on Human Stem and Tumor Cells

ABSTRACT CD46 is used by human group B adenoviruses (Ads) as a high-affinity attachment receptor. Here we show evidence that several group B Ads utilize an additional receptor for infection of human cells, which is different from CD46. We tentatively named this receptor receptor X. Competition studies with unlabeled and labeled Ads, recombinant Ad fiber knobs, and soluble CD46 and CD46 antibodies revealed three different subgroups of group B Ads, in terms of their receptor usage. Group I (Ad16, -21, -35, and -50) nearly exclusively uses CD46. Group II (Ad3, -7p, and -14) utilizes receptor X and not CD46. Group III (Ad11p) uses both CD46 and the alternative receptor X. Interaction of group II and III Ads with receptor X occurs via the fiber knob. Receptor X is an abundantly expressed glycoprotein that interacts with group II and III Ads at relatively low affinity in a Ca2+-dependent manner. This receptor is expressed at high levels on human mesenchymal and undifferentiated embryonic stem cells, as well as on human cancer cell lines. These findings have practical implications for stem cell and gene therapy.
Structured sparsity-inducing norms through submodular functions

Sparse methods for supervised learning aim at finding good linear predictors from as few variables as possible, i.e., with small cardinality of their supports. This combinatorial selection problem is often turned into a convex optimization problem by replacing the cardinality function by its convex envelope (tightest convex lower bound), in this case the l1-norm. In this paper, we investigate more general set-functions than the cardinality, that may incorporate prior knowledge or structural constraints which are common in many applications: namely, we show that for nondecreasing submodular set-functions, the corresponding convex envelope can be obtained from its Lovasz extension, a common tool in submodular analysis. This defines a family of polyhedral norms, for which we provide generic algorithmic tools (subgradients and proximal operators) and theoretical results (conditions for support recovery or high-dimensional inference). By selecting specific submodular functions, we can give a new interpretation to known norms, such as those based on rank-statistics or grouped norms with potentially overlapping groups; we also define new norms, in particular ones that can be used as non-factorial priors for supervised learning.
An efficient program for phylogenetic inference using simulated annealing

Inference of phylogenetic trees comprising thousands of organisms based on the maximum likelihood method is computationally expensive. A new program RAxML-SA (Randomized Axelerated Maximum Likelihood with Simulated-Annealing) is presented that combines simulated annealing and hill-climbing techniques to improve the quality of final trees. In addition, to the ability to perform backward steps and potentially escape local maxima provided by simulated-annealing, a large number of "good" alternative topologies is generated- which can be used to build a consensus tree on the fly. Though, slower than some of the fastest hill-climbing programs such as RAxML-III and PHYML, RAxML-SAfinds better trees for large real data alignments containing more than 250 sequences. Furthermore, the performance on 40 simulated500-taxon alignments is reasonable in comparison to PHYML. Finally, a straight-forward and efficient OpenMP parallelization of RAxML is presented.
Home unattended vs hospital telemonitored polysomnography in suspected obstructive sleep apnea syndrome: a randomized crossover trial.

STUDY OBJECTIVE To compare home unattended polysomnography (H-PSG) with polysomnography performed in a local hospital and telemonitored by a sleep laboratory (T-PSG) in the diagnosis of obstructive sleep apnea syndrome (OSAS). DESIGN Randomized crossover trial. PATIENTS Ninety-nine patients with suspected OSAS who underwent H-PSG and T-PSG on 2 consecutive nights, according to a randomized order. MEASUREMENTS H-PSG and T-PSG were compared in terms of (1) effectiveness, only recordings providing interpretable signals from at least one EEG, the electro-oculograph, the electromyograph, air flow, thoracic or abdominal movements, and arterial oxygen saturation for 180 min of sleep were considered to be effective; (2) patient preference assessed by a questionnaire; and (3) polysomnographic indexes and final interpretative results in patients for whom both recordings were legible. RESULTS Recordings were considered to be ineffective in 11.2% of T-PSG (95% confidence interval [CI], 4.9 to 17.4%) and in 23.4% of H-PSG (95% CI, 19.12 to 27.68%). Thermistor problems were the main cause of failure of H-PSG. Forty-one percent of patients preferred H-PSG, and 55% preferred T-PSG. H-PSG and T-PSG did not differ in terms of sleep and respiratory indexes in the 65 patients in whom both recordings were legible. H-PSG and T-PSG were concordant in 58 of 65 patients using a 10-event-per-hour apnea-hypopnea index cutoff value for the diagnosis of OSAS. CONCLUSIONS T-PSG is clearly superior to H-PSG from a technical point of view and tends to be preferred by patients. The site of recording (home vs hospital) has no influence on polysomnographic indexes.
The Relationship of Human Atrial Cellular Electrophysiology to Clinical Function and Ultrastructure

Although previous studies have described the electrophysiological and ultrastructural characteristics of human cardiac fibers, no attempt has been made as yet to describe quantitatively the relationship between the ultrastructural and cellular electrophysiological derangements occurring with cardiac disease, and their clinical manifestations. In this study, we used standard microelectrode techniques to record the action potential characteristics of human atrial fibers obtained during cardiac surgery and correlated the electrophysiological parameters with clinical and ultrastructural data. Ultrastructure was studied by optical and electron microscopy. We found a multiple linear regression among maximum diastolic potential, atrial size and pressure, P wave duration and ultrastructure changes. Proliferations of Z band material, widening of intercalated discs, and degenerative changes were quantified and correlated with electrophysiological and clinical data. These studies emphasize the relationship between hemodynamic anomalies and resultant changes in both human atrial fiber structure and electrical function. Finally, the likelihood of occurrence of arrhythmias can be predicted using the analytic method described.
Computational strategies for reducing annotation effort in language documentation

With the urgent need to document the world’s dying languages , it is important to explore ways to speed up language documentation efforts. One promising avenue is to use techniques from computational linguistics to automate some of the process. Here we consider unsupervised morphologica l segmentation and active learning for creating interlinear glossed text ( IGT) for the Mayan language Uspanteko. The practical goal is to produce a total ly annotated corpus that is as accurate as possible given limited time for man ual annotation. We discuss results from several experiments that suggest th ere is indeed much promise in these methods but also show that further developm ent is necessary to make them robustly useful for a wide range of conditions an d t sks. We also provide a detailed discussion of how two documentary lingui sts perceived machine support in IGT production and how their annotation p erformance varied with different levels of machine support. 1 LiLT Volume X, Issue Y, November 2009. Computational strategies for reducing annotation effort i n language documentation . Copyright c © 2009, CSLI Publications. 2 / L I LT VOLUME X, ISSUEY NOVEMBER 2009
Long-term movie popularity models in video-on-demand systems: or the life of an on-demand movie

Large scale video-on-demand systems require that the serv ers offering the video retrieval and playback services are arranged as a distributed system in order to support a lar ge number of concurrent streams. If such a system is hierarchical, an end-node serv er handles the requests from a particular area, the ne xt server in the hierarchy takes the request over for several end-node servers if those can not answer the request and so on. This architecture pro vides for cost efficiency, reliability and scalability of serv ers. The end-node servers store only a limited set of the o verall available information which changes over time due to user interests. If a video is requested which is not available, this server contacts the next server in the hierarchy. To decide the size and location of the video serv ers and the location of videos in the hierarch y, the access behaviour of users must be considered. Various models for the simulation of user behavior (and thus, of the load induced on the video serv ers) have been presented in the literature. Only a fe w of these models are designed to take long-term effects into account because the basis for most of the models are short-term influences on a single video server and the load on this single machine. In this paper we describe a new user behavior model and show that various assumptions made within other models are unrealistic.
Fast Distributed Multi-agent Plan Execution with Dynamic Task Assignment and Scheduling

An essential quality of a good partner is her responsiveness to other team members. Recent work in dynamic plan execution exhibits elements of this quality through the ability to adapt to the temporal uncertainties of others agents and the environment. However, a good teammate also has the ability to adapt on-the-fly through task assignment. We generalize the framework of dynamic execution to perform plan execution with dynamic task assignment as well as scheduling.This paper introduces Chaski, a multi-agent executive for scheduling temporal plans with online task assignment. Chaski enables an agent to dynamically update its plan in response to disturbances in task assignment and the schedule of other agents. The agent then uses the updated plan to choose, schedule and execute actions that are guaranteed to be temporally consistent and logically valid within the multi-agent plan. Chaski is made efficient through an incremental algorithm that compactly encodes all scheduling policies for all possible task assignments. We apply Chaski to perform multi-manipulator coordination using two Barrett Arms within the authors' hardware testbed. We empirically demonstrate up to one order of magnitude improvements in execution latency and solution compactness compared to prior art.
3-D Mapping With an RGB-D Camera

In this paper, we present a novel mapping system that robustly generates highly accurate 3-D maps using an RGB-D camera. Our approach requires no further sensors or odometry. With the availability of low-cost and light-weight RGB-D sensors such as the Microsoft Kinect, our approach applies to small domestic robots such as vacuum cleaners, as well as flying robots such as quadrocopters. Furthermore, our system can also be used for free-hand reconstruction of detailed 3-D models. In addition to the system itself, we present a thorough experimental evaluation on a publicly available benchmark dataset. We analyze and discuss the influence of several parameters such as the choice of the feature descriptor, the number of visual features, and validation methods. The results of the experiments demonstrate that our system can robustly deal with challenging scenarios such as fast camera motions and feature-poor environments while being fast enough for online operation. Our system is fully available as open source and has already been widely adopted by the robotics community.
The Role of Eph Receptor Tyrosine Kinases and Ephrin Ligands in Hematopoietic Cell Development and Function

The Eph receptor tyrosine kinases form the largest sub-family of the Receptor tyrosine kinases. Eph receptors interact with membrane bound ligands, termed ephrins. Eph-ephrin interactions have significant roles during mammalian development where they mediate such processes as cell adhesion and migration. Although Eph/ephrin expression is low in adult tissues evidence is accumulating which indicates that Eph and ephrins continue to play significant roles in postembryonic tissues. In this review we describe the current understanding of the function of Eph-ephrin signaling in human and mouse hematopoiesis. Ephs and ephrins have been shown to regulate the differentiation of hematopoietic cells, to direct lymphoid development as well as immune function. Whilst much still remains to be learned about the role of Ephephrin signaling in hematopoieis it is already clear that this system exerts important regulatory effects on differentiation, cell migration and effector function. The possibility that these molecules may be therapeutic targets is also discussed.
Increase of protein tyrosine phosphorylation in rat retina after ischemia-reperfusion injury.

PURPOSE This study was conducted to examine the effect of retinal ischemia-reperfusion injury on protein tyrosine phosphorylation, the production of angiogenic growth factors, and the activation of signal proteins in tyrosine kinase pathways. METHODS Ischemia-reperfusion injury was induced in rats by compression of the optic nerve for 2 hours. The rats were killed, and the retinas were collected at 0, 1, 6, 24, 48, 96, or 168 hours of reperfusion. Tyrosine phosphorylation of proteins in the retina was examined by Western blot analysis and immunohistochemistry. Angiogenic growth factors and their receptors, such as basic fibroblast growth factor (bFGF) and Flg, vascular endothelial growth factor (VEGF) and Flk-1, platelet-derived growth factor (PDGF)-B chain and PDGF-beta receptor, and five intracellular signal proteins (phosphatidylinositol 3-kinase [PI3K], phospholipase C gamma [PLC gamma], C-Src, SHC, and mitogen-activated protein kinase [MAPK]) were examined by Western blot analysis. RESULTS Protein tyrosine phosphorylation increased after ischemia-reperfusion injury, reaching a peak at 48 hours of reperfusion. Increased staining of tyrosine-phosphorylated proteins in the inner retina were evident on immunohistochemical examination. The amount of bFGF decreased after injury, but the amounts of VEGF and PDGF-B chain increased. Tyrosine phosphorylation of PLC gamma, SHC, and MAPK was increased at 48 hours of reperfusion, and tyrosine phosphorylation of PDGF-beta receptor and PI3K was increased at 168 hours of reperfusion. CONCLUSIONS Ischemia-reperfusion injury in the rat retina leads to activation of the tyrosine kinase pathway, increasing the amounts of angiogenic growth factors. The resultant activation of signal proteins PLC gamma, SHC, MAPK, PI3K, and PDGF-beta receptor may play an important role in ischemia-induced retinal changes such as cell proliferation.