Miracle-dz/UniFAR-FTUs huggingface dataset:
Random walks, arrangements, cell complexes, greedoids, and self-organizing libraries

The starting point is the known fact that some much-studied random walks on permutations, such as the Tsetlin library, arise from walks on real hyperplane arrangements. This paper explores similar walks on complex hyperplane arrangements. This is achieved by involving certain cell complexes naturally associated with the arrangement. In a particular case this leads to walks on libraries with several shelves. We also show that interval greedoids give rise to random walks belonging to the same general family. Members of this family of Markov chains, based on certain semigroups, have the property that all eigenvalues of the transition matrices are non-negative real and given by a simple combinatorial formula. Background material needed for understanding the walks is reviewed in rather great detail.
Omokage search: shape similarity search service for biomolecular structures in both the PDB and EMDB

Summary: Omokage search is a service to search the global shape similarity of biological macromolecules and their assemblies, in both the Protein Data Bank (PDB) and Electron Microscopy Data Bank (EMDB). The server compares global shapes of assemblies independent of sequence order and number of subunits. As a search query, the user inputs a structure ID (PDB ID or EMDB ID) or uploads an atomic model or 3D density map to the server. The search is performed usually within 1 min, using one-dimensional profiles (incremental distance rank profiles) to characterize the shapes. Using the gmfit (Gaussian mixture model fitting) program, the found structures are fitted onto the query structure and their superimposed structures are displayed on the Web browser. Our service provides new structural perspectives to life science researchers. Availability and implementation: Omokage search is freely accessible at http://pdbj.org/omokage/. Contact: hirofumi@protein.osaka-u.ac. jp Supplementary information: Supplementary data are available at Bioinformatics online.
Designing vertical bandwidth reconfigurable 3D NoCs for many core systems

As the number of processing elements increases in a single chip, the interconnect backbone becomes more and more stressed when serving frequent memory and cache accesses. Network-on-Chip (NoC) has emerged as a potential solution to provide a flexible and scalable interconnect in a planar platform. In the mean time, three-dimensional (3D) integration technology pushes circuit design beyond Moore's law and provides short vertical connections between different layers. As a result, the innovative solution that combines 3D integrations and NoC designs can further enhance the system performance. However, due to the unpredictable workload characteristics, NoC may suffer from intermittent congestions and channel overflows, especially when the network bandwidth is limited by the area and energy budget. In this work, we explore the performance bottlenecks in 3D NoC, and then leverage redundant TSVs, which are conventionally used for fault tolerance only, as vertical links to provide additional channel bandwidth for instant throughput improvement. Moreover, these shared redundant links can be dynamically allocated to the stressed routers for congestion alleviation. Experimental results show that our proposed NoC design can provide up to 40% performance improvement, with less than 1.5% area overhead.
Polynomial Expressions of Carries in p-ary Arithmetics

It is known that any $n$-variable function on a finite prime field of characteristic $p$ can be expressed as a polynomial over the same field with at most $p^n$ monomials. However, it is not obvious to determine the polynomial for a given concrete function. In this paper, we study the concrete polynomial expressions of the carries in addition and multiplication of $p$-ary integers. For the case of addition, our result gives a new family of symmetric polynomials, which generalizes the known result for the binary case $p = 2$ where the carries are given by elementary symmetric polynomials. On the other hand, for the case of multiplication of $n$ single-digit integers, we give a simple formula of the polynomial expression for the carry to the next digit using the Bernoulli numbers, and show that it has only $(n+1)(p-1)/2 + 1$ monomials, which is significantly fewer than the worst-case number $p^n$ of monomials for general functions. We also discuss applications of our results to cryptographic computation on encrypted data.
A low-complexity 2-point step size gradient projection method with selective function evaluations for smoothed total variation based CBCT reconstructions

The Barzilai–Borwein (BB) 2-point step size gradient method is receiving attention for accelerating Total Variation (TV) based CBCT reconstructions. In order to become truly viable for clinical applications, however, its convergence property needs to be properly addressed. We propose a novel fast converging gradient projection BB method that requires ‘at most one function evaluation’ in each iterative step. This Selective Function Evaluation method, referred to as GPBB-SFE in this paper, exhibits the desired convergence property when it is combined with a ‘smoothed TV’ or any other differentiable prior. This way, the proposed GPBB-SFE algorithm offers fast and guaranteed convergence to the desired 3DCBCT image with minimal computational complexity. We first applied this algorithm to a Shepp–Logan numerical phantom. We then applied to a CatPhan 600 physical phantom (The Phantom Laboratory, Salem, NY) and a clinically-treated head-and-neck patient, both acquired from the TrueBeam™ system (Varian Medical Systems, Palo Alto, CA). Furthermore, we accelerated the reconstruction by implementing the algorithm on NVIDIA GTX 480 GPU card. We first compared GPBB-SFE with three recently proposed BB-based CBCT reconstruction methods available in the literature using Shepp–Logan numerical phantom with 40 projections. It is found that GPBB-SFE shows either faster convergence speed/time or superior convergence property compared to existing BB-based algorithms. With the CatPhan 600 physical phantom, the GPBB-SFE algorithm requires only 3 function evaluations in 30 iterations and reconstructs the standard, 364-projection FDK reconstruction quality image using only 60 projections. We then applied the algorithm to a clinically-treated head-and-neck patient. It was observed that the GPBB-SFE algorithm requires only 18 function evaluations in 30 iterations. Compared with the FDK algorithm with 364 projections, the GPBB-SFE algorithm produces visibly equivalent quality CBCT image for the head-and-neck patient with only 180 projections, in 131.7 s, further supporting its clinical applicability.
Games and Traffic Safety - an Experimental Study in a Game-Based Simulation Environment

In this paper we report results from an experimental study of games and traffic safety performed in an advanced gaming environment. During car simulator-sessions we collected data over different traffic safety variables, such as speed, headway distance and lane change behavior, from 70 subjects. The data was analyzed in order to investigate possible individual learning effects and differences between groupings of subjects. The experiment shows clear positive individual learning effects for all traffic safety variables analyzed. Hence we conclude that game based simulations can be used to enhance learning in driving education.
Characterising arthralgia in the preclinical phase of rheumatoid arthritis using MRI

Background The phase of arthralgia is the earliest moment to clinically recognize patients who may develop Rheumatoid Arthritis (RA). Previous imaging studies in the arthralgia phase have shown that inflammation precedes RA development. It is unknown which symptoms/characteristics relate to subclinical joint inflammation as measured by MRI. Among all patients with arthralgia, those with clinically suspect arthralgia (CSA) are suspected to progress to arthritis according to the clinical judgement of their rheumatologists. We determined the symptoms/characteristics of patients with CSA who had inflammation on MRI. Methods 102 patients with CSA and without clinical arthritis were included. They completed questionnaires, underwent joint counts and unilateral 1.5 T MRI of MCP joints 2–4, wrist and MTP joints 1–5. Synovitis, bone marrow oedema (BME) and tenosynovitis were scored according to the OMERACT rheumatoid arthritis MRI scoring system. Symptoms and signs were related to MRI inflammation (based on MRI scores in symptom-free controls; a sum of synovitis, BME and tenosynovitis scores ≥3 was considered positive). Whether certain clinical characteristics frequently occurred together with MRI inflammation was studied by partial least squares analysis. Results MRI was performed in 93 patients with CSA, 44% of whom had subclinical MRI inflammation. Synovitis was the most prevalent inflammatory feature on MRI (20%). Patients with MRI inflammation were older and were more frequently positive for anti-citrullinated peptide antibodies than patients without MRI inflammation (p<0.001 and 0.049). In PLS analysis, including 16 clinical and serological characteristics as independent variables and MRI inflammation as dependent variable, no clear clusters of patients with and without MRI inflammation were identified. Conclusions Subclinical inflammation as measured by MRI is present in 44% of patients with CSA. A combination of symptoms/characteristics incompletely differentiated patients with and without MRI inflammation.
Comparison of three techniques for detection of Chlamydia trachomatis in endocervical specimens from asymptomatic women

Culture in DEAE-dextran-treated HeLa 229 cells, a solid-phase enzyme immunoassay (EIA) (Chlamydiazyme; Abbott Laboratories, North Chicago, Ill.), and a direct immunofluorescence test (DFA) (MicroTrak; Syva Co., Palo Alto, Calif.) were compared for the detection of Chlamydia trachomatis in endocervical specimens from 715 asymptomatic women. Response to antibiotic therapy was also monitored at least 4 weeks after completion of therapy. An additional sample was collected at a control visit, and a second culture was performed if discrepancies were observed between the three tests. A total of 48 infections were diagnosed, for a prevalence of 6.7%. At the first visit, 37 specimens were positive by culture. The respective sensitivities of EIA and DFA were 78.4 and 81.1% and the respective specificities were 96.8 and 97.9% when compared with the cell culture technique. The positive predictive values were 56.9 and 68.2%, respectively. When the additional 11 infections detected by the second culture were included to establish a new standard of positivity, the sensitivity of the first culture was estimated at 77.1%. The positive predictive values of EIA and DFA increased to 77.6 and 83.7%, respectively. EIA and DFA performed as well as culture for control of therapy; a 100% agreement among the three techniques was observed.
Impact of sack delay and link delay on failover performance in SCTP

The Stream Control Transmission Protocol (SCTP) was developedto support the transfer of telephony signaling overIP networks. One of the ambitions when designing SCTPwas to offer a robust transfer of traffic between hosts. Forthis reason SCTP was designed to support multihoming,which gives the possibility to set up several paths betweenthe same hosts in the same session. If the primary path betweena source machine and a destination machine breaksdown, the traffic may still be sent to the destination by utilizingone of the alternate paths. The failover that occurswhen changing path is to be transparent to the application.Consequently, the time between occurrence of a break onthe primary path until the traffic is run smoothly on one ofthe alternate paths is important. This paper presents experimentalresults concerning SCTP failover performance. Thefocus in this paper is to evaluate the impact of the SACKdelay and link delay on the failover time as well as on themaximum transfer time for a single message, which complementsearlier studies in this area. The results show asignificant performance impact of the SACK delay as wellas of the link delay. This suggests that the SACK delayis an important parameter to tune to enhance applicationtransparency in failure situations
The role of historical fire disturbance in the carbon dynamics of the pan-boreal region: A process-based analysis

[1] Wildfire is a common occurrence in ecosystems of northern high latitudes, and changes in the fire regime of this region have consequences for carbon feedbacks to the climate system. To improve our understanding of how wildfire influences carbon dynamics of this region, we used the process-based Terrestrial Ecosystem Model to simulate fire emissions and changes in carbon storage north of 45°N from the start of spatially explicit historically recorded fire records in the twentieth century through 2002, and evaluated the role of fire in the carbon dynamics of the region within the context of ecosystem responses to changes in atmospheric CO2 concentration and climate. Our analysis indicates that fire plays an important role in interannual and decadal scale variation of source/sink relationships of northern terrestrial ecosystems and also suggests that atmospheric CO2 may be important to consider in addition to changes in climate and fire disturbance. There are substantial uncertainties in the effects of fire on carbon storage in our simulations. These uncertainties are associated with sparse fire data for northern Eurasia, uncertainty in estimating carbon consumption, and difficulty in verifying assumptions about the representation of fires that occurred prior to the start of the historical fire record. To improve the ability to better predict how fire will influence carbon storage of this region in the future, new analyses of the retrospective role of fire in the carbon dynamics of northern high latitudes should address these uncertainties.
A partitioned algorithm for the image foresting transform

The Image Foresting Transform (IFT) is a powerful graph-based framework for the design and implementation of image processing operators. In this work we present the Partitioned IFT (PIFT), an algorithm that computes any IFT operator as a series of independent IFT-like computations. The PIFT makes parallelization of existing IFT operators easy, and allows the computation of IFTs in systems with scarce memory. We evaluate the PIFT for two image processing applications: watershed segmentation and Euclidean distance transforms.
Tracking a Mobile Receiver using the Unscented Kalman Filter

Technische Fakultät Institut fur Informatik Telecommunications Engineering Tracking a Mobile Receiver using the Unscented Kalman Filter by Joan Bordoy Andreu Indoor localization based on Time Difference of Arrival (TDOA) and Frequency Difference of Arrival (FDOA) has been a promising subject of study the last years. In this thesis, a moving target is tracked by receiving discrete signals from stationary beacons. These beacons are assumed to be small and inexpensive and they require no further communication. Moreover, they emit short discrete signals at regular intervals and are assumed to be distinguished. The interval can be different for each sender and they do not need to start emitting at the same time instant, they can be unsynchronized. The algorithm used to solve this situation is the unscented Kalman filter. First, an approach using only the TDOA or FDOA measurements is presented. Second, it is extended to the combination of both measurements. Finally, the performance of these algorithms is evaluated with multiple experiments such as changing the dimension of the space to three dimensions or changing the number of senders.
Fortschritte in der Ursachenforschung affektiver und schizophrener Störungen

Zusammenfassung Affektive und schizophrene Storungen sind haufige psychische Storungen, zu deren Entwicklung genetische Faktoren masgeblich beitragen. Die Identifizierung der krankheitsassozierten Gene beziehungsweise Mutationen hat begonnen. Die aufwendigen Untersuchungen sind nur in enger Kooperation zwischen klinischer Forschung, Humangenetik und genetischer Epidemiologie moglich. Wie auch bei anderen genetisch komplexen Krankheiten durfte affektiven und schizophrenen Storungen ein Muster von Genotypen zugrunde liegen, das fur eine Krankheitsdisposition verantwortlich ist. Ein einzelner Genotyp wird nur in sehr begrenztem Mase zur Atiologie der Storung beitragen. Die Identifikation der relevanten Gene wird ein tief greifendes Verstandnis fur die biologischen Grundlagen dieser oft langfristig beeintrachtigenden Krankheiten erlauben. Dies wird auch fur die Erforschung der umweltbedingten Einflusse an der Pathogenese grose Chancen eroffnen. Schlusselworter: Psychiatrische Genetik, Schizophrenie, affektive Storung, manische Depression, Genidentifizierung Summary
Migrants and International Economic Linkages: A Meta-Overview

Abstract The migration issue is a much debated subject in many developed countries. This study provides a review of the relationship between migrants and their international economic linkages. It then focuses on foreign direct investment (FDI), for both inward and outward FDI. This study aims to offer a synthesis by means of a meta-analysis of various studies, in order to test the robustness of the relationship between migration and FDI. Our results confirm that immigration has a positive impact on FDI investment in both directions (inward and outward), and that these impacts are higher when migrants are highly educated and skilled. RÉSUMÉ Le problème de la migration est un sujet qui suscite un intérêt considérable dans un grand nombre de pays évolués. Cette étude passe en revue les rapports entre les migrants et leurs liens économiques internationaux. Elle se penche en suite sur les investissements étrangers directs (IED), tant pour les IED étrangers que pour les investissements à l’étranger. L’étude s'efforce de présenter une synthèse par le biais de méta-analyses de différentes études, dans le but de tester la solidité des rapports entre migration et IED. Nos résultats confirment que la migration a eu un effet positif sur les investissements IED dans les deux sens (de l’étranger et à l’étranger, et qu'elle a un impact majeur lorsque les migrants sont des personnes haute ment qualifiées et spécialisées. RESUMEN La inmigración es un tema muy debatido en muchos países desarrollados. Este estudio proporciona una reseña de la relación entre los inmigrantes y sus enlaces económicos internacionales. Después se enfoca en la Inversión Extranjera Directa (IED), tanto de entrada como de salida. Este estudio tiene como objetivo ofrecer una síntesis mediante un metanáli sis de estudios varios para evaluar la solidez de la relación entre inmigración y la IED. Nuestros resultados confirman que la inmigración tiene un impacto positivo sobre la IED en ambas direcciones (entrada y salida), y que estos impactos son mayores cuando los inmigrantes tiene un alto nivel de educación y cualificación.
Effects of different orthodontic retention protocols on the periodontal health of mandibular incisors.

OBJECTIVES To test the following two hypotheses: 1) different types of retainers result in distinct levels of biomarkers in gingival crevicular fluid (GCF) and 2) the retainer bonded to all mandibular anterior teeth induces more detrimental outcomes to the periodontium. SETTING AND SAMPLE POPULATION The Department of Orthodontics at the University of Florida. The population consisted of individuals in the retention phase of orthodontic treatment. MATERIAL AND METHODS This was a cross-sectional study that enrolled 36 individuals. Subjects in group 1 had retainers bonded to the mandibular canines only. Group 2 consisted of individuals having retainers bonded to all mandibular anterior teeth. Group 3 included patients using mandibular removable retainers. After clinical examination, GCF was collected from the mandibular incisor and biomarker levels were compared between the groups. RESULTS Plaque accumulation and gingivitis differed significantly among groups, with the highest median values in group 2 subjects. Pairwise comparison of the groups with respect to gingivitis showed significant differences between groups 1 and 2. Significant differences among groups were detected for RANKL, OPG, OPN, M-CSF, MMP-3, and MMP-9. The ratio RANKL/OPG was significantly higher in group 2 subjects, with pairwise comparisons indicating that groups 1 and 2 differed from group 3. CONCLUSION An association was found between orthodontic retention groups and GCF biomarker levels, which should be further explored in longitudinal studies. The presence of retainers bonded to all anterior teeth seems to increase plaque accumulation and gingivitis.
Novel Antimicrobial Peptides with High Anticancer Activity and Selectivity

We describe a strategy to boost anticancer activity and reduce normal cell toxicity of short antimicrobial peptides by adding positive charge amino acids and non-nature bulky amino acid β-naphthylalanine residues to their termini. Among the designed peptides, K4R2-Nal2-S1 displayed better salt resistance and less toxicity to hRBCs and human fibroblast than Nal2-S1 and K6-Nal2-S1. Fluorescence microscopic studies indicated that the FITC-labeled K4R2-Nal2-S1 preferentially binds cancer cells and causes apoptotic cell death. Moreover, a significant inhibition in human lung tumor growth was observed in the xenograft mice treated with K4R2-Nal2-S1. Our strategy provides new opportunities in the development of highly effective and selective antimicrobial and anticancer peptide-based therapeutics.
Patient controlled analgesia (PCA) in paediatric surgery: a prospective study following laparoscopic and open appendicectomy

Patient controlled analgesia (PCA) has not yet gained universal acceptance for the management of postoperative pain in paediatric surgery. In a prospective study we evaluated feasibility and complications of PCA following 90 cases of laparoscopic or open appendicectomy. PCA proved to be a safe and feasible method with few complications (2% of medical complications, no abort of application, 17 technical checks in a total running time of 4125 h). Acceptance by patients was high and children of all age groups worked the system properly. Assessment of application protocols showed, that the consumption of analgesics was significantly reduced following laparoscopic appendicectomy (P < 0.05). PCA is a safe and feasible method for the management of postoperative pain in children and PCA recording provides an excellent insight into the consumptional behaviour of patients, enabling staff to evaluate postoperative pain for various procedures.