Miracle-dz/UniFAR-FTUs huggingface dataset:
Generic and robust method for automatic segmentation of PET images using an active contour model.

PURPOSE Although positron emission tomography (PET) images have shown potential to improve the accuracy of targeting in radiation therapy planning and assessment of response to treatment, the boundaries of tumors are not easily distinguishable from surrounding normal tissue owing to the low spatial resolution and inherent noisy characteristics of PET images. The objective of this study is to develop a generic and robust method for automatic delineation of tumor volumes using an active contour model and to evaluate its performance using phantom and clinical studies. METHODS MASAC, a method for automatic segmentation using an active contour model, incorporates the histogram fuzzy C-means clustering, and localized and textural information to constrain the active contour to detect boundaries in an accurate and robust manner. Moreover, the lattice Boltzmann method is used as an alternative approach for solving the level set equation to make it faster and suitable for parallel programming. Twenty simulated phantom studies and 16 clinical studies, including six cases of pharyngolaryngeal squamous cell carcinoma and ten cases of nonsmall cell lung cancer, were included to evaluate its performance. Besides, the proposed method was also compared with the contourlet-based active contour algorithm (CAC) and Schaefer's thresholding method (ST). The relative volume error (RE), Dice similarity coefficient (DSC), and classification error (CE) metrics were used to analyze the results quantitatively. RESULTS For the simulated phantom studies (PSs), MASAC and CAC provide similar segmentations of the different lesions, while ST fails to achieve reliable results. For the clinical datasets (2 cases with connected high-uptake regions excluded) (CSs), CAC provides for the lowest mean RE (-8.38% ± 27.49%), while MASAC achieves the best mean DSC (0.71 ± 0.09) and mean CE (53.92% ± 12.65%), respectively. MASAC could reliably quantify different types of lesions assessed in this work with good accuracy, resulting in a mean RE of -13.35% ± 11.87% and -11.15% ± 23.66%, a mean DSC of 0.89 ± 0.05 and 0.71 ± 0.09, and a mean CE of 19.19% ± 7.89% and 53.92% ± 12.65%, for PSs and CSs, respectively. CONCLUSIONS The authors' results demonstrate that the developed novel PET segmentation algorithm is applicable to various types of lesions in the authors' study and is capable of producing accurate and consistent target volume delineations, potentially resulting in reduced intraobserver and interobserver variabilities observed when using manual delineation and improved accuracy in treatment planning and outcome evaluation.
A multiresolution investigation on fatigue damage of aluminum alloys at micrometer level

Fatigue damage is a form of material degradation under repeated mechanical and/or thermal loading. A new multiresolution fatigue damage analysis is formulated and used to estimate low-cycle fatigue damage. The progressive fatigue damage is measured based on the X-ray computed tomography. Then, the measured microcracks and microvoids are transformed to mesoscale and macro-scale damage variables. The entire transformation process is achieved analytically by means of 3D finite element analysis and specially formulated super representative volume elements. The estimated macro-scale damage variables in terms of effective Young’s moduli are compared with those measured experimentally and found to be in agreement. Some lessons learned in this study are provided for the direction of future research.
High-Resolution Genotyping of Campylobacter Species by Use of PCR and High-Throughput Mass Spectrometry

ABSTRACT In this work we report on a high-throughput mass spectrometry-based technique for the rapid high-resolution identification of Campylobacter jejuni strain types. This method readily distinguishes C. jejuni from C. coli, has a resolving power comparable to that of multilocus sequence typing (MLST), is applicable to mixtures, and is highly automated. The strain typing approach is based on high-performance mass spectrometry, which “weighs” PCR amplicons with enough mass accuracy to unambiguously determine the base composition of each amplicon (i.e., the numbers of A's, G's, C's, and T's). Amplicons are derived from PCR primers which amplify short (<140-bp) regions of the housekeeping genes used by conventional MLST strategies. The results obtained with a challenge panel that comprised 25 strain types of C. jejuni and 25 strain types of C. coli are presented. These samples were parsed and resolved with demonstrated sensitivity down to 10 genomes/PCR from pure isolates.
Na+/H+ exchanger‐dependent intracellular alkalinization is an early event in malignant transformation and plays an essential role in the development of subsequent transformation‐associated phenotypes

In this study we investigate the mechanism of intracellular pH change and its role in malignant transformation using the E7 oncogene of human papillomavirus type 16 (HPV16). Infecting NIH3T3 cells with recombinant retroviruses expressing the HPV16 E7 or a transformation deficient mutant we show that alkalinization is transformation specific. In NIH3T3 cells in which transformation can be turned on and followed by induction of the HPV16 E7 oncogene expression, we demonstrate that cytoplasmic alkalinization is an early event and was driven by stimulation of Na+/H+ exchanger activity via an increase in the affinity of the intracellular NHE‐1 proton regulatory site. Annulment of the E7‐induced cytoplasmic alkalinization by specific inhibition of the NHE‐1, acidification of culture medium, or clamping the pHi to nontransformed levels prevented the development of later transformed phenotypes such as increased growth rate, serum‐independent growth, anchorage‐independent growth, and glycolytic metabolism. These findings were verified in human keratinocytes (HPKIA), the natural host of HPV. Results from both NIH3T3 and HPKIA cells show that alkalinization acts on pathways that are independent of the E2F‐mediated transcriptional activation of cell cycle regulator genes. Moreover, we show that the transformationdependent increase in proliferation is independent of the concomitant stimulation of glycolysis. Finally, treatment of nude mice with the specific inhibitor of NHE‐1, DMA, delayed the development of HPV16‐keratinocyte tumors. Our data confirm that activation of the NHE‐1 and resulting cellular alkalinization is a key mechanism in oncogenic transformation and is necessary for the development and maintenance of the transformed phenotype. —Reshkin, S. J., Bellizzi, A. , Caldeira, S. , Albarani, V. , Malanchi, I. , Poignee, M. , Alunni‐Fabbroni, M. , Casavola, V. , Tommasino, M. Na+/H+ exchanger‐dependent intracellular alkalinization is an early event in malignant transformation and plays an essential role in the development of subsequent transformation‐associated phenotypes.
A Study of the Potential Use of Asphalt Containing Synthetic Polymers for Asphalt Paving Mixes.

Chemically modified polymer derivatives of potentially useful polymer modifiers from solid wastes, i.e. polyolefins or EPDM, were prepared by chlorination or maleation to improve asphalt blend compatibility. Chlorination of polyethylene can be controlled to convert crystalline HDPE into semicrystalline polymeric additives. Environmental scanning electron microscopy shows that dispersed CPE rich phase was larger than the HDPE rich phase in asphalt blends. Introducing chlorine atoms on polyethylene chains can improve compatibility of the asphalt-polymer blends through adjusting interaction between the components of asphalt and polymer. The grafting of maleic anhydride to polyolefins or EPDM was carried out either in solution or in a melt process in the presence of free radicals. The extent of maleation (1-2.5%) achieved in either polyolefins or EPDM was determined by FTIR. DSC analysis revealed that all of the maleated polypropylene derivates were at least 45% amorphous. Most of maleated polymer/asphalt blends exhibited lower activation energies of flow and improved rhelogical properties relative to those of the pure asphalt matrix. Standard procedures for studying the physical and engineering properties of asphalt binders have been used to specify the PG grading of the blends according to Superpave protocols. The polymer/asphalt blends have significantly better properties than those of tank asphalts. The blends exhibit higher viscosity at high temperature, higher rutting resistance, reducing age hardening for long-
Asymmetrical design for non-relaxed near-UV AlGaN/GaN distributed Bragg reflectors

Towards the development of high efficient GaN-based Vertical Cavity devices, the fabrication of cracks-free high reflective semiconductor mirrors is still an issue. For near-UV operating devices, one of the best solution is the use of AlGaN/GaN materials family. With a relatively high Al molar fraction in AlGaN, a large enough index contrast can be achieved to fabricate high reflectivity mirrors. However, the lattice mismatch between AlGaN and GaN increases with the Al molar fraction and induces a lot of cracks in the structure which affect its optical and electrical properties. Moreover, for a regrowth of an active layer on the top of the mirror, it is necessary to suppress crack generations to achieve a smooth surface. In this work, asymmetrical designs were investigated for the modeling of fully-strained AlGaN/GaN distributed Bragg Reflectors with crack-free surfaces. First, the critical thickness of MOVPE-grown AlGaN on GaN-on-sapphire templates was experimentally determined and modeled. Then, several AlGaN/GaN mirrors with various Al molar fractions and asymmetry factors were simulated demonstrating that non relaxed DBRs could be obtained with adequate parameters. Finally, it has also been shown that there is a best suited Al molar fraction in AlGaN for each DBR centering wavelength.
Environmental, Policy, and Cultural Factors Related to Physical Activity in African American Women

SUMMARY Six focus groups were conducted in South Carolina with African American women (n = 42) aged 19–51 years to identify factors that influence physical activity. Transcripts were analyzed using NUD*IST. Cultural influences were seen as more important in determining the type of physical activity than its level. Barriers to and enablers of physical activity were identified in the social and physical environments, as were policy issues affecting physical activity in the community and at the work site. Potential community and work site interventions were suggested. Child care and monetary costs were frequently cited as barriers to physical activity.
Estimating Wheat Yield in China at the Field and District Scale from the Assimilation of Satellite Data into the Aquacrop and Simple Algorithm for Yield (SAFY) Models

Accurate yield estimation at the field scale is essential for the development of precision agriculture management, whereas at the district level it can provide valuable information for supply chain management. In this paper, Huan Jing (HJ) satellite HJ1A/B and Landsat 8 Operational Land Imager (OLI) images were employed to retrieve leaf area index (LAI) and canopy cover (CC) in the Yangling area (Central China). These variables were then assimilated into two crop models, Aquacrop and simple algorithm for yield (SAFY), in order to compare their performances and practicalities. Due to the models’ specificities and computational constraints, different assimilation methods were used. For SAFY, the ensemble Kalman filter (EnKF) was applied using LAI as the observed variable, while for Aquacrop, particle swarm optimization (PSO) was used, using canopy cover (CC). These techniques were applied and validated both at the field and at the district scale. In the field application, the lowest relative root-mean-square error (RRMSE) value of 18% was obtained using EnKF with SAFY. On a district scale, both methods were able to provide production estimates in agreement with data provided by the official statistical offices. From an operational point of view, SAFY with the EnKF method was more suitable than Aquacrop with PSO, in a data assimilation context.
Toward realtime transcription of broadcast news

In this paper, we describe our recent work in fast automatic transcription of broadcast news programming from radio and television. Given our state-of-the-art BBN BYBLOS primary system [1] running at 230 times real time (230xRT) we show that eliminating and approximating many computationally expensive components speeds up the system by a factor of more than 20 without significant loss in recognition accuracy. This is accomplished without retraining or changing the base-line system structure. The components of the primary system which are refined include segmentation, adaptation, decoding, cross-word rescoring with adaptation, and system combination.
An image descriptors extraction hardware-architecture inspired on Human Retina

We present a hardware architecture for the extraction of image feature descriptors, based on a model inspired on the Human Retina. This model comes from an analysis of a recent descriptor extractor, the FREAK (Fast Retina Keypoint) method, which has shown good performance results for different Computer Vision applications. From such analysis we decide the approximations that may be made to the original model so as to accomplish hardware requirements. The goal of our work is to implement FREAK on FPGA (Field-Programmable Gate Array), thinking about the development of future embedded systems. Finally we obtain an IP-core for image descriptor extraction, which can be integrated to a feature detector. We present the synthesis results of our proposed architecture focusing on the resource utilization.
Musical Expertise Modulates Early Processing of Syntactic Violations in Language

Syntactic violations in speech and music have been shown to elicit an anterior negativity (AN) as early as 100 ms after violation onset and a posterior positivity that peaks at roughly 600 ms (P600/LPC). The language AN is typically reported as left-lateralized (LAN), whereas the music AN is typically reported as right-lateralized (RAN). However, several lines of evidence suggest syntactic processing of language and music rely on overlapping neural systems. The current study tested the hypothesis that syntactic processing of speech and music share neural resources by examining whether musical proficiency modulates ERP indices of linguistic syntactic processing. ERPs were measured in response to syntactic violations in sentences and chord progressions in musicians and non-musicians. Violations in speech were insertion errors in normal and semantically impoverished English sentences. Violations in music were out-of-key chord substitutions from distantly and closely related keys. Phrase-structure violations elicited an AN and P600 in both groups. Harmonic violations elicited an LPC in both groups, blatant harmonic violations also elicited a RAN in musicians only. Cross-domain effects of musical proficiency were similar to previously reported within-domain effects of linguistic proficiency on the distribution of the language AN; syntactic violations in normal English sentences elicited a LAN in musicians and a bilateral AN in non-musicians. The late positivities elicited by violations differed in latency and distribution between domains. These results suggest that initial processing of syntactic violations in language and music relies on shared neural resources in the general population, and that musical expertise results in more specialized cortical organization of syntactic processing in both domains.
Handheld Augmented Reality

INTRODUCTION The idea of computers helping people in their everyday life has been around for quite a while. One way a computer can be used to assist a user to accomplish a task is by providing important information relevant to this task. But to know which information is relevant, which information is needed at the moment and how to display this information in the best possible way is a difficult task to solve. Luckily, a computer can take advantage of a wide range of input devices like different sensors, cameras and user interfaces as well as sophisticated devices for displaying data like screens and projectors. The combination of processing input from the environment, selecting relevant data and displaying the data in a for the situation suited fashion is called augmented reality (AR).
Barley powdery mildew , caused by the pathogen Blumeria graminis

Barley powdery mildew, caused by the pathogen Blumeria graminis f. sp. hordei is an important disease of barley (Hordeum vulgare L.). The random amplified polymorphic DNA (RAPD) method was used to detect DNA polymorphism among 7 Pallas near-isogenic lines (NILs) carrying Mla3, Mla12, Mlk, Mlp, Mlat, Mlg and MlLa genes for resistance to B. graminis f. sp. hordei. From among 500 random 10-mer primers tested, 3 were specific for NIL P2 (Mla3), 1 for P10 (Mla12), 6 for P17 (Mlk), 46 for P19 (Mlp), 4 for P20 (Mlat), 6 for P21 (Mlg), and 4 for P23 (MlLa). The results of this study demonstrated that the RAPD technique is a useful tool for detecting DNA polymorphism among Pallas NILs.
Modeling and Calibration of Coupled Fish-Eye CCD Camera and Laser Range Scanner for Outdoor Environment Reconstruction

Precise and realistic models of outdoor environments such as cities and roads are useful for various applications. In order to do so, geometry and photography of environments must be captured. We present in this paper a coupled system, based on a fish-eye lens CCD camera and a laser range scanner, aimed at capturing color and geometry in this context. To use this system, a revelant model and a accurate calibration method are presented. The calibration method uses a simplified fish-eye model; the method uses only one image for fish-eye parameters, and avoids the use of large calibration pattern as required in others methods. The validity and precision of the method are assessed and example of colored 3D points produced by the system is presented.
Selective Non-Steroidal Glucocorticoid Receptor Agonists Attenuate Inflammation but Do Not Impair Intestinal Epithelial Cell Restitution In Vitro

Introduction Despite the excellent anti-inflammatory and immunosuppressive action of glucocorticoids (GCs), their use for the treatment of inflammatory bowel disease (IBD) still carries significant risks in terms of frequently occurring severe side effects, such as the impairment of intestinal tissue repair. The recently-introduced selective glucocorticoid receptor (GR) agonists (SEGRAs) offer anti-inflammatory action comparable to that of common GCs, but with a reduced side effect profile. Methods The in vitro effects of the non-steroidal SEGRAs Compound A (CpdA) and ZK216348, were investigated in intestinal epithelial cells and compared to those of Dexamethasone (Dex). GR translocation was shown by immunfluorescence and Western blot analysis. Trans-repressive effects were studied by means of NF-κB/p65 activity and IL-8 levels, trans-activation potency by reporter gene assay. Flow cytometry was used to assess apoptosis of cells exposed to SEGRAs. The effects on IEC-6 and HaCaT cell restitution were determined using an in vitro wound healing model, cell proliferation by BrdU assay. In addition, influences on the TGF-β- or EGF/ERK1/2/MAPK-pathway were evaluated by reporter gene assay, Western blot and qPCR analysis. Results Dex, CpdA and ZK216348 were found to be functional GR agonists. In terms of trans-repression, CpdA and ZK216348 effectively inhibited NF-κB activity and IL-8 secretion, but showed less trans-activation potency. Furthermore, unlike SEGRAs, Dex caused a dose-dependent inhibition of cell restitution with no effect on cell proliferation. These differences in epithelial restitution were TGF-β-independent but Dex inhibited the EGF/ERK1/2/MAPK-pathway important for intestinal epithelial wound healing by induction of MKP-1 and Annexin-1 which was not affected by CpdA or ZK216348. Conclusion Collectively, our results indicate that, while their anti-inflammatory activity is comparable to Dex, SEGRAs show fewer side effects with respect to wound healing. The fact that SEGRAs did not have a similar effect on cell restitution might be due to a different modulation of EGF/ERK1/2 MAPK signalling.
Job-based queue delay modeling in a space-shared hypercube

Processor allocation problem in a space-shared hypercube parallel computer is considered. Since jobs are dynamically allocated and deallocated, existence of more free processors than required does not guarantee the immediate allocation due to the fragmentation problem. If the immediate allocation fails, the processor allocator should decide whether to wait or to assign a smaller subcube to the job. Here, the decision is made depending on the wait or queue delay time. There have been several attempts to predict the queue delay analytically based on the number of busy processors, not the busy subcubes. Main disadvantages of the processor-based prediction is that the number of busy processors does not accurately explain the queue delay. A subcube with the minimum number of running jobs is probably the best candidate for the future allocation even though it has less free processors. We propose a job-based queue delay prediction. We view the allocation moment when all the existing jobs, not the busy processors, in one of the possible subcubes complete their execution. We performed an extensive simulation study and it reveals that the predicted queue delay matches very well with the simulation results. Using the predicted queue delay time, the processor allocator is able to make a right decision and thus, enhances the system performance.
How regularity representations of short sound patterns that are based on relative or absolute pitch information establish over time: An EEG study

The recognition of sound patterns in speech or music (e.g., a melody that is played in different keys) requires knowledge about pitch relations between successive sounds. We investigated the formation of regularity representations for sound patterns in an event-related potential (ERP) study. A pattern, which consisted of six concatenated 50 ms tone segments differing in fundamental frequency, was presented 1, 2, 3, 6, or 12 times and then replaced by another pattern by randomly changing the pitch of the tonal segments (roving standard paradigm). In an absolute repetition condition, patterns were repeated identically, whereas in a transposed condition, only the pitch relations of the tonal segments of the patterns were repeated, while the entire patterns were shifted up or down in pitch. During ERP measurement participants were not informed about the pattern repetition rule, but were instructed to discriminate rarely occurring targets of lower or higher sound intensity. EPRs for pattern changes (mismatch negativity, MMN; and P3a) and for pattern repetitions (repetition positivity, RP) revealed that the auditory system is able to rapidly extract regularities from unfamiliar complex sound patterns even when absolute pitch varies. Yet, enhanced RP and P3a amplitudes, and improved behavioral performance measured in a post-hoc test, in the absolute as compared with the transposed condition suggest that it is more difficult to encode patterns without absolute pitch information. This is explained by dissociable processing of standards and deviants as well as a back propagation mechanism to early sensory processing stages, which is effective after less repetitions of a standard stimulus for absolute pitch.