Miracle-dz/UniFAR-FTUs huggingface dataset:
Developmental expression of perlecan during murine embryogenesis

Perlecan is a modular heparan sulfate proteoglycan that is an intrinsic constituent of all basement membranes and extracellular matrices. Because of its strategic position and unique structure, perlecan has been implicated in modulating the activity of various growth factors required for normal development and tissue homeostasis. To gain insights into the potential function of perlecan in vivo, we examined the spatiotemporal distribution of its mRNA and protein core during murine embryogenesis. We utilized a new affinity‐purified antibody that recognizes specifically the protein core of perlecan together with an in situ RT‐PCR approach to perform a systematic analysis of perlecan expression and deposition during murine ontogeny. Perlecan appeared early (E10.5) in tissues of vasculogenesis including heart, pericardium, and major blood vessels. Its early expression coincided with the development of the cardiovascular system. Subsequently (E11–13), the greatest deposition of perlecan occurred within the developing cartilage, especially the cartilage undergoing endochondral ossification, where it remained elevated throughout all the developmental stages, and up to adulthood. Interestingly, the mRNA levels of perlecan were always higher in all the vascularized tissues, principally within endothelial cells, while chondrocytes displayed relatively low mRNA levels. This suggests a higher biosynthesis and turnover rates in the blood vessels vis‐à‐vis those of cartilaginous and other mesenchymal tissues. During later stages of development (E13–17.5) perlecan mRNA levels progressively increased and its expression correlated with the onset of tissue differentiation of various parenchymal organs including the developing kidneys, lungs, liver, spleen, and gastrointestinal tract. The central nervous system showed no perlecan expression with the exception of the calvaria and choroid plexus. Collectively, the results indicate that perlecan may play crucial roles not only in vasculogenesis but also in the maturation and maintenance of differentiated tissues, including cartilage. Dev. Dyn. 1997;210:130–145. © 1997 Wiley‐Liss, Inc.
The Human Respiratory Syncytial Virus Nonstructural Protein 1 Regulates Type I and Type II Interferon Pathways

Respiratory syncytial viruses encode a nonstructural protein (NS1) that interferes with type I and III interferon and other antiviral responses. Proteomic studies were conducted on human A549 type II alveolar epithelial cells and type I interferon-deficient Vero cells (African green monkey kidney cells) infected with wild-type and NS1-deficient clones of human respiratory syncytial virus to identify other potential pathway and molecular targets of NS1 interference. These analyses included two-dimensional differential gel electrophoresis and quantitative Western blotting. Surprisingly, NS1 was found to suppress the induction of manganese superoxide dismutase (SOD2) expression in A549 cells and to a much lesser degree Vero cells in response to infection. Because SOD2 is not directly inducible by type I interferons, it served as a marker to probe the impact of NS1 on signaling of other cytokines known to induce SOD2 expression and/or indirect effects of type I interferon signaling. Deductive analysis of results obtained from cell infection and cytokine stimulation studies indicated that interferon-γ signaling was a potential target of NS1, possibly as a result of modulation of STAT1 levels. However, this was not sufficient to explain the magnitude of the impact of NS1 on SOD2 induction in A549 cells. Vero cell infection experiments indicated that NS1 targeted a component of the type I interferon response that does not directly induce SOD2 expression but is required to induce another initiator of SOD2 expression. STAT2 was ruled out as a target of NS1 interference using quantitative Western blot analysis of infected A549 cells, but data were obtained to indicate that STAT1 was one of a number of potential targets of NS1. A label-free mass spectrometry-based quantitative approach is proposed as a means of more definitive identification of NS1 targets.
Mapping Data-Flow Dependencies onto Distributed Embedded Systems

Model-driven development (MDD) is an emerging paradigm and has become state-of-the-art for embedded systems software design. In the overall design process, several steps have to be taken in order to get from a high-level system design to the deployed binaries on the target platform: starting from model design, software partitioning and code generation reaching down to task and bus scheduling. In this paper we focus on the later steps in the overall developing process and present a way to deploy clusters, which are tasks from an operational point of view, speci? ed using the Component Language (COLA). In this context, we introduce the notion of a Cluster Dependency Graph (CDG) which forms the basis for scheduling, address generation and estimation of memory requirements for the used middleware. Moreover the CDG provides clues about possibly parallelizable tasks. A case-study, namely an adaptive cruise control system (ACC), taken from the automotive domain serves as example throughout this paper to demonstrate our new approach.
My MOoD, a Multimedia and Multilingual Ontology Driven MAS: Design and First Experiments in the Sentiment Analysis Domain

In this paper we introduce the architecture of a Multimedia and Multilingual Ontology Driven Multiagent System (My MOoD) for classifying documents consisting of audiovisual and textual elements, according to classes described in a domain ontology. My MOoD will integrate software components devoted to the analysis of images, videos, and sound, with the multilingual text classifier based on BabelNet presented in this paper. All the integrated components will be wrapped by agents and will perform their classification based on a common domain ontology, which is a parameter of the multiagent system. Wrapper agents will interact in order to share the classification of the document's elements and agree on a coherent classification of the document as a whole, exploiting their background knowledge and reasoning capability to resolve ambiguities. Changing the ontology (and tuning or substituting the classifiers for dealing with the domain of interest) will allow the multiagent system to classify heterogeneous multimedia documents in whatever domain and for many different purposes. In the My MOoD instance discussed in this paper, the ontology (sentiHotel) describes the accommodation domain and the classification mines the sentiment of hotel reviews written in five different languages.
Spatial-Temporal Variations of Chlorophyll-a in the Adjacent Sea Area of the Yangtze River Estuary Influenced by Yangtze River Discharge

Carrying abundant nutrition, terrigenous freshwater has a great impact on the spatial and temporal heterogeneity of phytoplankton in coastal waters. The present study analyzed the spatial-temporal variations of Chlorophyll-a (Chl-a) concentration under the influence of discharge from the Yangtze River, based on remotely sensed Chl-a concentrations. The study area was initially zoned to quantitatively investigate the spatial variation patterns of Chl-a. Then, the temporal variation of Chl-a in each zone was simulated by a sinusoidal curve model. The results showed that in the inshore waters, the terrigenous discharge was the predominant driving force determining the pattern of Chl-a, which brings the risk of red tide disasters; while in the open sea areas, Chl-a was mainly affected by meteorological factors. Furthermore, a diversity of spatial and temporal variations of Chl-a existed based on the degree of influences from discharge. The diluted water extended from inshore to the east of Jeju Island. This process affected the Chl-a concentration flowing through the area, and had a potential impact on the marine environment. The Chl-a from September to November showed an obvious response to the discharge from July to September with a lag of 1 to 2 months.
SkiMap: An efficient mapping framework for robot navigation

We present a novel mapping framework for robot navigation which features a multi-level querying system capable to obtain rapidly representations as diverse as a 3D voxel grid, a 2.5D height map and a 2D occupancy grid. These are inherently embedded into a memory and time efficient core data structure organized as a Tree of SkipLists. Compared to the well-known Octree representation, our approach exhibits a better time efficiency, thanks to its simple and highly parallelizable computational structure, and a similar memory footprint when mapping large workspaces. Peculiarly within the realm of mapping for robot navigation, our framework supports real-time erosion and re-integration of measurements upon reception of optimized poses from the sensor tracker, so as to improve continuously the accuracy of the map.
Picking up the cues to a new consonant contrast: Danish learners' production and perception of English word-final /s/ - /z/

The present study examined how non-native speakers produce and perceive a voicing contrast that does not exist in their native language, and which is importantly signaled by an acoustic cue which has a very different function in the native language. Danish has no fricative voicing contrasts, which in English occur in initial, medial, and final position. An important acoustic cue for the final voicing contrasts in English is the duration of the preceding vowel. In Danish, vowel duration is used to contrast vowels. In Experiment 1, Danish learners of English produced only a small and nonsignificant difference in the vowel:fricative ratio, but Experiment 2 revealed that the same learners differentiated the final voicing contrast perceptually, influenced by vowel duration much like the native speakers. The overall results imply that although L2 learners do not produce certain unfamiliar contrasts native-like, they can use L2 cues to differentiate contrasts in perception.
Hybrid position-attitude control of DF-UAV based on generalized flight dynamics

For a ducted fan unmanned aerial vehicle (DF-UAV), the aerodynamic forces comprising the aerodynamic lift and drag as well as their induced angular moments are the real physical inputs dominating the flight state. These forces originate from the motions of the duct, propeller and control surfaces. Therefore, this study considered an integrated modeling of DF-UAV and proposed a layered design method for the hybrid position-attitude controller based on the reference feedback and dynamic decoupling.
Oxidative Metabolism of Rye (Secale cereale L.) after Short Term Exposure to Aluminum: Uncovering the Glutathione–Ascorbate Redox Network

One of the major limitations to plant growth and yield in acidic soils is the prevalence of soluble aluminum ions (Al3+) in the soil solution, which can irreversible damage the root apex cells. Nonetheless, many Al-tolerant species overcome Al toxicity and are well-adapted to acidic soils, being able to complete their life cycle under such stressful conditions. At this point, the complex physiological and biochemical processes inherent to Al tolerance remain unclear, especially in what concerns the behavior of antioxidant enzymes and stress indicators at early plant development. Since rye (Secale cereale L.), is considered the most Al-tolerant cereal, in this study we resort to seedlings of two genotypes with different Al sensitivities in order to evaluate their oxidative metabolism after short term Al exposure. Al-induced toxicity and antioxidant responses were dependent on rye genotype, organ and exposure period. Al affected biomass production and membrane integrity in roots and leaves of the sensitive (RioDeva) genotype. Catalase was the primary enzyme involved in H2O2 detoxification in the tolerant (Beira) genotype, while in RioDeva this task was mainly performed by GPX and POX. Evaluation of the enzymatic and non-enzymatic components of the ascorbate–glutathione cycle, as well the oxalate content, revealed that Beira genotype coped with Al stress by converting DHA into oxalate and tartarate, which posteriorly may bind to Al forming non-toxic chelates. In contrast, RioDeva genotype used a much more ineffective strategy which passed through ascorbate regeneration. So, remarkable differences between MDHAR and DHAR activities appear to be the key for a higher Al tolerance.
Role of diffusion tensor imaging in the diagnosis and management of post-traumatic anosmia

ABSTRACT Introduction: Anosmia is a possible complication of Traumatic Brain Injury (TBI). Psychometric and electrophysiological methods of olfaction measure and Magnetic Resonance Imaging (MRI) are the tools to evaluate the post-traumatic olfactory loss. Diffusion Tensor Imaging (DTI) provides useful data for a better understanding of etiopathogenesis TBI-related anosmia, in particular the loss of neural connections and their eventual recovery over time. Materials and methods: This study describes a case of TBI-related anosmia. The olfactory function was evaluated by Sniffin’ Sticks Test (SST), Olfactory Event-Related Potentials (OERPs), MRI and DTI at baseline (T0) and after one year (T1). Results: At baseline, SST highlighted a functional anosmia. The OERPs showed the presence of a small N1–P2 complex. MRI confirmed the presence of a scarring involved in the right orbitofrontal cortex (OFC). DTI detected a reduction in the average length and the number of neuronal fibre pathways of right OFC. At T1, a recovery of olfactory function was confirmed by SST and OERPs. Conclusion: While MRI images are unchanged from T0, DTI showed an increase in average length and number of fibre tracts in the right OFC. DTI could be a valid tool to display a post-traumatic loss of neural connections and to better understand TBI-recovery mechanisms.
Effect of prepregnancy body mass index and gestational weight gain on birth weight.

OBJECTIVE Nutritional status of women has been considered an important prognostic indicator of birth outcome. The study aims to show the effect of various prepregnancy Body Mass Index (BMI) categories and corresponding gestational weight gain on newborn birth weight. METHODS Two hundred women were included in the study. These women had regular antenatal visits and later delivered at The Aga Khan University Hospital (AKUH) between the period January 1, 1996 to December 31, 1997. RESULTS For women with prepregnancy BMI < 19. , mean birth weight of newborns was lower for those gaining < 12.5 kg than those gaining > 12.5 kg (P < 0.001). Women who started their pregnancy with BMI 19.8-26 and gained weight above expected range gave birth to high birth weight babies (P = 0.009). Gestational weight gain did not have a significant association with birth weight for women having prepregnancy BMI > 26. CONCLUSION Efforts should be made to attain adequate prepregnancy weight to reduce the likelihood of low birth weight babies. Hence, special attention should be paid to women with low prepregnancy BMI.
Not ready to use – overcoming pitfalls when dispersing nanoparticles in physiological media

Industrial nanoparticles are not developed to be compatible with in vitro cell culture assays which are carried out in isotonic solutions at physiological pH and often in the presence of proteins. The tendency of nanoparticles to deagglomerate or agglomerate is strongly sensitive to these parameters. The state of agglomeration and the protein corona bear an important influence on the level of toxic effects via the change of transport mechanisms and surface coating. Here we rigorously characterized the interaction of nanoparticles with physiological media for in vitro nanotoxicology experiments. Beyond adsorption of proteins on metal oxide and polymeric nanoparticles, we quantified nanoparticle deagglomeration due to adsorbing proteins acting as protection colloids. We report on previously neglected, but indispensable testing of sterility and measures to ensure it. Our findings result in a checklist of pre-requirements for dispersion of nanoparticles in physiological media and for reliable attribution of potential toxic effects.
Wavelet-based multiscale stochastic models for efficient tomographic discrimination of fractal fields

Proposes a technique for discrimination of fractal fields with different fractal dimensions, directly from the noisy and sparse tomographic projection data. This application is motivated from the medical field, where a change in fractal dimension is used to differentiate between normal and abnormal conditions in many different contexts, including diagnosis of liver abnormalities. The conventional method for discrimination of fractal fields from tomographic data is based on the calculation of the slope of the power spectra of the corresponding projections. This method, derived from the Radon transform results, breaks down in case the projection data are sparse and/or noisy. In order to avoid any restrictions on the duality and quantity of the projection data, we formulate our discrimination problem in a discrete hypothesis testing framework, the solution to which is given by the maximum-log-likelihood discrimination rule. The problem of discriminating fractal fields through likelihood calculations is, however, complicated by the fact that inverses and determinants of large, full, and generally ill conditioned fractal-field data covariance matrices are required. We show that these complications in the likelihood calculations can be removed by a transformation to the multiscale framework. The multiscale data covariance matrices are sparse and in addition, are naturally partitioned into ill conditioned coarsest scale approximation blocks and relatively well conditioned multiscale detail blocks. We simplify our likelihood calculations by using the class of multiscale stochastic models defined on trees to realize accurate approximations of the detail block of the data covariance matrices. <<ETX>>
Diagnostic Molecular Markers for Phosphine Resistance in U.S. Populations of Tribolium castaneum and Rhyzopertha dominica

Stored product beetles that are resistant to the fumigant pesticide phosphine (hydrogen phosphide) gas have been reported for more than 40 years in many places worldwide. Traditionally, determination of phosphine resistance in stored product beetles is based on a discriminating dose bioassay that can take up to two weeks to evaluate. We developed a diagnostic cleaved amplified polymorphic sequence method, CAPS, to detect individuals with alleles for strong resistance to phosphine in populations of the red flour beetle, Tribolium castaneum, and the lesser grain borer, Rhyzopertha dominica, according to a single nucleotide mutation in the dihydrolipoamide dehydrogenase (DLD) gene. We initially isolated and sequenced the DLD genes from susceptible and strongly resistant populations of both species. The corresponding amino acid sequences were then deduced. A single amino acid mutation in DLD in populations of T. castaneum and R. dominica with strong resistance was identified as P45S in T. castaneum and P49S in R. dominica, both collected from northern Oklahoma, USA. PCR products containing these mutations were digested by the restriction enzymes MboI and BstNI, which revealed presence or absence, respectively of the resistant (R) allele and allowed inference of genotypes with that allele. Seven populations of T. castaneum from Kansas were subjected to discriminating dose bioassays for the weak and strong resistance phenotypes. Application of CAPS to these seven populations confirmed the R allele was in high frequency in the strongly resistant populations, and was absent or at a lower frequency in populations with weak resistance, which suggests that these populations with a low frequency of the R allele have the potential for selection of the strong resistance phenotype. CAPS markers for strong phosphine resistance will help to detect and confirm resistant beetles and can facilitate resistance management actions against a given pest population.
L1-regularized Logistic Regression Stacking and Transductive CRF Smoothing for Action Recognition in Video

For the 2013 THUMOS challenge we built a bag-offeatures pipeline based on a variety of features extracted from both video and keyframe modalities. In addition to the quantized, hard-assigned features provided by the organizers, we extracted local HOG and Motion Boundary Histogram (MBH) descriptors aligned with dense trajectories in video to capture motion. We encode them as Fisher vectors. To represent action-specific scene context we compute local SIFT pyramids on grayscale (P-SIFT) and opponent color keyframes (P-OSIFT) extracted as the central frame of each clip. From all these features we built a bag-of-features pipeline using late classifier fusion to combine scores of individual classifier outputs. We further used two complementary techniques that improve on the basic baseline with late fusion. First, we improve accuracy by using L1-regularized logistic regression (L1LRS) for stacking classifier outputs. Second, we show how with a Conditional Random Field (CRF) we can perform transductive labeling of test samples to further improve classification performance. Using our features we improve on those provided by the contest organizers by 8%, and after incorporating L1LRS and the CRF by more than 11%, reaching a final classification accuracy of 85.7%.
Continuum damage mechanics modelling based on simulations of microstructural evolution kinetics

Abstract Continuum creep damage mechanics modelling of creep has been combined with the recently developed Monte Carlo simulations of precipitation kinetics in power plant ferritic steels. The precipitation simulation has been validated by applying it to a 9 wt-%Cr ferritic steel, P92 and using the microstructural data published in the literature. The microstructural evolution results of precipitation kinetics simulation are used in the continuum creep damage mechanics model to calculate the damage evolution instead of the model equations developed for specific creep damage. This approach has been applied to P92 to study the effects of different creep damage mechanisms on the creep behaviour. Reasonable agreement with experimental creep rupture data and creep curves has been obtained. The new approach shows promise to provide a useful tool for both new alloy development and component life prediction.
On the effectiveness of cooperative diversity in ad hoc networks: a MAC layer study

We investigate the effectiveness of cooperative diversity in interference limited ad hoc networks. The underlying cooperative techniques exploit space diversity through cooperative terminals' relaying signals for one another. We develop a relay selection policy and channel allocation scheme to provide contention-free transmissions while acquiring capacity benefits from cooperative diversity. Extensive simulation results show that careless/selfish usage of cooperative relays yields higher connection blocking probabilities. A proper source allocation scheme is essential to balance the tradeoff between cooperative diversity and interference mitigation.
Internal Erosion of Kaolin

Internal erosion is a great concern in the construction of water retaining embankments. Erosion of soils can be related to their dispersion characteristics. However, although a number of tests can be used to classify soils in terms of their dispersion, they can give contradictory results. Therefore a modified pinhole test was developed to assess erosion of soils. This internal erosion test was used to evaluate the behaviour of Kaolin clay, where specimens were formed using compaction and consolidation techniques and these were compared with slaking tests. Results showed that was a significant difference between the erodibility of the two sample preparation methods of compaction and consolidation, in both the internal erosion test and slaking test. Furthermore, significant differences were also noted in both tests between specimens prepared using the same technique (compaction and consolidation) but different effort (light vs. heavy and 900 kPa vs. 1500 kPa, respectively).