Miracle-dz/UniFAR-FTUs huggingface dataset:
A Global Approach for Medical Image Denoising via Sparse Representation

In this paper, a novel global noise reduction approach based on the sparse representation and nonlocal means algorithm is proposed to enhance the image qualities of various medical imaging modalities, including ultrasound images and magnetic resonance images. By using an overcomplete dictionary, a medical image is decomposed into a sparsest coefficients matrix populated primarily with zeros. A nonlocal means algorithm is developed to deal with these sparse coefficients to exploit the repetitive characters of structures in the whole image, realizing a “truly” global denoising. With synthetic and clinical data of ultrasound images and magnetic resonance images, this approach has been compared with other five state-of-the-art denoising methods. The experiments quantitative results demonstrate the effectiveness of our approach, especially superior in reducing the noise while well preserving the tissue details. It is concluded that our proposed approach is capable of enhancing image quality in both ultrasound and magnetic resonance images. It has a broad field of applications and will increase the diagnostic potential of the medical images.
Geographical parthenogenesis in Pacific Northwest hawthorns ( Crataegus ; Rosaceae )

We have demonstrated geographical parthenogenesis in Crataegus series Douglasianae, an agamic complex comprising exclusively tetraploid Crataegus douglasii sensu lato and the morphologically distinct Crataegus suksdorfii complex that comprises diploids and polyploids. Here we characterize ploidy level and breeding system by detailed flow cytometricmeasurements of the 2C nuclear DNA content of leaf, embryo, and endosperm tissues from 282 black-fruited hawthorns (Crataegus series Douglasianae) representing 33 localities in the Pacific Northwest, one in the Cypress Hills, and three more in the upper Great Lakes basin. We use existing climate and molecular data to place our flow cytometry results in an environmental and evolutionary context. Crataegus douglasii occupiesmore widely distributed sites that experiencemore extreme temperature andmoisture regimes than do the sites occupied by diploid C. suksdorfii.
A Neural Probabilistic Model for Context Based Citation Recommendation

Automatic citation recommendation can be very useful for authoring a paper and is an AI-complete problem due to the challenge of bridging the semantic gap between citation context and the cited paper. It is not always easy for knowledgeable researchers to give an accurate citation context for a cited paper or to find the right paper to cite given context. To help with this problem, we propose a novel neural probabilistic model that jointly learns the semantic representations of citation contexts and cited papers. The probability of citing a paper given a citation context is estimated by training a multi-layer neural network. We implement and evaluate our model on the entire CiteSeer dataset, which at the time of this work consists of 10,760,318 citation contexts from 1,017,457 papers. We show that the proposed model significantly outperforms other state-of-the-art models in recall, MAP, MRR, and nDCG.
Regeneration of Escherichia coli from Minicells through Lateral Gene Transfer

ABSTRACT Recently, artificial life has been created with artificial materials and methods. Life can be created when genomic DNA molecules are integrated in liposomes containing biochemical reactions for biogenic needs. However, it is not yet known whether the integration of these parts will be able to occur in nature and constitute a living system. I planned to regenerate bacteria from biologically active liposomes by inserting genomic DNA using only natural materials and methods. Minicells of Escherichia coli, containing plasmids and activated SOS proteins, act as protocells. Four new E. coli strains were regenerated from minicells by inserting the genomes by using the system for conjugation between F− and Hfr strains. Cells of the four regenerated strains showed the same genetic markers as the two genome donors. Pulse-field gel electrophoresis of their genomes showed admixing of those of both donors. In addition, the genomes of the four regenerated strains had chimeric genome of the two donors. These results show that synthesis of life can occur in nature without artificial arrangement. IMPORTANCE What is the difference between inanimate objects and organisms? Organisms always have genomic DNA. When organisms lose their genomes, they can neither grow nor reproduce. As the result, organisms turn into inanimate objects without their genomes. In this study, I regenerated microbes from cells that had lost their genomes (cell corpses) by inserting another genome. All steps of regeneration used the natural behavior of microbes. The same regeneration of microbes could happen in nature. These primitive lives have plasticity, which accelerates evolution and provides various kinds of life in the world.
Continuous expression of CD83 on activated human CD4+ T cells is correlated with their differentiation into induced regulatory T cells

CD83 is a widely recognized surface marker for mature dendritic cells, which are essential for priming naïve CD4+ T cells into effector cells. However, CD83 is also expressed on activated CD4+ T cells, which remains an enigma in T-cell mediated immunity. Therefore, the identification of the biological features and regulation of the expression of CD83 on activated CD4+ T cells is important in understanding the function of CD83 in the adaptive immune response. The present study revealed a time-dependent manner of the expression of CD83 on anti-CD3/CD28-stimulated human CD4+ T cells, which is characterized by the maximum expression at day 2 and a significant decrease at day 3. The reduced expression is not a result of a reduced rate of cell proliferation. The activation of interleukin-2 and secretion of interferon-γ accumulated progressively from day 1 to 3. Of note, sustained expression of CD83 was observed when CD4+ T cells were induced by transforming growth factor-β to differentiate into CD4+CD25+ forkhead box P3+ regulatory T (iTreg) cells. Confocal immunofluorescence microscopy analysis demonstrated that CD83 was highly co-localized with CD25 on activated CD4+ T cells. In conclusion, the findings of the present study suggested that the continuous expression of CD83 on activated human CD4+ T cells is correlated with their differentiation into iTreg cells.
Methodology of fever research : why are polyphasic fevers often thought to be biphasic ?

Romanovsky, Andrej A. , Vladimir A. Kulchitsky, Christopher T. Simons, and Naotoshi Sugimoto. Methodology of fever research: why are polyphasic fevers often thought to be biphasic? Am. J. Physiol. 275 (Regulatory Integrative Comp. Physiol. 44): R332–R338, 1998. —This study explains why the recently described triphasic lipopolysaccharide (LPS) fevers have been repeatedly mistaken for biphasic fevers. Experiments were performed in loosely restrained male Wistar rats with a catheter implanted into the right jugular vein. Each animal was injected with Escherichia coli LPS, and its colonic (Tc) and tail skin temperatures were monitored. The results are presented as time graphs and phase-plane plots; in the latter case the rate of change of Tc is plotted against Tc. At an ambient temperature (Ta) of 30.0°C, the response to the 10 μg/kg dose of LPS was triphasic, as is obvious from time graphs of Tc (3 peaks), time graphs of effector activity (3 waves of tail skin vasoconstriction), and phase-plane plots (3 complete loops). When the Ta was below neutral (22.0°C) or the LPS dose was higher (100 or 1,000 μg/kg), the time graph of Tc did not allow for the reliable detection of all three febrile phases, but the phase-plane plot and time graph of effector activity clearly revealed the triphasic pattern. In a separate experiment, LPS (10 μg/kg) or saline was injected via one of two different procedures: in the first group the injection was performed through the jugular catheter, from outside the experimental chamber; in the second group the same nonstressing injection was combined with opening the chamber and pricking the animal in its lower abdomen with a needle. In the first group the febrile response was obviously triphasic, and none of the phases was due to the procedure of injection per se (injection of saline did not affect Tc). In the second group the fever similarly consisted of three Tc rises, but it might have been readily mistaken for biphasic because the first rise was indistinguishable from stress hyperthermia occurring in the salineinjected (and needle-pricked) controls. We conclude that several methodological factors (dose of LPS, procedure of its injection, and Ta) have contributed, although each in a different way, to the common misbelief that there are only two febrile phases.
Clustering and switching as two components of verbal fluency: evidence from younger and older healthy adults.

Although verbal fluency is a frequently used neuropsychological test, little is known about the underlying cognitive processes. The authors proposed that 2 important components of fluency performance are clustering (i.e., the production of words within semantic or phonemic subcategories) and switching (i.e., the ability to shift between clusters). In Experiment 1, correlational data from 54 older and 41 younger adults indicated that both components were highly correlated with the number of words generated on semantic fluency, whereas switching was more highly correlated than clustering with the number of words generated on phonemic fluency. On semantic fluency, younger participants generated more words and switched more frequently than older participants; on phonemic fluency, older participants produced larger clusters than younger participants. In Experiment 2, among 22 young adults, divided attention decreased the number of words generated and decreased switching on phonemic fluency only. Overall, findings suggest that clustering and switching are dissociable fluency components and that switching is related to frontal-lobe functioning.
Learning to Read an Alphabet of Human Faces Produces Left-lateralized Training Effects in the Fusiform Gyrus

Numerous functional neuroimaging studies have shown that most orthographic stimuli, such as printed English words, produce a left-lateralized response within the fusiform gyrus (FG) at a characteristic location termed the visual word form area (VWFA). We developed an experimental alphabet (FaceFont) comprising 35 face–phoneme pairs to disentangle phonological and perceptual influences on the lateralization of orthographic processing within the FG. Using functional imaging, we found that a region in the vicinity of the VWFA responded to FaceFont words more strongly in trained versus untrained participants, whereas no differences were observed in the right FG. The trained response magnitudes in the left FG region correlated with behavioral reading performance, providing strong evidence that the neural tissue recruited by training supported the newly acquired reading skill. These results indicate that the left lateralization of the orthographic processing is not restricted to stimuli with particular visual-perceptual features. Instead, lateralization may occur because the anatomical projections in the vicinity of the VWFA provide a unique interconnection between the visual system and left-lateralized language areas involved in the representation of speech.
Phylogenetic Reconstruction of Atlantic Octocorallia (cnidaria: Anthozoa) Printer-friendly Version Interactive Discussion Comprehensive Phylogenetic Reconstruction of Relationships in Octocorallia (cnidaria: Anthozoa) from the Atlantic Ocean Using Mtmuts and Nad2 Genes Tree Reconstructions Bgd Phylo

Biogeosciences Discussions This discussion paper is/has been under review for the journal Biogeosciences (BG). Please refer to the corresponding final paper in BG if available. Abstract Despite being an abundant group of significant ecological importance the phylogenetic relationships of the Octocorallia remain poorly understood and very much understud-ied. We used 1132 bp of two mitochondrial protein-coding genes, nad2 and mtMutS (previously referred to as msh1), to construct a phylogeny for 161 octocoral specimens 5 from the Atlantic, including both Isididae and non-Isididae species. We found that four clades were supported using a concatenated alignment. Two of these (A and B) were in general agreement with the of Holaxonia–Alcyoniina and Anthomastus–Corallium clades identified by previous work. The third and fourth clades represent a split of the Calcaxonia–Pennatulacea clade resulting in a clade containing the Pennatulacea and 10 a small number of Isididae specimens and a second clade containing the remaining Calcaxonia. When individual genes were considered nad2 largely agreed with previous work with MtMutS also producing a fourth clade corresponding to a split of Isididae species from the Calcaxonia–Pennatulacea clade. It is expected these difference are a consequence of the inclusion of Isisdae species that have undergone a gene inver-15 sion in the mtMutS gene causing their separation in the MtMutS only tree. The fourth clade in the concatenated tree is also suspected to be a result of this gene inversion, as there were very few Isidiae species included in previous work tree and thus this separation would not be clearly resolved. A larger phylogeny including both Isididae and non Isididae species is required to further resolve these clades.
Chitosan Based Nanoparticles towards Biomedical Applications

This review outlines the bioapplications of newly developed chitosan based nanoparticles. Over the last decade, much interest has been developed in biopolymer based materials due to their biocompatible, biodegradable, nontoxic and non-allergenic nature. Here, we review the recent scientific advances in chitosan based nanoparticles not only for cancer therapy but also for various biomedical applications. An overview of chitosan, its derivatives and the formation of chitosan nanoparticles is provided along with the inherent and specific therapeutic efficacy. Major progresses in drug delivery approaches and gene delivery as well as tissue engineering applications have been summarized.
Phonological and motor errors in individuals with acquired sound production impairment.

PURPOSE This study aimed to compare sound production errors arising due to phonological processing impairment with errors arising due to motor speech impairment. METHOD Two speakers with similar clinical profiles who produced similar consonant cluster simplification errors were examined using a repetition task. We compared both overall accuracy and acoustic details of hundreds of productions with target consonant clusters to tokens with singletons. Changes in accuracy over the course of the study were also compared. RESULTS In target words with consonant cluster simplification, the individual whose errors reflected phonological impairment produced articulatory timing consistent with singleton onsets. These productions improved when resyllabification was possible, but error rates were not affected by exposure. In contrast, the individual with motoric-based errors produced simplifications that contained the articulatory timing associated with clusters. Accuracy was not affected by the ability to resyllabify, but it did significantly improve following repeated production. CONCLUSIONS Our findings reveal clear differences between errors arising in phonological processing and in motor planning that reflect the underlying systems. The changes over the course of the study suggest that error types with different sources are responsive to different intervention strategies.
Neuropsychological profile in a specific cohort of HIV patients infected postnatally: A cross-sectional study

: HIV-associated neurocognitive disorders (HANDs) are one of the most important complications of HIV infection reported in the current literature. Although HANDs have been closely studied in vertically infected HIV populations or in specific subgroups such as drug abusers or homosexuals, they have been completely understudied in hemophilia patients with HIV, infected through transfusions postnatally. For this reason, it seemed interesting to evaluate the presence of HAND in this specific population. The aim of this work is to present a study protocol aimed at assessing the neuropsychological profile of HIV + hemophilia patients compared with that of HIV − hemophilia patients. This is the first European study to evaluate the neuropsychological profile of HIV + adult hemophiliacs prospectively. in in HIV/ the and behavioral consequences of the disease, concomitant infections and specific antiretroviral therapy. The manuscript
INTEGRATED DATA MINING FRAMEWORK FOR NATURAL RESOURCE EXPLORATION

The study is aimed at developing spatio temporal data mining framework for natural resource exploration. A framework will be said as spatio temporal if it deals with changes in space over time. The study revealed different applications of existing and newly proposed spatio temporal data mining techniques on huge databases collected from diverse sources. The work is integrated on the basis of different proposed Techniques in a unified framework which could serve as a basic skeleton for hydrocarbon prospection. (Muhammad Shaheen), Muhammad Shahbaz, Syed Muhammad Ahsan, Syed Ather Masood. Integrated Data Mining Framework for Natural Resource Exploration. Life Science Journal. 2012;9(1):314-316) (ISSN:1097- 8135). http://www.lifesciencesite. com . 45
Study design considerations for irritable bowel syndrome clinical trials

Clinical trials of therapies intended to alleviate symptoms of irritable bowel syndrome (IBS) are prevalent. However, the ideal study design remains elusive since there is no obvious pathophysiological target and no universally accepted endpoint to assess symptom improvement in IBS. The purpose of this paper is to identify and discuss the most problematic issues in the design of clinical trials intended to evaluate the effectiveness of treatments for IBS symptoms. Lack of standardized diagnostic criteria, symptom variability, heterogeneous subject characteristics, large placebo effects, lack of statistical power, inappropriate endpoint selection, and poorly selected study design are the most critical issues that may confound study outcomes in IBS clinical trials.
Named Entity Recognition for User-Generated Tags

Content Based Multimedia Retrieval on nontextual documents is often constrained by available metadata. User-generated tags constitute an important source of information about a resource. To enable search scenarios exceeding traditional text-based search, such as exploratory and semantic search, this textual information must be complemented with semantic entities. Due to tag ambiguities and creative neologisms automatic semantic annotation based on user tags represents a major challenge. In this work, we show how to adopt context information and ontological knowledge to automatically assign semantic entities to user-generated tags for video data. Thus, a sophisticated semantic search on semantic entities is enabled. The algorithm combines co-occurence and link graph analysis using Linked Data. Also, a definition of context reliability in audio-visual content is described.
Investigation of low stress rupture properties in Inconel-718 super alloy

Inconel-718 is a Ni-Cr-Fe based super alloy. It is widely utilized in aircraft gas turbines, nuclear power systems, space vehicles and medical applications. Aim of the present study is to evaluate the effect of Ti and Nb content on high temperature stress rupture properties of Inconel718. OM, SEM and TEM were utilized for characterization of microstructure. Inconel718 is unique in that it forms large number of phases due to its composition and variety of heat treatments. γ"+ γ' precipitates and the effect of annealing on these precipitates have been studied using TEM. The main hardening phase was identified as metastable Ni3Nb (γ"). Other phases identified after annealing were secondary carbides (NbC) and stable acicular 5 phase. Effect of γ", 5, primary carbides and NbC on creep behavior was observed using OM and SEM. Higher Ti content(1.25 wt. %) resulted in poor creep properties due to large concentrations of primary carbides (TiC) at grain boundaries.
STRESS HORMONES IN TROPICAL BIRDS: PATTERNS AND FUTURE DIRECTIONS

Glucocorticoids are important stress hormones in birds that affect many aspects of physiol- ogy and behavior. Although these hormones have been well studied in temperate and Arctic-dwelling birds, much less is known about them in tropical species. Corticosterone, the primary avian glucocorticoid, is best-known for its involvement in energy balance. In ecological contexts, its main function is to re-direct an organism towards immediate survival of a biotic or abiotic stressor. As tropical environments are quite different from temperate and Arctic ones, corticosterone may have unique influences on avian physiology and behavior near the equator. For example, seasonality in the tropics is not characterized by the dramatic changes in ambient temperature as it is in the Arctic and temperate zones. In the tropics, other conditions, such as rainfall, may more strongly influence corticosterone and thus fitness. Likewise, threat of infection
GENERIC FEATURE MODULES : TWO-STAGED PROGRAM

With feature-oriented programming (FOP) and generics programmers have proper means for structuring software so that its elements can be reused and extended. This paper addresses the issue whether both approaches are equivalent. While FOP targets at large-scale building blocks and compositional programming, generics provide fine-grained customization at type-level. We contribute an analysis that reveals the individual capabilities of both approaches with respect to program customization. Therefrom, we extract guidelines for programmers in what situations which approach suffices. Furthermore, we present a fully implemented language proposal that integrates FOP and generics in order to combine their strengths. Our approach facilitates two-staged program customization: (1) selecting sets of features; (2) parameterizing features subsequently. This allows a broader spectrum of code reuse to be covered – reflected by proper language level mechanisms. We underpin our proposal by means of a case study.
Simulation of the Radiation Energy Release in Air Showers

A simulation study of the energy released by extensive air showers in the form of MHz radiation is performed using the CoREAS simulation code. We develop an efficient method to extract this radiation energy from air-shower simulations. We determine the longitudinal profile of the radiation energy release and compare it to the longitudinal profile of the energy deposit by the electromagnetic component of the air shower. We find that the radiation energy corrected for the geometric dependence of the geomagnetic emission scales quadratically with the energy in the electromagnetic component of the air shower with a second order dependency on the atmospheric density at the position of the maximum of the shower development X max . In a measurement where X max is not accessible, this second order dependence can be approximated using the zenith angle of the incoming direction of the air shower with only a minor deterioration in accuracy. This method results in an intrinsic uncertainty of 4% with respect to the electromagnetic shower energy which is well below current experimental uncertainties.