Miracle-dz/UniFAR-FTUs huggingface dataset:
Code Basket: Making Developers' Mental Model Visible and Explorable

One of software developers' most important activities is exploring the broader context of a certain programming task, which strongly requires navigating source code and working out a mental model of the collected information. Without tool support, creating and maintaining this mental model leads to significant cognitive load because developers have to handle both relating relevant source code entities to their mental model as well as remembering already explored search paths. Furthermore, the opposite direction, that is, recalling relevant facts out of the mental model, and subsequently, seeking corresponding entities within the source code, demands similar cognitive efforts. In this paper, we introduce Code Basket, an approach for making developers' mental model visible and explorable. As for that, Code Basket helps developers keeping their mental model persistent by providing a two-dimensional canvas on which they can freely arrange visual representations of source code entities, named eggs. Since those eggs are linked to the underlying source code, eventually, they can be used for navigating directly to related source code entities. We implemented a first prototype as a touch-enabled web application that is connected to a conventional integrated development environment. In order to get early feedback on our approach, we used Code Basket within a formative study.
Matrix Metalloproteinases and Their Tissue Inhibitors in Cuprizone-Induced Demyelination and Remyelination of Brain White and Gray Matter

Apart from their involvement in the pathogenesis of demyelinating diseases such as multiple sclerosis, there is emerging evidence that matrix metalloproteinases (MMPs) also promote remyelination. We investigated region-specific expression patterns of 11 MMPs and 4 tissueinhibitors of metalloproteinases (TIMPs) in the cuprizone murine demyelination model. Messenger RNA (mRNA) was extracted at different time points of exposure to cuprizone from microdissected samples of corpus callosum, cortex, and ex vivo isolated microglia and analyzedusing quantitative reverse transcription-polymerase chain reaction.Matrix metalloproteinase 12 and TIMP-1 mRNA were significantly upregulated versus age-matched controls in both areas during demyelination and remyelination. Matrix metalloproteinases 3, 11, and 14 mRNA were upregulated only in white matter during remyelination. Matrix metalloproteinase 24 mRNA was downregulated during both demyelination and remyelination. To identify potential cellular sources of the MMPs and TIMPs, we isolated microglia and detected high MMP-12and TIMP-2 mRNA upregulation at the peak of demyelination.By immunohistochemistry, MMP-3 protein was localized in astrocytes and MMP-12 was identified in microglia, astrocytes, and cells of oligodendrocyte lineage. These findings suggest that MMPs and TIMPs have roles in the regulation of demyelination and remyelination in thismodel. Moreover, differences in the expression levels of these genesbetween white and gray matter reveal region-specific molecularmechanisms.
Quantitative Control of Adaptive Cardiac Hypertrophy by Acetyltransferase p300

Background— Acetyltransferase p300 is essential for cardiac development and is thought to be involved in cardiac myocyte growth through MEF2- and GATA4-dependent transcription. However, the importance of p300 in the modulation of cardiac growth in vivo is unknown. Methods and Results— Pressure overload induced by transverse aortic coarctation, postnatal physiological growth, and human heart failure were associated with large increases in p300. Minimal transgenic overexpression of p300 (1.5- to 3.5-fold) induced striking myocyte and cardiac hypertrophy. Both mortality and cardiac mass were directly related to p300 protein dosage. Heterozygous loss of a single p300 allele reduced pressure overload–induced hypertrophy by ≈50% and rescued the hypertrophic phenotype of p300 overexpressers. Increased p300 expression had no effect on total histone deacetylase activity but was associated with proportional increases in p300 acetyltransferase activity and acetylation of the p300 substrates histone 3 and GATA-4. Remarkably, a doubling of p300 levels was associated with the de novo acetylation of MEF2. Consistent with this, genes specifically upregulated in p300 transgenic hearts were highly enriched for MEF2 binding sites. Conclusions— Small increments in p300 are necessary and sufficient to drive myocardial hypertrophy, possibly through acetylation of MEF2 and upstream of signals promoting phosphorylation or nuclear export of histone deacetylases. We propose that induction of myocardial p300 content is a primary rate-limiting event in the response to hemodynamic loading in vivo and that p300 availability drives and constrains adaptive myocardial growth. Specific reduction of p300 content or activity may diminish stress-induced hypertrophy and forestall the development of heart failure.
Color image processing using adaptive vector directional filters

A new class of filters for multichannel image processing is introduced and analyzed. This class constitutes a generalization of vector directional filters. The proposed filters use fuzzy transformations of the angles among the different vectors to adapt to local data in the image. The principle behind the new filters is explained and comparisons with other popular nonlinear filters are provided. The specific case of color image processing is studied as an important example of multichannel image processing. Simulation results indicate that the new filters offer some flexbility and have excellent performance.
Evasive mimicry: when (if ever) could mimicry based on difficulty of capture evolve?

We elucidate the conditions under which an easy–to–catch edible prey species may evolve to resemble another edible species that is much more difficult to capture (‘evasive Batesian mimicry’), and the conditions under which two or more edible but hard–to–catch species evolve a common resemblance (‘evasive Müllerian mimicry’). Using two complementary mathematical models, we argue that both phenomena are logically possible but that several factors will limit the prevalence of these forms of mimicry in nature. Evasive Batesian mimicry is most likely to arise when it is costly in time or energy for the predator species to pursue evasive prey, when mimics are encountered less frequently than evasive models and where there are abundant alternative prey. Evasive Müllerian mimicry, by contrast, is most likely to arise when evasive prey species differ in abundance, predators are slow to learn to avoid evasive prey and evading capture is costly to the prey. Unequivocal evidence for evasive Batesian or Müllerian mimicry has not yet been demonstrated in the field, and we argue that more empirical work is needed to test whether putative examples are indeed a result of selection to signal difficulty of capture.
Effect of Direction to be Used for the Timed Up and Go Test on Walking Time in Stroke Patients

Background: In the stroke patients with the characteristics of hemiplegic gait, turning direction of the affected and unaffected side influences turning time. Therefore, it is important to investigate the walking response to turning directions in stroke patients. Objects: This study aimed to measure the walking time while turning direction in hemiplegic patients depending on balance ability measured by Berg Balance Scale. Methods: A group of forty-five subjects with stroke (Berg Balance Scale score were twenty-eight, Berg Balance Scale score were seventeen) were enrolled in this study. Subjects were asked to perform the Timed Up and Go test. Testing indications included two directions for turning in each subject. These indications were for turning toward the affected and unaffected side in stroke patients. The duration of total analysis duration, sit to stand phase, stand to sit phase, mid-turning phase, and end turning phase were recorded. The obtained data were analyzed by using paired t-test and Wilcoxon signed rank test in the group that are below and above 45 points of Berg Balance Scale score. The significance level was set at . Results: There were significant increase time in the analysis duration and end turning phase duration while subjects were turned the unaffected side in stroke patients that presented a Berg Balance Scale score (p, revealed no significant differences of the measured parameters. Conclusion: This finding should be suggested in the specific definition of turning direction for evaluation with Timed Up and Go test in the Berg Balance Scale score, and other intervention for hemiplegic patients need to be suggested the direction of turning during walking training program.
Comment on "Long-Lived Giant Number Fluctuations in a Swarming Granular Nematic"

Narayan et al. (Reports, 6 July 2007, p. 105) reported giant number fluctuations attributed to curvature-driven active currents specific for nonequilibrium nematic systems. We present data demonstrating that similar results can be found in systems of spherical particles due either to inelastic clustering or persistent density inhomogeneity, suggesting two alternative explanations for their results.
Tag-assisted social-aware opportunistic device-to-device sharing for traffic offloading in mobile social networks

In recent years, the service demand for rich multimedia over mobile networks has continually been soaring at a tremendous pace. To solve the critical problem of mobile traffic explosion, substantial efforts have been made by researchers to try to offload mobile traffic from infrastructured cellular links to direct short-range communications locally among nearby users. In this article, we discuss the potential of combining users' online and offline social impacts to exploit D2D opportunistic sharing for offloading mobile traffic. We propose a tag-assisted social-aware D2D sharing framework, TASA, with corresponding optimization models, architecture design, and communication protocols. Through extensive simulations based on real data traces, we demonstrate that TASA can offload up to 78.9 percent of mobile traffic effectively.
The Role of Spinal Neuroimmune Activation in Morphine Tolerance/Hyperalgesia in Neuropathic and Sham-Operated Rats

Hypersensitivity resulting from nerve injury or morphine tolerance/hyperalgesia is predicted to involve similar cellular and molecular mechanisms. One expected but incompletely explored mechanism is the activation of central neuroimmune responses associated with these conditions. To begin to address this, we undertook three separate studies: First, we determined the acute antinociceptive action of morphine, the rate of development of opioid tolerance, and withdrawal-induced hyperalgesia/allodynia in nerve-injured and sham-operated rats using noxious (thermal and mechanical) and non-noxious (mechanical allodynia) behavioral paradigms. Second, we investigated the impact of chronic morphine treatment on spinal glial activation and cytokine expression after L5 spinal nerve transection or sham surgery. Third, we examined the consequences of spinal administration of cytokine inhibitors on the development of morphine tolerance and morphine withdrawal-induced hyperalgesia and allodynia. Results demonstrated that after nerve injury, the antinociceptive effect of acute morphine was significantly decreased, and the rate of development of tolerance and opioid withdrawal-induced hyperalgesia/allodynia was significantly enhanced compared with that after sham surgery. Chronic administration of morphine to sham-operated rats activated spinal glia and upregulated proinflammatory cytokines [interleukin (IL)-1β, IL-6, and tumor necrosis factor-α]. This neuroimmune activation was further enhanced in nerve-injured rats after chronic morphine treatment. Spinal inhibition of proinflammatory cytokines restored acute morphine antinociception in nerve-injured rats and also significantly reversed the development of morphine tolerance and withdrawal-induced hyperalgesia and allodynia in nerve-injured or sham-operated rats. Targeting central cytokine production and glial activation may improve the effectiveness of morphine and reduce the incidence of morphine withdrawal-induced hyperalgesia and allodynia in neuropathic pain conditions.
Regulation and function of somatostatin receptors

This review summarizes the latest advances that have been made to elucidate the somatostatinergic system in respect to somatostatin receptor evolution, the development of receptor agonists/antagonists, receptor regulation, signal transduction, effects on cell proliferation, receptor–receptor or receptor–protein interactions and receptor function.
Temporal interactions during paired-electrode stimulation in two retinal prosthesis subjects.

PURPOSE Since 2002, six blind patients have undergone implantation of an epiretinal 4 × 4 electrode array designed to directly stimulate the remaining cells of the retina after severe photoreceptor degeneration due to retinitis pigmentosa. This study was conducted to investigate how the brightness of percepts is affected by pulse timing across electrodes in two of these patients. METHODS Subjects compared the perceived brightness of a standard stimulus (synchronous pulse trains presented across pairs of electrodes) to the perceived brightness of a test stimulus (pulse trains across the electrode pair phase shifted by 0.075, 0.375, 1.8, or 9 ms). The current amplitude necessary for each phase-shifted test stimulus to match the brightness of the standard was determined. RESULTS Depending on the electrode pair, interactions between electrodes were either facilitatory (the perceived brightness produced by stimulating the pair of electrodes was greater than that produced by stimulating either electrode alone) or suppressive (the perceived brightness produced by stimulating the pair of electrodes was less than that produced by stimulating either electrode alone). The amount of interaction between electrodes decreased as a function of increased separation both in time (the phase-shift between pulse trains) and space (center-to-center distance between the electrode pair). CONCLUSIONS For visual prostheses to represent visual scenes that are changing in both space and time requires the development of spatiotemporal models describing the effects of stimulation across multiple electrodes. During multielectrode stimulation, interactions between electrodes have a significant influence on subjective brightness that includes both facilitatory and suppressive effects, and these interactions can be described with a simple computational model. (ClinicalTrials.gov number, NCT00279500.).
Progress in Lightning Impulse Characteristics of Grounding Electrodes With Soil Ionization

Grounding is the fundamental measure of lightning protection for power systems, industries, and buildings, and the lightning impulse behavior of grounding electrodes plays a very important role. How to correctly consider the lightning impulse characteristics of grounding electrodes is the fundament in lightning protection design. This paper summarized the progress in lightning impulse characteristics of grounding electrodes with soil ionization, including the images of soil ionization, the residual resistivity of ionized soil, the critical breakdown electrical field, the impulse breakdown delay characteristics of soil, and the impulse breakdown mechanism of soil. Finally, the numerical simulation methods for lightning impulse characteristics of grounding electrodes are classified, and some key performances of grounding electrodes under lightning impulse were presented.
Reducing electromagnetic coupling for bistatic subsurface pulse radar using EBG structures

The bistatic radars consist of transmitting antenna and receiving antenna. There antennas are placed side by side. However transmitted pulse from transmiting antenna is directly received by the receiving antenna. Therefore, if the radar and the target are close, transmitted pulse and wave which reflected from the target overlap each other and artificial image occurs. On the other hand, EBG (Electromagnetic Band-Gap) structure that is one of metamaterial reduces the electromagnetic coupling in specific frequency. This study shows that inserting EBG structures between the transmitting antenna and the receiving antenna reduce the artificial image.
Toponym Resolution in discourse

Toponym resolution involves two stages: toponym recognition and reference resolution. The present research proposes an integrative model for the resolution of Chinese toponym reference in discourse. The model employs the concept of cognitive salience, an inherent property of toponym references, to integrate different heuristic reference disambiguation methods into a coherent design. The heuristic methods involved in the model are category salience, geographic distance salience, co-occurrence frequency salience and discourse distance salience. An algorithm is also designed and implemented to evaluate the performance of the model. The evaluation is focused on the resolution of Chinese toponyms within the linguistic unit of discourse. Experiments of evaluation report satisfactory results with a best precision of 91.1% and a best recall of 73.6% for reference resolution.
Alignment of the Genomes of Brachypodium distachyon and Temperate Cereals and Grasses Using Bacterial Artificial Chromosome Landing With Fluorescence in Situ Hybridization

As part of an initiative to develop Brachypodium distachyon as a genomic “bridge” species between rice and the temperate cereals and grasses, a BAC library has been constructed for the two diploid (2n = 2x = 10) genotypes, ABR1 and ABR5. The library consists of 9100 clones, with an approximate average insert size of 88 kb, representing 2.22 genome equivalents. To validate the usefulness of this species for comparative genomics and gene discovery in its larger genome relatives, the library was screened by PCR using primers designed on previously mapped rice and Poaceae sequences. Screening indicated a degree of synteny between these species and B. distachyon, which was confirmed by fluorescent in situ hybridization of the marker-selected BACs (BAC landing) to the 10 chromosome arms of the karyotype, with most of the BACs hybridizing as single loci on known chromosomes. Contiguous BACs colocalized on individual chromosomes, thereby confirming the conservation of genome synteny and proving that B. distachyon has utility as a temperate grass model species alternative to rice.
High-Contrast Fluorescence Microscopy for a Biomolecular Analysis Based on Polarization Techniques Using an Optical Interference Mirror Slide

Fluorescence microscopy with an improved contrast for fluorescence images is developed using an optical interference mirror (OIM) slide, which can enhance the fluorescence from a fluorophore as a result of the double interference of the excitation light and emission light. To improve the contrast of a fluorescence image using an OIM slide, a linearly-polarized excitation light was employed, and the fluorescence emission polarized perpendicular to the polarization of the excitation light was detected. The image contrast with this optical system was improved 110-fold for rhodamine B spotted on the OIM, in comparison with a glass slide using a general fluorescence microscopy optical system. Moreover, a 24-fold improvement of the image contrast was achieved for the detection of Cy3-labeled streptavidin bound to immobilize biotin.
A Literary Excursion Into the Hidden (Fan) Fictional Worlds of Tetris, Starcraft, and Dreamfall

In this paper, we discuss a part of participatory culture that so far has not received much attention in the academic world; it is the writing and reading of game fan fiction. The focus in this paper is on fan fiction, based on three different games that represent three different game genres: Tetris, StarCraft and Dreamfall: The Longest Journey. The aim is to advance our understanding of how players experience and understand the game environment, and promote further research interest in fan fiction based on computer games. We do this by discussing narrative elements in the above mentioned computer games, and the fan fiction that is based on them.
Comparative proteomic analysis of mesenchymal stem cells derived from human bone marrow, umbilical cord, and placenta: Implication in the migration

Umbilical cord (UC) and placenta (P) have been suggested as alternatives to bone marrow (BM) as sources of mesenchymal stem cells (MSC) for cell therapy, with both UC‐ and P‐MSC possess immunophenotypic and functional characteristics similar to BM‐MSC. However, their migration capacity, which is indispensable during tissue regeneration process, is unclear. Under defined conditions, the migration capacity of BM‐ and P‐MSC was found 5.9‐ and 3.2‐folds higher than that of UC‐MSC, respectively. By the use of 2‐DE and combined MS and MS/MS analysis, six differentially expressed proteins were identified among these MSC samples, with five of them known to be involved in cell migration as migration enhancing or inhibiting proteins. Consistent with their migration capacity, the levels of migration enhancing proteins including cathepsin B, cathepsin D and prohibitin,were significantly lower in UC‐MSC when compared with those in BM‐ and P‐MSC. For the migration inhibiting proteins such as plasminogen activator inhibitor‐1 (PAI‐1) and manganese superoxide dismutase, higher expression was found in the UC‐MSC. We also showed that the overexpression of the PAI‐1 impaired the migration capacity of BM‐ and P‐MSC while silencing of PAI‐1 enhanced the migration capacity of UC‐MSC. Our study indicates that PAI‐1 and other migration‐related proteins are pivotal in governing the migration capacity of MSC.
Dietary protein and skeletal health: a review of recent human research

Purpose of review Both dietary calcium and vitamin D are undoubtedly beneficial to skeletal health. In contrast, despite intense investigation, the impact of dietary protein on calcium metabolism and bone balance remains controversial. A widely held view is that high intakes of animal protein result in increased bone resorption, reduced bone mineral density, and increased fractures because of its ability to generate a high fixed metabolic acid load. The purpose of this review is to present the recent or most important epidemiological and clinical trials in humans that evaluated dietary protein's impact on skeletal health. Recent findings Many epidemiological studies have found a significant positive relationship between protein intake and bone mass or density. Similarly, isotopic studies in humans have also demonstrated greater calcium retention and absorption by individuals consuming high-protein diets, particularly when the calcium content of the diet was limiting. High-protein intake may positively impact bone health by several mechanisms, including calcium absorption, stimulation of the secretion of insulin-like growth factor-1, and enhancement of lean body mass. The concept that an increase in dietary protein induces a large enough shift in systemic pH to increase osteoclastic bone resorption seems untenable. Summary Recent epidemiological, isotopic and meta-analysis studies suggest that dietary protein works synergistically with calcium to improve calcium retention and bone metabolism. The recommendation to intentionally restrict dietary protein to improve bone health is unwarranted, and potentially even dangerous to those individuals who consume inadequate protein.