Miracle-dz/UniFAR-FTUs huggingface dataset:
A novel bidirectional positive-feedback loop between Wnt–β-catenin and EGFR–ERK plays a role in context-specific modulation of epithelial tissue regeneration

ABSTRACT By operating as both a subunit of the cadherin complex and a key component of Wnt signalling, &bgr;-catenin acts as the lynchpin between cell–cell contact and transcriptional regulation of proliferation, coordinating epithelial tissue homeostasis and regeneration. The integration of multiple growth-regulatory inputs with &bgr;-catenin signalling has been observed in cancer-derived cells, yet the existence of pathway crosstalk in normal cells is unknown. Using a highly regenerative normal human epithelial culture system that displays contact inhibition, we demonstrate that the receptor tyrosine kinase (RTK)-driven MAPK and Wnt–&bgr;-catenin signalling axes form a bidirectional positive-feedback loop to drive cellular proliferation. We show that &bgr;-catenin both drives and is regulated by proliferative signalling cues, and its downregulation coincides with the switch from proliferation to contact-inhibited quiescence. We reveal a novel contextual interrelationship whereby positive and negative feedback between three major signalling pathways – EGFR–ERK, PI3K–AKT and Wnt–&bgr;-catenin – enable autocrine-regulated tissue homeostasis as an emergent property of physical interactions between cells. Our work has direct implications for normal epithelial tissue homeostasis and provides insight as to how dysregulation of these pathways could drive excessive and sustained cellular growth in disease.
MedSearch: a specialized search engine for medical information retrieval

People are thirsty for medical information. Existing Web search engines often cannot handle medical search well because they do not consider its special requirements. Often a medical information searcher is uncertain about his exact questions and unfamiliar with medical terminology. Therefore, he sometimes prefers to pose long queries, describing his symptoms and situation in plain English, and receive comprehensive, relevant information from search results. This paper presents MedSearch, a specialized medical Web search engine, to address these challenges. MedSearch uses several key techniques to improve its usability and the quality of search results. First, it accepts queries of extended length and reforms long queries into shorter queries by extracting a subset of important and representative words. This not only significantly increases the query processing speed but also improves the quality of search results. Second, it provides diversified search results. Lastly, it suggests related medical phrases to help the user quickly digest search results and refine the query. We evaluated MedSearch using medical questions posted on medical discussion forums. The results show that MedSearch can handle various medical queries effectively and efficiently.
Indoor localization by WiFi

The demand for accurate indoor localization techniques is increasing. The existing infrastructure of 802.11 WiFi networks can be exploited to position a device in a building. In this paper a positioning system is presented to locate a robot device in the Faculty of Computer Science building. Several techniques are experimented and the algorithms K Nearest-Neighbours (KNN), weighted KNN, weighted Centroid, and Gaussian kernel methods are implemented and compared.
Simpler Approximation of the Maximum Asymmetric Traveling Salesman Problem

We give a very simple approximation algorithm for the maximum asymmetric traveling salesman problem. The approximation guarantee of our algorithm is 2/3, which matches the best known approximation guarantee by Kaplan, Lewenstein, Shafrir and Sviridenko. Our algorithm is simple to analyze, and contrary to previous approaches, which need an optimal solution to a linear program, our algorithm is combinatorial and only uses maximum weight perfect matching algorithm.
Effects of Dietary Exposure to Zearalenone (ZEN) on Carp (Cyprinus carpio L.)

The mycotoxin zearalenone (ZEN) is frequently contaminating animal feeds including feed used in aquaculture. In the present study, the effects of dietary exposure to ZEN on carp (Cyprinus carpio L.) were investigated. ZEN at three different concentrations (low dose: 332 µg kg−1, medium dose: 621 µg kg−1 and high dose: 797 µg kg−1 final feed, respectively) was administered to juvenile carp for four weeks. Additional groups received the mycotoxin for the same time period but were fed with the uncontaminated diet for two more weeks to examine the reversibility of the ZEN effects. No effects on growth were observed during the feeding trial, but effects on haematological parameters occurred. In addition, an influence on white blood cell counts was noted whereby granulocytes and monocytes were affected in fish treated with the medium and high dose ZEN diet. In muscle samples, marginal ZEN and α-zearalenol (α-ZEL) concentrations were detected. Furthermore, the genotoxic potential of ZEN was confirmed by analysing formation of micronuclei in erythrocytes. In contrast to previous reports on other fish species, estrogenic effects measured as vitellogenin concentrations in serum samples were not increased by dietary exposure to ZEN. This is probably due to the fact that ZEN is rapidly metabolized in carp.
Transcriptional factors associated with epithelial-mesenchymal transition in choroidal neovascularization

Purpose To investigate the transcriptional factors associated with epithelial-mesenchymal transition (EMT) in choroidal neovascularization (CNV) secondary to age-related macular degeneration (AMD). Methods Paraffin sections of CNV obtained from patients with AMD (n=12) were stained for transcriptional factors related to EMT, i.e., Snail, Slug, SIP1, and Twist. As a control, postmortem sections of ocular normal tissue were used. Furthermore, using a human retinal pigment epithelial (RPE) cell line (ARPE-19), reverse transcription–polymerase chain reaction (RT–PCR) and immunofluorescence microscopy were performed to explore the cellular localization and expression levels of EMT-associated transcriptional factors upon cytokine stimulation. Results Of 12 specimens, 11 CNV tissues (91.6%) showed staining for Snail localized in cellular nuclei, particularly in those of RPE cells. Snail was strongly co-localized with α-smooth muscle antigen (SMA) in RPE cells. In contrast, postmortem human retina showed no Snail staining in RPE cells. Other transcriptional factors, Slug, Twist and SIP1 were not detected in CNV or normal human retina. In ARPE-19 cells, RT–PCR and immunofluorescence microscopy showed that Snail mRNA was upregulated by transforming growth factor (TGF)-β and VEGF stimulation. Furthermore, TGF-β induced relocalization of Snail to the nucleus in RPE cells. Conclusions The current data indicate that Snail is a major transcriptional factor for EMT changes of RPE cells in human CNV.
Knowledge, Attitude, and Practice of Rafsanjan University of Medical Sciences Students Concerning Fast Food

Background: Lifestyle changes and, consequently, changes in dietary habits have led people, especially young people, to consume more processed and fast food. This study evaluated the knowledge, attitude, and practice of fast-food consumption among medical sciences students in Rafsanjan, Iran. Methods: In this cross-sectional study, data were collected using a researcher-designed self-reported questionnaire, which was distributed among 350 medical sciences students in Rafsanjan, Iran, selected by stratified random sampling from 2019 to 2020. The validity and reliability of this questionnaire were confirmed before commencement. SPSS 20 was used for data analysis. Results: The results showed that university students had above-moderate knowledge (39.7±0.55) and positive attitudes (60.52±0.43) about fast food consumption. The mean number of times students consumed fast food in the past month was 12.41±0.46. There was a statistically significant and positive correlation between attitude and practice. Also, knowledge had a significant inverse correlation with attitude and practice. The level of women’s knowledge was significantly higher (P=0.001) than men’s knowledge, and the knowledge score of dental and medical students was significantly higher (P=0.04) than that of students from other schools. The men’s attitude score was significantly higher (P=0.04) than the women’s. Conclusion: Appropriate interventions should be implemented to improve students’ knowledge, attitude, and practice concerning fast food consumption. Food labeling, teaching healthy cooking and preparation, time management, improving university meal programs, and opening affordable, healthy on-campus restaurants are recommended.
Plasma Urate Level Is Directly Regulated by a Voltage-driven Urate Efflux Transporter URATv1 (SLC2A9) in Humans*

Hyperuricemia is a significant factor in a variety of diseases, including gout and cardiovascular diseases. Although renal excretion largely determines plasma urate concentration, the molecular mechanism of renal urate handling remains elusive. Previously, we identified a major urate reabsorptive transporter, URAT1 (SLC22A12), on the apical side of the renal proximal tubular cells. However, it is not known how urate taken up by URAT1 exits from the tubular cell to the systemic circulation. Here, we report that a sugar transport facilitator family member protein GLUT9 (SLC2A9) functions as an efflux transporter of urate from the tubular cell. GLUT9-expressed Xenopus oocytes mediated saturable urate transport (Km: 365 ± 42 μm). The transport was Na+-independent and enhanced at high concentrations of extracellular potassium favoring negative to positive potential direction. Substrate specificity and pyrazinoate sensitivity of GLUT9 was distinct from those of URAT1. The in vivo role of GLUT9 is supported by the fact that a renal hypouricemia patient without any mutations in SLC22A12 was found to have a missense mutation in SLC2A9, which reduced urate transport activity in vitro. Based on these data, we propose a novel model of transcellular urate transport in the kidney; Remunurate is taken up via apically located URAT1 and exits the cell via basolaterally located GLUT9, which we suggest be renamed URATv1 (voltage-driven urate transporter 1).
Incubation behavior adjustments, driven by ambient temperature variation, improve synchrony between hatch dates and caterpillar peak in a wild bird population

Abstract For organisms living in seasonal environments, synchronizing the peak energetic demands of reproduction with peak food availability is a key challenge. Understanding the extent to which animals can adjust behavior to optimize reproductive timing, and the cues they use to do this, is essential for predicting how they will respond to future climate change. In birds, the timing of peak energetic demand is largely determined by the timing of clutch initiation; however, considerable alterations can still occur once egg laying has begun. Here, we use a wild population of great tits (Parus major) to quantify individual variation in different aspects of incubation behavior (onset, duration, and daily intensity) and conduct a comprehensive assessment of the causes and consequences of this variation. Using a 54‐year dataset, we demonstrate that timing of hatching relative to peak prey abundance (synchrony) is a better predictor of reproductive success than clutch initiation or clutch completion timing, suggesting adjustments to reproductive timing via incubation are adaptive in this species. Using detailed in‐nest temperature recordings, we found that postlaying, birds improved their synchrony with the food peak primarily by varying the onset of incubation, with duration changes playing a lesser role. We then used a sliding time window approach to explore which spring temperature cues best predict variance in each aspect of incubation behavior. Variation in the onset of incubation correlated with mean temperatures just prior to laying; however, incubation duration could not be explained by any of our temperature variables. Daily incubation intensity varied in response to daily maximum temperatures throughout incubation, suggesting female great tits respond to temperature cues even in late stages of incubation. Our results suggest that multiple aspects of the breeding cycle influence the final timing of peak energetic demand. Such adjustments could compensate, in part, for poor initial timing, which has significant fitness impacts.
Amino Acid Metabolism of Thermoanaerobacter Strain AK90: The Role of Electron-Scavenging Systems in End Product Formation

The catabolism of the 20 amino acids by Thermoanaerobacter strain AK90 (KR007667) was investigated under three different conditions: as single amino acids without an electron-scavenging system, in the presence of thiosulfate, and in coculture with a hydrogenotrophic methanogen. The strain degraded only serine without an alternative electron acceptor but degraded 11 amino acids (alanine, cysteine, isoleucine, leucine, lysine, methionine, phenylalanine, serine, threonine, tyrosine, and valine) under both of the electron-scavenging systems investigated. Acetate was the dominant end product from alanine, cysteine, lysine, serine, and threonine under electron-scavenging conditions. The branched-chain amino acids, isoleucine, leucine, and valine, were degraded to their corresponding fatty acids under methanogenic conditions and to a mixture of their corresponding fatty acids and alcohols in the presence of thiosulfate. The partial pressure of hydrogen seems to be of importance for the branched-chain alcohol formation. This was suggested by low but detectable hydrogen concentrations at the end of cultivation on the branched-chain amino acid in the presence of thiosulfate but not when cocultured with the methanogen. A more detailed examination of the role of thiosulfate as an electron acceptor was performed with Thermoanaerobacter ethanolicus (DSM 2246) and Thermoanaerobacter brockii (DSM 1457).
Geometric modeling in shape space

We present a novel framework to treat shapes in the setting of Riemannian geometry. Shapes -- triangular meshes or more generally straight line graphs in Euclidean space -- are treated as points in a shape space. We introduce useful Riemannian metrics in this space to aid the user in design and modeling tasks, especially to explore the space of (approximately) isometric deformations of a given shape. Much of the work relies on an efficient algorithm to compute geodesics in shape spaces; to this end, we present a multi-resolution framework to solve the interpolation problem -- which amounts to solving a boundary value problem -- as well as the extrapolation problem -- an initial value problem -- in shape space. Based on these two operations, several classical concepts like parallel transport and the exponential map can be used in shape space to solve various geometric modeling and geometry processing tasks. Applications include shape morphing, shape deformation, deformation transfer, and intuitive shape exploration.
Chinese Morphological Analysis with Character-level POS Tagging

The focus of recent studies on Chinese word segmentation, part-of-speech (POS) tagging and parsing has been shifting from words to characters. However, existing methods have not yet fully utilized the potentials of Chinese characters. In this paper, we investigate the usefulness of character-level part-of-speech in the task of Chinese morphological analysis. We propose the first tagset designed for the task of character-level POS tagging. We propose a method that performs character-level POS tagging jointly with word segmentation and word-level POS tagging. Through experiments, we demonstrate that by introducing character-level POS information, the performance of a baseline morphological analyzer can be significantly improved.
Fabric-Based Wearable Dry Electrodes for Body Surface Biopotential Recording

A flexible and conformable dry electrode design on nonwoven fabrics is examined as a sensing platform for biopotential measurements. Due to limitations of commercial wet electrodes (e.g., shelf life, skin irritation), dry electrodes are investigated as the potential candidates for long-term monitoring of ECG signals. Multilayered dry electrodes are fabricated by screen printing of Ag/AgCl conductive inks on flexible nonwoven fabrics. This study focuses on the investigation of skin-electrode interface, form factor design, electrode body placement of printed dry electrodes for a wearable sensing platform. ECG signals obtained with dry and wet electrodes are comparatively studied as a function of body posture and movement. Experimental results show that skin-electrode impedance is influenced by printed electrode area, skin-electrode interface material, and applied pressure. The printed electrode yields comparable ECG signals to wet electrodes, and the QRS peak amplitude of ECG signal is dependent on printed electrode area and electrode on body spacing. Overall, fabric-based printed dry electrodes present an inexpensive health monitoring platform solution for mobile wearable electronics applications by fulfilling user comfort and wearability.
Does Plant Litter Become More Recalcitrant Under Elevated Atmospheric CO 2 Levels

Increases in atmospheric CO2 concentration exert several positive and negative effects on litter dynamics, but the net impact of climate change on litter decomposition and the carbon balance of the terrestrial ecosystem is yet unclear. The objective of this review is to summarize the current state of knowledge on litter dynamics under elevated CO2 levels with a view to using it as a basis for mitigating the negative effects of rising anthropogenic CO2 emissions. To understand the biogeochemical processes in response to elevated CO2 levels, we propose a conceptual model illustrating the interactive effects of rising CO2 levels on litter dynamics, which assumes that the expected positive effects on photosynthesis will be translated into higher detritus production. The general dilution of nitrogen within plant tissues grown under elevated CO2 and the consequent N constraints on microbes, however, may have a strong feedback effect on photosynthetic efficiency through depressed nutrient mineralization. Again, a concomitant rise in the atmospheric temperature may accelerate the process of litter decomposition. Significant regional variations in litter production and decomposition rates are also probable in view of the changes in precipitation intensity/patterns and/or biodiversity changes associated with global warming. Gains in litter accumulation on the forest floor under elevated CO2 levels may lead to increased carbon sequestration and could partially offset the negative effects of anthropogenic CO2 emissions into the atmosphere.
Fully distributed adaptive consensus control of multi-agent systems with LQR performance index

This paper deals with fully distributed consensus control of linear multi-agent systems in continuous-time. The subsystems or the agents are connected by an undirected graph with unknown network connectivity, which is then estimated by a carefully designed adaptive scheme. With this adaptive scheme, the proposed control design only uses the relative state information of the subsystems in a neighbourhood. This makes the proposed control fully distributed, without the use of the network connectivity that requires the Laplacian matrix of the entire network. The proposed control is also guaranteed to achieve an optimal control performance index.
The Effect of Noise in Dust Emission Maps on the Derivation of Column Density, Temperature, and Emissivity Spectral Index

We have mapped the central 10′ × 10′ of the dense core TMC-1C at 450, 850, and 1200 μm using SCUBA on the James Clerk Maxwell Telescope and MAMBO on the IRAM 30 m telescope. We show that although one can, in principle, use images at these wavelengths to map the emissivity spectral index, temperature, and column density independently, noise and calibration errors would have to be less than ~2% to accurately derive these three quantities from a set of three emission maps. Because our data are not this free of errors, we use our emission maps to fit the dust temperature and column density assuming a constant value of the emissivity spectral index and explore the effects of noise on the derived physical parameters. We find that the derived extinction values for TMC-1C are large for a starless core (~80 mag AV) and the derived temperatures are low (~6 K) in the densest regions of the core, using our derived value of β = 1.8.
Chronic administration of valproic acid inhibits activation of mouse hepatic stellate cells in vitro and in vivo

Hepatic stellate cell (HSC) activation is a pivotal step in the pathogenesis of liver fibrosis. The clarification of this transdifferentiation process is therefore important for the development of effective therapies for fibrosis. We analyzed the effect of a histone deacetylase inhibitor, valproic acid (VPA), on mouse HSC transdifferentiation in vitro and in vivo. The exposure of freshly isolated mouse HSCs to 2.5 mM VPA led to increased histone H4 acetylation and inhibited cell proliferation. Expression of stellate cell activation markers analyzed by quantitative polymerase chain reaction and western blotting revealed that treatment with VPA inhibited the induction of activation markers such as Acta2, Lox, Spp1, and Myh11. Treatment of mice with VPA decreased collagen deposition and in vivo activation of stellate cells in the livers of CCl4‐treated mice. Class I histone deacetylase silencing through RNA interference in mouse HSCs only partially mimicked treatment with VPA. Conclusion: Chronic administration of VPA results in a marked decrease in stellate cell activation both in vitro and in vivo. We hypothesize that the VPA effect results partially from class I histone deacetylase inhibition, but that also non‐histone deacetylase class I VPA targets are involved in the stellate cell activation process. (HEPATOLOGY 2010.)
Antioxidant mechanism of black garlic extract involving nuclear factor erythroid 2-like factor 2 pathway

BACKGROUN/OBJECTIVES Although studies have revealed that black garlic is a potent antioxidant, its antioxidant mechanism remains unclear. The objective of this study was to determine black garlic's antioxidant activities and possible antioxidant mechanisms related to nuclear factor erythroid 2-like factor 2 (Nrf2)-Keap1 complex. METHODS/MATERIALS After four weeks of feeding rats with a normal fat diet (NF), a high-fat diet (HF), a high-fat diet with 0.5% black garlic extract (HF+BGE 0.5), a high-fat diet with 1.0% black garlic extract (HF+BGE 1.0), or a high-fat diet with 1.5% black garlic extract (HF+BGE 1.5), plasma concentrations of glucose, insulin,homeostatic model assessment of insulin resistance (HOMA-IR) were determined. As oxidative stress indices, plasma concentrations of thiobarbituric acid reactive substances (TBARS) and 8-isoprostaglandin F2α (8-iso-PGF) were determined. To measure antioxidant capacities, plasma total antioxidant capacity (TAC) and activities of antioxidant enzymes in plasma and liver were determined. The mRNA expression levels of antioxidant related proteins such as Nrf2, NAD(P)H: quinone-oxidoreductase-1 (NQO1), heme oxygenase-1 (HO-1), glutathione reductase (GR), and glutathione S-transferase alpha 2 (GSTA2) were examined. RESULTS Plasma glucose level, plasma insulin level, and HOMA-IR in black garlic supplemented groups were significantly (P < 0.05) lower than those in the HF group without dose-dependent effect. Plasma TBARS concentration and TAC in the HF+BGE 1.5 group were significantly decreased compared to those of the HF group. The activities of catalase and glutathione peroxidase were significantly (P < 0.05) increased in the HF+BGE 1.0 and HF+BGE 1.5 groups compared to those of the HF group. The mRNA expression levels of hepatic Nrf2, NQO1, HO-1, and GSTA2 were significantly (P < 0.05) increased in the HF with BGE groups compared to those in the HF group. CONCLUSIONS The improvements of blood glucose homeostasis and antioxidant systems in rats fed with black garlic extract were related to mRNA expression levels of Nrf2 related genes.