Miracle-dz/UniFAR-FTUs huggingface dataset:
Green Tea Polyphenol Epigallocatechin-3-gallate (EGCG) Differentially Inhibits Interleukin-1β-Induced Expression of Matrix Metalloproteinase-1 and -13 in Human Chondrocytes

Interleukin-1β (IL-1β)-induced inflammatory response in arthritic joints include the enhanced expression and activity of matrix metalloproteinases (MMPs), and their matrix degrading activity contribute to the irreversible loss of cartilage and may also be associated with sustained chronic inflammation. We have earlier shown that green tea (Camellia sinensis) polyphenol epigallocatechin-3-gallate (EGCG) was non-toxic to human chondrocytes [Singh R, Ahmed S, Islam N, Goldberg VM, and Haqqi TM (2002) Arthritis Rheum 46: 2079–2086] and inhibits the expression of inflammatory mediators in arthritic joints [Haqqi TM, Anthony DD, Gupta S, Ahmed N, Lee MS, Kumar GK, and Mukhtar H (1999) Proc Natl Acad Sci USA 96: 4524–4529]. Here we show that EGCG at micromolar concentrations was highly effective in inhibiting the IL-1β-induced glycosaminoglycan (GAG) release from human cartilage explants in vitro. EGCG also inhibited the IL-1β-induced mRNA and protein expression of MMP-1 and MMP-13 in human chondrocytes. Importantly, EGCG showed a differential, dose-dependent inhibitory effect on the expression and activity of MMP-13 and MMP-1. A similar differential dose-dependent inhibition of transcription factors NF-κB and AP-1 by EGCG was also noted. These results for the first time demonstrate a differential dose-dependent effect of EGCG on the expression and activity of MMPs and on the activities of transcription factors NF-κB and AP-1 and provide insights into the molecular basis of the reported anti-inflammatory effects of EGCG. These results also suggest that EGCG or compounds derived from it may be therapeutically effective inhibitors of IL-1β-induced production of matrix-degrading enzymes in arthritis.
Optimization of a New Mass Spectrometry Method for Measurement of Breast Milk Iodine Concentrations and an Assessment of the Effect of Analytic Method and Timing of Within-Feed Sample Collection on Breast Milk Iodine Concentrations.

BACKGROUND Breast milk iodine concentration (BMIC) may be an indicator of iodine status during lactation, but there are few data comparing different analytical methods or timing of sampling. The aims of this study were: (i) to optimize a new inductively coupled plasma mass spectrometry (ICP-MS) method; and (ii) to evaluate the effect of analytical method and timing of within-feed sample collection on BMIC. METHODS The colorimetric Sandell-Kolthoff method was evaluated with (a) or without (b) alkaline ashing, and ICP-MS was evaluated using a new (129)I isotope ratio approach including Tellurium (Te) for mass bias correction (c) or external standard curve (d). From iodine-sufficient lactating women (n = 97), three samples were collected within one breast-feeding session (fore-, mid-, and hind-feed samples) and BMIC was analyzed using (c) and (d). RESULTS Iodine recovery from NIST SRM1549a whole milk powder for methods (a)-(d) was 67%, 24%, 105%, and 102%, respectively. Intra- and inter-assay coefficients of variation for ICP-MS comparing (c) and (d) were 1.3% versus 5.6% (p = 0.04) and 1.1% versus 2.4% (p = 0.33). The limit of detection (LOD) was lower for (c) (0.26 μg/kg) than it was for (d) (2.54 μg/kg; p = 0.02). Using (c), the median [95% confidence interval (CI) obtained by bootstrap] BMIC (μg/kg) in foremilk (179 [CI 161-206]) and in mid-feed milk (184 [CI 160-220]) were not significantly different (p = 0.017), but were higher than in hindmilk (175 [CI 153-216]; p < 0.001). In foremilk using (d), BMIC was 199 ([CI 182-257]; p < 0.001 vs. (c)). The variation in BMIC comparing (c) and (d) (13%) was greater than variation within feeding (5%; p < 0.001). CONCLUSIONS Because of poor recoveries, (a) and (b) should not be used to measure BMIC. Compared with (d), (c) has the advantages of higher precision and a lower LOD. In iodine-sufficient women, BMIC shows low variation within a breast-feeding session, so timing of sampling is not a major determinant of BMIC.
Feeding a High Concentration Diet Induces Unhealthy Alterations in the Composition and Metabolism of Ruminal Microbiota and Host Response in a Goat Model

There is limited knowledge about the impact of long-term feeding a high-concentrate (HC) diet on rumen microbiota, metabolome, and host cell functions. In this study, a combination of mass spectrometry-based metabolomics techniques, 454 pyrosequencing of 16S rDNA genes, and RT-PCR was applied to evaluate the changes of ruminal microbiota composition, ruminal metabolites, and related genes expression in rumen epithelial cells of lactating goats received either a 35% concentrate diet or a 65% concentrate diet for 4 or 19 weeks, respectively. Results show that feeding a HC diet reduced the microbiota diversity and led to the disorders of metabolism in the rumen. The concentrations of lactate, phosphorus, NH3-N and endotoxin Lipopolysaccharide in ruminal fluids, and plasma histamine, lactate and urine N (UN) were increased significantly in goats fed with a HC diet. A significant increase of genes expression related to volatile fatty acids transport, cell apoptosis, and inflammatory responses were also observed in goats fed with a HC diet. Correlation analysis revealed some potential relationships between bacteria abundance and metabolites concentrations. Our findings indicate that a HC diet can induce ruminal microbiota dysbiosis and metabolic disorders, thus increasing risks to host health and potential harm to the environment.
A case‐control study for differences among hepatitis B virus infections of genotypes A (subtypes Aa and Ae) and D

There are two subtypes of hepatitis B virus genotype A (HBV/A) and they are provisionally designated Aa (“a” standing for Africa/Asia) and Ae (“e” for Europe). In a case‐control study, 78 HBV/Aa, 78HBV/Ae, and 78HBV/D carriers from several countries were compared. The prevalence of HBe antigen (HBeAg) in serum was significantly lower in carriers of HBV/Aa than in carriers of HBV/Ae (31% vs. 49%; P = .033), with a difference more obvious in the carriers aged 30 years or younger (34% vs. 67%; P = .029). HBV DNA levels in the carriers of HBV/Aa (median, 3.46 log copies/mL; 95% CI, 2.93–3.95) were significantly lower than those of carriers of HBV/Ae (6.09 log copies/mL; 95% CI, 4.24–7.64) or of carriers of HBV/D (5.48 log copies/mL; 95% CI, 4.06–7.02), regardless of the HBeAg status (P < .001). The most specific and frequent substitutions in 54 HBV/Aa isolates were double substitutions for T1809 (100%) and T1812 (96%) immediately upstream of the precore initiation codon, which would interfere with the translation of HBeAg in HBV/Aa infections. They were not detected in 57 HBV/Ae or 61 HBV/D isolates examined. The double mutation in the core promoter (T1762/A1764) was more frequent in both HBV/Aa (50%) and HBV/Ae (44%) than in HBV/D isolates (25%; P < .01), whereas the precore mutation (A1896) occurred in HBV/D isolates only (48%; P < .0001). In conclusion, the clearance of HBeAg from serum may occur by different mechanisms in HBV/Aa, HBV/Ae, and HBV/D infections, which may influence clinical manifestations in the Western countries where both genotypes A and D are prevalent. (HEPATOLOGY 2004;40:747–755.)
Putative pacemakers of crayfish show clock proteins interlocked with circadian oscillations

SUMMARY Although the molecular mechanisms that control circadian rhythms in many animals, particularly in the fly, are well known, molecular and biochemical studies addressing the location and function of the proteins and genes contributing to the cycling of the clock in crayfish Procambarus clarkii are scarce. In this study, we investigated whether three proteins that interact in the feedback loop of the molecular clock described for Drosophila are expressed in the putative circadian pacemakers of crayfish retina, eyestalk and brain and whether their expression cycles in a manner consistent with elements of the circadian clock. Here we identified PER, TIM and CLK immunoreactivity in the cytoplasm and nucleus of cells located in the retina as well as in clusters of cells and neuropils of the optic ganglia, lateral protocerebrum and brain. Brain clusters 6, 10, 9 and 11, in particular, showed Per, Tim and Clk-like immunoreactivity at the perikarya and nucleus, and these antigens colocalized at Zeitgeber time (ZT) 0 and/or ZT 12. A biochemical assay demonstrated circadian functionality of Per, Tim and Clk proteins. Both in the eyestalk and in the brain, these proteins demonstrated apparent daily and circadian rhythms. The presence and colocalization of these clock proteins in the cytoplasm and/or nucleus of several cells of retina, optic lobe and brain, depending on time, as well as their circadian oscillations, suggest interactions between positive and negative transcription factors and clock proteins similar to those forming the feedback loop of the canonical model proposed for different animals.
End-to-end congestion control schemes: utility functions, random losses and ECN marks

We present a framework for designing end-to-end congestion control schemes in a network where each user may have a different utility function. We first show that there exists an additive increase-multiplicative decrease scheme using only end-to-end measurable losses such that a socially-optimal solution can be reached. We incorporate non-congestion-related random losses and round-trip delay in this model, and show that one can generalize observations regarding TCP-type congestion avoidance to more general window flow control schemes. We then consider explicit congestion notification (ECN) as an alternate mechanism (instead of losses) for signaling congestion and show that ECN marking levels can be designed to nearly eliminate losses in the network by choosing the marking level independently for each node in the network. While the ECN marking level at each node may depend on the number of flows through the node, the appropriate marking level can be estimated using only aggregate flow measurements, i.e., per-flow measurements are not required.
A new bistatic model for electromagnetic scattering from perfectly conducting random surfaces: numerical evaluation and comparison with SPM

Abstract This paper is a companion to our previous contribution deriving a new approximate bistatic model for electromagnetic scattering from perfectly conducting rough surfaces. We evaluate this model numerically and compare it with an ‘exact’ numerical solution of the scattering problem. This comparison shows good agreement between our approximation and numerical solution for a wide range of incident and scattering angles. However, for horizontal-incident horizontal-scattered polarization (HH-pol), the model exhibits strong deviation from the ‘exact’ solution for near-grazing scattering angles. The model shows a similar divergence at HH-pol when compared with the small-perturbation method (SPM). The cause of this divergence is explained. During the SPM comparison, we noticed that the integral equation method model also does not reproduce the SPM limit except for forward and backscatter geometries. We propose in this paper a simple modification of our model to ensure agreement with the bistatic SPM approximation when applicable, and show that the modified model also yields close agreement with numerical computations even when the surface roughness does not satisfy the SPM condition.
Max-Min Fair Resource Allocation in Millimetre-Wave Backhauls

5G mobile networks are expected to provide pervasive high speed wireless connectivity and support increasingly resource intensive user applications. Network hyper-densification therefore becomes necessary, though connecting to the Internet tens of thousands of base stations is non-trivial, especially in urban scenarios where optical fibre is difficult and costly to deploy. The millimetre wave (mm-wave) spectrum is a promising candidate for inexpensive multi-Gbps wireless backhauling, but exploiting this band for effective multi-hop data communications is challenging. In particular, resource allocation and scheduling of very narrow transmission/ reception beams require to overcome terminal deafness and link blockage problems, while managing fairness issues that arise when flows encounter dissimilar competition and traverse different numbers of links with heterogeneous quality. In this paper, we propose WiHaul, an airtime allocation and scheduling mechanism that overcomes these challenges specific to multi-hop mm-wave networks, guarantees max-min fairness among traffic flows, and ensures the overall available backhaul resources are fully utilised. We evaluate the proposed WiHaul scheme over a broad range of practical network conditions, and demonstrate up to 5× individual throughput gains and a five-fold improvement in terms of measurable fairness, over recent mm-wave scheduling solutions.
An Interaction-aware Attention Network for Speech Emotion Recognition in Spoken Dialogs

Obtaining robust speech emotion recognition (SER) in scenarios of spoken interactions is critical to the developments of next generation human-machine interface. Previous research has largely focused on performing SER by modeling each utterance of the dialog in isolation without considering the transactional and dependent nature of the human-human conversation. In this work, we propose an interaction-aware attention network (IAAN) that incorporate contextual information in the learned vocal representation through a novel attention mechanism. Our proposed method achieves 66.3% accuracy (7.9% over baseline methods) in four class emotion recognition and is also the current state-of-art recognition rates obtained on the benchmark database.
Heavy Tailed Distributions of Effect Sizes in Systematic Reviews of Complex Interventions

Background Systematic reviews of complex interventions commonly find heterogeneity of effect sizes among similar interventions which cannot be explained. Commentators have suggested that complex interventions should be viewed as interventions in complex systems. We hypothesised that if this is the case, the distribution of effect sizes from complex interventions should be heavy tailed, as in other complex systems. Thus, apparent heterogeneity may be a feature of the complex systems in which such interventions operate. Methodology/Principal Findings We specified three levels of complexity and identified systematic reviews which reported effect sizes of healthcare interventions at two of these levels (interventions to change professional practice and personal interventions to help smoking cessation). These were compared with each other and with simulated data representing the lowest level of complexity. Effect size data were rescaled across reviews at each level using log-normal parameters and pooled. Distributions were plotted and fitted against the inverse power law (Pareto) and stretched exponential (Weibull) distributions, heavy tailed distributions which are commonly reported in the literature, using maximum likelihood fitting. The dataset included 155 studies of interventions to change practice and 98 studies of helping smoking cessation. Both distributions showed a heavy tailed distribution which fitted best to the inverse power law for practice interventions (exponent = 3.9, loglikelihood = −35.3) and to the stretched exponential for smoking cessation (loglikelihood = −75.2). Bootstrap sensitivity analysis to adjust for possible publication bias against weak results did not diminish the goodness of fit. Conclusions/Significance The distribution of effect sizes from complex interventions includes heavy tails as typically seen in both theoretical and empirical complex systems. This is in keeping with the idea of complex interventions as interventions in complex systems.
All-Moves-As-First Heuristics in Monte-Carlo Go

We present and explore the effectiveness of sev- eral variations on the All-Moves-As-First (AMAF) heuristic in Monte-Carlo Go. Our results show that: Random play-outs provide more information about the goodness of moves made earlier in the play-out. AMAF updates are not just a way to quickly initialize counts, they are useful after every play-out. Updates even more aggressive than AMAF can be even more beneficial.
Intrinsic Evaluations of Word Embeddings: What Can We Do Better?

This paper presents an analysis of existing methods for the intrinsic evaluation of word embeddings. We show that the main methodological premise of such evaluations is “interpretability” of word embed-dings: a “good” embedding produces re-sults that make sense in terms of traditional linguistic categories. This approach is not only of limited practical use, but also fails to do justice to the strengths of distributional meaning representations. We argue for a shift from abstract ratings of word embedding “quality” to exploration of their strengths and weaknesses.
A binary approximating method for graspable region determination of biped climbing robots

For a biped pole-climbing robot (BiPCR) with grippers, it is an essential demand to determine the target grasp configuration for climbing and transiting between poles, with the graspable region as a priori knowledge. The graspable region on the target pole is critically important for climbing path planning and motion control. To efficiently compute the graspable region for a BiPCR, we propose a novel binary approximating method in this paper. This method may also be applied to generate the three-dimensional (3-D) workspace of a manipulator with constant orientation. The grasping problem and the concept of graspable region for a BiPCR are first introduced. The binary approximating method and the corresponding algorithms are then presented to generate the graspable region. Additional constraints on a biped climbing robot with five degrees of freedom (DoFs) are presented as a supplement to the algorithm. A series of comprehensive simulations are conducted with the five-DoF and six-DoF climbing robots to verify the effectiveness of the proposed method. Finally, the dexterity of biped climbing robots with different DoFs is discussed. Graphical Abstract
Active Pathways: Using Active Tangibles and Interactive Tabletops for Collaborative Modeling in Systems Biology

We present Active Pathways, an active tangible and tabletop system that aims to support collaborative discovery and learning in biochemical modeling. Our work extends ideas from embodied cognition that suggest that interactive systems that support model building by coupling actions made with the motor system to the dynamic properties of external and internal models can enhance the potential for insight and discoveries. We describe the motivation for our work and the design and development of our system. We also present the results of a user study with pairs of novice modelers, which suggest that our system is not only easy to use and learn but also successful at facilitating an understanding of complex systems and supporting collaboration.
Biomass production in experimental grasslands of different species richness during three years of climate warming

Abstract. Here we report on the single and combined impacts of climate warming and species richness on the biomass production in experimental grassland communities. Projections of a future warmer climate have stimulated studies on the response of terrestrial ecosystems to this global change. Experiments have likewise addressed the importance of species numbers for ecosystem functioning. There is, however, little knowledge on the interplay between warming and species richness. During three years, we grew experimental plant communities containing one, three or nine grassland species in 12 sunlit, climate-controlled chambers in Wilrijk, Belgium. Half of these chambers were exposed to ambient air temperatures (unheated), while the other half were warmed by 3°C (heated). Equal amounts of water were added to heated and unheated communities, so that warming would imply drier soils if evapotranspiration was higher. Biomass production was decreased due to warming, both aboveground (–29%) and belowground (–25%), as negative impacts of increased heat and drought stress in summer prevailed. Complementarity effects, likely mostly through both increased aboveground spatial complementarity and facilitative effects of legumes, led to higher shoot and root biomass in multi-species communities, regardless of the induced warming. Surprisingly, warming suppressed productivity the most in 9-species communities, which may be attributed to negative impacts of intense interspecific competition for resources under conditions of high abiotic stress. Our results suggest that warming and the associated soil drying could reduce primary production in many temperate grasslands, and that this will not necessarily be mitigated by efforts to maintain or increase species richness.
Output torque ripple for a cycloidal gear train

The article discusses the problem of a torque ripple on the output shaft of a cycloidal gearbox. To investigate the phenomenon, numerical simulations were performed and compared with the experimental results. Simulations were performed with multibody dynamic software—one with rigid and second with flexible elements. The dynamic model of the gearbox for the determination of the amplitude of the torque change was introduced, where the model utilizes periodical change of the stiffness of gear components as well as geometrical parameters, which are the results of machining and assembly tolerances. The test was made on a gearbox that was calculated, designed, and tested by the authors of the article. To perform the test, a test bench was built. The bench included electric motors, torque meters, and a control application.
Prognostic and diagnostic value of HE 4 expression in patients with chronic kidney diseases

Background: Chronic kidney diseases (CKD) is a progressive loss in renal function, of which the advanced stage is renal fibrosis caused by excessive accumulation of collagen I and other extracellular matrix. The HE4 gene encodes a putative serine protease inhibitor that is upregulated in human fibrotic kidneys and the serum of patients with kidney fibrosis. The expression and clinical significance of HE4 in patients with chronic kidney diseases are not clear. Methods: Here, we detected the expression and localization of HE4 in renal biopsies, correlated their immunostaining scores with clinical and histological parameters, and analyzed whether the HE4 protein level in the renal interstitium was correlated with renal survival. In addition, we detected serum HE4 concentrations in patients with CKD by enzyme-linked immunosorbent assay (ELISA). Receiver operating characteristic (ROC) curves and Cox analyses were used to evaluate its diagnostic and prognostic efficacy, respectively. Results: We found that HE4 was strongly expressed in the cytoplasm of tubular epithelial cells from kidneys of patients with CKDs. HE4 protein expression in the tubulointerstitium was inversely correlated with eGFR and positively correlated with the percent of tubulointerstitial fibrosis. Moreover, HE4 levels were higher in the serum of patients with CKD than in controls. The correlations between serum HE4 concentrations and tubulointerstitial fibrosis or eGFR were significant (P < 0.05). Conclusions: Our results suggested that HE4 was an available biomarker for the progression of renal fibrosis.