Miracle-dz/UniFAR-FTUs huggingface dataset:
Accurate Motion Control of Linear Motors With Adaptive Robust Compensation of Nonlinear Electromagnetic Field Effect

Many control methodologies have been applied to the motion control of linear motor drive systems. Compensations of nonlinearities such as frictions and cogging forces have also been carried out to obtain better tracking performance. However, the relationship between the driving current and the resulting motor force has been assumed to be linear, which is invalid for high driving coil currents due to the saturating electromagnetic field effect. This paper focuses on the effective compensation of nonlinear electromagnetic field effect so that the system can be operated at even higher acceleration or heavier load without losing achievable control performance. Specifically, cubic polynomials with unknown weights are used for an effective approximation of the unknown nonlinearity between the electromagnetic force and the driving current. The effectiveness of such an approximation is verified by offline identification experiments. An adaptive robust control (ARC) algorithm with online tuning of the unknown weights and other system parameters is then developed to account for various uncertainties. Theoretically, the proposed ARC algorithm achieves a guaranteed transient and steady-state performance for position tracking, as well as zero steady-state tracking error when subjected to parametric uncertainties only. Comparative experiments of ARC with and without compensation of electromagnetic nonlinearity done on both axes of a linear-motor-driven industrial gantry are shown. The results show that the proposed ARC algorithm achieves better tracking performance than existing ones, validating the effectiveness of the proposed approach in practical applications.
Construction and application of dynamic protein interaction network based on time course gene expression data

In recent years, researchers have tried to inject dynamic information into static protein interaction networks (PINs). The paper first proposes a three‐sigma method to identify active time points of each protein in a cellular cycle, where three‐sigma principle is used to compute an active threshold for each gene according to the characteristics of its expression curve. Then a dynamic protein interaction network (DPIN) is constructed, which includes the dynamic changes of protein interactions. To validate the efficiency of DPIN, MCL, CPM, and core attachment algorithms are applied on two different DPINs, the static PIN and the time course PIN (TC‐PIN) to detect protein complexes. The performance of each algorithm on DPINs outperforms those on other networks in terms of matching with known complexes, sensitivity, specificity, f‐measure, and accuracy. Furthermore, the statistics of three‐sigma principle show that 23–45% proteins are active at a time point and most proteins are active in about half of cellular cycle. In addition, we find 94% essential proteins are in the group of proteins that are active at equal or great than 12 timepoints of GSE4987, which indicates the potential existence of feedback mechanisms that can stabilize the expression level of essential proteins and might provide a new insight for predicting essential proteins from dynamic protein networks.
Angiopoietin-like 4 is a potent angiogenic factor and a novel therapeutic target for patients with proliferative diabetic retinopathy

Significance In proliferative diabetic retinopathy (PDR), the most vision-threatening sequela of diabetic eye disease, retinal ischemia leads to increased expression of angiogenic factors that promote neovascularization. Although therapies targeting the potent angiogenic mediator vascular endothelial growth factor have been remarkably successful for the treatment of diabetic macular edema, this approach has not proven sufficient to prevent the development of retinal neovascularization, implicating additional angiogenic factor(s) in PDR pathogenesis. We demonstrate here that angiopoietin-like 4 is a potent angiogenic mediator with markedly increased expression in the eyes of PDR patients. Our studies identify a novel therapeutic target for the treatment of ocular neovascular disease and may have broad implications for the treatment of other diseases dependent on pathologic angiogenesis. Diabetic eye disease is the most common cause of severe vision loss in the working-age population in the developed world, and proliferative diabetic retinopathy (PDR) is its most vision-threatening sequela. In PDR, retinal ischemia leads to the up-regulation of angiogenic factors that promote neovascularization. Therapies targeting vascular endothelial growth factor (VEGF) delay the development of neovascularization in some, but not all, diabetic patients, implicating additional factor(s) in PDR pathogenesis. Here we demonstrate that the angiogenic potential of aqueous fluid from PDR patients is independent of VEGF concentration, providing an opportunity to evaluate the contribution of other angiogenic factor(s) to PDR development. We identify angiopoietin-like 4 (ANGPTL4) as a potent angiogenic factor whose expression is up-regulated in hypoxic retinal Müller cells in vitro and the ischemic retina in vivo. Expression of ANGPTL4 was increased in the aqueous and vitreous of PDR patients, independent of VEGF levels, correlated with the presence of diabetic eye disease, and localized to areas of retinal neovascularization. Inhibition of ANGPTL4 expression reduced the angiogenic potential of hypoxic Müller cells; this effect was additive with inhibition of VEGF expression. An ANGPTL4 neutralizing antibody inhibited the angiogenic effect of aqueous fluid from PDR patients, including samples from patients with low VEGF levels or receiving anti-VEGF therapy. Collectively, our results suggest that targeting both ANGPTL4 and VEGF may be necessary for effective treatment or prevention of PDR and provide the foundation for studies evaluating aqueous ANGPTL4 as a biomarker to help guide individualized therapy for diabetic eye disease.
Genetic Susceptibility to Renal Cell Carcinoma: The Role of DNA Double-Strand Break Repair Pathway

Alterations in DNA repair genes have been shown to cause a reduction in host DNA repair capacity and may influence host susceptibility to carcinogenesis. The double-strand break repair is a major DNA-repair pathway. This study tested the hypothesis that common sequence variants of the double-strand break pathway genes predispose susceptible individuals to an increased risk for renal cell carcinoma. Toward this end, we evaluated the associations of 13 single-nucleotide polymorphisms in 10 candidate genes involved in the double-strand break pathway with renal cell carcinoma risk in a population-based case-control study that included 326 Caucasian renal cell carcinoma patients and 335 controls. Using the homozygous wild type as the reference group, we observed a significantly increased renal cell carcinoma risk associated with the homozygous variant genotype of NBS1 (rs1805794; odds ratio, 2.13; 95% confidence interval (95% CI), 1.17-3.86). Carrying of at least one copy of the variant XRCC4 allele was also associated with a significantly increased risk (rs1805377; odds ratio, 1.56; 95% CI, 1.08-2.26). Importantly, in pathway analysis, compared with the reference group (1 or less adverse alleles), individuals with two (odds ratio, 1.26; 95% CI, 0.83-1.91), three (odds ratio, 1.00; 95% CI, 0.64-1.56), and more than three adverse alleles (odds ratio, 1.75; 95% CI, 1.03-2.98) were at increased risk for renal cell carcinoma with significant association in subjects carrying more than 3 adverse alleles. Results from this study provide evidence that individuals with a higher number of genetic variations in the DBS repair pathway are at an increased risk for renal cell carcinoma. These findings require further validation in independent populations. (Cancer Epidemiol Biomarkers Prev 2008;17(9):2366–73)
Vision-based body tracking: turning Kinect into a clinical tool

Abstract Purpose: Vision-based body tracking technologies, originally developed for the consumer gaming market, are being repurposed to form the core of a range of innovative healthcare applications in the clinical assessment and rehabilitation of movement ability. Vision-based body tracking has substantial potential, but there are technical limitations. Method: We use our “stories from the field” to articulate the challenges and offer examples of how these can be overcome. Results: We illustrate that: (i) substantial effort is needed to determine the measures and feedback vision-based body tracking should provide, accounting for the practicalities of the technology (e.g. range) as well as new environments (e.g. home). (ii) Practical considerations are important when planning data capture so that data is analysable, whether finding ways to support a patient or ensuring everyone does the exercise in the same manner. (iii) Home is a place of opportunity for vision-based body tracking, but what we do now in the clinic (e.g. balance tests) or in the home (e.g. play games) will require modifications to achieve capturable, clinically relevant measures. Conclusions: This article articulates how vision-based body tracking works and when it does not to continue to inspire our clinical colleagues to imagine new applications. Implications for Rehabilitation Vision-based body tracking has quickly been repurposed to form the core of innovative healthcare applications in clinical assessment and rehabilitation, but there are clinical as well as practical challenges to make such systems a reality. Substantial effort needs to go into determining what types of measures and feedback vision-based body tracking should provide. This needs to account for the practicalities of the technology (e.g. range) as well as the opportunities of new environments (e.g. the home). Practical considerations need to be accounted for when planning capture in a particular environment so that data is analysable, whether it be finding a chair substitute, ways to support a patient or ensuring everyone does the exercise in the same manner. The home is a place of opportunity with vision-based body tracking, but it would be naïve to think that we can do what we do now in the clinic (e.g. balance tests) or in the home (e.g. play games), without appropriate modifications to what constitutes a practically capturable, clinically relevant measure.
3-O-Deacylation of Lipid A by PagL, a PhoP/PhoQ-regulated Deacylase of Salmonella typhimurium, Modulates Signaling through Toll-like Receptor 4*

Toll-like receptor 4 (TLR4)-mediated responses, which are induced by the lipid A portion of lipopolysaccharide, are important for host defense against Salmonellae infection. A variety of different data indicate that the acylation state of lipid A can alter TLR4-mediated responses. The S. typhimurium virulence gene product PhoP/PhoQ signals the presence of host microenvironments to regulate the expression of a lipid A 3-O-deacylase, PagL, and a lipid A palmitoyltransferase, PagP. We now demonstrate that 3-O-deacylation and palmitoylation of lipid A decreases its ability to induce TLR4-mediated signaling. Deacylated lipid A, deacylated and palmitoylated lipid A, palmitoylated lipid A, and unmodified lipid A species were purified from Escherichia coli heterologously expressing PagL and/or PagP. The purified lipid A preparations showed spectra of a single lipid A species on mass spectrometry and gave a single band on thin layer chromatography. The activity of purified lipid A species was examined using human and mouse cell lines that express recombinant human TLR4. Compared with unmodified lipid A, the modified lipid A species are 30–100-fold less active in the ability to induce NF-κB-dependent reporter activation. These results suggest that the lipid A modifications reduce TLR4-signaling as part of Salmonellae adaptation to host environments.
Initiation of network bursts by Ca2+‐dependent intrinsic bursting in the rat pilocarpine model of temporal lobe epilepsy

1 Chronically epileptic rats, produced by prior injection of pilocarpine, were used to investigate whether changes in intrinsic neuronal excitability may contribute to the epileptogenicity of the hippocampus in experimental temporal lobe epilepsy (TLE). 2 Paired extra‐/intracellular electrophysiological recordings were made in the CA1 pyramidal layer in acute hippocampal slices prepared from control and epileptic rats and perfused with artificial cerebrospinal fluid (ACSF). Whereas orthodromic activation of CA1 neurons evoked only a single, stimulus‐graded population spike in control slices, it produced an all‐or‐none burst of population spikes in epileptic slices. 3 The intrinsic firing patterns of CA1 pyramidal cells were determined by intrasomatic positive current injection. In control slices, the vast majority (97 %) of the neurons were regular firing cells. In epileptic slices, only 53 % the pyramidal cells fired in a regular mode. The remaining 47 % of the pyramidal cells were intrinsic bursters. These neurons generated high‐frequency bursts of three to six spikes in response to threshold depolarizations. A subgroup of these neurons (10.1 % of all cells) also burst fired spontaneously even after suppression of synaptic activity. 4 In epileptic slices, burst firing in most cases (ca 70 %) was completely blocked by adding the Ca2+ channel blocker Ni2+ (1 mm) to, or removing Ca2+ from, the ACSF, but not by intracellular application of the Ca2+ chelater 1,2‐bis(o‐aminophenoxy)ethane‐N,N,N′,N′‐tetra‐acetic acid (BAPTA), suggesting it was driven by a Ca2+ current. 5 Spontaneously recurring population bursts were observed in a subset of epileptic slices. They were abolished by adding 2 μm 6‐cyano‐7‐nitro‐quinoxaline‐2,3‐dione (CNQX) to the ACSF, indicating that synaptic excitation is critical for the generation of these events. 6 All sampled pyramidal cells fired repetitively during each population burst. The firing of spontaneously active bursters anteceded the population discharge, whereas most other pyramidal cells began to fire conjointly with the first population spike. Thus, spontaneous bursters are likely to be the initiators of spontaneous population bursts in epileptic slices. 7 The dramatic up‐regulation of intrinsic bursting in CA1 pyramidal cells, particularly the de novo appearance of Ca2+‐dependent bursting, may contribute to the epileptogenicity of the hippocampus in the pilocarpine model of TLE. These findings have important implications for the pharmacological treatment of medically refractory human TLE.
Incorporating Multiple Supervised Learning Algorithms for Effective Intrusion Detection

— As internet continues to expand its usage with an enormous number of applications, cyber-threats have significantly increased accordingly. Thus, accurate detection of malicious traffic in a timely manner is a critical concern in today’s Internet for security. One approach for intrusion detection is to use Machine Learning (ML) techniques. Several methods based on ML algorithms have been introduced over the past years, but they are largely limited in terms of detection accuracy and/or time and space complexity to run. In this work, we present a novel method for intrusion detection that incorporates a set of supervised learning algorithms. The proposed technique provides high accuracy and outperforms existing techniques that simply utilizes a single learning method. In addition, our technique relies on partial flow information (rather than full information) for detection, and thus, it is light-weight and desirable for online operations with the property of early identification. With the mid-Atlantic CCDC intrusion dataset publicly available, we show that our proposed technique yields a high degree of detection rate over 99% with a very low false alarm rate (0.4%).
Supplemental to : “ Variational Stokes : A Unified Pressure-Viscosity Solver for Accurate Viscous Liquids "

Free Surface Test (2D). Our free surface Stokes test case is a fluid disk of radius r = 0.75 centred at the origin, with density ρ = 1 and viscosity μ = 0.1, computed over a timestep ∆t = 1 . For simplicity of presentation, we describe the final velocity field in terms of a stream function,ψ , where the velocity field can be derived as uf inal = ∇ ×ψ . This also guarantees that the velocity field is divergence free. The stream function is:
Domain and Nucleotide Dependence of the Interaction between Saccharomyces cerevisiae Translation Elongation Factors 3 and 1A*

Eukaryotic translation elongation factor 3 (eEF3) is a fungal-specific ATPase proposed to catalyze the release of deacylated-tRNA from the ribosomal E-site. In addition, it has been shown to interact with the aminoacyl-tRNA binding GTPase elongation factor 1A (eEF1A), perhaps linking the E and A sites. Domain mapping demonstrates that amino acids 775–980 contain the eEF1A binding sites. Domain III of eEF1A, which is also involved in actin-related functions, is the site of eEF3 binding. The binding of eEF3 to eEF1A is enhanced by ADP, indicating the interaction is favored post-ATP hydrolysis but is not dependent on the eEF1A-bound nucleotide. A temperature-sensitive P915L mutant in the eEF1A binding site of eEF3 has reduced ATPase activity and affinity for eEF1A. These results support the model that upon ATP hydrolysis, eEF3 interacts with eEF1A to help catalyze the delivery of aminoacyl-tRNA at the A-site of the ribosome. The dynamics of when eEF3 interacts with eEF1A may be part of the signal for transition of the post to pre-translocational ribosomal state in yeast.
Bio-psycho-social correlates of the perceived crowding in different contexts.

BACKGROUND This paper analyzes the experience of crowding through a biopsychosocial approach to human behavior which empirically joins different dimensions that the literature has analyzed separately. The main aim consists of identifying factors involved in perceived crowding from (a) the emotional response and affective meaning (BIO dimension); (b) the perception of psychological well-being and personality traits (PSYCHO dimension), and (c) sociodemographic characteristics (SOCIO dimension). METHOD 761 adults completed an online questionnaire that included an assessment of images representing four high- and low-density functional and residential contexts. The data were analyzed through four hierarchical regressions, one for each spatial context. RESULTS Although the results vary depending on the contexts analyzed, the prevalence of the variables from the BIO dimension in functional contexts, as opposed to residential contexts, is highlighted. The latter spaces show greater heterogeneity regarding the explanatory power of the experience of crowding. CONCLUSIONS The response to crowding experienced in residential environments shows a greater range of variables involved, supporting the idea of these spaces’ greater complexity, insofar as they are psychologically adaptive.
Caco-2 versus Caco-2/HT29-MTX co-cultured cell lines: permeabilities via diffusion, inside- and outside-directed carrier-mediated transport.

PURPOSE The objective of this study was a systematic characterization and evaluation of cell culture models based on mixtures of Caco-2/HT29-MTX co-cultures for their use in screening for drug absorption and intestinal permeability in comparison to the properties of the respective mono-cultures. METHODS Co-cultures of Caco-2 cells (absorptive-type) and HT29-MTX cells (goblet-type) were set up. Three different co-cultures (initial seeding ratios Caco-2/HT29-MTX: 90/10, 70/30, and 50/50) were grown on permeable filter supports, and monolayers were used for permeability studies with model compounds for paracellular absorption (atenolol, furosemide, H334/75, mannitol, terbutaline), transcellular absorption (antipyrine, ketoprofen, metoprolol, piroxicam), carrier-mediated absorption (D-glucose, Gly-Pro, and L-phenylalanine) as well as substrates for carrier-mediated secretion via P-glycoprotein (cimetidine and talinolol). Electrophysiological and microscopic controls were performed to characterize the cell cultures. RESULTS For compounds undergoing passive intestinal absorption permeabilities were generally higher in co-cultures than in Caco-2 monolayers, yielding highest values in pure HT29-MTX monolayers. This difference was most obvious for compounds transported via the paracellular pathway, where HT29-MTX cells may be up to 30 times more permeable than Caco-2 cells, whereas for lipophilic and highly permeable compounds, the difference in permeability values was less obvious. For drugs undergoing intestinal secretion mediated by P-glycoprotein, co-cultivation of Caco-2 cells with HT29-MTX cells led to increased apical to basolateral permeability which was decreased in the opposite direction, consistent with the fact that HT29-MTX cells do not express P-glycoprotein. When a carrier-mediated absorption mechanism is involved, the permeabilities observed were lower than the values reported for human small intestine and co-cultivation of HT29-MTX cells with Caco-2 cells resulted in even lower values as compared to the plain Caco-2 cultures. CONCLUSIONS Co-cultures of HT29-MTX and Caco-2 cells offer the opportunity of modifying the permeability barrier of the cell monolayers both with respect to paracellular resistance and secretory transport via P-gp. Thus, in special cases, they allow more flexibility in adapting the in vitro system to the in vivo situation as compared to the monocultures. Another advantage is the obvious robustness of the method with respect to the reproducibility of the results. A problem remaining, however, is the quantitative expression of carriers involved in intestinal uptake of many nutrients and drugs.
Forensic Postmortem Interval Estimation from Skeletal Muscle Tissue: A Lipidomics Approach

Lipidomic analyses of human skeletal muscle tissue were conducted to detect biomarkers of time-dependent postmortem degradation and to test the predictive capacity of lipids in human skeletal muscle cell membranes. High-resolution mass spectrometry analytical platforms were used to isolate phospholipids in muscle cell membranes that are specific to the corpse tissues and not invading microbes, thus eliminating potential noise from the surrounding microenvironment. The most consistently extracted cell membrane phospholipids were phosphatidylglycerol (PG) 34:0 and phosphatidylethanolamine (PtdE) 36:4. The actual accumulated degree days of all validation samples fell within the 95% prediction interval limits for the simple linear regression models with PtdE 36:4 and PG 34:0, though the prediction intervals for the latter were wider. The analysis requires only a small amount of tissue, is less subjective than visual methods for estimating postmortem interval, and is robust to drastic fluctuations in temperature. Sophisticated quantitative methods for estimating PMI from biomolecules unique to the corpse, and the human microbiome may provide a means of overcoming the geographic limitations of methods based on subjective visual observations of decomposition changes.