Miracle-dz/UniFAR-FTUs huggingface dataset:
Expression of the dermatomyositis autoantigen Mi-2 in regenerating muscle.

OBJECTIVE Autoantibodies against the chromatin remodeler Mi-2 are found in a distinct subset of patients with dermatomyositis (DM). Previous quantitative immunoblotting experiments demonstrated that Mi-2 protein levels are up-regulated in DM muscle. This study was undertaken to define the population of cells expressing high levels of Mi-2 in DM muscle and to explore the regulation and functional role of Mi-2 during muscle regeneration. METHODS The expression of Mi-2 was analyzed by immunofluorescence microscopy in human muscle biopsy specimens. In an experimental mouse model, cardiotoxin was used to induce muscle injury and repair, and expression of Mi-2 during muscle regeneration was studied in this model by immunofluorescence and immunoblotting analyses. In addition, a cell culture system of muscle differentiation was utilized to artificially modulate Mi-2 levels during proliferation and differentiation of myoblasts. RESULTS In human DM muscle tissue, increased Mi-2 expression was found preferentially in the myofibers within fascicles affected by perifascicular atrophy, particularly in the centralized nuclei of small perifascicular muscle fibers expressing markers of regeneration. In injured mouse muscle tissue, Mi-2 levels were dramatically and persistently up-regulated during muscle regeneration in vivo. Premature silencing of Mi-2 with RNA interference in vitro resulted in accelerated myoblast differentiation. CONCLUSION Expression of Mi-2 is markedly up-regulated during muscle regeneration in a mouse model of muscle injury and repair. It is also up-regulated in human DM myofibers expressing markers of regeneration. Results of the in vitro studies indicate that this protein may play a role in modulating the kinetics of myoblast differentiation. Our findings thus suggest that high levels of Mi-2 expression in muscle biopsy tissue from patients with DM reflect the presence of incompletely differentiated muscle cells.
A systematic study of modulation of ADAM-mediated ectodomain shedding by site-specific O-glycosylation

Significance Ectodomain shedding is a central event in a range of biological processes and pathways, however the underlying mechanisms are still not fully understood. Here we present evidence that site-specific O-glycosylation regulated by individual GalNAc-Transferase isoforms, serve to coregulate ectodomain shedding, predominantly through blocking of cleavage. Our general finding is exemplified by the specific role of a single GalNAc-T isoform (GalNAc-T2) in coregulating TNF-alpha release in vitro, ex vivo in isogenic cell models, and in vivo in mouse Galnt2 knockouts. Adding the large family of GalNAc-T isoforms to regulation of ectodomain shedding substantially increase the ability to fine-tune this important process on a substrate level. Regulated shedding of the ectodomain of cell membrane proteins by proteases is a common process that releases the extracellular domain from the cell and activates cell signaling. Ectodomain shedding occurs in the immediate extracellular juxtamembrane region, which is also where O-glycosylation is often found and examples of crosstalk between shedding and O-glycosylation have been reported. Here, we systematically investigated the potential of site-specific O-glycosylation mediated by distinct polypeptide GalNAc-transferase (GalNAc-T) isoforms to coregulate ectodomain shedding mediated by the A Disintegrin And Metalloproteinase (ADAM) subfamily of proteases and in particular ADAM17. We analyzed 25 membrane proteins that are known to undergo ADAM17 shedding and where the processing sites included Ser/Thr residues within ± 4 residues that could represent O-glycosites. We used in vitro GalNAc-T enzyme and ADAM cleavage assays to demonstrate that shedding of at least 12 of these proteins are potentially coregulated by O-glycosylation. Using TNF-α as an example, we confirmed that shedding mediated by ADAM17 is coregulated by O-glycosylation controlled by the GalNAc-T2 isoform both ex vivo in isogenic cell models and in vivo in mouse Galnt2 knockouts. The study provides compelling evidence for a wider role of site-specific O-glycosylation in ectodomain shedding.
Impairments of Antigen-Presenting Cells in Pulmonary Tuberculosis

The phenotype and functional properties of antigen-presenting cells (APC), that is, circulating monocytes and generated in vitro macrophages and dendritic cells, were investigated in the patients with pulmonary tuberculosis (TB) differing in lymphocyte reactivity to M. tuberculosis antigens (PPD-reactive versus PPD-anergic patients). We revealed the distinct impairments in patient APC functions. For example, the monocyte dysfunctions were displayed by low CD86 and HLA-DR expression, 2-fold increase in CD14+CD16+ expression, the high numbers of IL-10-producing cells, and enhanced IL-10 and IL-6 production upon LPS-stimulation. The macrophages which were in vitro generated from peripheral blood monocytes under GM-CSF were characterized by Th1/Th2-balance shifting (downproduction of IFN-γ coupled with upproduction of IL-10) and by reducing of allostimulatory activity in mixed lymphocyte culture. The dendritic cells (generated in vitro from peripheral blood monocytes upon GM-CSF + IFN-α) were characterized by impaired maturation/activation, a lower level of IFN-γ production in conjunction with an enhanced capacity to produce IL-10 and IL-6, and a profound reduction of allostimulatory activity. The APC dysfunctions were found to be most prominent in PPD-anergic patients. The possible role of APC impairments in reducing the antigen-specific T-cell response to M. tuberculosis was discussed.
Brønsted Acidic Ionic Liquid Accelerated Halogenation of Organic Compounds with N-Halosuccinimides (NXS)

The Brønsted-acidic ionic liquid 1-methyl-3-(4-sulfobutyl)imidazolium triflate [BMIM(SO3H)][OTf] was demonstrated to act efficiently as solvent and catalyst for the halogenation of activated organic compounds with N-halosuccinimides (NXS) under mild conditions with short reaction times. Methyl aryl ketones were converted into α-halo and α,α-dihaloketones, depending on the quantity of NXS used. Ketones with activated aromatic rings were selectively halogenated, however in some cases mixtures of α-halogenated ketone and ring-halogenated ketones were obtained. Activated aromatics were regioselectively ring halogenated to give mono- and dihalo-substituted products. The [BMIM(SO3H)][OTf] ionic liquid (IL-A) was successfully reused eight times in a representative monohalogenation reaction with no noticeable decrease in efficiency. An effective halogenation scale-up in this IL is also presented. The reactivity trend and the observed chemo- and regioselectiivities point to an ET process in these IL-promoted halofunctionalization reactions.
Evaluating Content Selection in Summarization: The Pyramid Method

We present an empirically grounded method for evaluating content selection in summarization. It incorporates the idea that no single best model summary for a collection of documents exists. Our method quantiﬁes the relative importance of facts to be conveyed. We argue that it is reliable, predictive and diagnostic, thus improves considerably over the shortcomings of the human evaluation method currently used in the Document Understanding Conference.
Seedling Quality in Serbia – Results from a Three-Year Survey

During a three-year survey in 14 forest nurseries in Serbia we measured seedlings of 19 species and 96 stocktypes of both conifers and broadleaves. Seedlings were measured in the nurseries for height and diameter, and subsamples was taken for measurements of shoot and root dry weight, and presence of mycorrhiza. Results of mean values and variation of measured morphological attributes are presented and compared to Serbian standard for seedlings quality. We found mycorrhiza on seedlings root from almost every nursery, seedbed and tray. Our results show that current nursery cultural practice need to be improved and that seedlings quality standards should be updated.
The Latest on Carbohydrate Loading: A Practical Approach

High dietary carbohydrate (CHO) intake for several days before competition (CHO loading) is known to increase muscle glycogen stores, with subsequent ergogenic performance benefits often seen in events longer than 90 min in duration. CHO-loading strategies vary in characteristics such as type and duration of dietary manipulation and the accompanying exercise/training activities. Additionally, glycogen concentration may remain elevated for up to 5 d. This versatility in CHO-loading strategies allows the athlete greater flexibility in tailoring pre-event preparation. Women who attempt to CHO load should be particularly attentive to both total energy intake and relative CHO intake; dietary CHO should exceed 8 g·kg body mass−1 ·d−1 or 10 g·kg lean body mass−1 ·d−1. As long as the amount ingested is adequate for loading, the type of CHO is less important, with the exception of 1-d loading protocols where the glycemic index may be an important consideration.
0-Bit Consistent Weighted Sampling

We develop 0-bit consistent weighted sampling (CWS) for efficiently estimating min-max kernel, which is a generalization of the resemblance kernel originally designed for binary data. Because the estimator of 0-bit CWS constitutes a positive definite kernel, this method can be naturally applied to large-scale data mining problems. Basically, if we feed the sampled data from 0-bit CWS to a highly efficient linear classifier (e.g., linear SVM), we effectively (and approximately) train a nonlinear classifier based on the min-max kernel. The accuracy improves as we increase the sample size. In this paper, we first demonstrate, through an extensive classification study using kernel machines, that the min-max kernel often provides an effective measure of similarity for nonnegative data. This helps justify the use of min-max kernel. However, as the min-max kernel is nonlinear and might be difficult to be used for industrial applications with massive data, we propose to linearize the min-max kernel via 0-bit CWS, a simplification of the original CWS method. The previous remarkable work on {\em consistent weighted sampling (CWS)} produces samples in the form of (i*, t*) where the i* records the location (and in fact also the weights) information analogous to the samples produced by classical minwise hashing on binary data. Because the t* is theoretically unbounded, it was not immediately clear how to effectively implement CWS for building large-scale linear classifiers. We provide a simple solution by discarding t* (which we refer to as the "0-bit" scheme). Via an extensive empirical study, we show that this 0-bit scheme does not lose essential information. We then apply 0-bit CWS for building linear classifiers to approximate min-max kernel classifiers, as extensively validated on a wide range of public datasets. We expect this work will generate interests among data mining practitioners who would like to efficiently utilize the nonlinear information of non-binary and nonnegative data.
Current treatment of oral candidiasis: A literature review

Candidiasis or oral candidosis is one of the most common human opportunistic fungal infections of the oral cavity. This pathology has a wide variety of treatment which has been studied until these days. The present study offers a literature review on the treatment of oral candidiasis, with the purpose of establish which treatment is the most suitable in each case. Searching the 24 latest articles about treatment of candidiasis it concluded that the incidence depends on the type of the candidiasis and the virulence of the infection. Although nystatin and amphotericin b were the most drugs used locally, fluconazole oral suspension is proving to be a very effective drug in the treatment of oral candidiasis. Fluconazole was found to be the drug of choice as a systemic treatment of oral candidiasis. Due to its good antifungal properties, its high acceptance of the patient and its efficacy compared with other antifungal drugs. But this drug is not always effective, so we need to evaluate and distinguish others like itraconazole or ketoconazole, in that cases when Candida strains resist to fluconazole. Key words:Candidiasis, treatment, miconazole, fluconazole, nystatin.
Preliminary and Incomplete 1 General Equilibrium of a Monetary Model with State-Dependent Pricing ∗

There is a long standing debate on whether nominal shocks have real effects on the economy. According to one theory, frictions in the price adjustment process can lead to the non-neutrality of money. Macroeconomic models of optimal price setting that nest these price adjustment frictions, however, have proven to be difficult to construct and apply to the data. This paper provides a rational expectations equilibrium model of optimal price setting that is solved numerically. The solution requires the speciÞcation and estimation of a price forecast rule. The structural parameters of the model, focusing on the parameters of the price adjustment cost process, are estimated through an indirect inference procedure using aggregate data from the U.S. economy. According to the estimated results, large and variable adjustment costs are required for the model to match up against U.S. data. ∗This paper is a revised version of the third chapter of my Ph.D. dissertation. I would like to thank Russell Cooper, Simon Gilchrist, John Leahy, and Chris House for their valuable comments. The views expressed herein are solely those of the author and do not necessarily reßect the views of the Federal Reserve Bank of Kansas City or the Federal Reserve System. Correspondence to: Jonathan Willis; Economic Research Department; Federal Reserve Bank of Kansas City; 925 Grand Boulevard; Kansas City, MO 64198. Email: jonathan.willis@kc.frb. org.
Roles of learning rates, artificial process noise and square root filtering for extended Kalman filter training

Singhal and Wu (1989) introduced the extended Kalman filter (EKF) neural network training algorithm. Since then, many modifications, simplifications and improvements of the EKF procedure have been developed and applied to difficult problems in pattern classification, signal processing and control. Recently, a number of enhancements related to learning rates and square root filtering for EKF training have been proposed, and performance superior to previously reported methods has been claimed. This paper serves to clarify issues related to the proper treatment of learning rates, artificial process noise and square root filtering for EKF training.
Reverse remodeling of cardiac myocyte hypertrophy in hypertension and failure by targeting of the renin-angiotensin system.

BACKGROUND ACE inhibitors (ACEIs) and angiotensin II type 1 (AT(1)) receptor blockers are effective in reducing left ventricular mass in hypertension and heart failure. However, the ability of these drugs to reverse excessive myocyte lengthening and transverse growth in heart failure is unknown. METHODS AND RESULTS L-158,809 (an AT(1) blocker; AT(1)), enalapril (an ACEI), and hydralazine (a vasodilator) were administered to spontaneously hypertensive heart failure rats between 6 and 10 months of age (early treatment) and between 18 and 22 months of age (late treatment). After 4 months of treatment, hemodynamics and chamber dimensions were collected before left ventricular myocyte isolation and subsequent analysis of myocyte shape. Each drug reduced systolic blood pressures to normal values. In the early and late studies, the ACEI reduced myocyte volume. Myocyte length was also reduced in the late study. However, the AT(1) was most effective in reversing myocyte dimensions to near-normal values in both studies. Hydralazine was ineffective in reducing cell size but arrested progression of myocyte lengthening in the late study. Changes in myocyte shape reflected alterations in chamber dimensions and wall thickness. CONCLUSIONS Reversal of myocyte hypertrophy was produced in hypertensive/heart failure rats with an AT(1). The ACEI was effective but to a lesser extent. Results indicate that it is possible to significantly reverse myocyte remodeling pharmacologically even if therapy is initiated near the onset of failure. Further work is needed to determine whether similar results can be obtained in humans.
Impact of aboriginal ethnicity on HCV core‐induced IL‐10 synthesis: Interaction with IL‐10 gene polymorphisms

The host immune response is a critical determinant in viral infection outcome. Epidemiological studies indicate that North American indigenous peoples are more resistant to chronic HCV infection than other populations. Due to the prominence of IL‐10 in chronic HCV infection, we investigated the genetic tendency to produce IL‐10 in Caucasian (CA) and First Nation (FN) populations. Peripheral blood mononuclear cells (PBMCs) from CA subjects had a greater tendency to produce IL‐10 defined by allelic polymorphisms, as well as genotypes and haplotypes, at the ‐1082, ‐819, and ‐592 positions of the IL‐10 promoter. More importantly, we directly evaluated the influence of ethnicity on the ability of HCV core protein to induce IL‐10 synthesis and found significantly higher IL‐10 production by PBMCs isolated from healthy CA subjects compared with FN subjects. Further examination of the underlying relationship between core‐induced IL‐10 with the high, intermediate, and low phenotypes at the ‐1082, ‐819, and ‐592 position revealed that spontaneous and core‐induced IL‐10 synthesis tended to interact negatively with defined polymorphisms. This was particularly evident for the FN cohort, in which the relationship was strengthened by a stronger interaction of core with the low–IL‐10–producing phenotypes. As with previous studies, concanavalin A induced IL‐10 synthesis from the CA cohort positively associated with defined genetic phenotypes. Conclusion: Cells from FN subjects had a reduced capacity to produce IL‐10 in response to HCV core protein, suggesting that reduced susceptibility of FN immunity to virally induced IL‐10 synthesis might contribute to epidemiological observations of enhanced HCV clearance. (HEPATOLOGY 2007;45:623–630.)
Pilot Study of Acupuncture Point Laterality: Evidence from Heart Rate Variability

The specificity of acupuncture points (acupoints) is one of the key concepts in traditional acupuncture theory, but the question of whether there is adequate scientific evidence to prove or disprove specificity has been vigorously debated in recent years. Laterality, or the tendency for acupoints on the right or left side of the body to produce different physiological effects, is an important aspect of acupoint specificity. Data is particularly scarce regarding the laterality of the same channel, same-named acupoint located on opposite sides of the body. The aim of this study was to investigate whether Neiguan (PC6) has laterality. A total of eighteen healthy female volunteers were recruited for this study. Electrocardiograms were recorded and heart rate variability was analyzed before, during, and after PC6 was stimulated on either the left or the right side. The results show that during acupuncture, there were significant differences in the standard deviation of RR intervals (STDRR), root mean square of successive differences between RR intervals (RMSSD), and total power between the left PC6 stimulation group and the right PC6 stimulation group, which indicates that PC6 may have laterality.
The local and global effects of traffic shaping in the internet

The Internet is witnessing explosive growth in traffic, in large part due to bulk transfers. Delivering such traffic is expensive for ISPs because they pay other ISPs based on peak utilization. To limit costs, many ISPs are deploying ad-hoc traffic shaping policies that specifically target bulk flows. However, there is relatively little understanding today about the effectiveness of different shaping policies at reducing peak loads and what impact these policies have on the performance of bulk transfers. In this paper, we compare several traffic shaping policies with respect to (1) the achieved reduction in peak network traffic and (2) the resulting performance loss for bulk transfers. We identified a practical policy that achieves peak traffic reductions of up to 50% with only limited performance loss for bulk transfers. However, we found that the same policy leads to large performance losses for bulk transfers when deployed by multiple ISPs along a networking path. Our analysis revealed that this is caused by certain TCP characteristics and differences in local peak utilization times.
Comparative Analysis of Telomerase Activity in CD117+CD34+ Cardiac Telocytes with Bone Mesenchymal Stem Cells, Cardiac Fibroblasts and Cardiomyocytes

Background: This study characterized the cardiac telocyte (TC) population both in vivo and in vitro, and investigated its telomerase activity related to mitosis. Methods: Using transmission electron microscopy and a phase contrast microscope, the typical morphological features of cardiac TCs were observed; by targeting the cell surface proteins CD117 and CD34, CD117+CD34+ cardiac TCs were sorted via flow cytometry and validated by immunofluorescence based on the primary cell culture. Then the optimized basal nutrient medium for selected population was examined with the cell counting kit 8. Under this conditioned medium, the process of cell division was captured, and the telomerase activity of CD117+CD34+ cardiac TCs was detected in comparison with bone mesenchymal stem cells (BMSCs), cardiac fibroblasts (CFBs), cardiomyocytes (CMs). Results: Cardiac TCs projected characteristic telopodes with thin segments (podomers) in alternation with dilation (podoms). In addition, 64% of the primary cultured cardiac TCs were composed of CD117+CD34+ cardiac TCs; which was verified by immunofluorescence. In a live cell imaging system, CD117+CD34+ cardiac TCs were observed to enter into cell division in a short time, followed by an significant invagination forming across the middle of the cell body. Using a real-time quantitative telomeric-repeat amplification assay, the telomerase concentration in CD117+CD34+ cardiac TCs was obviously lower than in BMSCs and CFBs, and significantly higher than in CMs. Conclusions: Cardiac TCs represent a unique cell population and CD117+CD34+ cardiac TCs have relative low telomerase activity that differs from BMSCs, CFBs and CMs and thus they might play an important role in maintaining cardiac homeostasis.