Miracle-dz/UniFAR-FTUs huggingface dataset:
Lipopolysaccharide induces aberrant hypermethylation of Hic-1 in mouse embryonic fibroblasts lacking p53 gene.

BACKGROUND The present study asked whether continuous administration with lipopolysaccharide (LPS), a potent inflammatory agent, induces aberrant methylation in the promoter region of tumor suppressor genes and p53 and/or inducible nitric oxide synthase (iNOS) genes involved in its aberrant methylation. MATERIALS AND METHODS Mouse embryonic fibroblasts (MEFs) were prepared from mice harboring four different genotypes (p53+/+iNOS+/+, p53++iNOS-/-, p53-/-iNOS+/+ and p53-/-iNOS-/-). The MEFs were immortalized by 3T3 procedure and continuously cultured under a medium containing LPS or LPS plus interferon (IFN)-gamma during 40 passages. The methylation status in the CpG site of hypermethylated in cancer-1 (Hic-1) exon la and p16 promoter region was monitored using bisulfite-sequencing methods. RESULTS LPS and LPS plus IFN-gamma induced de novo methylation in the CpG sites of the Hic-1 gene. This site was methylated only in p53-/- MEFs, and the mRNA expression of Hic-1 decreased in p53-/- MEFs compared to p53+/+ MEFs. The methylation patterns of Hic-1, however, were not affected by iNOS gene status. The promoter region of p16 was methylated by increasing the passage, even under the control medium, with LPS administration promoting methylation, particularly in MEFs lacking the iNOS gene. However, the methylation pattern was not significantly different between the p53 genotypes. CONCLUSION Our preliminary study suggests that LPS induces de novo methylation in the CpG site in MEFs. For the Hic-1 gene, but not p16, the p53 gene might protect against aberrant methylation. The iNOS gene might not be involved in methylation of the Hic-1 gene, whereas the promoter region of p16 could be prone to methylation in MEFs lacking the iNOS gene.
Deployment and the Citizen Soldier: Need and Resilience

Background:The wars in Iraq and Afghanistan have made unprecedented demands on the nation's citizen soldiers, the National Guard and Reserve. A major concern involves the repeated deployment of these forces overseas. Objectives:Using data from the Department of Defense Survey of Health Related Behaviors among the Guard and Reserve Force, we examined the effects of deployment on 6 health outcomes. Subjects:The Department of Defense Survey of Health Related Behaviors among the Guard and Reserve Force is a sample (n = 17,754) of all Reserve component personnel (including full time and/or activated Guard and Reservists) serving in all pay grades throughout the world. Research Design:We relied on inverse probability of treatment weights to adjust for observed confounders and used sensitivity analyses to examine the sensitivity of our findings to potential unobserved confounding. Results:Observed confounders explain much of the apparent effect of deployment. For men, the adjusted relationships could very well reflect further confounding involving unobserved factors. However, for women, effects of deployment on marijuana use, symptoms of post-traumatic stress disorder, and suicidal ideation are robust to adjustments for multiple testing and possible unobserved confounding. Conclusions:These effects are large in practical terms and troubling but suggest that media reports of the harm caused by deployment may be overstated. Such exaggerations run the risk of stigmatizing those who serve.
New insights into the haemostatic function of platelets

Considerable progress has been made over the last two decades in delineating the key molecular events regulating the haemostatic function of platelets. Much of this new insight has been derived from the study of mouse models, in which the expression or structure of one or more platelet proteins has been genetically altered. Despite these advances on the research front, clinical progress in diagnosing patients with unexplained surgical bleeding or recurrent haemorrhage from mucocutaneous sites has been comparatively limited. There is a dearth of literature available to help physicians integrate and apply the burgeoning knowledge on platelet biology to diagnosing patients with atypical or unexplained platelet dysfunction. The purpose of this review is to summarise the major primary platelet disorders relevant to pathological bleeding in humans (excluding those primarily due to thrombocytopenia or acquired functional disorders), with a focus on lesions identified in mouse models that could represent candidate molecules for study in patients with impaired platelet function.
Treatment of Chronic Viral Hepatitis in Woodchucks by Prolonged Intrahepatic Expression of Interleukin-12

ABSTRACT Chronic hepatitis B is a major cause of liver-related death worldwide. Interleukin-12 (IL-12) induction accompanies viral clearance in chronic hepatitis B virus infection. Here, we tested the therapeutic potential of IL-12 gene therapy in woodchucks chronically infected with woodchuck hepatitis virus (WHV), an infection that closely resembles chronic hepatitis B. The woodchucks were treated by intrahepatic injection of a helper-dependent adenoviral vector encoding IL-12 under the control of a liver-specific RU486-responsive promoter. All woodchucks with viral loads below 1010 viral genomes (vg)/ml showed a marked and sustained reduction of viremia that was accompanied by a reduction in hepatic WHV DNA, a loss of e antigen and surface antigen, and improved liver histology. In contrast, none of the woodchucks with higher viremia levels responded to therapy. The antiviral effect was associated with the induction of T-cell immunity against viral antigens and a reduction of hepatic expression of Foxp3 in the responsive animals. Studies were performed in vitro to elucidate the resistance to therapy in highly viremic woodchucks. These studies showed that lymphocytes from healthy woodchucks or from animals with low viremia levels produced gamma interferon (IFN-γ) upon IL-12 stimulation, while lymphocytes from woodchucks with high viremia failed to upregulate IFN-γ in response to IL-12. In conclusion, IL-12-based gene therapy is an efficient approach to treat chronic hepadnavirus infection in woodchucks with viral loads below 1010 vg/ml. Interestingly, this therapy is able to break immunological tolerance to viral antigens in chronic WHV carriers.
Identification of a novel autoantigen in inflammatory bowel disease by protein microarray

Background: Patients with inflammatory bowel disease (IBD) display immunoreactivity to self‐antigens and microbial antigens. We used a protein microarray approach to identify novel autoantigens in IBD. Methods: ProtoArray Human Protein Microarray v4.0 containing 8268 human proteins from Invitrogen (La Jolla, CA) was used. Results: Twenty‐five IBD patients and five healthy controls were screened for candidate autoantigens. For 256 antigens, IBD patients had a higher seroreactivity than controls. Twenty antigens were selected for further evaluation in a larger cohort (60 ulcerative colitis [UC] patients, 60 Crohn's disease [CD] patients, 60 healthy controls, and 60 gastrointestinal‐diseased controls) by means of a customized protein microarray. Out of these 20 antigens, one antigen, family with sequence similarity 84 member A (FAM84A), was identified as a target antigen in IBD. Antibodies to FAM84A were significantly more prevalent in IBD patients (19%) than in gastrointestinal‐diseased controls (1.7%) (P = 0.0008) and healthy controls (5%) (P = 0.01). Anti‐FAM84A antibodies were found in 26.6% of UC patients and in 11.7% of CD patients. FAM84A was confirmed as target antigen in IBD by means of Western blotting in a large independent cohort (100 UC patients, 106 CD patients, 102 healthy controls, and 100 gastrointestinal‐diseased controls). Antibodies to FAM84A were significantly more prevalent in IBD patients (20%) than in gastrointestinal‐diseased controls (5%) (P = 0.0004) and healthy controls (0%) (P < 0.0001). Anti‐FAM84A antibodies were found in 18% of UC patients and in 22% of CD patients. Conclusions: We identified FAM84A as a novel autoantigen in IBD. (Inflamm Bowel Dis 2011;)
EEG Ocular Artefacts and Noise Removal

The general framework of this research is the pre-processing of the electroencephalographic (EEG) signals. The goal of this paper is to compare several combinations of wavelet denoising (WD) and independent component analysis (ICA) algorithms for noise and artefacts removal. These methods are tested on simulated EEG, using different evaluation criteria. According to our results, the most effective method consists in source separation by SOBI-RO [1], followed by wavelet denoising by SURE thresholding [2].
Solar Powered Variable Speed Power Factor Corrected BLDC Motor drive

Renewable energy sources have more importance. This importance is mainly because of limited resource and environmental problems of the conventional energy. Among the all renewable energy resources available, solar energy seems to be a major competitor as it is abundant in nature and also pollution-free. And we can convert this dc from solar panel to single phase AC source by using single phase inverter. This AC source is the supply for BLDC motor drive. And speed control method of BLDC motor with low cost for low power applications can be done by using a power factor corrected bridgeless buck-boost converter. Speed control is by controlling the dc link voltage of the voltage source inverter (VSI). Bridgeless converter reduces the conduction losses in the diode bridge rectifier. Commutation of the BLDC motor is by using VSI, which reduces the switching losses and it avoid the sparking and wear and tear by mechanical commutation and it is known as electronic commutation. Power factor improvement is done by designing the converter in discontinuous inductor current mode (DCM). As compared with other speed controlling method, speed control of BLDC motor by power factor corrected bridge less buck-boost convertor uses reduced number of components. This method has high efficiency and low cost as compared with other speed controlling method of BLDC motor and improved power quality is also achieved.
Parameter Dependent Lyapunov functions for stability of Linear Parameter Varying systems

the problem in this paper consists in developing a new robust stability condition for Linear Parameter Varying (LPV) continuous systems, under polytopic uncertainty structure. The main skill is the use of Parameter Dependent Lyapunov functions with (PDLFs) particular forms. The article hinges upon an analysis stability test for polytopic uncertain systems. The main result is given in terms of LMI-based conditions. A numerical example illustrates the accuracy of the proposed approach and some comparisons with previously established results show its efficiency.
Triplet pregnancies: perinatal outcome evolution.

PURPOSE To evaluate the obstetric and perinatal outcomes evolution of triplet pregnancies. METHODS A prospective observational study was conducted in triplet pregnancies delivered over 16 years in a tertiary obstetric center with differentiated perinatal support. Evaluation of demographic factors, obstetric complications, gestational age at delivery, mode of delivery, birth weight and immediate newborn outcome were done over a 16 years period. A global characterization of the sample was performed considering the listed parameters. Variables were categorized in three groups according to year of occurrence: 1996-2000, 2001-2006, 2007-2011, and all parameters were compared. RESULTS Of the 33 triplets included, 72.7% resulted from induced pregnancies. All except one patient received prenatal corticosteroids and five received tocolytics. All women delivered prenatally and no significant differences were seen in the mean gestational age at delivery or birth weight towards time. There were three intrauterine fetal deaths. Neonatal immediate outcomes were not significantly different over the years. CONCLUSION Despite remarkable progresses in perinatal and neonatal cares, no noticeable impact in triplet gestations' outcomes was seen, sustaining that triplets should be avoided due to their great risk of prematurity and neonatal morbidities, either by limiting the numbers of embryos transferred or by fetal reduction.
The Bioinformatics of Psychosocial Genomics in Alternative and Complementary Medicine

The bioinformatics of alternative and complementary medicine is outlined in 3 hypotheses that extend the molecular-genomic revolution initiated by Watson and Crick 50 years ago to include psychology in the new discipline of psychosocial and cultural genomics. Stress-induced changes in the alternative splicing of genes demonstrate how psychosomatic stress in humans modulates activity-dependent gene expression, protein formation, physiological function, and psychological experience. The molecular messengers generated by stress, injury, and disease can activate immediate early genes within stem cells so that they then signal the target genes required to synthesize the proteins that will transform (differentiate) stem cells into mature well-functioning tissues. Such activity-dependent gene expression and its consequent activity-dependent neurogenesis and stem cell healing is proposed as the molecular-genomic-cellular basis of rehabilitative medicine, physical, and occupational therapy as well as the many alternative and complementary approaches to mind-body healing. The therapeutic replaying of enriching life experiences that evoke the novelty-numinosum-neurogenesis effect during creative moments of art, music, dance, drama, humor, literature, poetry, and spirituality, as well as cultural rituals of life transitions (birth, puberty, marriage, illness, healing, and death) can optimize consciousness, personal relationships, and healing in a manner that has much in common with the psychogenomic foundations of naturalistic and complementary medicine. The entire history of alternative and complementary approaches to healing is consistent with this new neuroscience world view about the role of psychological arousal and fascination in modulating gene expression, neurogenesis, and healing via the psychosocial and cultural rites of human societies.
Analysis of losses and thermal model in a surface-mounted permanent-magnet synchronous machine over a wide- voltage range of rated output power operation

This paper shows the results of permanent magnet eddy current loss, iron core loss and Copper loss of a surface permanent magnet synchronous machine. A thermal model for the temperature of all motor components is also presented in the paper. This PMSM will be operated at the voltage 700-1000V powered by the battery pack. So the losses are calculated separately at four different DC link voltages (700V, 800V, 900V, 1000V). The analysis shows that this motor should stop working to avoid damage at very low voltage.
Capsular Sialic Acid of Streptococcus suis Serotype 2 Binds to Swine Influenza Virus and Enhances Bacterial Interactions with Virus-Infected Tracheal Epithelial Cells

ABSTRACT Streptococcus suis serotype 2 is an important swine bacterial pathogen, and it is also an emerging zoonotic agent. It is unknown how S. suis virulent strains, which are usually found in low quantities in pig tonsils, manage to cross the first host defense lines to initiate systemic disease. Influenza virus produces a contagious infection in pigs which is frequently complicated by bacterial coinfections, leading to significant economic impacts. In this study, the effect of a preceding swine influenza H1N1 virus (swH1N1) infection of swine tracheal epithelial cells (NTPr) on the ability of S. suis serotype 2 to adhere to, invade, and activate these cells was evaluated. Cells preinfected with swH1N1 showed bacterial adhesion and invasion levels that were increased more than 100-fold compared to those of normal cells. Inhibition studies confirmed that the capsular sialic acid moiety is responsible for the binding to virus-infected cell surfaces. Also, preincubation of S. suis with swH1N1 significantly increased bacterial adhesion to/invasion of epithelial cells, suggesting that S. suis also uses swH1N1 as a vehicle to invade epithelial cells when the two infections occur simultaneously. Influenza virus infection may facilitate the transient passage of S. suis at the respiratory tract to reach the bloodstream and cause bacteremia and septicemia. S. suis may also increase the local inflammation at the respiratory tract during influenza infection, as suggested by an exacerbated expression of proinflammatory mediators in coinfected cells. These results give new insight into the complex interactions between influenza virus and S. suis in a coinfection model.
Review of: Fundamentals of Parameterized Complexity by Rodney G. Downey and Michael R. Fellows

Most interesting optimization problems on graphs are NP-hard, which means that (unless P=NP) there is no polynomial time algorithm that solves all the instances of such a problem exactly. However as noted by Garey and Johnson [3], hardness results such as NP-hardness should merely constitute the beginning of research. The traditional way to combat the intractability is to design approximation algorithms or randomized algorithms which run in polynomial time. These methods have their own shortcomings: we either get an approximate solution or lose the guarantee that the output is always correct. All problems in NP have trivial exponential time algorithms which just search and verify all the witnesses. Any algorithm which beats the brute-force algorithm can be thought of as making a clever search in the big space of all candidate solutions. expressing it as a function of only the input size n, one Parameterized Complexity is essentially a two-dimensional analogue of P vs NP. Unlike classical complexity, we define a parameter which is a non-negative integer often denoted by k and perform a refined multivariate analysis of the running time by expressing it as a function of both the input size n and the parameter k, instead of expressing it as solely as a function of n. The goal is to design algorithms that work efficiently if the parameters of the input instance are small, even if the size of the input is large. More precisely, a NP-hard problem is said to be fixed-parameter tractable (FPT) with respect to parameter k if the problem can be solved in time f(k) · nO(1) where f is a computable function and n is the input size. A straightforward generalization is to define more than one parameter. Parameterized complexity allows us to completely determine the effect of a parameter on the complexity of a certain problem. In particular, if one can design an FPT algorithm for a problem with respect to a parameter k then this means that instances of the problem where k is small are easier to handle than others. This theory of multivariate analysis has found applications to problems in varied areas such as social networks, streaming algorithms, game theory, coding theory, machine learning, etc. Since the first book on this area by Downey and Fellows [1] there have been two other books viz. by Flum and Grohe [2] and by Niedermeier [4] which appeared in 2006. Since then there was no book to cover the new developments in the field of parameterized complexity and this book fulfills exactly this void.
Reconstructive Surgery with a Dermal Regeneration Template: Clinical and Histologic Study

Integra artificial skin was introduced in 1981 and its use in acute surgical management of burns is well established, but Integra has also been used in patients undergoing reconstructive surgery. Over a period of 25 months, the authors used Integra to cover 30 anatomic sites in 20 consecutive patients requiring reconstructive surgery and then analyzed the clinical and histologic outcomes. The most common reason for surgery was release of contracture followed by resurfacing of tight or painful scars. The authors assessed patients’ satisfaction using a visual analog scale and scar appearance using a modified Vancouver Burn Index Scale. They evaluated the progress of wound healing by examining weekly punch‐biopsy specimens with standard and immunohistochemical stains. Patients reported a 72 percent increase in range of movement, a 62 percent improvement in softness, and a 59 percent improvement in appearance compared with their preoperative states. Pruritus and dryness were the main complaints, and neither was improved much. Four distinct phases of dermal regeneration could be demonstrated histologically: imbibition, fibroblast migration, neovascularization, and remodeling and maturation. Full vascularization of the neodermis occurred at 4 weeks. The color of the wound reflected the state of neodermal vascularization. No adnexa, nerve endings, or elastic fibers were seen in any of the specimens. The new collagen was histologically indistinguishable from normal dermal collagen. The authors conclude that Integra is a useful tool in reconstructive surgery. The additional cost of its use can be justified by its distinct benefits compared with current methodology. (Plast. Reconstr. Surg. 108: 93, 2001.)
Value at Risk Models in the Indian Stock Market

This paper provides empirical tests of different risk management models in the Value at Risk (VaR) framework in the Indian stock market. It is found that the GARCH-GED (Generalised Auto-Regressive Conditional Heteroscedasticity with Generalised Error Distribution residuals) performs exceedingly well at all common risk levels (ranging from 0.25% to 10%). The EWMA (Exponentially Weighted Moving Average) model used in J. P. Morgan’s RiskMetrics® methodology does well at the 10% and 5% risk levels but breaks down at the 1% and lower risk levels. The paper then suggests a way of salvaging the EWMA model by using a larger number of standard deviations to set the VaR limit. For example, the paper suggests using 3 standard deviations for a 1% VaR while the normal distribution indicates 2.58 standard deviations and the GED indicates 2.85 standard deviations. With this modification the EWMA model is shown to work quite well. Given its greater simplicity and ease of interpretation, it may be more convenient in practice to use this model than the more accurate GARCH-GED specification. The paper also provides evidence suggesting that it may be possible to improve the performance of the VaR models by taking into account the price movements in foreign stock markets.
Closed Form Modal Green's Functions for Accelerated Computation of Bodies of Revolution

To solve problems of bodies of revolution (BoR) using the method of moments, the modal Green's function is used, which is defined as the radiation field of a circular loop antenna with sinusoidal current distribution. It is a group of oscillating integrals that forms the bottleneck for further accelerating the computation of BoR problems. In this paper, we propose closed-form expressions for near-axis far-distance modal Green's functions, which can be used to accelerate the computation of BoR problems especially when the object is slim. A criterion is presented based on a rigorous error analysis to guarantee its range of applications. Both the scattering and radiation examples are presented to demonstrate the validity and efficiency of the proposed expressions.