Miracle-dz/UniFAR-FTUs huggingface dataset:
Molecular Determinants of Arenavirus Z Protein Homo-Oligomerization and L Polymerase Binding

ABSTRACT The arenavirus Z is a zinc-binding RING protein that has been implicated in multiple functions during the viral life cycle. These roles of Z involve interactions with viral and cellular proteins that remain incompletely understood. In this regard, Z inhibits viral RNA transcription and replication through direct interaction with the viral L polymerase. Here, we defined the L-binding domain of Tacaribe virus (TCRV) Z protein and the structural requirements mediating Z homo-oligomerization. By using site-directed mutagenesis, coimmunoprecipitation, and functional assays, we showed that residues R37, N39, W44, L50, and Y57, located around the zinc coordination site I, play a critical role in the Z-L interaction. We also found that Z protein from either TCRV or the pathogenic Junin virus (JUNV) self-associates into oligomeric forms in mammalian cells. Importantly, mutation of the myristoylation site, the strictly conserved residue G at position 2, severely impaired the ability of both TCRV Z and JUNV Z to self-interact as well as their capacity to accumulate at the plasma membrane, strongly suggesting that Z homo-oligomerization is associated with its myristoylation and cell membrane targeting. In contrast, disruption of the RING structure or substitution of W44 or N39, which are critical for L protein recognition, did not affect Z self-binding. Overall, the data presented here indicate that homo-oligomerization is not a requirement for Z-L interaction or Z-mediated polymerase activity inhibition.
Non-parametric expectation maximization: a learning automata approach

The famous expectation maximization technique suffers two major drawbacks. First, the number of components has to be specified apriori. Also, the expectation maximization is sensitive to initialization. In this paper, we present a new stochastic technique for estimating the mixture parameters. Parzen Window is used to estimate a discrete estimate of the PDF of the given data. Stochastic learning automata is then used to select the mixture parameters that minimize the distance between the discrete estimate of the PDF and the estimate of the expectation maximization. The validity of the proposed approach is verified using bivariate simulation data.
Light Regulates COP1-Mediated Degradation of HFR1, a Transcription Factor Essential for Light Signaling in Arabidopsis

Arabidopsis thaliana seedlings undergo photomorphogenesis in the light and etiolation in the dark. Long Hypocotyl in Far-Red 1 (HFR1), a basic helix-loop-helix transcription factor, is required for both phytochrome A–mediated far-red and cryptochrome 1–mediated blue light signaling. Here, we report that HFR1 is a short-lived protein in darkness and is degraded through a 26S proteasome-dependent pathway. Light, irrespective of its quality, enhances HFR1 protein accumulation via promoting its stabilization. We demonstrate that HFR1 physically interacts with Constitutive Photomorphogenesis 1 (COP1) and that COP1 exhibits ubiquitin ligase activity toward HFR1 in vitro. In addition, we show that COP1 is required for degradation of HFR1 in vivo. Furthermore, plants overexpressing a C-terminal 161–amino acid fragment of HFR1 (CT161) display enhanced photomorphogenesis, suggesting an autonomous function of CT161 in promoting light signaling. This truncated HFR1 gene product is more stable than the full-length HFR1 protein in darkness, indicating that the COP1-interacting N-terminal portion of HFR1 is essential for COP1-mediated destabilization of HFR1. These results suggest that light enhances HFR1 protein accumulation by abrogating COP1-mediated degradation of HFR1, which is necessary and sufficient for promoting light signaling. Additionally, our results substantiate the E3 ligase activity of COP1 and its critical role in desensitizing light signaling.
An efficient FPGA implementation of a flexible JPEG2000 decoder for Digital Cinema

The image compression standard JPEG2000 proposes a large set of features, useful for today's multimedia applications. Unfortunately, its complexity is greater than older standards. A hardware implementation brings a solution to this complexity for real-time applications, such as Digital Cinema. In this paper, a decoding scheme is proposed with two main characteristics. First, the complete scheme takes place in an FPGA without accessing any external memory, allowing integration in a secured system. Secondly, a customizable level of parallelization allows to satisfy a broad range of constraints, depending on the signal resolution.
Novel slow-wave ladder microstrip line filters

We report an investigation of novel slow-wave ladder microstrip line bandpass filters. The investigation has shown that the ladder microstrip line filters can be designed based on the knowledge of the conventional microstrip coupled line filters. The new type of filter has a smaller size than the conventional one because of the slowwave effect on the ladder line. Two filters of this type have for the first time been designed and fabricated. The measured performances are presented.
Differential expression of CD 146 in tissues and endothelial cells derived from infantile haemangioma and normal human skin

Haemangioma is the most common tumour of endothelial origin, occurring in 4–10% of Caucasian infants. It is characterized by rapid growth during the first year of postnatal life, followed by spontaneous regression from 1 to 7 years of age. The cell surface adhesion molecule CD146 has been identified as an endothelial cell marker. Despite advances in understanding the functional role of CD146 in normal endothelial cells and tumour progression, its expression and a possible role in an endothelial tumour have not been studied. As part of an investigation of endothelial cell alterations in infantile haemangioma, differential expression studies were performed with several known antigens and endothelial cell markers. Using immunohistochemical and flow cytometric analyses, cultured human dermal microvascular endothelial cells isolated from newborn foreskin (HDMEC) were compared with endothelial cells derived from haemangioma tissue (HemECs). In addition, immunohistochemistry was used to compare haemangioma tissues with normal human skin. Unexpectedly, cultured HemECs showed a significantly lower level of CD146 than HDMECs by both flow cytometric analysis and immunofluorescence staining. Using immunohistochemical studies, it was further demonstrated that endothelia in all haemangioma tissues, regardless of the tumour phase, showed negative immunoreactivity for CD146. In contrast, strong positive staining for CD146 was observed in the pericytelike cells that surround the endothelial layers. These findings are believed to be relevant to the molecular basis of haemangioma. Furthermore, it is possible that antibodies against CD146 may be useful for separating haemangioma-derived endothelial cells from normal endothelial cells and pericytes. Copyright  2003 John Wiley & Sons, Ltd.
Chapter 2 Review on Image Guided Lung Biopsy

Lung biopsy is an established field. Throughout years physician and scientist have been exploring the field, from technical and clinical point of view. Mainly there are three types of lung biopsy, open, bronchoscopic, and fine needle aspiration biopsy. Open biopsy is essentially a surgery, thus not really dependent on image guiding system. On the other hand, bronchoscopic and fine needle aspiration biopsy relay heavily in image guiding system. Curiously, it is rare to find both biopsy types talked side by side. In this paper, both biopsy types explored and compared from technical and clinical point of view. Technical wise, bronchoscopic biopsy trend is toward path finding algorithm, while fine needle aspiration biopsy trend is toward breathing compensation algorithm and automatization. Clinical wise, there is no evidence that one type hold better diagnostic value than the other. M.Q. Rizqie N.S. Mohd Yusof R.F. Surakusumah D.E. Octorina Dewi E. Supriyanto (&) IJN-UTM Cardiovascular Engineering Center, Universiti Teknologi Malaysia, 81310 Skudai, Malaysia e-mail: eko@biomedical.utm.my M.Q. Rizqie e-mail: qurhanul.rizqie@gmail.com N.S. Mohd Yusof e-mail: nurulshafiqayusof@yahoo.com R.F. Surakusumah e-mail: rinoferdian@gmail.com D.E. Octorina Dewi e-mail: dyah@utm.my; dyah.ekashanti@gmail.com M.Q. Rizqie Faculty of Computer Science, Universitas Sriwijaya, Palembang, Indonesia K.W. Lai Biomedical Engineering Department, Faculty of Engineering University Malaya, Kuala Lumpur 50603, Malaysia e-mail: lai.khinwee@um.edu. my © Springer Science+Business Media Singapore 2015 K.W. Lai and D.E. Octorina Dewi (eds.), Medical Imaging Technology, Lecture Notes in Bioengineering, DOI 10.1007/978-981-287-540-2_2 41
Evaluation of Microsatellite Instability, hMLH1 Expression and hMLH1 Promoter Hypermethylation in Defining the MSI Phenotype of Colorectal Cancer

About 10-15% of all colorectal cancers (CRCs) demonstrate high levels of microsatellite instability (MSI-H) and are currently best identified by molecular analysis of microsatellite markers. Most sporadic CRCs with MSI-H are known to be associated with the methylation of the hMLH1 promoter. Promoter methylation coincides with lack of the hMLH1 expression. We aimed to investigate the association between MSI status, hMLH1 protein expression and methylation status of the hMLH1 promoter, and to determine the usefulness of each method in defining the MSI phenotype in sporadic CRCs. Methods: CRCs from 173 patients from the Cancer and Leukemia Group B (CALGB) were assessed for their MSI status. An additional cohort of 18 MSI-H tumors from the University of California San Diego (UCSD) was included in the analysis of the MSI-H subgroup. MSI testing was performed by PCR using five standard MSI markers. hMLH1 promoter analysis was investigated by methylation specific PCR (MSP), and expression of the MMR genes hMLH1 and hMSH2 was examined by immunohistochemistry (IHC). Results: Of the 173 CALGB tumors, 111 (64%) were MSS, 35 (20%) were MSI-L and 27 (16%) MSI-H, respectively. Data on hMLH1 protein expression, MSH2 protein expression and hMLH1 methylation are available on 128, 173 and 81 of these tumors, respectively. Presence of hMLH1 and hMSH2 protein expression was significantly associated with MSI status. Four of 45 (8.9%) MSI-H tumors and 0 of 146 (0%) MSS/MSI-L tumors did not express hMSH2 (p=0.0028). hMLH1 protein expression was present in 107 of 108 (99%) MSS and MSI-L tumors versus 11 of 20 (55%) MSI-H tumors (p
A state observer approach to filter stochastic nonlinear differential systems

This paper investigates the state estimation problem for stochastic nonlinear differential systems with multiplicative noise. Our purpose is to combine the noise filtering properties of the Extended Kalman Filter with the global convergence properties of high-gain observers. We propose an observer-based algorithm and provide conditions under which a bound on the estimation error can be guaranteed. Simulations show that this algorithm reveals to be more efficient than the Extended Kalman Bucy filter for systems with large measurement errors.
ARE MORE ALTERNATIVES BETTER FOR DECISION-MAKERS ?

While the traditional economic wisdom believes that an individual will become better off by being given a larger opportunity set to choose from, in this paper we question this belief and build a formal theoretical model that introduces decision costs into the rational decision process. We show, under some reasonable conditions, that a larger feasible set may actually lower an individual’s level of satisfaction. This provides a solid economic underpinning for the Simon prediction.
Intima-media thickness of the common carotid artery is the significant predictor of angiographically proven coronary artery disease.

BACKGROUND Previous studies have shown a relationship between intima-media thickness (IMT) of the common carotid artery and coronary artery disease (CAD). The role of IMT in the prediction of significant CAD has not been established. OBJECTIVES To investigate the diagnostic accuracy of IMT measurement and the detection of carotid plaques in relation to cardiovascular risk factors in the prediction of significant CAD. PATIENTS AND METHODS One hundred and seventy patients (121 men and 49 women; average age 58 +/- 11 years) undergoing selective coronary angiography were examined by carotid ultrasound. IMT was measured. Plasma lipid concentrations and other risk factors were determined. RESULTS Angiographically proven significant CAD was found in 138 (81%) of all patients. Carotid plaques were detected in 98 (58%) of all patients. Presence of carotid plaques in common carotid artery (P<0.001) and male sex (P<0.005) were found to be categorical risk factors for significant CAD but in multiple regression analysis only age (P=0.15), IMT (P<0.01), high density lipoprotein (HDL) cholesterol (P=0.02) and, less significantly, total cholesterol (P=0.09) were found to be independent parameters for the prediction of significant CAD. IMT of 0.75 mm was determined as a cut-off point for the detection of significant CAD (sensitivity 78%, specificity 79%, positive predictive value 95%, negative predictive value 41%, odds ratio 12.9, 95% CI 3.5 to 47.6). CONCLUSION The increase in IMT is the significant positive predictor of angiographically proven CAD; other predictors are high age, low HDL cholesterol and, less significantly, high total cholesterol. Presence of carotid plaques and male sex do not add any new information for the prediction of CAD once the predictors are considered.
Optimization of Vitamin Suppletion After Roux-En-Y Gastric Bypass Surgery Can Lower Postoperative Deficiencies

Abstract Iron, vitamin B12, and folic acid deficiencies are among the most common deficiencies occurring after laparoscopic Roux-en-Y gastric bypass (LRYGB). The present study evaluates the effectiveness of a specially designed multivitamin supplement (WLS Forte, FitForMe, Rotterdam, the Netherlands) specifically developed for LRYGB patients. A triple-blind, randomized, 12-month study was conducted comparing WLS forte with a standard multivitamin supplement (sMVS) containing approximately 100% of the recommended daily allowance (RDA) for iron, vitamin B12, and folic acid. WLS Forte contains vitamin B12 14000% RDA, iron 500% RDA, and folic acid 300% RDA. In total, 148 patients (74 in each group) underwent a LRYGB procedure. Baseline characteristics were similar for both groups. Per protocol analysis demonstrated that sMVS treatment was associated with a decline in ferritin (−24.4 ± 70.1 &mgr;g/L) and vitamin B12 (−45.9 ± 150.3 pmol/L) over 12 months, whereas in WLS Forte patients, ferritin remained stable (+3.2 ± 93.2 &mgr;g/L) and vitamin B12 increased significantly (+55.1 ± 144.2 pmol/L). The number of patients developing ferritin or vitamin B12 deficiency was significantly lower with WLS Forte compared with sMVS (P < 0.05). Iron deficiency (ID) was reduced by 88% after WLS Forte compared with sMVS. Adverse events related to supplement use did not occur. An optimized multivitamin supplement is safe and reduces the development of iron and vitamin B12 deficiencies after LRYGB.
L'innovation gap et le performance gap dans les économies de services: un défi pour les politiques publiques

Ce travail est consacre a l'analyse de la relation innovation-performance dans les economies developpees contemporaines. Il met en evidence un double « gap » relatif a l'innovation et a la performance. L'« innovation gap » traduit la difference entre la realite de l'innovation produite dans une economie et ce que les indicateurs traditionnels de l'innovation (R-D, brevets) percoivent. Le « performance gap » quant a lui mesure la difference entre la realite de la performance dans une economie et la performance evaluee par les outils economiques traditionnels (essentiellement la productivite et la croissance). Il correspond a la performance cachee, invisible a ces outils. Ces deux « gaps » brouillent la relation innovation-performance. Ils sont a l'origine d'un certain nombre de paradoxes dont ce travail entend rendre compte, et ils conduisent a s'interroger sur le bien-fonde de certaines politiques publiques de soutien a l'innovation.
Prospective, randomized, double-blind study about effectiveness of levothyroxine suppressive therapy in prevention of recurrence after operation: result at the third year of follow-up.

BACKGROUND Levothyroxine has often been given to patients operated on for nodular goiter to prevent recurrence. The rationale is that suppression of thyroid-stimulating hormone (TSH), considered to be the main growth factor in this disease, can be obtained by administration of levothyroxine. METHODS Sixty patients undergoing operation for nontoxic nodular goiter were randomized in two groups: (1) thirty-two were administered levothyroxine at substitutive dosage (100 micrograms) or placebo and (2) twenty-eight were given levothyroxine at suppressive dosage (2.2 to 3 micrograms/kg/day). Levels of thyroid hormones and TSH were evaluated every 6 months. Recurrences detected by echography were then considered. RESULTS After a 3-year follow-up we observed 25 of 32 recurrences in group 1 and 6 of 28 in group 2 (p < 0.005). Subjects with endemic goiter problems responded better to therapy. Patients with a multinodular goiter responded better than patients with a uninodular goiter. No difference was found regarding the type of surgical treatment (subtotal thyroidectomy vs lobectomy). CONCLUSIONS The results confirmed suppressive therapy as actually being effective in preventing recurrences at least in iodine-deficient regions like Italy. Thus for these patients it may be suggested as a prophylactic treatment after operation.
Pareto Density Estimation: Probability Density Estimation for Knowledge Discovery

Pareto Density Estimation (PDE) as defined in this work is a method for the estimation of probability density functions using hyperspheres. The radius of the hyperspheres is derived from optimizing information while minimizing set size. It is shown, that PDE is a very good estimate for clusters of Gaussian structure. The robustness of the method is tested with respect to cluster overlap, number of clusters, different variances in different clusters and application to high dimensional data. For high dimensional data PDE is found to be appropriate for the purpose of cluster analysis. The method is tested successfully on a difficult high dimensional real world problem: stock picking in falling markets.
Nonradiating and radiating modes excited by quantum emitters in open epsilon-near-zero cavities

Quantum emitters embedded in arbitrarily shaped epsilon-near-zero cavities can selectively excite both nonradiating and radiating modes. Controlling the emission and interaction properties of quantum emitters (QEs) embedded within an optical cavity is a key technique in engineering light-matter interactions at the nanoscale, as well as in the development of quantum information processing. State-of-the-art optical cavities are based on high quality factor photonic crystals and dielectric resonators. However, wealthier responses might be attainable with cavities carved in more exotic materials. We theoretically investigate the emission and interaction properties of QEs embedded in open epsilon-near-zero (ENZ) cavities. Using analytical methods and numerical simulations, we demonstrate that open ENZ cavities present the unique property of supporting nonradiating modes independently of the geometry of the external boundary of the cavity (shape, size, topology, etc.). Moreover, the possibility of switching between radiating and nonradiating modes enables a dynamic control of the emission by, and the interaction between, QEs. These phenomena provide unprecedented degrees of freedom in controlling and trapping fields within optical cavities, as well as in the design of cavity opto- and acoustomechanical systems.
Secondary traumatization in children of Vietnam veterans.

The profound psychological effect of combat experience on some veterans of the Vietnam War is well documented. The most common symptoms experienced by veterans suffering from posttraumatic stress disorder (PTSD) are flashbacks, nightmares, startle responses, mntability, depression, and violent behavior (1). Veterans with PTSD experience a high incidence ofdivorce, marital conflict, and domestic violence; however, there have been no neports of the impact of the disorder on their children. In contrast, there is an extensive literature on the children of survivors of the Nazi concentration camps. These children have been reported to suffer from problems with separaiion and individuation, pathologic identification with their traumatized parents, depression, guilt, and aggressiveness (2). Since initiating a small child therapy program at the West Hayen Veterans Administration Medical Center three years ago, we have encountered many troubled and symptomatic children whose fathers are being treated for
Identifying and Managing Malnutrition Stemming from Different Causes

Protein–energy malnutrition (PEM) is highly prevalent among peritoneal dialysis (PD) patients and is a strong predictor of morbidity and mortality. A wide range of factors can lead to PEM and associated wasting (PEM/W) in PD patients, but persistent inflammation and the presence of diabetes have been identified as the two main reasons. An important body of literature has been reporting studies of methods suitable for detecting malnutrition in its early phase so that appropriate intervention can be provided. Although assessment of nutrition status has been substantially improved, no definitive single method of assessing nutrition status has been decided. Rather, several different markers of nutrition should be evaluated together. Because of the complexity of treating malnutrition in PD patients, nontraditional strategies such as appetite stimulants, anti-inflammatory diets, and anti-inflammatory pharmacologic agents are recommended to be combined with more traditional forms of nutritional support, so as to provide a better chance of recovery. The present review briefly discusses the causes of PEM/W, the methods most commonly used to identify the condition, and the new management strategies available.
The potential applications of Apolipoprotein E in personalized medicine

Personalized medicine uses various individual characteristics to guide medical decisions. Apolipoprotein (ApoE), the most studied polymorphism in humans, has been associated with several diseases. The purpose of this review is to elucidate the potential role of ApoE polymorphisms in personalized medicine, with a specific focus on neurodegenerative diseases, by giving an overview of its influence on disease risk assessment, diagnosis, prognosis, and therapy. This review is not a systematic inventory of the literature, but rather a summary and discussion of novel, influential and promising works in the field of ApoE research that could be valuable for personalized medicine. Empirical evidence suggests that ApoE genotype informs pre-symptomatic risk for a wide variety of diseases, is valuable for the diagnosis of type III dysbetalipoproteinemia, increases risk of dementia in neurodegenerative diseases, and is associated with a poor prognosis following acute brain damage. ApoE status appears to influence the efficacy of certain drugs, outcome of clinical trials, and might also give insight into disease prevention. Assessing ApoE genotype might therefore help to guide medical decisions in clinical practice.