Miracle-dz/UniFAR-FTUs huggingface dataset:
PIASy-Mediated Sumoylation of Yin Yang 1 Depends on Their Interaction but Not the RING Finger

ABSTRACT As a multifunctional protein, Yin Yang 1 (YY1) has been demonstrated to regulate both gene expression and protein posttranslational modifications. However, gaps still exist in our knowledge of how YY1 can be modified and what the consequences of its modifications are. Here we report that YY1 protein can be sumoylated both in vivo and in vitro. We have identified lysine 288 as the major sumoylation site of YY1. We also discovered that PIASy, a SUMO E3 ligase, is a novel YY1-interacting protein and can stimulate the sumoylation of YY1 both in vitro and in vivo. Importantly, the effects of PIASy mutants on in vivo YY1 sumoylation correlate with the YY1-PIASy interaction but do not depend on the RING finger domain of PIASy. This regulation is unique to YY1 sumoylation because PIASy-mediated p53 sumoylation still relies on the integrity of PIASy, which is also true of all of the previously identified substrates of PIASy. In addition, PIASy colocalizes with YY1 in the nucleus, stabilizes YY1 in vivo, and differentially regulates YY1 transcriptional activity on different target promoters. This study demonstrates that YY1 is a target of SUMOs and reveals a novel feature of a SUMO E3 ligase in the PIAS family that selectively stimulates protein sumoylation independent of the RING finger domain.
Sugar Overconsumption during Adolescence Selectively Alters Motivation and Reward Function in Adult Rats

Background There has been a dramatic escalation in sugar intake in the last few decades, most strikingly observed in the adolescent population. Sugar overconsumption has been associated with several adverse health consequences, including obesity and diabetes. Very little is known, however, about the impact of sugar overconsumption on mental health in general, and on reward-related behavioral disorders in particular. This study examined in rats the effects of unlimited access to sucrose during adolescence on the motivation for natural and pharmacological rewards in adulthood. Methodology/Principal Findings Adolescent rats had free access to 5% sucrose or water from postnatal day 30 to 46. The control group had access to water only. In adulthood, rats were tested for self-administration of saccharin (sweet), maltodextrin (non-sweet), and cocaine (a potent drug of abuse) using fixed- and progressive-ratio schedules, and a concentration-response curve for each substance. Adult rats, exposed or not exposed to sucrose, were tested for saccharin self-administration later in life to verify the specificity of adolescence for the sugar effects. Sugar overconsumption during adolescence, but not during adulthood, reduced the subsequent motivation for saccharin and maltodextrin, but not cocaine. This selective decrease in motivation is more likely due to changes in brain reward processing than changes in gustatory perception. Conclusions/Significance Sugar overconsumption induces a developmental stage-specific chronic depression in reward processing that may contribute to an increase in the vulnerability to reward-related psychiatric disorders.
Network Infusion to Infer Information Sources in Networks

Several significant models have been developed that enable the study of diffusion of signals across biological, social and engineered networks. Within these established frameworks, the inverse problem of identifying the source of the propagated signal is challenging, owing to the numerous alternative possibilities for signal progression through the network. In real world networks, the challenge of determining sources is compounded as the true propagation dynamics are typically unknown, and when they have been directly measured, they rarely conform to the assumptions of any of the well-studied models. In this paper we introduce a method called Network Infusion (NI) that has been designed to circumvent these issues, making source inference practical for large, complex real world networks. The key idea is that to infer the source node in the network, full characterization of diffusion dynamics, in many cases, may not be necessary. This objective is achieved by creating a diffusion kernel that well-approximates standard diffusion models such as the susceptible-infected diffusion model, but lends itself to inversion, by design, via likelihood maximization or error minimization. We apply NI for both single-source and multi-source diffusion, for both single-snapshot and multi-snapshot observations, and for both homogeneous and heterogeneous diffusion setups. We prove the mean-field optimality of NI for different scenarios, and demonstrate its effectiveness over several synthetic networks. Moreover, we apply NI to a real-data application, identifying news sources in the Digg social network, and demonstrate the effectiveness of NI compared to existing methods. Finally, we propose an integrative source inference framework that combines NI with a distance centrality-based method, which leads to a robust performance in cases where the underlying dynamics are unknown.
FOOD AND NUTRITION FOR LIFE : MALNUTRITION IN OLDER AMERICANS BIBLIOGRAPHY

This study determined the prevalence of underweight and hypoalbuminia in VA nursing home residents and the frequency with which physicians, nurses and dietitians document their awareness of these problems, and found a high prevalence of calorie and protein undernutrition among 2,811 residents, with wide variation across 26 nursing homes, and a frequent lack of documentation of these problems by physicians and nurses Abraham NE, Stroh K. Establishing linkages in a community setting-Delaware Nutrition Screening Program. Nutrition Screening 2: New Approaches to Care, An Interdisciplinary Strategy. [May 10,1993: Washington, DC] Washington, DC: Nutrition Screening Initiative, 1993.
Analysis of Property Based Attestation in Trusted Platforms

Binary attestation in trusted computing platforms provide the ability to reason about the state of a system using hash measurements. Property based attestation on the other hand enables more meaningful attestation by abstracting low level binary values to high level security properties or functions of systems. In this paper, we try to understand the kind of security properties that trusted platforms can attest. We propose that security properties can have different levels of granularity and provide a pyramid model that classifies properties at four different levels. We leverage the Common Criteria framework for security requirements to provide examples of such properties. The model is then implemented in the context of authorisation for Web services.
Elongator is a histone H3 and H4 acetyltransferase important for normal histone acetylation levels in vivo

The elongating, hyperphosphorylated form of RNA polymerase II is associated with the Elongator complex, which has the histone acetyltransferase (HAT) Elp3 as a subunit. Here we show that, in contrast to the isolated Elp3 subunit, the activity of intact Elongator complex is directed specifically toward the amino-terminal tails of histone H3 and H4, and that Elongator can acetylate both core histones and nucleosomal substrates. The predominant acetylation sites are lysine-14 of histone H3 and lysine-8 of histone H4. The three smallest Elongator subunits—Elp4, Elp5, and Elp6—are required for HAT activity, and Elongator binds to both naked and nucleosomal DNA. By using chromatin immunoprecipitation, we show that the levels of multiply acetylated histone H3 and H4 in chromatin are decreased in vivo in yeast cells lacking ELP3.
Parametric Construction of Improved Nyquist Filters Based on Inner and Outer Functions

In this paper, we explore the concept of inner and outer functions to come up with two novel parametric families of Nyquist pulses. Aside from requiring only two design parameters, the proposed pulses yield an enhanced performance compared to the sophisticated flipped-inverse hyperbolic secant (asech) pulse, that was recently presented in the literature. While the construction of parametric families originates from the work of Beaulieu and Damen, the usage of inner and outer functions guarantees a higher flexibility in the choice of the composite family members. The proposed pulses may have a slower decay rate than the well-known raised-cosine (RC) pulse, but exhibit a more pronounced decrease in the amplitudes of the two largest sidelobes and this accounts for their improved robustness to error probabilities. In the following, it is clearly demonstrated that a lower bit error rate (BER), compared to the existing pulses, can be achieved for different values of the roll-off factor and timing jitter. Moreover, a smaller maximum distortion along with a more open eye diagram are attained as well.
Choosing project risk management techniques. A theoretical framework

The pressure for increasing quality while reducing time and costs places particular emphasis on managing risk in projects. To this end, several models and techniques have been developed in literature and applied in practice, so that there is a strong need for clarifying when and how each of them should be used. At the same time, knowledge about risk management is becoming a matter of paramount importance to effectively deal with the complexity of projects. However, communication and knowledge creation are not easy tasks, especially when dealing with uncertainty, because decision-making is often fragmented and a comprehensive perspective on the goals, opportunities and threats of a project is missing. With the purpose of providing guidelines for the selection of risk techniques taking into account the most relevant aspects characterising the managerial and operational scenario of a project, a theoretical framework to classify these techniques is proposed. Based on a literature review of the criteria to categorise risk techniques, three dimensions are defined: the phase of the risk management process, the phase of the project life cycle and the corporate maturity towards risk. The taxonomy is then applied to a wide selection of risk techniques according to their documented applications. This work helps to integrate the risk management and the knowledge management processes. Future research efforts will be directed towards refining the framework and testing it in multiple industries.
Effects of age, gender, and environmental exposures on exhaled nitric oxide level in healthy 12 to 18 years Qatari children

CONTEXT: Fractional exhaled nitric oxide (FENO) is a useful noninvasive diagnostic tool for asthma and some other pediatric respiratory diseases. Factors affecting FENO level are variable in different populations and studies. AIMS: To estimate the normal values of exhaled nitric oxide for Qataris 12 to 18 years of age. Other objectives were to measure the correlation of anthropometric and other potential factors with FENO levels. SETTINGS AND DESIGN: Community-based, cross-sectional study. METHODS: A total of 438 Qatari national school children from both genders were randomly recruited in cross-sectional study. Of them, 203 were non-atopic and hence included in the statistical analysis. Questionnaires including personal data, demographic data, and other factors that may affect FENO level were distributed. STATISTICAL ANALYSIS USED: Comparison of means done using t-test. We performed Spearman's rho test to measure correlations. Data analysis was done using PASW 18.0 Release 18.0. 0, 2009. RESULTS: The geometric mean of FENO levels for all subjects was 14.1 ppb (upper level CI 95% - 36.3 ppb). FENO was significantly higher in males (R2 = −0.254, P<0.0001) and was negatively correlated with increasing age for the whole study population (P=0.036). This decline was interrupted by a significant upraise at the age of 15 years (P=0.0462) which seems to be driven by the males (P=0.0244). FENO levels were lower in subjects exposed to cats (P=0.019). We could not find significant correlation between FENO and other factors studied. CONCLUSIONS: Estimated FENO level with 95% CI in Qatari children, which is probably close to those in other Gulf countries, will be helpful clinically. The lower level of FENO with female gender, increasing age, and exposure to cats needs to be further studied to establish the association and to understand the underlying mechanisms.
Face recognition using improved local line binary pattern

This paper presents a new technique, named Improved Local Line Binary Pattern (ILLBP), which is an operator for illumination-robust face recognition from a single training image. In order to empirically demonstrate effectiveness of the proposed approach, we use Principal Component Analysis-Nearest Neighbour (PCA-NN) and multi-class Support Vector Machine (SVM) as the classifiers. Comparisons to the Local Line Binary Pattern (LLBP) on Yale Face Database B are also conducted. The advantages of our technique include higher accuracy, lesser complexity and faster computational time compared to LLBP technique.
Shedding of tumor necrosis factor receptors by activated human neutrophils

The capacity of human neutrophils (PMN) to bind tumor necrosis factor (TNF) was rapidly lost when the cells were incubated in suspension with agents that can stimulate their migratory and secretory responses. Both physiological (poly)peptides (FMLP, C5a, CSF-GM) and pharmacologic agonists (PMN, calcium ionophore A23187) induced the loss of TNF receptors (TNF-R) from the cell surface. Half-maximal loss in TNF-R ensued after only approximately 2 min with 10(-7) M FMLP at 37 degrees C, and required only 10(-9) M FMLP during a 30-min exposure. However, there were no such changes even with prolonged exposure of PMN to FMLP at 4 degrees or 16 degrees C. Scatchard analysis revealed loss of TNF- binding sites without change in their affinity (Kd approximately 0.4 nM) as measured at incompletely modulating concentrations of FMLP, C5a, PMA, or A23187. The binding of anti-TNF-R mAbs to PMN decreased in parallel, providing independent evidence for the loss of TNF-R from the cell surface. At the same time, soluble TNF-R appeared in the medium of stimulated PMN. This inference was based on the PMN- and FMLP-dependent generation of a nonsedimentable activity that could inhibit the binding of TNF to fresh human PMN or to mouse macrophages, and the ability of mAbs specific for human TNF-R to abolish inhibition by PMN-conditioned medium of binding of TNF to mouse macrophages. Soluble TNF-R activity was associated with a protein of Mr approximately 28,000 by ligand blot analysis of cell-free supernatants of FMLP-treated PMN. Thus, some portion of the FMLP-induced loss of TNF-R from human PMN is due to shedding of TNF-R. Shedding was unaffected by inhibitors of serine and thiol proteases and could not be induced with phosphatidylinositol- specific phospholipase C. Loss of TNF-R from PMN first stimulated by other agents may decrease their responsiveness to TNF. TNF-R shed by PMN may be one source of the TNF-binding proteins found in body fluids, and may blunt the actions of the cytokine on other cells.
Absence of Right Visual Field Attentional Bias in Reading in Dyslexic Children

A parafoveal word is better identified in the right visual field (RVF) than in the left visual field (LVF), in adults [4] and in school-age children [5]. Attention may play a role, at least partially, in this RVF superiority in reading. The hypothesis is that attention is not symmetrically distributed in the state of expectancy prior to the presentation of parafoveal words, and a bias in favor of the RVF exists. This attentional bias may be the consequence of the left hemispheric control when the subject is engaged in a linguistic task [2], and of scanning habits [1]. Many investigators have hypothesized a failure of left-hemisphere posterior brain systems to function properly during reading in dyslexia [6]. A possibility is that this hemispheric dysfunctioning may influence the distribution of spatial attention and affect the RVF bias in reading. We studied the distribution of attention when identifying parafoveal words in dyslexic children and agematched skilled readers. We compared performance in a condition in which a word was presented alone in the LVF or RVF, and a condition in which a distractor was simultaneously presented in the visual field opposite the word. The distribution of attention should be affected by the presence of the distractor, and the distractor effect is stronger in the LVF than in the RVF in normal
Cytochemistry of Ovarian Hormone Binding Sites in Human Breast Cancer

Since quantitative assays for estrogen (ER) and progesterone (PR) binding sites in the homogenate of human breast cancer biopsies are inaccurate due to the heterogeneity of cell population in small needle biopsies, cytochemistry of ER and PR is a method of choice to visualize small number of cancer cells positive for these binding sites. Our current study confirmed this hypothesis. We have found about 15-25% under-reported results for PR and ER respectively. This makes a great difference in the management of breast cancer patients with regard to the administration of tamoxifen or other anti-estrogen drugs following surgery and or radiation therapy.
Meta-scheduling in advance using red-black trees in heterogeneous Grids

The provision of Quality of Service in Grid environments is still an open issue that needs attention from the research community. One way of contributing to the provision QoS in Grids is by performing meta-scheduling of jobs in advance, that is, jobs are scheduled some time before they are actually executed. In this way, the aproppriate resources will be available to run the job when needed, so that QoS requirements (i.e., deadline) are met. This paper presents two new techniques, implemented over the red-black tree data structure, to manage the idle/busy periods of resources. One of them takes into account the heterogeneity of resources when estimating the execution times of jobs. A performance evaluation using a real testbed is presented that illustrates the efficiency of this approach to meet the QoS requirements of users.
Increases in cardiac output can reverse flow deficits from vasospasm independent of blood pressure: a study using xenon computed tomographic measurement of cerebral blood flow.

INTRODUCTION Vasospasm after subarachnoid hemorrhage remains a management challenge. The accepted treatment involves hypertensive, hypervolemic, hemodilution therapy. However, there is variation in the application of this treatment. Most authors increase mean arterial pressure (MAP), which can be associated with significant morbidity. Others increase cardiac output (CO). In this study, we examined the relationship between volume status, CO, and MAP and cerebral blood flow (CBF) in the setting of vasospasm. METHODS A xenon blood flow tomography-based system was used to quantitate CBF. Sixteen patients with vasospasm after subarachnoid hemorrhage were treated with hypervolemia, phenylephrine to increase MAP, or dobutamine to increase CO. Direct CBF measurements were obtained before and after treatment. A strength of this study is that only one variable (central venous pressure, MAP, or CO) was manipulated in each patient, and the effect of this change was measured immediately. RESULTS With phenylephrine, mean MAP increased from 102.4 to 132.1 mm Hg. In regions of diminished CBF due to vasospasm, mean CBF increased from 19.2 to 33.7 ml/100 g/min. Similarly, dobutamine increased the cardiac index from a mean of 4.1 to 6.0 L/min/m(2) and slightly decreased MAP. CBF increased from a mean of 24.8 to 35.4 ml/100 g/min. Both were statistically significant changes. With hypervolemia, the average central venous pressure increased from a mean of 5.4 to 7.3 cm H(2)O; no changes in mean CBF were noted. CONCLUSION This article reports the first human study that shows with direct measurements the independent influence of CO in the setting of vasospasm. Increases in CO without changes in MAP can elevate CBF. This finding has immediate clinical application because CO manipulation is much safer than increasing MAP. Because both interventions were equally efficacious, our protocol has been changed to augment CO as a first measure. Induced hypertension is reserved for patients in whom this initial treatment fails.
Incremental Fusion of Structure-from-Motion and GPS Using Constrained Bundle Adjustments

Two problems occur when bundle adjustment (BA) is applied on long image sequences: large calculation time and drift (or error accumulation). In recent work, the calculation time is reduced by local BAs applied in an incremental scheme. The drift may be reduced by fusion of GPS and Structure-from-Motion. An existing fusion method is BA minimizing a weighted sum of image and GPS errors. This paper introduces two constrained BAs for fusion which enforce an upper bound for the reprojection error. These BAs are alternatives to the existing fusion BA which does not guarantee a small reprojection error and requires a weight as input. Then, the three fusion BAs are integrated in an incremental Structure-from-Motion method based on local BA. Last, we will compare the fusion results on long monocular image sequences and low cost GPS.
Variable effects of chronic subcutaneous administration of rotenone on striatal histology

When infused in rats, rotenone, a mitochondrial complex I inhibitor, induces alterations that resemble the histological changes of Parkinson's disease, particularly degeneration of the nigrostriatal dopaminergic system. However, the specificity of rotenone effects has been challenged recently. We have re‐examined the alterations caused by rotenone in the substantia nigra and the striatum of rats after infusion of rotenone (2 mg/kg per day s.c.) for 21 days. Three patterns of striatal tyrosine‐hydroxylase immunoreactivity (TH‐IR) were observed: 46% of animals showed no reduction, and 46% of animals showed diffuse reduction in TH‐IR, whereas one animal presented a focal loss of TH‐IR in the striatum. Confocal microscopy analysis showed that the vesicular monoamine transporter (VMAT2) was decreased in parallel with TH‐IR, strongly suggesting a loss of striatal DA nerve terminals in animals with diffuse or central TH‐IR loss. However, no significant loss of TH‐IR neurons was observed in the substantia nigra. Analysis of NeuN and DARPP‐32 immunoreactivity, and Nissl staining, in the striatum showed no striatal neuronal loss in animals with either preserved TH‐IR or diffuse TH‐IR reduction. However, in the animal with focal TH‐IR loss, severe neuronal loss was evident in the center and the periphery of the striatum, together with microglial activation detected by OX‐6 and OX‐42 staining. Thus, in most cases, chronic subcutaneous infusion of low doses of rotenone does not induce significant striatal neuronal loss, despite TH‐IR and VMAT‐IR reduction in a subset of animals, supporting the use of rotenone as a model of Parkinson's disease under carefully controlled experimental conditions. J. Comp. Neurol. 478:418–426, 2004. © 2004 Wiley‐Liss, Inc.
Automatic video system for aircraft identification

Advanced surface movement guidance and control systems need the identification of aircraft and vehicles in airport movement areas. In this work, a video identification algorithm based on tail number recognition is proposed as a part of a global surveillance video system. The aircraft identification problem has to deal with three fundamental aspects: capturing and preprocessing the images, international regulations defining tail number grammar, and pattern recognition methodology. Considering these aspects, the developed system is based on three ideas: using the local grey level contrast to detect characters of the tail number; finding the zone where the fail number is written to isolate it from the rest of the image; and processing this zone to identify the aircraft, using an aircraft database.