Miracle-dz/UniFAR-FTUs huggingface dataset:
DNA-binding specificity of Mcm1: operator mutations that alter DNA-bending and transcriptional activities by a MADS box protein

The yeast Mcm1 protein is a member of the MADS box family of transcriptional regulatory factors, a class of DNA-binding proteins found in such diverse organisms as yeast, plants, flies, and humans. To explore the protein-DNA interactions of Mcm1 in vivo and in vitro, we have introduced an extensive series of base pair substitutions into an Mcm1 operator site and examined their effects on Mcm1-mediated transcriptional regulation and DNA-binding affinity. Our results show that Mcm1 uses a mechanism to contact the DNA that has some significant differences from the one used by the human serum response factor (SRF), a closely related MADS box protein in which the three-dimensional structure has been determined. One major difference is that 5-bromouracil-mediated photo-cross-linking experiments indicate that Mcm1 is in close proximity to functional groups in the major groove at the center of the recognition site whereas the SRF protein did not exhibit this characteristic. A more significant difference is that mutations at a position outside of the conserved CC(A/T)6GG site significantly reduce Mcm1-dependent DNA bending, while these substitutions have no effect on DNA bending by SRF. This result shows that the DNA bending by Mcm1 is sequence dependent and that the base-specific requirements for bending differ between Mcm1 and SRF. Interestingly, although these substitutions have a large effect on DNA bending and transcriptional activation by Mcm1, they have a relatively small effect on the DNA-binding affinity of the protein. This result suggests that the degree of DNA bending is important for transcriptional activation by Mcm1.
Pituitary Adenylate Cyclase Activating Peptide Deficient Mice Exhibit Impaired Thymic and Extrathymic Regulatory T Cell Proliferation during EAE

We have shown that mice deficient in pituitary adenylate cyclase-activating polypeptide (PACAP, gene name ADCYAP1) manifest enhanced sensitivity to experimental autoimmune encephalomyelitis (EAE), supporting the anti-inflammatory actions described for this neuropeptide. In addition to an increased proinflammatory cytokine response in these mice, a reduction in regulatory T cell (Treg) abundance in the lymph nodes (LN) was observed, suggesting altered Treg kinetics. In the present study, we compared in PACAP deficient (KO) vs. wild type mice the abundances and rates of proliferation FoxP3+ Tregs in three sites, the LN, central nervous system (CNS) and thymus and the relative proportions of Th1, Th2, and Th17 effector subsets in the LN and CNS. Flow cytometry analyses revealed a decrease in Treg proliferation and an increased T effector/Tregs ratio in the LN and CNS of PACAP KO mice. In the thymus, the primary site of do novo natural Treg production, the total numbers and proliferative rates of FoxP3+ Tregs were significantly reduced. Moreover, the expression of IL-7, a cytokine implicated in thymic Treg expansion during EAE, failed to increase at the peak of the disease in the thymus and LN of PACAP KO mice. In addition to these Treg alterations, a specific reduction of Th2 cells (about 4-fold) was observed in the lymph nodes in PACAP KO mice, with no effects on Th1 and Th17 subsets, whereas in the CNS, Th1 and Th17 cells were increased and Th2 decreased. Our results suggest that endogenous production of the neuropeptide PACAP protects against EAE by modulating Treg expansion and Th subsets at multiple sites.
Abnormal Salivary Total and Oligomeric Alpha-Synuclein in Parkinson’s Disease

In Parkinson’s disease (PD), alpha-synuclein (a-syn) can be detected in biological fluids including saliva. Although previous studies found reduced a-syn total (a-syntotal) concentration in saliva of PD patients, no studies have previously examined salivary a-syn oligomers (a-synolig) concentrations or assessed the correlation between salivary a-syntotal, a-synolig and clinical features in a large cohort of PD patients. Is well known that a-synolig exerts a crucial neurotoxic effect in PD. We collected salivary samples from 60 PD patients and 40 age- and sex-comparable healthy subjects. PD was diagnosed according to the United Kingdom Brain Bank Criteria. Samples of saliva were analyzed by specific anti-a-syn and anti-oligomeric a-syn ELISA kits. A complete clinical evaluation of each patient was performed using MDS-Unified Parkinson's Disease Rating Scale, Beck Depression Inventory, Montreal Cognitive Assessment and Frontal Assessment Battery. Salivary a-syntotal was lower, whereas a-synolig was higher in PD patients than healthy subjects. The a-synolig/a-syntotal ratio was also higher in patients than in healthy subjects. Salivary a-syntotal concentration negatively correlated with that of a-synolig and correlated with several patients’ clinical features. In PD, decreased salivary concentration of a-syntotal may reflect the reduction of a-syn monomers (a-synmon), as well as the formation of insoluble intracellular inclusions and soluble oligomers. The combined detection of a-syntotal and a-synolig in the saliva might help the early diagnosis of PD.
Optimal Asset Allocation Based on Utility Maximization in the Presence of Market Frictions

We develop a model of optimal asset allocation based on a utility framework. This applies to a more general context than the classical mean-variance paradigm since it can also account for the presence of constraints in the portfolio composition. Using this approach, we study the distribution of a measure of wealth compensative variation, we propose a benchmark and portfolio efficiency test and a procedure to estimate the implicit risk aversion parameter of a power utility function. Our empirical analysis makes use of the S&P 500 and industry portfolios time series to show that although the market index cannot be considered an efficient investment in the mean-variance metric, the wealth loss associated with such an investment is statistically different from zero but rather small (lower than 0.5%). The wealth loss is at its minimum for a representative agent with a constant risk aversion index not higher than 5. Furthermore we show that, for reasonable levels of risk aversion, the use of an equally weighted portfolio is surprisingly consistent with an expected utility maximizing behavior.
Basic fibroblast growth factor-induced activation of latent transforming growth factor beta in endothelial cells: regulation of plasminogen activator activity

Exposure of bovine aortic or capillary endothelial cells to basic FGF (bFGF) for 1 h resulted in an approximately sixfold increase in plasminogen activator (PA) activity by 18 h that returned nearly to basal levels by 36 h. We hypothesized that the decrease in PA activity following bFGF stimulation was mediated by transforming growth factor beta (TGF-beta) formed from its inactive precursor. Conditioned medium collected from endothelial cells 36 h after a 1-h exposure to bFGF, but not control medium, inhibited basal levels of PA activity when transferred to confluent monolayers of bovine aortic endothelial cells. Antibody to TGF-beta neutralized the inhibitory activity of this conditioned medium, indicating that the medium contained active TGF- beta. Northern blot analysis and quantitation of acid activatable latent TGF-beta in conditioned medium demonstrated that bFGF exposure did not increase the amount of transcription or secretion of latent TGF- beta by the endothelial cells. Both aprotinin, an inhibitor of plasmin, and anti-urokinase type PA IgG blocked the generation of active TGF- beta in cultures exposed to bFGF. These results demonstrated that plasmin generated by uPA activity is required for the activation of latent TGF-beta in endothelial cell cultures treated with bFGF. Activation of TGF-beta by endothelial cells exposed to bFGF appears to limit both the degree and duration of PA stimulation. Thus, in bFGF- stimulated endothelial cell cultures, PA levels are controlled by a negative feedback loop: PA, whose expression is stimulated by bFGF, contributes to the formation of TGF-beta, which in turn opposes the effects of bFGF by limiting PA synthesis and activity. These studies suggest a role for TGF-beta in reversing the invasive stage of angiogenesis and contributing to the formation of quiescent capillaries.
SLAM algorithm with parallel localization loops: TinySLAM 1.1

This paper presents the tinySLAM algorithm, which enables a mobile robot to perform automatic localization and mapping, called SLAM. Indeed, it is one of the essential bricks to build an autonomous robot that can evolve in an unknown environment. Several methods and algorithms have been developed to solve this problem, using various techniques and sensors. TinySLAM is a SLAM algorithm based on the principle of IML (Incremental Maximum Likelihood). It uses data from a laser sensor to estimate the most probable position of the robot in a 2D map. We have worked extensively on improving the computation speed of this estimate. Results obtained allowed us to run two loops of position estimation in parallel, with different characteristics. The algorithm has a better chance to find a good estimate of the position. In previous work, we presented a first version of this algorithm. This paper talks about the advances made in improving the tinySLAM algorithm, until version 1.1.
An improved robust predictive current regulation algorithm

Current regulation techniques for pulsewidth-modulated (PWM) voltage source inverters (VSIs) can be classified as either linear or nonlinear. Linear techniques consist principally of either a proportional-integral (PI) or a predictive current control strategy, while nonlinear schemes are usually based on a hysteresis strategy. Of the two linear strategies, predictive current control offers the advantages of precise current tracking with minimal distortion and can also be fully implemented on a digital platform. However, the conventional implementation of the predictive current regulation (PCR) algorithm is sensitive to noise and errors in the load inductance estimate, particularly when the back EMF is also estimated. This paper presents an improved PCR algorithm that retains all the benefits associated with PCR while achieving significantly increased robustness to load parameter mismatch and reduced zero current clamped oscillation effects. It is also relatively insensitive to noise in the sampled current measurements. The algorithm is equally applicable to variable fundamental frequency applications such as variable speed drives and to fixed fundamental frequency applications such as PWM rectifier systems or active filters. Simulation and experimental results are presented to confirm the improved robustness of the new algorithm.
Atmospheric Chemistry and Physics First Long-term Study of Particle Number Size Distributions and New Particle Formation Events of Regional Aerosol in the North China Plain

Atmospheric particle number size distributions (size range 0.003–10µm) were measured between March 2008 and August 2009 at Shangdianzi (SDZ), a rural research station in the North China Plain. These measurements were made in an attempt to better characterize the tropo-spheric background aerosol in Northern China. The mean particle number concentrations of the total particle, as well as the nucleation, Aitken, accumulation and coarse mode were determined to be 1. A general finding was that the particle number concentration was higher during spring compared to the other seasons. The air mass origin had an important effect on the particle number concentration and new particle formation events. Air masses from northwest (i.e. inner Asia) favored the new particle formation events, while air masses from southeast showed the highest particle mass concentration. Significant diurnal variations in particle number were observed, which could be linked to new particle formation events, i.e. gas-to-particle conversion. During particle formation events, the number concentration of the nucleation mode rose up to maximum value of 10 4 cm −3. New particle formation events were observed on 36% of the effective measurement days.
Independent transient plane design for protection in OpenFlow-based networks

Network protection against link failure is required to allow packets to reach the destination with minimal packet loss when a failure occurs. When a link fails, traffic that attempts to use the failed link is interrupted. Typically, routers in the network discover the failure and find a new route to bypass the failed link. Alternatively, well-known segment protection schemes can also be used to speed up the link recovery time by rerouting packets locally through precalculated protection paths. However, several backup paths have to be prepared for each primary path, making path configuration rather complex and poorly scalable. This paper proposes a design for fast rerouting in an OpenFlow-based network. This new design reduces the number of flow entries and the number of configuration messages needed for network rerouting, which in turn reduces the memory size needed in each switch and the CPU load at the controller. We show empirically and using simulations that our design can reduce the number of flow entries and configuration messages needed by about 60% and 75%, respectively, when compared with an existing OpenFlow-based segment protection design. Furthermore, we implement the proposed design on a pan-European network and show that our design can recover from a link failure in as little as 25 ms.
Human Apolipoprotein E Isoform‐Specific Differences in Neuronal Sprouting in Organotypic Hippocampal Culture

Abstract : The apolipoprotein E (ApoE) ε4 allele is a major risk factor for neurodegenerative conditions, including Alzheimer's disease. A role for ApoE is implicated in regeneration of synaptic circuitry after neural injury. In the in vitro mouse organotypic hippocampal slice culture system, we previously showed that cultures derived from ApoE‐knockout mice are defective in mossy fiber sprouting into the dentate gyrus molecular layer. This sprouting defect was rescued in cultures from transgenic mice expressing ApoE3 under the control of the human promoter and in ApoE‐knockout cultures treated with ApoE3‐conditioned media. Although the ApoE3 transgene fully restored sprouting, ApoE4 restored sprouting to only 58% of ApoE3 levels. These data indicate that ApoE isoform‐specific effects on neuroregeneration may contribute to its genetic risk for Alzheimer's disease.
Parenting perceptions among college students: A qualitative examination

ABSTRACT This study assessed the knowledge and attitudes of young adults without children in regard to discipline and parenting practices. A qualitative design was utilized (n = 26) with semistructured focus groups. Results indicated participants believed discipline is important, with spanking and loss of privileges being the most effective strategy for behavior change. The majority of participants reported plans to discipline future children the way in which they were disciplined, suggesting a high percentage intend to utilize spanking. Findings suggest that personal experiences shape parenting beliefs, attitudes, and knowledge. Results inform efforts at educating future parents on appropriate parenting practices and indicate the need for protocols for young adults to educate about practices that may diverge from their personal experiences.
Comparative Study of Adhoc Routing Protocol AODV , DSR and DSDV in Mobile Adhoc NETwork

A Mobile Ad hoc NETwork is a kind of wireless ad-hoc network, and is a self configuring network of mobile routers connected by wireless links. Mobile Ad-Hoc Network (MANET) is a wireless network without infrastructure. Self configurability and easy deployment feature of the MANET resulted in numerous applications in this modern era. Efficient routing protocols will make MANETs reliable. Various research communities are working in field of MANET and trying to adopt the protocols and technology in other applications as well. In this paper, an attempt has been made to compare three well know protocols AODV, DSR and DSDV by using three performance metrics packet delivery ratio, average end to end delay and routing overhead. The comparison has been done by using simulation tool NS2 which is the main simulator, NAM (Network Animator) and excel graph which is used for preparing the graphs from the trace files.
Ceramide-Coated Balloon Catheters Limit Neointimal Hyperplasia After Stretch Injury in Carotid Arteries

Neointimal hyperplasia at the site of surgical intervention is a common and deleterious complication of surgery for cardiovascular diseases. We hypothesized that direct delivery of a cell-permeable growth-arresting lipid via the balloon tip of an embolectomy catheter would limit neointimal hyperplasia after stretch injury. We have previously demonstrated that sphingolipid-derived ceramide arrested the growth of smooth muscle cell pericytes in vitro. Here, we show that ceramide-coated balloon catheters significantly reduced neointimal hyperplasia induced by balloon angioplasty in rabbit carotid arteries in vivo. This ceramide treatment decreased the number of vascular smooth muscle cells entering the cell cycle without inducing apoptosis. In situ autoradiographic studies demonstrated that inflating the balloon catheter forced cell-permeable ceramide into the intimal and medial layers of the artery. Intercalation of ceramide into vascular smooth muscle cells correlated with rapid inhibition of trauma-associated phosphorylation of extracellular signal–regulated kinase and protein kinase B. These studies demonstrate the utility of cell-permeable ceramide as a novel therapy for reducing neointimal hyperplasia after balloon angioplasty.
Knowledge, Attitudes and Beliefs about Dementia in an Urban Xhosa-Speaking Community in South Africa

Background: Dementia, a debilitating condition, requires particular attention in Southern Africa where there is a dearth of prevalence data. Population ageing and other risk factors are driving an increasing incidence of dementia. However, limited knowledge and understanding may impact the attitudes and practices towards persons with dementia. Aim: To investigate the relationship between the knowledge of dementia, its effect on the attitudes and practices toward people with dementia in an urban community setting. To determine the perceived availability of services for those with dementia, the awareness of elder abuse and care-giver burden. Methods: A descriptive, cross-sectional study was performed in Khayelitsha. An interviewer administered questionnaire was used with assistance from isiXhosa speaking translators. A sample of 100 individuals was surveyed door-to-door from both the informal and formal housing settlements, using cluster random sampling methods. Results: There was deficient knowledge about dementia, with an average accuracy of 53.44% on the knowledge test. Only 10% reported knowing what dementia was. Participants had generally tolerant views about people with dementia. No significant relationship was found between knowledge and attitudes about dementia. There was a significant difference between people who would share their house with a family member with dementia or send them to nursing homes (p = 0.03). 64% of participants knew what elder abuse was. 19% knew of an elder who had been abused; amongst the most common forms reported were being locked alone in their house and being deprived of food. Conclusions: This study showed that knowledge about dementia was limited with no relationship to attitudes of high tolerance towards people with dementia. Elder abuse was well recognized, but poorly reported. Appropriate health promotion strategies and education should be conducted and further research should be done into dementia in South Africa.
Individual and couple-level risk factors for hepatitis C infection among heterosexual drug users: a multilevel dyadic analysis.

BACKGROUND Hepatitis C virus (HCV) is the most common bloodborne pathogen in the United States and is a leading cause of liver-related morbidity and mortality. Although it is known that HCV is most commonly transmitted among injection drug users, the role of sexual transmission in the spread of HCV remains controversial because of inconsistent findings across studies involving heterosexual couples. METHODS A novel multilevel modeling technique designed to overcome the limitations of previous research was performed to assess multiple risk factors for HCV while partitioning the source of risk at the individual and couple level. The analysis was performed on risk exposure and HCV screening data obtained from 265 drug-using couples in East Harlem, New York City. RESULTS In multivariable analysis, significant individual risk factors for HCV included a history of injection drug use, tattooing, and older age. At the couple level, HCV infection tended to cluster within couples, and this interdependence was accounted for by couples' drug-injection behavior. Individual and couple-level sexual behavior was not associated with HCV infection. CONCLUSIONS Our results are consistent with prior research indicating that sexual contact plays little role in HCV transmission. Rather, couples' injection behavior appears to account for the clustering of HCV within heterosexual dyads.
The Integration Project Among White Teachers and Racial/Ethnic Minority Youth: Understanding Bias in School Practice

In 1954, the Supreme Court ruled schools in the United States needed to desegregate and begin integration. The decision was a radical departure from the facilities argument initially presented; it added the issue that the segregation of Black students was having a deleterious effect on their self-concept. Many scholars argue the integration has not been sustained (Orfield and Frankenberg, 2014); in fact, a recent report highlights Black, Latino and Native American students are less integrated with White and Asian students than in 1954 (Orfield and Frankenberg, 2014). However the Brown decision set forth another integration project – the integration of White practitioners (i.e., teachers and principals) with Black, Latino and Native American student populations! This article brings together an array of social interaction research that articulates the complexity of this integration project. More specifically, the article focuses on demographic patterns of intimate interactions (i.e., friendship networks, interracial marriage), research studies that document race-based ideas of learning and achievement; the presence of “passive” lowered expectations occurring through interactions such as stereotype threat (Steele and Aronson, 1995) and racial/ethnic microaggressions (Wing Sue, 2010) and “active” lowered expectations through school structures such as curriculum (Anyon, 1983) and resource allocation (Campaign for Fiscal Equity v. NYS, 2003).