Miracle-dz/UniFAR-FTUs huggingface dataset:
Dendritic cells during Epstein Barr virus infection

Epstein Barr virus (EBV) causes persistent infection in more than 90% of the human adult population and is associated with 2% of all tumors in humans. This γ-herpes virus infects primarily human B and epithelial cells, but it has been reported to be sensed by dendritic cells (DCs) during primary infection. These activated DCs are thought to contribute to innate restriction of EBV infection and initiate EBV-specific adaptive immune responses via cross-priming. The respective evidence and their potential importance for EBV-specific vaccine development will be discussed in this review.
Kinetics of nitrogen uptake by Populus tremuloides in relation to atmospheric CO(2) and soil nitrogen availability.

Sustained increases in plant production in response to elevated atmospheric carbon dioxide (CO(2)) concentration may be constrained by the availability of soil nitrogen (N). However, it is possible that plants will respond to N limitation at elevated CO(2) concentration by increasing the specific N uptake capacity of their roots. To explore this possibility, we examined the kinetics of (15)NH(4) (+) and (15)NO(3) (-) uptake by excised roots of Populus tremuloides Michx. grown in ambient and twice-ambient CO(2) concentrations, and in soils of low- and high-N availability. Elevated CO(2) concentration had no effect on either NH(4) (+) or NO(3) (-) uptake, whereas high-N availability decreased the capacity of roots to take up both NH(4) (+) and NO(3) (-). The maximal rate of NH(4) (+) uptake decreased from 12 to 8 &mgr;mol g(-1) h(-1), and K(m) increased from 49 to 162 &mgr;mol l(-1), from low to high soil N availability.Because NO(3) (-) uptake exhibited mixedkinetics over the concentration range we used (10-500 &mgr;mol l( -1)), it was not possible to calculate V(max) and K(m). Instead, we used an uptake rate of 100 &mgr;mol g(-1) h(-1) as our metric of NO(3) (-) uptake capacity, which averaged 0.45 and 0.23 &mgr;mol g(-1) h(-1) at low- and high-N availability, respectively. The proximal mechanisms for decreased N uptake capacity at high-N availability appeared to be an increase in fine-root carbohydrate status and a decrease in fine-root N concentration. Both NH(4) (+) and NO(3) (-) uptake were inversely related to fine-root N concentration, and positively related to fine-root total nonstructural carbohydrate concentration. We conclude that soil N availability, through its effects on fine-root N and carbohydrate status, has a much greater influence on the specific uptake capacity of P. tremuloides fine roots than elevated atmospheric CO(2). In elevated atmospheric CO(2), changes in N acquisition by P. tremuloides appeared to be driven by changes in root architecture and biomass, rather than by changes in the amount or activity of N-uptake enzymes.
Computational model of axon guidance

Axon guidance (AG) towards their target during embryogenesis or after injury is an important issue in the development of neuronal networks. During their growth, axons often face complex decisions that are difficult to understand when observing just a small part of the problem. In this work we propose a computational model of AG based on activity-independent mechanisms that takes into account the most important aspects of AG. The model includes the main elements (neurons, with soma, axon and growth cone; glial cells acting as guideposts) and mechanisms (attraction/repulsion guidance cues, growth cone adaptation, tissue-gradient intersections, axonal transport, changes in the growth cone complexity and a range of responses for each receptor). The growth cone guidance is defined as a function that maps the receptor activation by ligands into a repulsive or attractive force. This force is then converted into a turn- ing angle using spherical coordinates. A regulatory network between the receptors and the intracellular proteins is considered, leading to more complex and realistic behaviors. The ligand diffusion through the extracellular environment is modeled with linear or exponential functions. Concerning experimentation, it was developed the first computational model and a new theoretical model of the midline crossing of Drosophila axons that focus all the decision points. The computational model created allows describing to a great extent the behaviors that have been reported in the literature, for three different pathfinding scenarios: (i) normal, (ii) comm mutant and (iii) robo mutant. Moreover, this model suggests new hypotheses, being the most relevant the existence of an inhibitory link between the DCC receptor and the Comm protein that is Netrin-mediated or mediated by a third unknown signal.
Burkholderia phytofirmans PsJN reduces impact of freezing temperatures on photosynthesis in Arabidopsis thaliana

Several plant growth-promoting rhizobacteria (PGPR) are known to improve plant tolerance to multiple stresses, including low temperatures. However, mechanisms underlying this protection are still poorly understood. The aim of this study was to evaluate the role of the endophytic PGPR, Burkholderia phytofirmans strain PsJN (Bp PsJN), on Arabidopsis thaliana cold tolerance using photosynthesis parameters as physiological markers. Under standard conditions, our results indicated that Bp PsJN inoculation led to growth promotion of Arabidopsis plants without significant modification on photosynthesis parameters and chloroplast organization. However, bacterial colonization induced a cell wall strengthening in the mesophyll. Impact of inoculation modes (either on seeds or by soil irrigation) and their effects overnight at 0, -1, or -3°C, were investigated by following photosystem II (PSII) activity and gas exchanges. Following low temperatures stress, a decrease of photosynthesis parameters was observed. In addition, during three consecutive nights or days at -1°C, PSII activity was monitored. Pigment contents, RuBisCO protein abundance, expression of several genes including RbcS, RbcL, CBF1, CBF2, CBF3, ICE1, COR15a, and COR78 were evaluated at the end of exposure. To assess the impact of the bacteria on cell ultrastructure under low temperatures, microscopic observations were achieved. Results indicated that freezing treatment induced significant changes in PSII activity as early as the first cold day, whereas the same impact on PSII activity was observed only during the third cold night. The significant effects conferred by PsJN were differential accumulation of pigments, and reduced expression of RbcL and COR78. Microscopical observations showed an alteration/disorganization in A. thaliana leaf mesophyll cells independently of the freezing treatments. The presence of bacteria during the three successive nights or days did not significantly improved A. thaliana responses but prevented the plasmalemma disruption under freezing stress.
Support Vector Regression Model Based on Empirical Mode Decomposition and Auto Regression for Electric Load Forecasting

Electric load forecasting is an important issue for a power utility, associated with the management of daily operations such as energy transfer scheduling, unit commitment, and load dispatch. Inspired by strong non-linear learning capability of support vector regression (SVR), this paper presents a SVR model hybridized with the empirical mode decomposition (EMD) method and auto regression (AR) for electric load forecasting. The electric load data of the New South Wales (Australia) market are employed for comparing the forecasting performances of different forecasting models. The results confirm the validity of the idea that the proposed model can simultaneously provide forecasting with good accuracy and interpretability.
Applications of All-Atom Molecular Dynamics to Nanofluidics

In recent years, due to the progress in the fabrication of micro and nanodevices, nanofluidics has become an intense research field. The interest of the scientific community is evident from the large amount of published papers and by the issuing of dedicated journals. In this scenario, a better understanding of the key aspects of fluid motion in nanoscale systems is fundamental and hence computational techniques able to provide a deeper insight in the complex phenomena involved in nanoscale mass transport play a crucial role in nanofluidic research. The aim of this chapter is to introduce the reader to the application of classical all-atom molecular dynamics (MD) to nanofluidic problems. Nanofluidics is the study of the fluid motion in confined structures whose characteristic size is some nanometers, typically 1 − 100 nm (Eijkel & Berg, 2005). Confined fluids in nanoscale geometries exhibit physical behaviors that, in several cases, largely differ from macroscale dynamics. The crucial difference is that in nanoscale systems the usual mathematical description for continuum fluid dynamics often fails to reproduce the correct behavior. Here we deal with simple liquids (Hansen & McDonald, 2006) and the appropriate macroscopic model is given by the incompressible Navier-Stokes equations for mass and momentum conservation
Social Determinants and Access to Induced Abortion in Burkina Faso: From Two Case Studies

Unsafe abortion constitutes a major public health problem in Burkina Faso and concerns mainly young women. The legal restriction and social stigma make abortions most often clandestine and risky for women who decide to terminate a pregnancy. However, the exposure to the risk of unsafe induced abortion is not the same for all the women who faced unwanted pregnancy and decide to have an abortion. Drawn from a qualitative study on the issue of abortion in Ouagadougou, Burkina Faso's capital, the contrasting cases of two young women who had abortion allow us to show how the women's personal resources (such as the school level, financial resources, the compliance to social norms, the social network, etc.) may determine the degree of vulnerability of women, the delay to have an abortion, the type of care they are likely to benefit from, and the cost they have to face. This study concludes that the poorest always pay more (cost and consequences), take longer to have an abortion, and have more exposure to the risk of unsafe abortion.
Eco-friendly Synthesis and Characterization of Silver Nanoparticles and Evaluation of Their Antibacterial Activity

Generally, most of the metallic nanoparticles have been synthesized using chemical techniques, where the chemicals used are generally toxic and combustible. Therefore there is a growing need to develop environment friendly synthesis techniques without using toxic chemicals. In this paper we present a simple and green/eco-friendly/chemical free biosynthesis of silver nanoparticles using Elettaria cardamom seed extract as reducing agents. The as synthesized nanoparticles were characterized by UV-vis absorbance spectroscopy, XRD and SEM measurements. The experimental study confirmed the formation of highly crystalline nanoparticles with uniform shape. Further, the antibacterial activity against the Bacillus subtilis was also evaluated for Elettaria cardamom seeds extract assisted silver nanoparticles and the later found to exhibit significant activity.
Impact of Similarity Measures on Web-page Clustering

Clustering of web documents enables (semi-)automated categorization, and facilitates certain types of search. Any clustering method has to embed the documents in a suitable similarity space. While several clustering methods and the associated similarity measures have been proposed in the past, there is no systematic comparative study of the impact of similarity metrics on cluster quality, possibly because the popular cost criteria do not readily translate across qualitatively different metrics. We observe that in domains such as YAHOO that provide a categorization by human experts, a useful criteria for comparisons across similarity metrics is indeed available. We then compare four popular similarity measures (Euclidean, cosine, Pearson correlation and extended Jaccard) in conjunction with several clustering techniques (random, self-organizing feature map, hyper-graph partitioning, generalized kmeans, weighted graph partitioning), on high dimensionai sparse data representing web documents. Performance is measured against a human-imposed classification into news categories and industry categories. We conduct a number of experiments and use t-tests to assure statistical significance of results. Cosine and extended Jaccard similarities emerge as the best measures to capture human categorization behavior, while Euclidean performs poorest. Also, weighted graph partitioning approaches are clearly superior to all others.
Sepiapterin Decreases Acute Rejection and Apoptosis in Cardiac Transplants Independently of Changes in Nitric Oxide and Inducible Nitric-Oxide Synthase Dimerization

Tetrahydrobiopterin (BH4), a cofactor of inducible nitric-oxide synthase (iNOS), is an important post-translational regulator of NO bioactivity. We examined whether treatment of cardiac allograft recipients with sepiapterin [S-(-)-2-amino-7,8-dihydro-6-(2-hydroxy-1-oxopropyl)-4-(1H)-pteridinone], a precursor of BH4, inhibited acute rejection and apoptosis in cardiac transplants. Heterotopic cardiac transplantation was performed in Wistar-Furth donor to Lewis recipient strain rats. Recipients were treated daily after transplantation with 10 mg/kg sepiapterin. Grafts were harvested on post-transplant day 6 for analysis of BH4 (high-performance liquid chromatography), expression of inflammatory cytokines (reverse transcription- and real-time polymerase chain reaction), iNOS (Western blots), and NO (Griess reaction and NO analyzer). Histological rejection grade was scored, and graft function was determined by echocardiography. Apoptosis, protein nitration, and oxidative stress were determined by immunohistochemistry. Treatment of allografts with sepiapterin increased cardiac BH4 levels by 3-fold without changing protein levels of GTP cyclohydrolase, the enzyme that regulates de novo BH4 synthesis. Sepiapterin decreased inflammatory cell infiltrate and significantly inhibited histological rejection scores and apoptosis similar in magnitude to cyclosporine. Sepiapterin also decreased nitrative and oxidative stress. Sepiapterin caused a smaller increase in left ventricular mass versus untreated allografts but without improving fractional shortening. Sepiapterin did not alter tumor necrosis factor-α and interferon-γ expression, whereas it decreased interleukin (IL)-2 expression. Sepiapterin did not change total iNOS protein or monomer levels, or plasma and tissue NO metabolites levels. It is concluded that the mechanism(s) of antirejection are due in part to decreased apoptosis, protein nitration, and oxidation of cardiomyocytes, which seems to be mediated at the immune level by limiting inflammatory cell infiltration via decreased IL-2-mediated T-lymphocyte expansion.
Gravitational Shunts in Longstanding Overt Ventriculomegaly in Adults

OBJECTIVE:A new entity of chronic hydrocephalus was introduced recently in the international literature: longstanding overt ventriculomegaly in adults. Previous experience with this disorder has demonstrated that shunt therapy for such patients involves a considerable risk of overdrainage. In the present study, we aimed to clarify whether this risk could be avoided by use of gravitational shunts. METHODS:A total of 26 adults (age range, 17–75 yr) with macrocephaly and progressive hydrocephalus symptoms underwent implantation of either an adjustable Codman Hakim gravity-assisted shunt (Codman Medos, LeLocle, Switzerland) plus an Aesculap-Miethke ShuntAssistant (Miethke KG, Kleinmachnow, Germany) or a nonadjustable gravitational shunt (Aesculap-Miethke gravity-assisted valve). The follow-up period averaged 29 ± 13 months (range, 6–48 mo). RESULTS:Significant sustained clinical improvement was achieved in 87% of patients. In more than 90% of patients, Evans index decreased postoperatively by less than 10%. No correlation was documented between the degree of ventricle width reduction and clinical improvement. Only two patients developed subdural hematoma, which was caused by insufficient hydrostatic pressure compensation owing to errors in estimation of intraperitoneal pressure. CONCLUSION:Unlike conventional differential pressure shunts, gravitational shunts can be used in the treatment of high-risk patients with longstanding overt ventriculomegaly in adults. Significant risk of overdrainage can be avoided. Gravitational shunts offer a viable alternative to endoscopic third ventriculostomy, provided the choice and adjustment of the shunt opening pressure is based on a correct assessment of the hydrostatic pressure to be compensated for.
TAM - A Compiler Controlled Threaded Abstract Machine

Abstract The Threaded Abstract Machine (TAM) refines dataflow execution models to address the critical constraints that modern parallel architectures place on the compilation of general-purpose parallel programming languages. TAM defines a self-scheduled machine language of parallel threads, which provides a path from data-flow-graph program representations to conventional control flow. The most important feature of TAM is the way it exposes the interaction between the handling of asynchronous message events, the scheduling of computation, and the utilization of the storage hierarchy. This paper provides a complete description of TAM and codifies the model in terms of a pseudo machine language TL0. Issues in compilation from a high level parallel language to TL0 are discussed in general and specifically in regard to the Id90 language. The implementation of TL0 on the CM-5 multiprocessor is explained in detail. Using this implementation, a cost model is developed for the various TAM primitives. The TAM approach is evaluated on sizable Id90 programs on a 64 processor system. The scheduling hierarchy of quanta and threads is shown to provide substantial locality while tolerating long latencies. This allows the average thread scheduling cost to be extremely low.
Mitochondrial Fusion/Fission, Transport and Autophagy in Parkinson's Disease: When Mitochondria Get Nasty

Understanding the molecular basis of Parkinson's disease (PD) has proven to be a major challenge in the field of neurodegenerative diseases. Although several hypotheses have been proposed to explain the molecular mechanisms underlying the pathogenesis of PD, a growing body of evidence has highlighted the role of mitochondrial dysfunction and the disruption of the mechanisms of mitochondrial dynamics in PD and other parkinsonian disorders. In this paper, we comment on the recent advances in how changes in the mitochondrial function and mitochondrial dynamics (fusion/fission, transport, and clearance) contribute to neurodegeneration, specifically focusing on PD. We also evaluate the current controversies in those issues and discuss the role of fusion/fission dynamics in the mitochondrial lifecycle and maintenance. We propose that cellular demise and neurodegeneration in PD are due to the interplay between mitochondrial dysfunction, mitochondrial trafficking disruption, and impaired autophagic clearance.
The Role of Mindfulness in Healthcare Reform: a Policy Paper

REFORM By now it is clear to everyone— economists , lawmakers, health professionals, and the public—that healthcare reform is an urgent need, a national emergency that requires immediate and focused attention. Costs continue to spiral out of control, large numbers of Americans are uninsured (medical bills are a leading cause of bankruptcy), and the aging of the so-called baby boomer generation threatens to burden Medicare beyond its capacity. The United States spends over $2 trillion annually on healthcare, yet some key national health indicators lag significantly behind other developed nations (eg, infant mortality rates in the United States rank 23rd globally, on par with Po-land and Slovakia). As a percentage of gross domestic product, healthcare spending exceeds 16% and is projected to reach 17.7% by 2012. 2 Clearly, our healthcare system is unsustainable both in terms of its financial and human costs. However, despite a nearly unanimous call for reform, there remains a lack of consensus about what form the changes should take, and different stake-holders have put forth a variety of approaches. At this stage, one of the most important questions we can ask is, " What is driving healthcare costs? " It is reasonable to assume that if we can identify the underlying problem, we will increase our chances of arriving at an effective solution. Like most commodities, healthcare is subject to the rule of supply and demand. Right now, we have a high demand for healthcare procedures characterized by sophisticated and expensive medical technology. The evidence suggests that advances in medical technology are the single biggest factor driving up healthcare costs over the last 50 years or so, eclipsing all the other factors such as aging population , costs of health insurance, rising incomes , defensive medicine, administrative costs, lower productivity, end-of-life care, and the like. 2 However, since advances in medical technology have also tended to produce better health outcomes for certain conditions, 3 we do not want to thwart technological progress. The problem is that the nation, regardless of who pays for healthcare, can no longer afford to keep supplying the ever-increasing demand. One solution is to put limits on the sup-ply—to engage in healthcare rationing. There are many serious objections to this approach, chief among them the moral issue of denying potentially life-saving procedures to human beings. Fortunately, there is another more humane and sensible solution: reducing the demand by leverag-ing preventive medicine. " …
Toward Human-Aware Robot Task Planning

Human-robot interaction requires explicit reasoning on human environment and on robot capacities to achieve its tasks in a collaborative way with a human partner. We have devised a decisional framework for human-robot interactive task achievement that is aimed to allow the robot not only to accomplish its tasks but also to produce behaviors that support its engagement visa -vis its human partner and to interpret human behaviors and intentions. Together and in coherence with this framework, we intend to develop and experiment various task planners and interaction schemes that will allow the robot to select and perform its tasks while taking into account explicitly the human abilities as well as the constraints imposed by the presence of humans, their needs and preferences. We present the first results obtained by our "human-aware" task and motion planners and discuss how they can be extended.
Deducing Linguistic Structure from the Statistics of Large Corpora

Two experiments that strongly suggest that largely distributional techniques might be developed to automatically provide both a set of part of speech tags for English and a skeletal parsing of free English text are described. In one experiment the authors have developed a constituent boundary parsing algorithm that derives an (unlabeled) bracketing, given text annotated for part of speech as input. In other experiment the authors have investigated whether a distributional analysis can discover a part of speech tag set which might prove adequate to support experiments. The state of a tagged natural language corpus to aid such experiments is summarized. <<ETX>>