Miracle-dz/UniFAR-FTUs huggingface dataset:
Extending the MODPATH Algorithm to Rectangular Unstructured Grids

The recent release of MODFLOW‐USG, which allows model grids to have irregular, unstructured connections, requires a modification of the particle‐tracking algorithm used by MODPATH. This paper describes a modification of the semi‐analytical particle‐tracking algorithm used by MODPATH that allows it to be extended to rectangular‐based unstructured grids by dividing grid cells with multi‐cell face connections into sub‐cells. The new method will be incorporated in the next version of MODPATH which is currently under development.
New energy sources: the enzymatic biofuel cell

The continuous search for alternative energy sources, imposed by economic and environmental concerns, has motivated investigations into clean and efficient alternatives for energy production. Studies have shown that fuel cells are a potentially efficient strategy for energy conversion. Biofuel cells constitute a subclass of fuel cells with promising application in low-power devices (generally in the order of micro to milli watts). Instead of metallic catalysts, biological power sources employ biological molecules such as enzymes, organelles, or microorganisms to convert chemical energy into electricity. Biofuel cells offer several advantages over traditional batteries, including the use of renewable and non-toxic components, reaction selectivity, fuel flexibility, and ability to operate at lower temperatures and near neutral pH. Indeed, recent papers have demonstrated the promising characteristics of these devices; however, some challenges remains to be faced despite the several advances in this area. This review aims to provide the readers of the Journal of the Brazilian Chemical Society with an overview of enzymatic biofuel cells, their development since its first description in 1964, and the most recent outcomes. The latest papers in this field (including implantable technology) and an outlook for future research in this area are also presented.
Lactobacillus paracasei feeding improves immune control of influenza infection in mice

Respiratory tract infections such as flu cause severe morbidity and mortality and are among the leading causes of death in children and adults worldwide. Commensal microbiota is critical for orchestrating tissue homeostasis and immunity in the intestine. Probiotics represent an interesting source of immune modulators and several clinical studies have addressed the potential beneficial effects of probiotics against respiratory infections. Therefore, we have investigated the mechanisms of protection conferred by L. paracasei CNCM I-1518 strain in a mouse model of influenza infection. Notably, local myeloid cells accumulation is generated in the lungs after seven days feeding with L. paracasei prior to viral infection. L. paracasei-fed mice showed reduced susceptibility to the influenza infection, associated with less accumulation of inflammatory cells in the lungs, faster viral clearance and general health improvement. Interestingly, Allobaculum was significantly increased in L. paracasei-fed mice 7 days after influenza infection, even if the gut microbiota composition was not altered overall. L. paracasei-purified peptidoglycan partially recapitulated the protective phenotype observed with the entire bacteria. Collectively, our results demonstrate that oral consumption of L. paracasei CNCM I-1518 modulates lung immunity was associated with an improved control of influenza infection. These results further extend the beneficial role for certain lactobacilli to alleviate the burden of respiratory tract infections.
Factors Associated with Succession of Abandoned Agricultural Lands along the Lower Missouri River, U.S.A.

The 1993 flood of the Missouri River led to the abandonment of agriculture on considerable land in the floodplain. This abandonment led to a restoration opportunity for the U.S. Federal Government, purchasing those lands being sold by farmers. Restoration of this floodplain is complicated, however, by an imperfect understanding of its past environmental and vegetative conditions. We examined environmental conditions associated with the current placement of young forests and wet prairies as a guide to the potential successional trajectory for abandoned agricultural land subject to flooding. We used Bayesian mixed‐effects logistic regression to examine the effects of flood frequency, soil drainage, distance from the main channel, and elevation on whether a site was in wet prairie or in forest. Study site was included as a random effect, controlling for site‐specific differences not measured in our study. We found, after controlling for the effect of site, that early‐successional forest sites were closer to the river and at a lower elevation but occurred on drier soils than wet prairie. In a regulated river such as the lower Missouri River, wet prairie sites are relatively isolated from the main channel compared to early‐successional forest, despite occurring on relatively moister soils. The modeled results from this study may be used to predict the potential successional fate of the acquired agricultural lands, and along with information on wildlife assemblages associated with wet prairie and forest can be used to predict potential benefit of these acquisitions to wildlife conservation.
Ignition and Propagation of an Atmospheric-Pressure Helium Plasma Jet

The ignition and propagation of an atmospheric-pressure plasma jet is examined using fast imaging techniques. The plasma jet consists of a single electrode, fabricated using a transparent and conductive polymer film, wrapped around a quartz dielectric tube; this allows the entire ignition and propagation process to be observed without the usual obstruction of a nontransparent electrode. It is shown that the discharge is always triggered at the electrode edges and that the plasma propagation mechanism differs significantly depending on the polarity of the applied voltage.
The nature of spatiotemporal changes in cerebral hemodynamics as manifested in functional magnetic resonance imaging

The nature of changes in rapidly acquired magnetic resonance images of the brain was studied by using a denoising method and spectral techniques optimally suited to short time series. It was found that the stimulus related changes have a complex spatiotemporal structure even for simple visual stimuli. Apart from a low frequency window, the non‐stimulusrelated changes were found to correspond in detail to either breathing or heartbeat, although these two sources show different patterns of spatial coherence in the image. At low frequencies, oscillations with frequencies around 0.1 Hz were observed, also with nontrivial space‐time structure, which are likely to be vasomotor in origin.
Inhibiting Cxcr 2 disrupts tumor-stromal interactions and improves survival in a mouse model of pancreatic ductal adenocarcinoma

1Department of Gastroenterology, Graduate School of Medicine, University of Tokyo, Tokyo, Japan. 2Department of Cancer Biology and 3Vanderbilt-Ingram Comprehensive Cancer Center, Vanderbilt University, Nashville, Tennessee, USA. 4Whitehead Institute for Biomedical Research, Cambridge, Massachusetts, USA. 5Department of Medicine and Clinical Oncology, Graduate School of Medicine, Chiba University, Chiba, Japan. 6Department of Gastroenterology, Graduate School of Medicine, Yokohama City University, Kanagawa, Japan. 7Division of Clinical Genome Research, Institute of Medical Sciences, University of Tokyo, Tokyo, Japan. 8Cell and Developmental Biology and 9Vanderbilt University Program in Developmental Biology, Vanderbilt University, Nashville, Tennessee, USA. 10Yamanashi Prefectural Central Hospital, Yamanashi, Japan.
Formation of cytoplasmic heat shock granules in tomato cell cultures and leaves

Biochemical and electron microscopic analyses of heat-shocked suspension cultures of Peruvian tomato (Lycopersicon peruvianum) revealed that a considerable part of the dominant small heat shock proteins (hsps) with an Mr of approximately 17,000 are structural proteins of newly forming granular aggregates in the cytoplasm (heat shock granules), whose formation strictly depends on heat shock conditions (37 to 40 degrees C) and the presence or simultaneous synthesis of hsps. However, under certain conditions, e.g., in preinduced cultures maintained at 25 degrees C, hsps also accumulate as soluble proteins without concomitant assembly of heat shock granules. Similar heat shock-induced cytoplasmic aggregates were also observed in other cell cultures and heat-shocked tomato leaves and corn coleoptiles.
ESTIMATIVA SIMBÓLICA DE INTERVALOS ASSUMIDOS POR VARIÁVEIS INTEIRAS DURANTE A EXECUÇÃO DE PROGRAMAS

Range analyses attempt to statically infer intervals that conservatively encompass all values a given program variable can assume during execution. These types of analyses are widely useful for program optimization, in cases such as variable bitwidth reduction, integer overflow and buffer overflow check elimination, and more. Some range-like analyses suffer from a few issues, such as lack of precision due to being tailored for specific program constructs, i.e. scalar evolution, or compromised scalability, i.e. polyhedral model. This dissertation presents a symbolic range analysis which leverages the expressibility of symbolic algebra and variable renaming techniques to overcome some limitations of previously available analyses, providing one that is a positive mixture of precision and scalability. We expose use cases in which our analysis contributes to software security, automation techniques, and general program optimization, and we also experiment with several tweaks and modifications, such as our novel pointer-arithmetic elimination anti-optimization. In a bounds check elimination case study, we eliminate 48% of all checks produced by AddressSanitizer and produce code that is 17% faster on SPEC CPU2006 and also reduce AddressSanitizer’s overhead from 112% to 14% on Polybench through bounds check hoisting techniques. For page migration on NUMA architectures, our range analysis is the base for heuristics which achieve 50% greater performance when compared to state-of-the-art options.
Bayesian network-based identification of driver lane-changing intents using eye tracking and vehicle-based data

A Bayesian network decision-making method is proposed by combining driver's eye-tracking data and vehicle-based data together to identify driver lane-changing intents. First, experiments are conducted in a driving simulator with eye-tracker device to obtain the data when a subject driver makes lane-changing maneuvers. Second, collected data are analyzed in machine learning method using Bayesian decision-making approach to predict driver's lane-changing intents. Last, to show the benefits of our proposed method, comparison experiments are made between the data fusion way and only using eye tracking data or vehicle-based data. The results show that the Bayesian network with data fusion method performs better than using single information to recognize driver's lane-changing intents. At the same time, thresholds of Lane-changing probability and vehicle-based data as restricting condition choosing work is discussed in order to select the best identification parameter. Topic: Active safety and driver assistance systems, Driver modeling
Investigation of Heat Treatment of Gears Using a Simultaneous Dual Frequency Induction Heating Method

This paper presents the development of a simultaneous dual frequency (SDF) induction hardening apparatus for gear hardening. First, a 2-D finite-element (FE) modeling for a thermal-electromagnetic coupled field is introduced for gear hardening and then the analytical results are investigated. By modeling the gear hardening as 2-D FE model, we can calculate for the coupled field more efficiently. In addition, optimum process parameters can also be found through this analysis. A real SDF heat treatment equipment is manufactured using analytical results, like input frequency, and gear hardening experiments are conducted. Through analysis and experiments, we can validate the performance of the developed machine.
Load balancing, cost and response time minimisation issues in agent-based multi cloud service composition

In multi cloud environments, we need to find services from multiple clouds, if a single cloud cannot give us all the required component services. In such a situation, however, it is challenging to find an appropriate composition sequence by taking into consideration load balancing between the different clouds and in the same time by minimising the composite service cost and response time. In this paper, an agent-based cloud service composition architecture is presented. It includes two main agents CSCA and CMA which use MCDA methods to support cloud services selection. These agents use load balancing mechanisms and the CNP in order to evolve and adapt cloud service composition. We have performed a comprehensive analytical and experimental study to evaluate the effectiveness of our approach. The experimental results, based on CloudSim simulator, show that the proposed architecture can effectively achieve good performance (load balancing), improve the response time and minimise cost.
Feature extraction for BCIs based on electromagnetic source localization and Common Spatial Patterns

Brain-Computer Interfaces (BCIs) provide a way to communicate without movement and can offer significant clinical benefits. Electrical brain activity recorded using electroencephalography (EEG) can be automatically interpreted by supervised learning classifiers according to the descriptive features of the signal. This paper investigates the performance of novel feature extraction based on a signal source localization and Common Spatial Patterns (CSP) methods. The proposed approach was evaluated by the reference EEG dataset yielding an average classification accuracy of 74.6 % for a chosen group of subjects. It is shown that CSP feature extraction performs significantly better when applied to source components compared to features from the original sensor domain.
Examining associations between disordered eating and serotonin transporter gene polymorphisms.

OBJECTIVE The serotonin system has been implicated in mood and appetite regulation, and the serotonin transporter gene (SLC6A4) is a commonly studied candidate gene for eating pathology. However, most studies have focused on a single polymorphism (5-HTTLPR) in SLC6A4; little research has utilized multiple single nucleotide polymorphisms (SNPs) to investigate associations between SLC6A4 and eating pathology more comprehensively. METHOD Family-based association tests were conducted for seven polymorphisms in or near SLC6A4, using families from the Colorado Center for Antisocial Drug Dependence. Data were available for 135 families, with phenotypic data available for female twins and female nontwin siblings. Seven items assessed two disordered eating characteristics: weight and shape concerns and behaviors (WSCB) and binge eating (BE). RESULTS No significant associations were found between any genetic variant and the two disordered eating characteristics. DISCUSSION This study suggests that utilizing polymorphisms in and near SLC6A4, including 5-HTTLPR, may not be useful in identifying genetic risk factors for disordered eating.
Inflammation‐associated repression of vasodilator‐stimulated phosphoprotein (VASP) reduces alveolar‐capillary barrier function during acute lung injury

Acute lung injury (ALI) is an inflammatory disorder associated with reduced alveolar‐capillary barrier function, increased pulmonary vascular permeability, and infiltration of leukocytes into the alveolar space. Pulmonary function might be compromised, its most severe form being the acute respiratory distress syndrome. A protein central to physiological barrier properties is vasodilator‐stimulated phosphoprotein (VASP). Given the fact that VASP expression is reduced during periods of cellular hypoxia, we investigated the role of VASP during ALI. Initial studies revealed reduced VASP expressional levels through cyto‐kines in vitro. Studies in the putative human VASP promoter identified NF‐κB as a key regulator of VASP transcription. This VASP repression results in increased paracellular permeability and migration of neutrophils in vitro. In a model of LPS‐induced ALI, VASP −/− mice demonstrated increased pulmonary damage compared with wild‐type animals. These findings were confirmed in a second model of ventilator‐induced lung injury. Studies employing bone marrow chimeric animals identified tissue‐specific repression of VASP as the underlying cause of decreased barrier properties of the alveolar‐capillary barrier during ALI. Taken together these studies identify tissue‐specific VASP as a central protein in the control of the alveolar‐capillary barrier properties during ALI. —Henes, J., Schmit, M. A. , Morote‐Garcia, J. C. , Mirakaj, V. , Kohler, D. , Glover, L. , Eldh, T. , Walter, U. , Karhausen, J., Colgan, S. P., Rosenberger, P. Inflammation‐associated repression of vasodilator‐stimulated phosphoprotein (VASP) reduces alveolar‐capillary barrier function during acute lung injury. FASEB J. 23, 4244‐4255 (2009). www.fasebj. org
A molecular genetic and statistical approach for the diagnosis of dual-site cancers.

BACKGROUND Concurrent tumors can be synchronous, independently derived, non-metastatic tumors or metastatic tumors. The prognosis and clinical management of patients with these different concurrent tumor types are different. METHODS DNA from normal and tumor tissues of 62 patients with synchronous endometrial and ovarian, bilateral ovarian, or endometrial and bilateral ovarian tumors was analyzed for loss of heterozygosity and microsatellite instability using eight polymorphic microsatellite markers at loci frequently deleted in ovarian and/or endometrial cancers. A statistical algorithm was designed to assess the clonal relationship between the tumors. RESULTS The original histopathology reports classified 26 (42%) case patients with single primary tumors and related metastatic lesions and 21 (34%) with independent primary tumors; 15 (24%) were unclassified. Genetic data identified 35 (56%) case patients with single primary tumors and related metastatic lesions, 18 (29%) with independent primary tumors, and nine (15%) that could not be typed. Excluding case patients with histopathology reports for which a clonal relationship was uncertain or was not reported, there was 53% concordance between genetic and histopathology diagnoses. Increasing the stringency of the statistical analysis increased the number of uncertain diagnoses but did not affect the proportion of discordant genetic and histologic diagnoses. CONCLUSIONS We have developed a rapid and robust combined genetic and statistical method to establish whether multiple tumors from the same patient represent distinct primary tumors or whether they are clonally related and therefore metastatic. For the majority of case patients, histopathology reports and genetic analyses were in agreement and diagnostic confidence was improved. Importantly, in approximately one-fourth of all case patients, genetic and histopathologic analyses suggested alternative diagnoses. The results suggest that genetic analysis has implications for clinical management and can be performed rapidly as a diagnostic test with paraffin-embedded tissues.
The Acute-phase Response Is Not Predictive for the Development of Arthritis in Seropositive Arthralgia – A Prospective Cohort Study

Objective. To evaluate whether markers of the acute-phase response in patients presenting with arthralgia and positive anticitrullinated protein antibodies (ACPA) and/or immunoglobulin M rheumatoid factor (IgM-RF) could be predictive for the development of arthritis. Methods. In total, 137 ACPA- and/or IgM-RF-positive patients were included. Patients were followed annually for the development of arthritis, defined as presence of 1 or more swollen joints at clinical examination. High-sensitivity C-reactive protein (hsCRP), procalcitonin (PCT), secretory phospholipase A2 (SPLA2), tumor necrosis factor-α (TNF-α), interleukin 6 (IL-6), IL-12p70, IL-10, and interferon-γ (IFN-γ) were measured in baseline serum samples. Gene expression focusing on a predefined panel of genes coding for inflammatory molecules was measured by multiplex ligation-dependent probe amplification. Results. Thirty-five patients (26%) developed arthritis within a median time of 11 months (interquartile range 3.7–18 mo). Circulating levels of cytokines, SPLA2, hsCRP, and PCT were not different between patients with progression to clinical arthritis and those without progression. However, a trend for IL-12p70, TNF-α, IL-10, IL-6, and SPLA2 was observed. No correlation between messenger RNA (mRNA) expression levels of inflammatory genes and progression to arthritis was found. Subgroup analysis of patients with early progression to arthritis showed higher levels of mRNA expression of poly(A)-specific ribonuclease and polycomb complex protein BMI-1 compared to patients without progression to arthritis. Conclusion. Although low-grade inflammation is present before onset of clinical arthritis in large cohorts and can be detected using consecutive measurements, a single measurement of acute-phase reactants seems to have limited value for prediction of development of arthritis in individual patients.
Towards ubiquitous indoor spatial awareness on a worldwide scale

While a remarkable effort has been put in developing indoor spatial awareness systems, they are still isolated efforts that are tailored to specific deployments. A truly ubiquitous indoor spatial awareness system is envisioned to be deployed on a large scale worldwide, with minimum overhead, and to work with the heterogeneous IoT devices. Such a system will enable a wide set of new applications including worldwide seamless direction finding between indoor locations, anywhere anytime health monitoring, enhanced first responders' safety, and providing richer context for indoor mobile computing applications. In this paper, we describe our vision and work towards achieving ubiquitous indoor spatial awareness systems as well as the open challenges that need to be addressed to materialize this dream.
Oil Consumption, Economic Growth, and Oil Futures∗

I present evidence that increases in the cost of hedging oil price exposure in futures markets from 2005 to 2012 coincided with increases in uncertainty about long-run oil supplies. Motivated by these results, I provide new evidence on the relations between oil consumption, oil prices, and economic growth, and build on this evidence to develop a quantitative real business cycle model to study oil price risk. Calibrated model results can match relations between oil prices and economic quantities, and can rationalize behavior in equity and futures markets as a consequence of changing risk premia driven by increases in long-run oil supply uncertainty.
Removing noises caused by motion artefacts in microcirculation maps of human skin in vivo

This paper presents a zero‐padding and cross‐correlation technique‐based correlation mapping optical coherence tomography (ZPCC‐cmOCT) to reconstruct microcirculation maps of human skin in vivo, which can remove the background decorrelation noise caused by motion artefacts. In conventional correlation mapping optical coherence tomography method, the correlation degree of static tissue may be lowered by the motion artefacts due to cardiac and respiratory motion, resulting in background decorrelation noise in microcirculation maps. In zero‐padding and cross‐correlation technique‐based correlation mapping optical coherence tomography method, structural images are first obtained by performing Fourier transform on zero‐padded interference fringes, and then cross‐correlation‐based image registration is utilized to align local areas in two adjacent structural images. Finally, correlation mapping optical coherence tomography method is performed to generate microcirculation maps. Both phantom experiments and in vivo experiments were implemented and the results demonstrate that the proposed method is capable of providing microcirculation maps with the background decorrelation noise removed.