Miracle-dz/UniFAR-FTUs huggingface dataset:
Blood pressure distribution in microvascular networks

Blood rheology is complex and non­linear. The effective viscosity variations are important due to red blood cells packing inside capillaries, the so­called Fahraeus­Lindquist effect, whilst concomitantly phase segregation appears in bifurcations. We have performed direct numerical simulations of different non­linear rheological models of the blood on realistic three­dimensional micro­vascular networks. These simulations point out two significant results. First, various rheological models lead to very similar pressure distributions over the whole range of physiologically relevant hematocrits. Secondly, different models for phase segregation lead to very distinct hematocrit distributions in the micro­vascular network. Moreover, for all the investigated rheological models, the hematocrit distribution very weakly affects the pressure distribution, when prescribing uniform pressure boundary conditions.
Understanding MicroRNA Regulation: A computational perspective

This paper aims to provide researchers with a computational background, a comprehensive discussion on the importance of miRNA (microRNA), the related high-throughput technology and databases, the current development of computational algorithms for elucidating miRNA regulatory functions, and the prospective directions on related topics. Some topics discussed were about miRNA target recognition, silencing, expression profiling, transfection experiments, target predictions, databases, microarray data, biochemical approaches, rule-based algorithms, data-driven algorithms, prediction algorithms, transcription factors, and other computational techniques.
When and How Using Structural Information to Improve IR-Based Traceability Recovery

Information Retrieval (IR) has been widely accepted as a method for automated traceability recovery based on the textual similarity among the software artifacts. However, a notorious difficulty for IR-based methods is that artifacts may be related even if they are not textually similar. A growing body of work addresses this challenge by combining IR-based methods with structural information from source code. Unfortunately, the accuracy of such methods is highly dependent on the IR methods. If the IR methods perform poorly, the combined approaches may perform even worse. In this paper, we propose to use the feedback provided by the software engineer when classifying candidate links to regulate the effect of using structural information. Specifically, our approach only considers structural information when the traceability links from the IR methods are verified by the software engineer and classified as correct links. An empirical evaluation conducted on three systems suggests that our approach outperforms both a pure IR-based method and a simple approach for combining textual and structural information.
Towards Unsupervised Approaches For Aspects Extraction

One of the most recent opinion mining research directions falls in the extraction of polarities referring to specific entities (called “aspects”) contained in the analyzed texts. The detection of such aspects may be very critical especially when the domain which documents belong to is unknown. Indeed, while in some contexts it is possible to train domain-specific models for improving the effectiveness of aspects extraction algorithms, in others the most suitable solution is to apply unsupervised techniques by making the used algorithm independent from the domain. In this work, we implemented different unsupervised solutions into an aspect-based opinion mining system. Such solutions are based on the use of semantic resources for performing the extraction of aspects from texts. The algorithms have been tested on benchmarks provided by the SemEval campaign and have been compared with the results obtained by domain-adapted techniques.
Pitavastatin Reduces Inflammation in Atherosclerotic Plaques in Apolipoprotein E-Deficient Mice with Late Stage Renal Disease

Objectives Chronic renal disease (CRD) accelerates atherosclerosis and cardiovascular calcification. Statins reduce low-density lipoprotein-cholesterol levels in patients with CRD, however, the benefits of statins on cardiovascular disease in CRD remain unclear. This study has determined the effects of pitavastatin, the newest statin, on arterial inflammation and calcification in atherogenic mice with CRD. Methods and Results CRD was induced by 5/6 nephrectomy in cholesterol-fed apolipoprotein E-deficient mice. Mice were randomized into three groups: control mice, CRD mice, and CRD mice treated with pitavastatin. Ultrasonography showed that pitavastatin treatment significantly attenuated luminal stenosis in brachiocephalic arteries of CRD mice. Near-infrared molecular imaging and correlative Mac3 immunostaining demonstrated a significant reduction in macrophage accumulation in pitavastatin-treated CRD mice. Pitavastatin treatment reduced levels of osteopontin in plasma and atherosclerotic lesions in CRD mice, but did not produce a significant reduction in calcification in atherosclerotic plaques as assesses by histology. CRD mice had significantly higher levels of phosphate in plasma than did control mice, which did not change by pitavastatin. In vitro, pitavastatin suppressed the expression of osteopontin in peritoneal macrophages stimulated with phosphate or calcium/phosphate in concentrations similar to those found in human patients with CRD. Conclusion Our study provides in vivo evidence that pitavastatin reduces inflammation within atherosclerotic lesions in CRD mice.
Leishmania donovani Argininosuccinate Synthase Is an Active Enzyme Associated with Parasite Pathogenesis

Background Gene expression analysis in Leishmania donovani (Ld) identified an orthologue of the urea cycle enzyme, argininosuccinate synthase (LdASS), that was more abundantly expressed in amastigotes than in promastigotes. In order to characterize in detail this newly identified protein in Leishmania, we determined its enzymatic activity, subcellular localization in the parasite and affect on virulence in vivo. Methodology/Principal Findings Two parasite cell lines either over expressing wild type LdASS or a mutant form (G128S) associated with severe cases of citrullinemia in humans were developed. In addition we also produced bacterially expressed recombinant forms of the same proteins. Our results demonstrated that LdASS has argininosuccinate synthase enzymatic activity that is abolished using an ASS specific inhibitor (MDLA: methyl-D-L-Aspartic acid). However, the mutant form of the protein is inactive. We demonstrate that though LdASS has a glycosomal targeting signal that binds the targeting apparatus in vitro, only a small proportion of the total cellular ASS is localized in a vesicle, as indicated by protection from protease digestion of the crude organelle fraction. The majority of LdASS was found to be in the cytosolic fraction that may include large cytosolic complexes as indicated by the punctate distribution in IFA. Surprisingly, comparison to known glycosomal proteins by IFA revealed that LdASS was located in a structure different from the known glycosomal vesicles. Significantly, parasites expressing a mutant form of LdASS associated with a loss of in vitro activity had reduced virulence in vivo in BALB/c mice as demonstrated by a significant reduction in the parasite load in spleen and liver. Conclusion/Significance Our study suggests that LdASS is an active enzyme, with unique localization and essential for parasite survival and growth in the mammalian host. Based on these observations LdASS could be further explored as a potential drug target.
Investigation of Bamboo Mosaic Virus Satellite RNA(satBaMV)-Encoded p20 in the Movement of satBaMV in p20 Transgenic Tobacco

The satellite RNA of Bamboo mosaic virus (BaMV) contains an open reading frame for a 20-kDa nonstructural protein, which facilitates the long distance movement of satBaMV in plants. To determine whether the frame shift mutant of satBaMV (F6) could move systemically or could be complemented or promoted by P20, sucrose-synthase- promoter-driven P20 (SSP20) transgenic Nicotiana benthamiana plants have been developed via Agrobacterium- mediated transformation. Homozygous transgenic plants have been obtained through two generations of selection on MS medium supplemented with 20 mg/L of hygromycin. The integrated transgene in transgenic plants was confirmed by PCR, but not by Southern blot, which maybe due to too low level of integration of transgene in host chromosome. RT-PCR results have shown that the transgene could be successfully expressed at transcriptional level. Positive results have been obtained in tissue printing of stem section of F2 transgenic plants. No signal could be detected from RNA blot of tissue printing and phloem sap. There are more branches in F2 transgenic plants than in WT. Both dot blot and Northern blot showed that BSF4 and its frame shift mutant BSF6 could move systemically in both WT and SSP20 transgenic N. benthamiana line SP3-4 and SP4-4, which indicates that P20 is not essential for the of replication and movement BaMV and satBaMV. P20 is helpful for satBaMV replication and movement because the stronger signal of BSF4 was detected in systemic leaves than that in BSF6 and BSGFP both in WT and transgenic plants by dot blot and Northern blot assay. No much difference between WT and transgenic plants in the expression of BSF4 and BSF6 both in inoculated and systemic leaves. The expression level of BSGFP in transgenic plants was slightly higher than that in WT. RT-PCR and subsequent sequencing data revealed the correct sequence of inoculated BSF4, BSF6, and BSGFP, respectively.
Exploring the “In-Between” Place: Dialogue, Hermeneutics, and Transformation in Governance

The vocabulary of governance has yet to come to terms with hermeneutic processes. This article explores the emergence and transformation in governance of Ohio’s Cuyahoga River using an interpretive approach based on philosophical hermeneutics. Drawing on Gadamer’s hermeneutic concepts of tradition, authority, and prejudice, this research reveals how hermeneutic space is created in dialogue, deliberations, and collaborative work. This more fluid understanding for the governance process has key ramifications for public administration research and practice in terms of an ontological understanding of governance, rethinking of the practice of administrative skills, and shifting the manner in which authority is understood and exercised.
Planning With Information States: A Survey Term Project for cs397sml — Spring 2002

Classical planning generally depends on the assumption that the outcome of each action is known. That is, even though there may be some a priori uncertainty about which state will result from a given action, classical planning methods assume that there is no a postieriori uncertainty – that after an action is taken, the resulting state is immediately known with certainty. In practice this assumption can be problematic. At best, sensors that report the current state will be subject to some noise; at worst, no state information at all will be available. This paper surveys work on this imperfect state information problem. In Section 2, we formalize the problem. Section 3 summarizes a number of papers that address specific instances of the problem. Finally, Section 4 is a discussion of several questions that have yet to be satisfactorily answered.
PRSice: Polygenic Risk Score software

Summary: A polygenic risk score (PRS) is a sum of trait-associated alleles across many genetic loci, typically weighted by effect sizes estimated from a genome-wide association study. The application of PRS has grown in recent years as their utility for detecting shared genetic aetiology among traits has become appreciated; PRS can also be used to establish the presence of a genetic signal in underpowered studies, to infer the genetic architecture of a trait, for screening in clinical trials, and can act as a biomarker for a phenotype. Here we present the first dedicated PRS software, PRSice (‘precise'), for calculating, applying, evaluating and plotting the results of PRS. PRSice can calculate PRS at a large number of thresholds (“high resolution”) to provide the best-fit PRS, as well as provide results calculated at broad P-value thresholds, can thin Single Nucleotide Polymorphisms (SNPs) according to linkage disequilibrium and P-value or use all SNPs, handles genotyped and imputed data, can calculate and incorporate ancestry-informative variables, and can apply PRS across multiple traits in a single run. We exemplify the use of PRSice via application to data on schizophrenia, major depressive disorder and smoking, illustrate the importance of identifying the best-fit PRS and estimate a P-value significance threshold for high-resolution PRS studies. Availability and implementation: PRSice is written in R, including wrappers for bash data management scripts and PLINK-1.9 to minimize computational time. PRSice runs as a command-line program with a variety of user-options, and is freely available for download from http://PRSice.info Contact: jack.euesden@kcl.ac. uk or paul.oreilly@kcl.ac. uk Supplementary information: Supplementary data are available at Bioinformatics online.
Substrate application of magnetic metamaterial

The main relations for designing a metamaterial rectangular patch antenna with a magnetically enhanced substrate are obtained. It is supposed that the substrate is to be fabricated of metamaterial with a large value in the real part of the effective permeability instead of a conventional homogenous high dielectric or magnetic material. It results in antenna miniaturization. The specific type of metamaterial that can be used as a substrate is suggested.
Land mobile GNSS availability and multipath evaluation tool

Applications of global navigation satellite system (GNSS) in land transportation systems are already extensively deployed and will certainly continue to grow especially in the framework of intelligent transport systems. However, one of the best-known drawbacks of such a system is the lack of satellite visibility in dense urban areas as well as in some specific embedded railway environments. This restricts considerably GNSS use for extended safety related applications. In this paper, a new tool is proposed to predict the availability of a satellite constellation from the point of view of the land transportation user. Knowing the trajectory of a land vehicle, the tool predicts the number of satellites that will be received and produces a safety criterion able to qualify the GNSS localization result. A first version of the tool, already in operation, merges an image processing approach providing the knowledge of the land environment, and the output of a satellite tracking program predicting satellite positions in the sky. This allows us to determine, using a simple optical approach, the number of satellites received in line-of-sight or blocked, with regard to the nearby environment of the receiving antenna. Results obtained in railway as well as in road environments show that satellite signals received by multipath are often used by GNSS receivers in the localization process. Thus, propagation characteristics of the satellite signals in an urban canyon configuration were characterized to determine when a signal received by reflected ray is used by the receiver or not. A criterion related to the satellite elevation is defined to improve the overall performance of the predictive tool. Comparisons with real measurements are commented on. Both simulations and measurements are very similar.
Network design for mesoscale inversions of CO2 sources and sinks

ABSTRACT Recent instrumental deployments of regional observation networks of atmospheric CO2 mixing ratios have been used to constrain carbon sources and sinks using inversion methodologies. In this study, we performed sensitivity experiments using observation sites from the Mid Continent Intensive experiment to evaluate the required spatial density and locations of CO2 concentration towers based on flux corrections and error reduction analysis. In addition, we investigated the impact of prior flux error structures with different correlation lengths and biome information. We show here that, while the regional carbon balance converged to similar annual estimates using only two concentration towers over the region, additional sites were necessary to retrieve the spatial flux distribution of our reference case (using the entire network of eight towers). Local flux corrections required the presence of observation sites in their vicinity, suggesting that each tower was only able to retrieve major corrections within a hundred of kilometres around, despite the introduction of spatial correlation lengths (~100 to 300 km) in the prior flux errors. We then quantified and evaluated the impact of the spatial correlations in the prior flux errors by estimating the improvement in the CO2 model-data mismatch of the towers not included in the inversion. The overall gain across the domain increased with the correlation length, up to 300 km, including both biome-related and non-biome-related structures. However, the spatial variability at smaller scales was not improved. We conclude that the placement of observation towers around major sources and sinks is critical for regional-scale inversions in order to obtain reliable flux distributions in space. Sparser networks seem sufficient to assess the overall regional carbon budget with the support of flux error correlations, indicating that regional signals can be recovered using hourly mixing ratios. However, the smaller spatial structures in the posterior fluxes are highly constrained by assumed prior flux error correlation lengths, with no significant improvement at only a few hundreds of kilometres away from the observation sites.
Where Do Open Source Requirements Come From ( And What Should We Do About It ) ?

The collection and specification of software requirements is one of the most intense areas of software engineering research. This makes it a natural area to explore when considering open-source software. In this paper, I argue that the sources of open-source software requirements differ in some important respects from the sources of commercial software project requirements. This has some interesting implications for both open-source and commercial development. The collection and specification of software requirements is one of the most intense areas of software engineering research. This makes it a natural area to explore when considering open-source software. In this paper, I argue that the sources of open-source software requirements differ in some important respects from the sources of commercial software project requirements. This has some interesting implications for both open-source and commercial development.
Maturity Model for IT Service Catalogues An Approach to Assess the Quality of IT Service Documentation

Information technology (IT) has to face many challenges regarding the increasing business requirements for flexibility, complexity, and availability of IT. Thus, a restructuring of the IT portfolio into IT services is necessary to provide an effective and business-driven IT support. The design of IT service catalogues is generally difficult in the managerial context of an enterprise. The current situation of the IT service structure can hardly be analyzed because no approaches exist that support such an analysis. In this paper we intend to develop a maturity model to assess the current situation of the quality of IT service catalogues. We describe the model structure, its components, and present empirical key findings of its practical application in a benchmarking study.
Radiation-induced chromosome aberrations: insights gained from biophysical modeling.

Enzymatic misrepair of ionizing-radiation-induced DNA damage can produce large-scale rearrangements of the genome, such as translocations and dicentrics. These and other chromosome exchange aberrations can cause major phenotypic alterations, including cell death, mutation and neoplasia. Exchange formation requires that two (or more) genomic loci come together spatially. Consequently, the surprisingly rich aberration spectra uncovered by recently developed techniques, when combined with biophysically based computer modeling, help characterize large-scale chromatin architecture in the interphase nucleus. Most results are consistent with a picture whereby chromosomes are mainly confined to territories, chromatin motion is limited, and interchromosomal interactions involve mainly territory surfaces. Aberration spectra and modeling also help characterize DNA repair/misrepair mechanisms. Quantitative results for mammalian cells are best described by a breakage-and-reunion model, suggesting that the dominant recombinational mechanism during the G(0)/G(1) phase of the cell cycle is non-homologous end-joining of radiogenic DNA double strand breaks. In turn, better mechanistic and quantitative understanding of aberration formation gives new insights into health-related applications.
Modeling the Spread of Smoking in Adolescent Social Networks

Objectives: Using a systems-level approach, develop a large-scale, individual-based, simulation framework for analyzing the spread and control of smoking behavior in adolescent populations. Methods: We create a synthetic information environment that combines Add Health data with synthetic population data to create a model of smoking behavior diffusion in middle and high schools. This also involves generating synthetic friendship networks based on real friendship networks from the Add Health data. Simulations are done for a three-year period, using an efficient parallel simulation engine. Results: We derive diffusion curves by smoking rate, age, gender, and parents’ smoking status, separately for the middle and high schoolers. We also compare them with similar diffusion curves obtained from the real friendship networks from Add Health. Conclusions: This research builds a synthetic laboratory for social epidemiologists where a rich representation of individual characteristics and contextual factors can be taken into account to understand the global dynamics of a variety of individual behaviors pertaining to smoking.
Membrane Incorporation, Channel Formation, and Disruption of Calcium Homeostasis by Alzheimer's β-Amyloid Protein

Oligomerization, conformational changes, and the consequent neurodegeneration of Alzheimer's β-amyloid protein (AβP) play crucial roles in the pathogenesis of Alzheimer's disease (AD). Mounting evidence suggests that oligomeric AβPs cause the disruption of calcium homeostasis, eventually leading to neuronal death. We have demonstrated that oligomeric AβPs directly incorporate into neuronal membranes, form cation-sensitive ion channels (“amyloid channels”), and cause the disruption of calcium homeostasis via the amyloid channels. Other disease-related amyloidogenic proteins, such as prion protein in prion diseases or α-synuclein in dementia with Lewy bodies, exhibit similarities in the incorporation into membranes and the formation of calcium-permeable channels. Here, based on our experimental results and those of numerous other studies, we review the current understanding of the direct binding of AβP into membrane surfaces and the formation of calcium-permeable channels. The implication of composition of membrane lipids and the possible development of new drugs by influencing membrane properties and attenuating amyloid channels for the treatment and prevention of AD is also discussed.