Miracle-dz/UniFAR-FTUs huggingface dataset:
Computing Hopf Bifurcations. II: Three Examples From Neurophysiology

In [Guckenheimer, Myers, and Sturmfels, SIAM J. Numer. Anal. , 34 (1997)] we present algorithms for detecting Hopf bifurcations in two-parameter families of vector fields based on classical algebraic constructions. In addition to their utility as augmented systems for use with standard Newton-type continuation methods, they are shown to be particularly well adapted for solution by computer algebra techniques for vector fields of small or moderate dimension. The present study examines the performance of these methods on test problems selected from models of current research interest in neurophysiology. Implementation issues are examined and the numerical properties of the proposed methods are compared with several alternative algorithms for Hopf pathfollowing that appear in the literature.
Wage Dispersion and Wage Dynamics within and Across Firms

This paper examines wage dispersion and wage dynamics in a stock-flow matching economy with on-the-job search. Under stock-flow matching, job seekers immediately become fully informed about the stock of viable vacancies. If only one option is available, monopsony wages result. With more than one firm bidding, Bertrand wages arise. The initial and expected threat of competition determines the evolution of wages and thereby introduces a novel way of understanding wage differences among similar workers. The resulting wage distribution has an interior mode and prominent, well-behaved tails. The model also generates job-to-job transitions with both wage cuts and jumps.
Differences in genetic alterations between primary lobular and ductal breast cancers detected by comparative genomic hybridization

Infiltrating ductal (DC) and lobular carcinoma (LC) of the breast represent the most frequently observed varieties of invasive breast cancer, characterized by differences in their histological and clinical properties. Although comparative genomic hybridization (CGH) of invasive breast carcinomas has revealed a complex and consistent pattern of DNA copy number changes, the data with regard to type specific aberrations are limited. A comprehensive study was therefore performed on 19 LCs and 29 DCs to ascertain type‐specific differences of unbalanced DNA copy number changes by CGH. Statistical analysis revealed significantly higher frequencies for underrepresentation of chromosomes 16q (p<0.01), 22 (p<0.05), and 17q (p<0.05), and a lower frequency for overrepresentation of chromosome 8q (p<0.01) in LC. Similar frequencies of non‐random chromosomal changes in LC and DC were obtained for gain of 1q (74%/59%) and loss of 19p (53%/52%), parts of 1p (42%/41%) and 11q (21%/24%). Less frequently, gains mainly involving parts of chromosomes 20q, 20p, 3q, and 5p and partial losses of chromosomes 17p and 13 were observed in both groups of tumours. Minimal regions of overlapping amplifications were mapped to 17q23 exclusively in DC (17%) and 11q13–q14 in both DC and LC (21% and 11%, respectively). High occurrences of DNA copy number decreases were detected at the distal part of chromosomes 1p, 19 and 22, but further analysis is required to confirm these imbalances. It is suggested that the observed differences are involved in the development of type‐specific properties of DC and LC. Copyright © 2000 John Wiley & Sons, Ltd.
Evaluation of the Broth Microdilution Method Using 2,3-Diphenyl-5-thienyl-(2)-tetrazolium Chloride for Rapidly Growing Mycobacteria Susceptibility Testing

As the incidence of nontuberculous mycobacterial infection has been increasing recently in Korea, the importance of drug susceptibility test for clinical isolates of mycobacteria has become larger. In this study we determined the antimicrobial susceptibility patterns of clinical isolates of M. fortuitum and M. abscessus in Korea, and evaluated the efficacy of a modified broth microdilution method using 2,3-diphenyl-5-thienyl-(2)-tetrazolium chloride (STC), in terms of its ability to provide accurate and easy-to-read minimal inhibitory concentration (MIC) endpoints for the susceptibility testing of rapidly growing mycobacteria. Most isolates of M. fortuitum and M. abscessus in Korea are susceptible or intermediately susceptible to amikacin, cefoxitin, ciprofloxacin, and clarithromycin. Many isolates of M. fortuitum are susceptible to doxycycline, sulfamethoxazole, and imipenem, while many M. abscessus isolates are resistant to these drugs. In the present study, the modified broth microdilution method using STC was found to be reliable, easy to read, and inexpensive for M. fortuitum and M. abscessus susceptibility testing. The modified colorimetric MIC testing method using STC was proven to be a useful surrogate for RGM antibiotic susceptibility testing.
The salicylate 1,2‐dioxygenase as a model for a conventional gentisate 1,2‐dioxygenase: crystal structures of the G106A mutant and its adducts with gentisate and salicylate

The salicylate 1,2‐dioxygenase (SDO) from the bacterium Pseudaminobacter salicylatoxidans BN12 is a versatile gentisate 1,2‐dioxygenase (GDO) that converts both gentisate (2,5‐dihydroxybenzoate) and various monohydroxylated substrates. Several variants of this enzyme were rationally designed based on the previously determined enzyme structure and sequence differences between the SDO and the ‘conventional’ GDO from Corynebacterium glutamicum. This was undertaken in order to define the structural elements that give the SDO its unique ability to dioxygenolytically cleave (substituted) salicylates. SDO variants M103L, G106A, G111A, R113G, S147R and F159Y were constructed and it was found that G106A oxidized only gentisate; 1‐hydroxy‐2‐naphthoate and salicylate were not converted. This indicated that this enzyme variant behaves like previously known ‘conventional’ GDOs. Crystals of the G106A SDO variant and its complexes with salicylate and gentisate were obtained under anaerobic conditions, and the structures were solved and analyzed. The amino acid residue Gly106 is located inside the SDO active site cavity but does not directly interact with the substrates. Crystal structures of G106A SDO complexes with gentisate and salicylate showed a different binding mode for salicylate when compared with the wild‐type enzyme. Thus, salicylate coordinated in the G106A variant with the catalytically active Fe(II) ion in an unusual and unproductive manner because of the inability of salicylate to displace a hydrogen bond that was formed between Trp104 and Asp174 in the G106A variant. It is proposed that this type of unproductive substrate binding might generally limit the substrate spectrum of ‘conventional’ GDOs.
Stability in the Cuntz semigroup of a commutative C*‐algebra

Let A be a C*‐algebra. The Cuntz semigroup W(A) is an analogue for positive elements of the semigroup V(A) of Murray‐von Neumann equivalence classes of projections in matrices over A. We prove stability theorems for the Cuntz semigroup of a commutative C*‐algebra which are analogues of classical stability theorems for topological vector bundles over compact Hausdorff spaces.
Effectiveness of Shrinkage-Reducing Admixtures on Different Concrete Mixtures

The shrinkage of concrete originates stresses on restrained structural elements which can cause cracks. In some cases, for instance to reduce the number of structural joints, it is important to decrease drying shrinkage by the use of a shrinkage reduction admixture (SRA). The effectiveness of a SRA depends on porosity and stiffness of concrete. In order to evaluate the performance of two SRA products, shrinkage tests have been done on concretes with and without SRA. Two different concrete mixtures were evaluated: (1) a low strength concrete mixture (for housing purposes and (2) a medium strength concrete mixture (used in bridges). Results show the effectiveness of the SRA on the two reference concrete mixtures, with different W/C and different cement contents.
Folksonomy-Based Tag Recommendation for Collaborative Tagging Systems

Collaborative tagging has emerged as a common solution for labelling and organising online digital content. However, collaborative tagging systems typically suffer from a number of issues such as tag scarcity or ambiguous labelling. As a result, the organisation and browsing of tagged content is far from being optimal. In this work the authors present a general scheme for building a folksonomy-based tag recommendation system to help users tagging online content resources. Based on this general scheme, the authorse describe eight tag recommendation methods and extensively evaluate them with data coming from two real-world large-scale datasets of tagged images and sound clips. Their results show that the proposed methods can effectively recommend relevant tags, given a set of input tags and tag co-occurrence information. Moreover, the authors show how novel strategies for selecting the appropriate number of tags to be recommended can significantly improve methods performances. Approaches such as the one presented here can be useful to obtain more comprehensive and coherent descriptions of tagged resources, thus allowing a better organisation, browsing and reuse of online content. Moreover, they can increase the value of folksonomies as reliable sources for knowledge-mining.
Tool Support for Reuse-Driven Elicitation and Specification of User Requirements

Reuse is a promising approach meet the constantly increasing demand for prompt solutions and high-quality implementations. Systematic reuse has to start in requirements elicitation and specification. This paper presents an approach emphasizing the direct involvement of end users and domain experts. It is based on tool support promoting requirements reuse as a way for users to easily match their needs with the specifications of existing solutions. The approach has been implemented as an extension to a Web-based requirements management tool. It received positive feedback from professional requirements engineers and users, indicating following benefits: (1) Reduced time and effort for requirements engineering, (2) improved quality of specifications, and (3) better mapping to approved solutions.
Stereoselective urinary excretion of formoterol and its glucuronide conjugate in human.

AIMS Formoterol is an inhaled beta2-adrenoceptor agonist used as a racemic mixture of the active (R; R)- and inactive (S; S)-enantiomers (rac-formoterol). Glucuronidation is an important route of metabolism in humans which occurs faster for (S; S)-formoterol in human liver microsomes. The aim of this study was to investigate the stereoselectivity of urinary excretion of formoterol and its glucuronide conjugate after oral dosing with rac-formoterol. METHODS Seven nonsmoking volunteers (six males, one female) were included in the study. After an overnight fast, a single 60 micro g oral dose of rac-formoterol fumarate dihydrate was ingested. Urine samples were collected at 1 h intervals for the first 4 h, and at 6, 8, 12 and 24 h after dosing. Formoterol enantiomers were analysed by chiral h.p.l.c. assay and formoterol glucuronides were determined as formoterol enantiomers after enzymatic cleavage with beta-glucuronidase. RESULTS The female subject displayed a different pattern of metabolism and statistical analysis was therefore limited to data for the six males. The median (range) of the total urinary excretion of formoterol was 37.8% (20.9-51.2%) of the dose. The medians (ranges) of the amounts of (R; R)- and (S; S)-formoterol and of (R; R)- and (S; S)-formoterol glucuronide excreted were 2.1 (1.0-2.9), 3.5 (2.6-3.8), 21.0 (13.1-31.0) and 10.3 (4.2-14.6)%, respectively, of the dose. Unchanged (S; S)-formoterol excretion was significantly greater than that of unchanged (R; R)-formoterol and (R; R)-formoterol glucuronide excretion was significantly greater than that of (S; S)-formoterol glucuronide. The total RR-formoterol (unchanged drug plus glucuronide) excreted was significantly greater than the total (S; S)-formoterol. CONCLUSIONS Our study demonstrates that the urinary excretion of formoterol in male humans after oral administration of rac-formoterol is stereoselective with preferential excretion of the active (R; R)-formoterol as unchanged drug and glucuronide. The different pattern of metabolism in the female subject provides impetus for further studies of the effect of gender on the stereoselective metabolism and pharmacokinetics of formoterol.
Diet-induced Obesity Up-regulates the Abundance of GPR43 and GPR120 in a Tissue Specific Manner

Background/Aims: GPR43 and GPR120 have recently been deorphanised as receptors for fatty acids. Fatty acids mediate a variety of metabolic processes in the body, however, the effect these receptors have on metabolism is not fully understood. Here, we characterise the effect of diet-induced obesity on the expression of GPR43 and GPR120 in tissues important in maintaining metabolic health. Methods: Six-week old male Sprague Dawley rats were fed either a high fat diet (HFD; 22% fat) or control diet (5% fat; n = 8-9/group) for 12 weeks. Rats were euthanized and the heart, liver, soleus and extensor digitorum longus (EDL) skeletal muscles were excised. GPR43 and GPR120 receptor abundance was quantified by ‘real-time’ PCR. Results: GPR43 mRNA abundance was significantly up-regulated by a HFD in liver and soleus and EDL skeletal muscles compared to control (p ≤ 0.05). Whilst a HFD significantly up-regulated GPR120 gene transcripts in cardiac tissue and EDL skeletal muscle when compare to control (p ≤ 0.05). Conclusion: We have shown for the first time that up-regulation of GPR43 and GPR120 in response to a HFD, is tissue specific. This suggests these receptors have different roles in mediating metabolic function in a number of tissues in the human body.
Norepinephrine Inhibits Macrophage Migration by Decreasing CCR2 Expression

Increased incidences of infectious and septic complications during post-burn courses represent the main contributor to burn injury mortality. Sustained increases in catecholamine levels, especially norepinephrine (NE), contribute to immune disturbances in severely burned patients. The precise mechanisms underlying NE-mediated immunoregulation are not fully understood. Here we hypothesize that persistently elevated NE levels are associated with immunodysfunctions. We examined the effects of NE on the phenotype and functions of bone marrow-derived macrophages (BMMs). Whole mouse bone marrow cells were treated in vitro with 40 ng/mL of M-CSF and with 1 x 10-6 M or 1 x 10-8 M of NE or without NE for 7 days; cells were collected and stained with antibodies for CD11b, F4/80, MHC II and the inflammatory CC chemokine receptor 2 (CCR2). We found 1 x 10-6 M of NE inhibited MHC II and CCR2 expression on CD11b+/F4/80+ BMM cells. It also inhibited BMM proliferation by inhibiting CSF-1R expression. On the contrary, 1 x 10-8 M of NE slightly increased both MHC II and CCR2 expression on CD11b+/F4/80+ BMM cells but inhibited CD11b+/F4/80+ BMM proliferation. MCP-1 based migration assay showed that the migration of 1 x 10-6 M of NE-treated BMM toward MCP-1 was significantly decreased compared to BMM without NE treatment. Both 1 x 10-8 M and 1 x 10-6 M of NE enhanced TNF-α production and phagocytosis of FITC-Dextran. Intracellular staining of transcriptional factor MafB showed that 1 x 10-6 M of NE treatment enhanced its expression, whereas 1 x 10-8 M of NE decreased expression. Stimulation with LPS in the last 24-hours of BMM culture further decreased CCR2 and MHC II expression of these BMM, suggesting the synergistic effect of LPS and NE on macrophage. Our results demonstrate that NE regulates macrophage differentiation, proliferation and function, and may play a critical role in the dysfunctional immune response post-burn.
Automated detection and delineation of mitochondria in electron micrographs of human skeletal muscles

Morphometric measurements of mitochondria in human skeletal muscles provide useful information relating to tissue oxidative energy production, nutrition, exercise, and aging. Morphometric data such as area, perimeter, long axis, and short axis can be obtained by delineating individual mitochondria in electron micrographs. However, manual counting and delineating of individual mitochondria is a formidable task. The purpose of this study was to develop a fully automated computer algorithm for quantifying mitochondrial morphometry in electron micrographs. The algorithm locates mitochondria with a two‐dimensional matched filter and then traces the borders of individual mitochondria. The delineation is accomplished by edge detection along radial lines launched outwards from the center of each mitochondrion. Shape descriptors applied to delineated mitochondria are used to reject likely false‐positive selections. The results show that the fully automated algorithm detects mitochondria with a false‐positive rate of 2% and a false‐negative rate of 36%. The errors are easily and rapidly corrected by user intervention using a second semiautomated delineation algorithm. Morphometric measurements collected with the automated algorithm are equivalent to those obtained manually by human experts. The algorithm significantly improves the speed of image analysis and it also provides copious quantities of high‐quality mitochondrial morphometric data. Microsc. Res. Tech. 63:133–139, 2004. © 2004 Wiley‐Liss, Inc.
Tetraspanin CD9 determines invasiveness and tumorigenicity of human breast cancer cells

Interaction of breast cancer cells (BCCs) with stromal components is critical for tumor growth and metastasis. Here, we assessed the role of CD9 in adhesion, migration and invasiveness of BCCs. We used co-cultures of BCCs and bone marrow-derived multipotent mesenchymal stromal cells (MSCs), and analyzed their behavior and morphology by dynamic total internal reflection fluorescence, confocal and scanning electron microscopy. 83, 16 and 10% of contacts between MDA-MB-231 (MDA), MA-11 or MCF-7 cells and MSCs, respectively, resulted in MSC invasion. MDA cells developed long magnupodia, lamellipodia and dorsal microvilli, whereas long microvilli emerged from MA-11 cells. MCF-7 cells displayed large dorsal ruffles. CD9 knockdown and antibody blockage in MDA cells inhibited MSC invasion by 95 and 70%, respectively, suggesting that CD9 is required for this process. Remarkably, CD9-deficient MDA cells displayed significant alteration of their plasma membrane, harboring numerous peripheral and dorsal membrane ruffles instead of intact magnupodium/lamellipodium and microvillus, respectively. Such modification might explain the delayed adhesion, and hence MSC invasion. In agreement with this hypothesis, CD9-knockdown suppressed the metastatic capacity of MDA cells in mouse xenografts. Our data indicate that CD9 is implicated in BCC invasiveness and metastases by cellular mechanisms that involve specific CD9+ plasma membrane protrusions of BCCs.
Toward a Framework for Detecting Privacy Policy Violations in Android Application Code

Mobile applications frequently access sensitive personal informa- tion to meet user or business requirements. Because such informa- tion is sensitive in general, regulators increasingly require mobile- app developers to publish privacy policies that describe what infor- mation is collected. Furthermore, regulators have fined companies when these policies are inconsistent with the actual data practices of mobile apps. To help mobile-app developers check their pri- vacy policies against their apps’ code for consistency, we propose a semi-automated framework that consists of a policy terminology- API method map that links policy phrases to API methods that pro- duce sensitive information, and information flow analysis to detect misalignments. We present an implementation of our framework based on a privacy-policy-phrase ontology and a collection of map- pings from API methods to policy phrases. Our empirical eval- uation on 477 top Android apps discovered 341 potential privacy policy violations.
Detecting semantic merge conflicts with variability-aware execution

In collaborative software development, changes made in parallel by multiple developers may conflict. Previous research has shown that conflicts are common and occur as textual conflicts or semantic conflicts, which manifest as build or test failures. With many parallel changes, it is desirable to identify conflicts early and pinpoint the (minimum) set of changes involved. However, the costs of identifying semantic conflicts can be high because tests need to be executed on many merge scenarios. We propose Semex, a novel approach to detect semantic conflicts using variability-aware execution. We encode all parallel changes into a single program, in which "if" statements guard the alternative code fragments. Then, we run the test cases using variability-aware execution, exploring all possible concrete executions of the combined program with regard to all possible merge scenarios, while exploiting similarities among the executions to speed up the process. Variability-aware execution returns a formula describing all failing merge scenarios. In our preliminary experimental study on seven PHP programs with a total of 50 test cases and 19 semantic conflicts, Semex correctly detected all 19 conflicts.
Laser induced synthesis of nanoparticles in liquids

The review of results on nanoparticles formation is presented under laser ablation of Ag, Au, and Cu-containing solid targets in liquid environments (H2O, C2H5OH, C2H4Cl2, etc.). X-ray diffractometry (XRD), UV-Vis optical transmission spectrometry, and High Resolution Transmission Electron Microscopy (HRTEM) characterize the nanoparticles. The morphology of nanoparticles is studied as the function of both laser fluence and nature of the liquid. The possibility to control the shape of nanoparticles by ablation of an Au target by an interference pattern of two laser beams is demonstrated. Formation of alloyed Au-Ag and Ag-Cu nanoparticles is reported under laser exposure of a mixture of individual nanoparticles. Self-influence of the beam of a femtosecond laser is discussed under ablation of the Ag target in liquids under Ti:sapphire laser. The factors are discussed that determine the distribution function of particles size under laser ablation. The influence of laser parameters as well as the nature on the liquid on the properties of nanoparticles is elucidated.
Connecting mobile things to global sensor network middleware using system-generated wrappers

Internet of Things (IoT) will create a cyberphysical world where all the things around us are connected to the Internet, sense and produce "big data" that has to be stored, processed and communicated with minimum human intervention. With the ever increasing emergence of new sensors, interfaces and mobile devices, the grand challenge is to keep up with this race in developing software drivers and wrappers for IoT things. In this paper, we examine the approaches that automate the process of developing middleware drivers/wrappers for the IoT things. We propose ASCM4GSN architecture to address this challenge efficiently and effectively. We demonstrate the proposed approach using Global Sensor Network (GSN) middleware which exemplifies a cluster of data streaming engines. The ASCM4GSN architecture significantly speeds up the wrapper development and sensor configuration process as demonstrated for Android mobile phone based sensors as well as for Sun SPOT sensors.