Miracle-dz/UniFAR-FTUs huggingface dataset:
DeMIMA: A Multilayered Approach for Design Pattern Identification

Design patterns are important in object-oriented programming because they offer design motifs, elegant solutions to recurrent design problems, which improve the quality of software systems. Design motifs facilitate system maintenance by helping to understand design and implementation. However, after implementation, design motifs are spread throughout the source code and are thus not directly available to maintainers. We present DeMIMA, an approach to identify semi-automatically micro-architectures that are similar to design motifs in source code and to ensure the traceability of these micro-architectures between implementation and design. DeMIMA consists of three layers: two layers to recover an abstract model of the source code, including binary class relationships, and a third layer to identify design patterns in the abstract model. We apply DeMIMA to five open-source systems and, on average, we observe 34% precision for the considered 12 design motifs. Through the use of explanation-based constraint programming, DeMIMA ensures 100% recall on the five systems. We also apply DeMIMA on 33 industrial components.
B. Atrophaeus and G. Stearothermophilus Biological Indicators for Chlorine Dioxide Gas Decontamination

In anticipation of a validation program for the use of chlorine dioxide (CD) gas in the decontamination of laminar flow biological safety cabinets, the use of Bacillus atrophaeus (BA) and Geobacillus stearothermophilus (GS) endospores for biological indicators (BIs) of CD gas decontaminations were studied. This work includes studies of BIs having either paper or steel substrates. BI analyses were performed with both enumeration and fractionation methods. Among the conclusions it was found that in using paper GS BIs, results from enumeration analysis proved to be too variable to monitor CD decontaminations. Targeted CD exposure levels provided significantly less than a 6-log spore reduction of GS spores on steel substrates, but were very effective for GS BIs with paper substrates. BA spores on paper proved to be suitable and repeatable for validation work with either enumeration or fractionation analysis. Formaldehyde decontamination conditions used in standard practices were largely ineffective to decontaminate the GS indicators.
Understanding Supporting Ontology Evolution by Observing the WWW Conference

Ontologies which represent domain knowledge in information systems are efficient to enhance information retrieval. However, domain knowledge is evolving over time and thus it should be also expressible at ontology level. Unfortunately, we consider that ontology evolution is barely study and its basic principles have not been yet precisely defined according to our notion of evolution. In this paper, we have followed a bottom-up approach consisting in a rigorous analysis of the evolution of a particular domain over a significant period of time (namely the WWW series of conference over a decade) to highlight concrete domain knowledge evolutions. We then have generalized and we present a precise set of evolution features that should be offered by ontology metamodels. We also evaluate the modelling capabilities of OWL to represent these features and finally, we show the contribution of ontology evolution support to improve Web information retrieval.
Whole Body Mechanics of Stealthy Walking in Cats

The metabolic cost associated with locomotion represents a significant part of an animal's metabolic energy budget. Therefore understanding the ways in which animals manage the energy required for locomotion by controlling muscular effort is critical to understanding limb design and the evolution of locomotor behavior. The assumption that energetic economy is the most important target of natural selection underlies many analyses of steady animal locomotion, leading to the prediction that animals will choose gaits and postures that maximize energetic efficiency. Many quadrupedal animals, particularly those that specialize in long distance steady locomotion, do in fact reduce the muscular contribution required for walking by adopting pendulum-like center of mass movements that facilitate exchange between kinetic energy (KE) and potential energy (PE) [1]–[4]. However, animals that are not specialized for long distance steady locomotion may face a more complex set of requirements, some of which may conflict with the efficient exchange of mechanical energy. For example, the “stealthy” walking style of cats may demand slow movements performed with the center of mass close to the ground. Force plate and video data show that domestic cats (Felis catus, Linnaeus, 1758) have lower mechanical energy recovery than mammals specialized for distance. A strong negative correlation was found between mechanical energy recovery and diagonality in the footfalls and there was also a negative correlation between limb compression and diagonality of footfalls such that more crouched postures tended to have greater diagonality. These data show a previously unrecognized mechanical relationship in which crouched postures are associated with changes in footfall pattern which are in turn related to reduced mechanical energy recovery. Low energy recovery was not associated with decreased vertical oscillations of the center of mass as theoretically predicted, but rather with posture and footfall pattern on the phase relationship between potential and kinetic energy. An important implication of these results is the possibility of a tradeoff between stealthy walking and economy of locomotion. This potential tradeoff highlights the complex and conflicting pressures that may govern the locomotor choices that animals make.
Inhibition of Angiogenesis and Invasion by 3 , 3 ¶-Diindolylmethane Is Mediated by the NFK B Downstream Target Genes MMP-9 and uPA that Regulated Bioavailability of VEGF in Prostate Cancer

Progression of prostate cancer is believed to be dependent on angiogenesis induced by tumor cells. 3,3¶-Diindolylmethane (DIM) has been shown to repress neovascularization in a Matrigel plug assay and inhibit cell proliferation, migration, invasion, and capillary tube formation of cultured human umbilical vein endothelial cells. However, the molecular mechanism, by which DIM inhibits angiogenesis and invasion, has not been fully elucidated. Therefore, we sought to explore the molecular mechanism by which DIM inhibits angiogenesis and invasion, specifically by investigating the role of angiogenic factors secreted by prostate cancer cells which control all steps of angiogenesis. We found that BioResponse DIM (B-DIM), a formulated DIM with higher bioavailability, inhibited angiogenesis and invasion by reducing the bioavailability of vascular endothelial growth factor (VEGF) via repressing extracellular matrix–degrading proteases, such as matrix metalloproteinase (MMP)-9 and urokinase-type plasminogen activator (uPA), in human prostate cancer cells and reduced vascularity (angiogenesis) in vivo using Matrigel plug assay. We also found that B-DIM treatment inhibited DNA binding activity of nuclear factor-KB (NF-KB), which is known to mediate the expression of many NF-KB downstream target genes, including VEGF, IL-8, uPA, and MMP-9, all of which are involved in angiogenesis, invasion, and metastasis. Our data suggest that inhibition of NF-KB DNA binding activity by B-DIM contributes to the regulated bioavailability of VEGF by MMP-9 and uPA and, in turn, inhibits invasion and angiogenesis, which could be mechanistically linked with the antitumor activity of B-DIM as observed previously by our laboratory in a prostate cancer animal model. [Cancer Res 2007;67(7):3310–9]
Impaired Balance of Mitochondrial Fission and Fusion in Alzheimer's Disease

Mitochondrial dysfunction is a prominent feature of Alzheimer's disease (AD) neurons. In this study, we explored the involvement of an abnormal mitochondrial dynamics by investigating the changes in the expression of mitochondrial fission and fusion proteins in AD brain and the potential cause and consequence of these changes in neuronal cells. We found that mitochondria were redistributed away from axons in the pyramidal neurons of AD brain. Immunoblot analysis revealed that levels of DLP1 (also referred to as Drp1), OPA1, Mfn1, and Mfn2 were significantly reduced whereas levels of Fis1 were significantly increased in AD. Despite their differential effects on mitochondrial morphology, manipulations of these mitochondrial fission and fusion proteins in neuronal cells to mimic their expressional changes in AD caused a similar abnormal mitochondrial distribution pattern, such that mitochondrial density was reduced in the cell periphery of M17 cells or neuronal process of primary neurons and correlated with reduced spine density in the neurite. Interestingly, oligomeric amyloid-β-derived diffusible ligands (ADDLs) caused mitochondrial fragmentation and reduced mitochondrial density in neuronal processes. More importantly, ADDL-induced synaptic change (i.e., loss of dendritic spine and postsynaptic density protein 95 puncta) correlated with abnormal mitochondrial distribution. DLP1 overexpression, likely through repopulation of neuronal processes with mitochondria, prevented ADDL-induced synaptic loss, suggesting that abnormal mitochondrial dynamics plays an important role in ADDL-induced synaptic abnormalities. Based on these findings, we suggest that an altered balance in mitochondrial fission and fusion is likely an important mechanism leading to mitochondrial and neuronal dysfunction in AD brain.
Using LIDAR to Validate the Performance of Vehicle Classification Stations

Vehicle classification is an important traffic parameter for transportation planning and infrastructure management. Vehicle classification stations depend on accurate calibration and validation to yield meaningful results. Operating agencies spend millions of dollars to deploy vehicle classification stations to collect classified count data, yet very few of these stations are ever subjected to a rigorous performance evaluation to ensure that they are reporting accurate data. To date such performance monitoring has been prohibitively labor intensive and prone to human error. To address this problem we develop a classification performance monitoring system to allow operating agencies to rapidly assess the health of their classification stations on a per vehicle basis. We eliminate most of the labor demands and instead deploy a portable nonintrusive vehicle classification system (PNVCS) to classify vehicles, concurrent with an existing classification station. This article uses a LIDAR-based PNVCS but our approach is compatible with many other PNVCSs. The processing requires several intermediate steps, developed herein, including synchronizing the independent clocks and matching observations of a given vehicle between the two classification systems. The performance monitoring methodology automatically compares the vehicle classification between the existing classification station and the PNVCS for each vehicle. If the two classification systems agree, the given vehicle is automatically taken as a success. A human only looks at the vehicle when the two systems disagree, and for this task we have developed tools to semi-automate the manual validation process, greatly increasing the efficiency and accuracy of the human user. Thus, the PNVCS must be accurate enough to be used as a baseline, as verified herein. The methodology is applied to over 21,000 vehicles from several permanent and temporary vehicle classification stations to evaluate the performance of axle and length-based classification stations. The automated process does the bulk of the work, with only 8% of the vehicles requiring manual intervention. The user typically spent 3–5 seconds per vehicle reviewed, translating into only a few minutes to process the exceptions from all lanes over 1 hour of data. This approach offers a cost-effective solution to ensure that classification stations are providing accurate data, and for permanent classification stations the additional labor is a fraction of the cost to deploy the station in the first place.
The distribution of the ISM in the Milky Way - A three-dimensional large-scale model

We use the COBE/DIRBE (1.2, 2.2, 60, 100, 140, and 240 µm) maps and the COBE/FIRAS spectra (for the wavelength range 100−1000 µm) to constrain a model for the spatial distribution of the dust, the stars, and the gas in the Milky Way. By assuming exponential axisymmetric distributions for the dust and the stars and by performing the corresponding radiative transfer calculations we closely (given the simple geometry of the model) reproduce the FIR and NIR maps of the Milky Way. Similar distributions for the atomic and molecular hydrogen in the disk are used (with an inner cut-off radius for the atomic hydrogen) to fit the gas data. The star formation rate as a function of the Galactic radius is derived from the FIR emission and is well in agreement with existing estimates from various star formation tracers. The gas surface density is plotted against the star formation rate density and an “intrinsic” Galactic Schmidt law is derived with excellent agreement with the “external” Schmidt law found for spiral galaxies. The Milky Way is found to consume ∼1% and ∼10% of its gas in the outer and inner regions respectively (for a period of 0.1 Gyr) to make stars. The dust-induced B − V color excess observed in various directions and distances (up to ∼6.5 kpc) with well-studied Cepheid stars is compared with the model predictions showing a good agreement. The simple assumption of exponential distributions of stars and dust in the Galaxy is found to be quite instructive and adequate in modeling all the available data sets from 0.45 µ m( B-band) to 1000 µm.
The World at War: Three and a Half Decades of New York Times Conflict Coverage

This quantitative content analysis uses 36 years of New York Times international news to understand how conflict coverage is presented to audiences in terms of quantity and geographic focus, whether conflict is covered because of its linkage to US interests, and whether the Times relies on its own personnel for first-hand coverage. Additionally, a contemporary history approach gauges how representative coverage is of conflicts in varying regions. Quantitative data reveal an imbalance in coverage; stories about low-income nations focused more on conflict and were more likely to link events to US interests. However, the volume of coverage of these countries was minimal and arguably failed to report some of the most severe internal crises in those nations. According to social construction of reality theorists, this imbalance and distortion can lead to audience perception that more conflict occurs in low-income nations than in other, more developed parts of the world.
NOX2 Inhibition Impairs Early Muscle Gene Expression Induced by a Single Exercise Bout

Reactive oxygen species (ROS) participate as signaling molecules in response to exercise in skeletal muscle. However, the source of ROS and the molecular mechanisms involved in these phenomena are still not completely understood. The aim of this work was to study the role of skeletal muscle NADPH oxidase isoform 2 (NOX2) in the molecular response to physical exercise in skeletal muscle. BALB/c mice, pre-treated with a NOX2 inhibitor, apocynin, (3 mg/kg) or vehicle for 3 days, were swim-exercised for 60 min. Phospho–p47phox levels were significantly upregulated by exercise in flexor digitorum brevis (FDB). Moreover, exercise significantly increased NOX2 complex assembly (p47phox–gp91phox interaction) demonstrated by both proximity ligation assay and co-immunoprecipitation. Exercise-induced NOX2 activation was completely inhibited by apocynin treatment. As expected, exercise increased the mRNA levels of manganese superoxide dismutase (MnSOD), glutathione peroxidase (GPx), citrate synthase (CS), mitochondrial transcription factor A (tfam) and interleukin-6 (IL-I6) in FDB muscles. Moreover, the apocynin treatment was associated to a reduced activation of p38 MAP kinase, ERK 1/2, and NF-κB signaling pathways after a single bout of exercise. Additionally, the increase in plasma IL-6 elicited by exercise was decreased in apocynin-treated mice compared with the exercised vehicle-group (p < 0.001). These results were corroborated using gp91-dstat in an in vitro exercise model. In conclusion, NOX2 inhibition by both apocynin and gp91dstat, alters the intracellular signaling to exercise and electrical stimuli in skeletal muscle, suggesting that NOX2 plays a critical role in molecular response to an acute exercise.
Probabilistic tractography recovers a rostrocaudal trajectory of connectivity variability in the human insular cortex

The insular cortex of macaques has a wide spectrum of anatomical connections whose distribution is related to its heterogeneous cytoarchitecture. Although there is evidence of a similar cytoarchitectural arrangement in humans, the anatomical connectivity of the insula in the human brain has not yet been investigated in vivo. In the present work, we used in vivo probabilistic white‐matter tractography and Laplacian eigenmaps (LE) to study the variation of connectivity patterns across insular territories in humans. In each subject and hemisphere, we recovered a rostrocaudal trajectory of connectivity variation ranging from the anterior dorsal and ventral insula to the dorsal caudal part of the long insular gyri. LE suggested that regional transitions among tractography patterns in the insula occur more gradually than in other brain regions. In particular, the change in tractography patterns was more gradual in the insula than in the medial premotor region, where a sharp transition between different tractography patterns was found. The recovered trajectory of connectivity variation in the insula suggests a relation between connectivity and cytoarchitecture in humans resembling that previously found in macaques: tractography seeds from the anterior insula were mainly found in limbic and paralimbic regions and in anterior parts of the inferior frontal gyrus, while seeds from caudal insular territories mostly reached parietal and posterior temporal cortices. Regions in the putative dysgranular insula displayed more heterogeneous connectivity patterns, with regional differences related to the proximity with either putative granular or agranular regions. Hum Brain Mapp 33:2005–2034, 2012. © 2011 The Authors. Human Brain Mapping Published by Wiley Periodicals, Inc.
The necessary and sufficient conditions of copositive tensors

In this paper, it is proved that (strict) copositivity of a symmetric tensor $\mathcal{A}$ is equivalent to the fact that every principal sub-tensor of $\mathcal{A}$ has no a (non-positive) negative $H^{++}$-eigenvalue. The necessary and sufficient conditions are also given in terms of the $Z^{++}$-eigenvalue of the principal sub-tensor of the given tensor. This presents a method of testing (strict) copositivity of a symmetric tensor by means of the lower dimensional tensors. Also the equivalent definition of strictly copositive tensors is given on entire space $\mathbb{R}^n$.
Deficiency and Also Transgenic Overexpression of Timp-3 Both Lead to Compromised Bone Mass and Architecture In Vivo

Tissue inhibitor of metalloproteinases-3 (TIMP-3) regulates extracellular matrix via its inhibition of matrix metalloproteinases and membrane-bound sheddases. Timp-3 is expressed at multiple sites of extensive tissue remodelling. This extends to bone where its role, however, remains largely unresolved. In this study, we have used Micro-CT to assess bone mass and architecture, histological and histochemical evaluation to characterise the skeletal phenotype of Timp-3 KO mice and have complemented this by also examining similar indices in mice harbouring a Timp-3 transgene driven via a Col-2a-driven promoter to specifically target overexpression to chondrocytes. Our data show that Timp-3 deficiency compromises tibial bone mass and structure in both cortical and trabecular compartments, with corresponding increases in osteoclasts. Transgenic overexpression also generates defects in tibial structure predominantly in the cortical bone along the entire shaft without significant increases in osteoclasts. These alterations in cortical mass significantly compromise predicted tibial load-bearing resistance to torsion in both genotypes. Neither Timp-3 KO nor transgenic mouse growth plates are significantly affected. The impact of Timp-3 deficiency and of transgenic overexpression extends to produce modification in craniofacial bones of both endochondral and intramembranous origins. These data indicate that the levels of Timp-3 are crucial in the attainment of functionally-appropriate bone mass and architecture and that this arises from chondrogenic and osteogenic lineages.
The Political Economy of Market Reform in Jordan

The Political Economy of Market Reform in Jordan, by Timothy J. Piro. Lanham, MD: Rowman & Littlefield, 1998. xvii + 131 pages. Bibl. to p. 123. Index to p. 131. $54 cloth; $19.95 paper. In this slim monograph, Timothy J. Piro has concisely and clearly described the role of stateowned enterprises (SOEs) in the Jordanian economy and the difficulties of privatizing them, even when they are money losers and a drain on the state. In a country where the private economic sector is very small and the state is weak, state and SOEs are linked together as are Siamese twins: cutting them apart results in the death of both. In the 1970s and 1980s, using money from the oil-rich Arab states, the Jordanian government ascribed to the state a privileged position, allowed labor remittances from those working in the Gulf to be used for consumptive purposes, and rewarded the groups which supported its policies. Afraid of being toppled by riots, demonstrations, and violent action, the government did not demand much from the people in the form of taxes. It did not encourage the growth of private industry, preferring, instead, to rely on remittances by expatriates, customs duties on imports, and economic assistance from foreign countries. It tied important parts of the private and public sectors into a "close, and ultimately parasitic, relationship" (p. 70), which enfeebled the private sector. The end result was a rentier economy, which differed only slightly from those of the oil-rich states of the Arabian Peninsula. Piro examines the "Big Five" Jordanian enterprises: the Jordan Cement Factory Company, the Jordan Phosphate Mines Company, the Jordan Petroleum and Refinery Company, the Arab Potash Company, and the Jordan Fertilizer Industries Company. All but one of these were established in the 1950s to promote economic development, national sovereignty, and international prestige. The state provided the capital, appointed the directors, and influenced the selection of managers. Thus, the enterprises did not have much autonomy, were not profit-oriented, and (along with other institutions) served as pillars of the patrimonial political system, in which the king divvied out awards to families, tribes, business interests, and political factions in order to keep them off balance and somewhat happy with the regime. But today the call from international organizations, such as the World Bank and the International Monetary Fund (IMF), is for "market reform," which, for the Jordanian government is not easy to implement. Because of the Gulf War (1990-91), economic assistance to Jordan from oil-rich Arab states and remittances from workers in the Gulf have ceased. …
The merging/AGN connection - II. Ionization of the circumnuclear regions

We report the first results of a study of a sample of 20 galaxy mergers/interacting systems, using the VIMOS and PMAS integral field spectrographs. For each object, we extracted the integrated spectrum of the central regions and analyzed the ionization state using classical diagnostic diagrams (Veilleux & Osterbrock 1987). There is evidence of AGN ionization in 4 of the objects, i.e. 20% of the sample, a considerably higher fraction than found in previous studies (∼4%). An increase of the nuclear activity with the far infrared temperature may account for the difference.