Miracle-dz/UniFAR-FTUs huggingface dataset:
Saliency Density and Edge Response Based Salient Object Detection

SUMMARY We propose a novel threshold-free salient object detection approach which integrates both saliency density and edge response. The salient object with a well-deﬁned boundary can be automatically detected by our approach. Saliency density and edge response maximization is used as the quality function to direct the salient object discovery. The global optimal window containing a salient object is e ﬃ ciently located through the proposed saliency density and edge response based branch-and-bound search. To extract the salient object with a well-deﬁned boundary, the GrabCut method is applied, initialized by the located window. Experimental results show that our approach outperforms the methods only using saliency or edge response and achieves a comparable performance with the best state-of-the-art method, while being without any threshold or multiple iterations of GrabCut.
Synthetic antibodies as therapeutics

Synthetic antibody libraries, whose repertoires are designed, have advanced in the last decade to rival natural repertoire-based libraries. Many types of diversity design have been shown to generate highly functional libraries. Defined template and defined diversity in synthetic antibody libraries improve the process of discovering and optimizing new antibodies. Synthetic libraries with different diversity design have targeted different epitopes on antigens, including epitopes that are unlikely to be targeted by immunization and hybridoma. Cross-species binding antibodies are prime examples of products generated by synthetic antibody libraries, and they are becoming the tools of choice to validate the selection of targeted molecules in therapeutic development. Synthetic antibody libraries complement the existing natural repertoire-based antibody libraries and hybridoma approach to maximize the potentials of antibodies as therapeutics.
Normal map recovery using bundle adjustment

Although modern reconstruction methods have advanced considerably, their ability to retrieve fine details, small features of a surface is limited. Applying texture can be used to conceal lack of geometry to some extent, but it becomes apparent when lighting varies. A more sophisticated solution is to map normal vectors to the surface of the model in order to alter the way it is rendered under different illuminations in accordance with the properties of the real object. The principle of photometric stereo is to reconstruct normals from a series of images. By illuminating the object with different directional light sources local surface orientation can be inferred. The contribution of this study is that the authors successfully applied the widely used bundle adjustment algorithm to photometric stereo problems when non-parallel light rays illuminate the objects.
Assessing the risk of skin damage due to femtosecond laser irradiation

We irradiated freshly excised skin biopsies with four irradiation regimes usually taken for multiphoton imaging. If there is any skin damaging, it is mainly an effect similar to the damaging effects of UV‐irradiation. Using fluorescent antibodies against cyclobutane‐pyrimidin‐dimers (CPDs) in combination with immuno‐fluorescence image analysis we quantitatively compared fs‐irradiation effects with UV‐irradiation (solar simulator). Based on these results we are giving a risk assessment. The results show that multi photon imaging using the parameters described here is in the ballpark of damaging occurring from every day sun exposure. (© 2008 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
The ontology based FMEA of lead free soldering process

Paper is directed to improvement of a FMEA (Failure Mode and Effects Analysis) procedure in the area of reflow lead free soldering by the use of an ontology paradigm. Some ontology editor tools suitable for our intention are presented. Particular phases of ontology utilization for development of more exact approach to the FMEA procedure of reflow lead free soldering are analyzed. The goal of our work, a proposal of a user's guide for the FMEA procedure based on an ontology paradigm is presented. This user's guide is included in our university courses Management of Production Quality and Complex Quality Control provided by the Department of Electro-Technology of our faculty.
Binding and Agglutination of Streptococcus pneumoniae by Human Surfactant Protein D (SP-D) Vary between Strains, but SP-D Fails To Enhance Killing by Neutrophils

ABSTRACT Recombinant human surfactant protein D (SP-D) expressed in Escherichia coli, consisting of the head and neck regions of the native molecule, bound to all strains of Streptococcus pneumoniae that were tested, but the extent of binding varied between strains of differing capsular serotypes. The recombinant protein expressed in the yeast Pichia pastoris did not bind. Full-length native SP-D aggregated pneumococci in a calcium-dependent manner that was inhibited by maltose acting as a competitive sugar. The ability of SP-D to modulate the uptake and killing of pneumococci by human neutrophils was also addressed. Neither recombinant truncated SP-D nor native full-length SP-D enhanced the killing of pneumococci by human neutrophils. Aggregation of pneumococci varied not only between strains of the same multilocus sequence type and different serotypes but also between strains of the same serotype. However, use of recombinant strains in which the serotype had been changed showed that the degree of aggregation was influenced by the capsular type. Indeed, a 19F serotype strain which was not aggregated by SP-D did exhibit aggregation when the original isogenic strain was capsule switched to capsular serotype 3. However, although our results show that SP-D is capable of aggregating most pneumococci, no correlation between the degree of aggregation and the capsule or multilocus sequence type of the pneumococcus was clearly apparent. Therefore, although the capsule serotype is not the only determinant of aggregation by SP-D, the data presented here indicate that it does have a role to play.
Color standardization in whole slide imaging using a color calibration slide

Background: Color consistency in histology images is still an issue in digital pathology. Different imaging systems reproduced the colors of a histological slide differently. Materials and Methods: Color correction was implemented using the color information of the nine color patches of a color calibration slide. The inherent spectral colors of these patches along with their scanned colors were used to derive a color correction matrix whose coefficients were used to convert the pixels′ colors to their target colors. Results: There was a significant reduction in the CIELAB color difference, between images of the same H & E histological slide produced by two different whole slide scanners by 3.42 units, P < 0.001 at 95% confidence level. Conclusion: Color variations in histological images brought about by whole slide scanning can be effectively normalized with the use of the color calibration slide.
Résolution de systèmes linéaires et non linéaires creux sur grappes de GPUs. (Solving sparse linear and nonlinear systems on GPU clusters)

Depuis quelques annees, les grappes equipees de processeurs graphiques GPUs sont devenues des outils tres attrayants pour le calcul parallele haute performance. Dans cette these, nous avons concu des algorithmes iteratifs paralleles pour la resolution de systemes lineaires et non lineaires creux de tres grandes tailles sur grappes de GPUs. Dans un premier temps, nous nous sommes focalises sur la resolution de systemes lineaires creux a l'aide des methodes iteratives CG et GMRES. Les experimentations ont montre qu'une grappe de GPUs est plus performante que son homologue grappe de CPUs pour la resolution de systemes lineaires de tres grandes tailles. Ensuite, nous avons mis en oeuvre des algorithmes paralleles synchrones et asynchrones des methodes iteratives Richardson et de relaxation par blocs pour la resolution de systemes non lineaires creux. Nous avons constate que les meilleurs solutions developpees pour les CPUs ne sont pas necessairement bien adaptees aux GPUs. En effet, les simulations effectuees sur une grappe de GPUs ont montre que les algorithmes Richardson sont largement plus efficaces que ceux de relaxation par blocs. De plus, elles ont aussi montre que la puissance de calcul des GPUs permet de reduire le rapport entre le temps d'execution et celui de communication, ce qui favorise l'utilisation des algorithmes asynchrones sur des grappes de GPUs. Enfin, nous nous sommes interesses aux grappes geographiquement distantes pour la resolution de systemes lineaires creux. Dans ce contexte, nous avons utilise la methode de multi-decomposition a deux niveaux avec GMRES parallele adaptee aux grappes de GPUs. Celle-ci utilise des iterations synchrones pour resoudre localement les sous-systemes lineaires et des iterations asynchrones pour resoudre la globalite du systeme lineaire.
Activated Platelets in Heparinized Shed Blood: The “Second Hit” of Acute Lung Injury in Trauma/Hemorrhagic Shock Models

ABSTRACT The return of heparinized shed blood (SB) in trauma/hemorrhagic shock (T/HS) models remains controversial because of potential anti-inflammatory properties. Although ubiquitous as an anticoagulant, heparin is ineffective on cellular coagulation as an antithrombotic agent. Therefore, we hypothesized that returning heparinized SB would paradoxically enhance acute lung injury (ALI) after T/HS because of the infusion of activated platelets. Sprague-Dawley rats, anesthetized with pentobarbital, underwent laparotomy and hemorrhage-induced shock (MAP of 30 mmHg × 45 min). Animals were resuscitated with a combination of normal saline and returned SB. Shed blood was collected in either 80 U/kg of heparin, 800 U/kg of heparin, or citrate or diluted 1:8 with normal saline. An additional group of animals were pretreated with a platelet P2Y12 receptor antagonist (clopidogrel) before T/HS. Bronchoalveolar lavage, lung myeloperoxidase assays, pulmonary immunofluorescence, and blood smears were conducted. Bronchoalveolar lavage protein increased in animals resuscitated with heparinized SB (T/HS + 80 U/kg Hep 1.62 ± 0.29, T/HS + 800 U/kg Hep 1.30 ± 0.15 vs. T/SS 0.51 ± 0.16 and T/HS Citrate 0.7 ± 0.09) (P < 0.0001). Blood smears and platelet function assays revealed platelet aggregates and increased platelet activation. Animals pretreated with a platelet P2Y12 receptor antagonist were protected from postinjury ALI (P < 0.0001). Animals with return of SB had increased pulmonary polymorphonuclear leukocyte sequestration (P < 0.0001). Pulmonary immunofluorescence demonstrated microthrombi only in the T/HS group receiving heparinized SB (P < 0.0001). The return of heparinized SB functions as a “second hit” to enhance ALI, with activated platelets propagating microthrombi and pulmonary polymorphonuclear leukocyte recruitment.
Inducible Nitric-oxide Synthase Expression Is Regulated by Mitogen-activated Protein Kinase Phosphatase-1*

Inducible nitric-oxide (NO) synthase (iNOS) plays a critical role in the eradication of intracellular pathogens. However, the excessive production of NO by iNOS has also been implicated in the pathogenesis of septic shock syndrome. Previously, we have demonstrated that mice deficient in mitogen-activated protein kinase phosphatase-1 (MKP-1) exhibit exaggerated inflammatory responses and rapidly succumb to lipopolysaccharide (LPS). In response to LPS, MKP-1−/− mice produce greater amounts of inflammatory cytokines and NO than do wild-type mice, and the MKP-1−/− mice exhibit severe hypotension. To understand the molecular basis for the increase in NO production, we studied the role of MKP-1 in the regulation of iNOS expression. We found that LPS challenge elicited a stronger iNOS induction in MKP-1 knock-out mice than in wild-type mice. Likewise, LPS treatment also resulted in greater iNOS expression in macrophages from MKP-1−/− mice than in macrophages from wild-type mice. Both accelerated gene transcription and enhanced mRNA stability contribute to the increases in iNOS expression in LPS-stimulated MKP-1−/− macrophages. We found that STAT-1, a transcription factor known to mediate iNOS induction by interferon-γ, was more potently activated by LPS in MKP-1−/− macrophages than in wild-type cells. MicroRNA array analysis indicated that microRNA (miR)-155 expression was increased in MKP-1-deficient macrophages compared with wild-type macrophages. Transfection of miR-155 attenuated the expression of Suppressor of Cytokine Signal (SOCS)-1 and enhanced the expression of iNOS. Our results suggest that MKP-1 may negatively regulate iNOS expression by controlling the expression of miR-155 and consequently the STAT pathway via SOCS-1.
A simple position-sensorless algorithm for rotor-side field-oriented control of wound-rotor induction machine

A simple position-sensorless method for the rotor-side field-oriented control of a wound-rotor induction machine is described in this paper. The algorithm is based on axis transformations. Compared to the previously proposed methods, it is more direct and the dependence on machine parameters is also largely reduced. The algorithm can be started on the fly without the knowledge of the initial rotor position. Operation at synchronous speed, corresponding to zero rotor frequency, is stable, thus making it suitable for variable speed constant frequency operations. Simulation and experimental results show excellent performance of the scheme.
Measuring Long-Run Exchange Rate Pass-Through Economics : The Open-Access

The paper discusses the issue of estimating shortand long-run exchange rate pass-through to import prices in euro area countries and reviews some problems with the measures recently proposed in the literature. Theoretical considerations suggest a cointegrating relationship (between import unit values, the exchange rate and foreign prices), which is typically ignored in existing empirical studies. We use time series and up-to-date panel data techniques to test for cointegration with the possibility of structural breaks and show how the long run may be restored in the estimation. The main finding is that allowing for possible breaks around the formation of EMU and the appreciation of the euro starting in 2001 helps restore a long run cointegration relationship, where over the sample period the fixed component of the pass-through decreased while the variable component tended to increase. JEL: F14, F31, F36, F42, C23
Molecular phylogeny of Entomobrya (Collembola: Entomobryidae) from China: Color pattern groups and multiple origins

Highly diversified colorations among springtails (Collembola) have been widely used for species diagnosis, but their phylogenetic significance is poorly known. We addressed this issue in the largest Entomobryinae genus Entomobrya, which possesses variable color patterns among species. The relationships within the genus and to other genera have also rarely been studied. Based on material mainly from China, we have conducted a multilocus phylogeny and topology tests with likelihood and Bayesian algorithms, and accordingly demonstrated the non‐monophyly of Chinese Entomobrya. The division of five clades, including Entomobrya and several related genera, coincided well with five types of colorations, respectively. Further analyses of divergence time and historical biogeography revealed that Chinese Entomobrya originated mainly from Palearctic (northern and western) China in the Paleocene and Eocene. This study highlights the great phylogenetic values as well as taxonomic uses of coloration in Chinese Entomobrya. Multiple phylogenetic and biogeographic origins of Entomobrya imply its complicated relationships with both scaled and unscaled genera of Entomobryinae.
Genomic profiling of the neuronal target genes of the plasticity‐related transcription factor – Zif268

The later phases of neuronal plasticity are invariably dependent on gene transcription. Induction of the transcription factor Zif268 (Egr‐1) in neurones is closely associated with many forms of functional plasticity, yet the neuronal target genes modulated by Zif268 have not been characterized. After transfection of a neuronal cell line with Zif268 we identified genes that show altered expression using high density microarrays. Although some of the genes identified have previously been associated with forms of neuronal plasticity, the majority have not been linked with neuronal plasticity or Zif268 action. Altered expression of a representative sample of the novel target genes was confirmed in Zif268‐transfected PC12 neurones, and in in vitro and in vivo models of Zif268‐associated neuronal plasticity. In particular, altered expression of the protease inhibitor Cystatin C and the chemokine Cxcl10 was observed in striatal tissue after haloperidol administration. Surprisingly, the group of identified genes is enriched for components of the proteasome and the major histocompatibility complex. Our findings suggest that altered expression of these genes following Zif268 induction may be a key component of long lasting plasticity in the CNS.
Complex network theory approach to the assessment on collective knowledge advancement through scientific discourse in CSCL

This study discusses the possibility of the integrated analytic approach to discourse in CSCL by the combination of macro network analysis and micro analysis of argument on students' written discourse. Although studies have established fine-grained analytic approaches to discourse or argumentation in CSCL environments, we still have difficulty with evaluating collective knowledge advancement. The Complex Network Theory would be a promising approach to challenging this difficulty. We can visualize a variety of network structures with identifying ideas as nodes, and co-presence of words as links. Several indices numerically inform us how a target network is structured. In this paper, we report our attempt to describe how the network of ideas represented in discourse is structured in CSCL environments and its relation to the network structure analysis.
Fading correlations in wireless MIMO communication systems

We investigate the effects of fading correlations on wireless communication systems employing multiple antennas at both the receiver and the transmitter side of the link, so called multiple-input multiple-output (MIMO) systems. It turns out that the amount of transmitter sided channel knowledge plays an important part when dealing with fading correlations. Furthermore, the possible availability of time diversity in a time-selective channel can have essential influence on performance. To study the influence of time-selectivity, the concept of sample-mean outage is introduced and applied to information theoretic measures, like capacity or cutoff rate. It will be shown, that in some cases correlated fading may offer better performance than uncorrelated fading permits, which is due to exploitable antenna gain, that will also be defined in a general form for MIMO systems.
The Purification and Functional Analysis of Human CD4+CD25high Regulatory T Cells

Regulatory T cells were initially identified and isolated in the mouse, by virtue of their endogenous expression of CD25 (IL‐2R αchain) and shown to inhibit both the in vivo development of autoimmunity and the in vitro proliferation of nonregulatory, CD4+CD25− T cells. In contrast to mouse cells, human regulatory T cells are not purified by isolating all CD25‐expressing CD4 T cells ex vivo. Such cells can be isolated by targeting only the small percentage of human CD4 T cells that express high levels of CD25. This is best achieved by FACS sorting using the level of CD25 expressed on CD4− T cells to place the gate for discriminating high expression of CD25. This unit provides two widely used methods to isolate (FACS) or to enrich (magnetic beads) human CD4+CD25+ regulatory T cells from blood, along with an in vitro coculture assay to measure the anergic and suppressive features of human CD4+CD25+ regulatory T cells.
Predation risk, competition, and territorial damselfishes as drivers of herbivore foraging on Caribbean coral reefs

Food availability, competition, habitat complexity, and territorial damselfish shape foraging decisions of herbivorous coral reef fishes. However, relatively little is known about how predators affect herbivore diet selection. We examined diets of 2 common reef herbivores, Sparisoma aurofrenatum and Acanthurus coeruleus, in the Florida Keys, across sites of varying predator biomass. We used stable isotope analysis to understand the importance of predation risk relative to other known drivers of herbivore foraging decisions. For S. aurofrenatum, we found that greater predator biomass was associated with an increase in the diversity of resources consumed within populations. In contrast, increasing densities of damselfishes, which aggressively defend resource-rich algal gardens, were associated with lower diet diversity. However, within A. coeruleus populations, diet diversity increased with damselfish abundance, but was unrelated to predator biomass. Stomach content analyses and direct observation of diet selection in the field corroborated the stable isotope analysis. Importantly, both predator and damselfish abundance impacted diet diversity in different ways for these 2 fishes, which may be linked to differences in sociality and group foraging. A. coeruleus is more likely to forage in schools, potentially reducing predation risk and allowing them to overwhelm damselfishes and access their territories. Interestingly, damselfish abundance was positively correlated with predator biomass, suggesting that predators may influence herbivore diets indirectly via altered densities or behavior of damselfishes. Our work argues for more emphasis on the role of predation risk in affecting herbivore foraging in order to understand the implications of human-mediated predator removal and recovery in coral reef ecosystems.
Extracellular Ca2(+)-dependent inducible alkaline phosphatase from extremely halophilic archaebacterium Haloarcula marismortui

When starved of inorganic phosphate, the extremely halophilic archaebacterium Haloarcula marismortui produces the enzyme alkaline phosphatase and secretes it to the medium. This inducible extracellular enzyme is a glycoprotein whose subunit molecular mass is 160 kDa, as estimated by sodium dodecyl sulfate-gel electrophoresis. The native form of the enzyme is heterogeneous and composed of multiple oligomeric forms. The enzymatic activity of the halophilic alkaline phosphatase is maximal at pH 8.5, and the enzyme is inhibited by phosphate. Unlike most alkaline phosphatases, the halobacterial enzyme requires Ca2+ and not Zn2+ ions for its activity. Both calcium ions (in the millimolar range) and NaCl (in the molar range) are required for the stability of the enzyme.