Miracle-dz/UniFAR-FTUs huggingface dataset:
Listeriolysin O‐dependent activation of endothelial cells during infection with Listeria monocytogenes: activation of NF‐κB and upregulation of adhesion molecules and chemokines

The facultative intracellular bacterium Listeria monocytogenes is an invasive pathogen that crosses the vascular endothelium and disseminates to the placenta and the central nervous system. Its interaction with endothelial cells is crucial for the pathogenesis of listeriosis. By infecting in vitro human umbilical vein endothelial cells (HUVEC) with L. monocytogenes, we found that wild‐type bacteria induced the expression of the adhesion molecules (ICAM‐1 and E‐selectin), chemokine secretion (IL‐8 and monocyte chemotactic protein‐1) and NF‐κB nuclear translocation. The activation of HUVEC required viable bacteria and was abolished in prfA‐deficient mutants of L. monocytogenes, suggesting that virulence genes are associated with endothelial cell activation. Using a genetic approach with mutants of virulence genes, we found that listeriolysin O (LLO)‐deficient mutants inactivated in the hly gene did not induce HUVEC activation, as opposed to mutants inactivated in the other virulence genes. Adhesion molecule expression, chemokine secretion and NF‐κB activation were fully restored by a strain of Listeria innocua transformed with the hly gene encoding LLO. The relevance in vivo of endothelial cell activation for listerial pathogenesis was investigated in transgenic mice carrying an NF‐κB‐responsive lacZ reporter gene. NF‐κB activation was visualized by a strong lacZ expression in endothelial cells of capillaries of mice infected with a virulent haemolytic strain, but was not seen in those infected with a non‐haemolytic isogenic mutant. Direct evidence that LLO is involved in NF‐κB activation in transgenic mice was provided by injecting intravenously purified LLO, thus inducing stimulation of NF‐κB in endothelial cells of blood capillaries. Our results demonstrate that functional listeriolysin O secreted by bacteria contributes as a potent inflammatory stimulus to inducing endothelial cell activation during the infectious process.
Terahertz spectral fingerprints detection with Hilbert-Huang Transform

We applied Hilbert-Huang Transform to analyze terahertz spectra in order to improve the state-of-art detection sensitivity of inconspicuous spectral fingerprints for materials with low concentrations and remote sensing. We conducted experiments on ammonia gas and water vapor with terahertz time domain spectroscopy. The temporal terahertz signal is decomposed into a series of intrinsic mode functions using Hilbert-Huang Transform. By comparing the frequency and absorption spectra obtained from the original signals and their intrinsic mode functions, we have showed the validity of low-order intrinsic mode functions and demonstrated that basically the first two orders of functions are capable to show the spectral fingerprints clearly. Therefore, Hilbert-Huang Transform has the potential to become an effective supplementary tool for terahertz spectroscopy.
Two approaches for incorporating linguistic constraints to improve the usability of Telugu dependency parser

Statistical systems with high accuracy are very useful in real-world applications. If these systems can capture basic linguistic information, then the usefulness of these statistical systems improves a lot. This paper is an attempt at incorporating linguistic constraints in statistical dependency parsing. We consider a simple linguistic constraint that a verb should not have multiple subjects or direct objects as its children in the dependency tree. We first describe the importance of this constraint considering machine translation systems which use dependency parser output, as an example application. We then show how the current state-of-the-art dependency parsers violate this constraint. We describe two methods to handle this constraint. We evaluate our methods on the state-of-the-art dependency Telugu parser. Our results show that we can build a statistical parser which handles linguistic constraints and thus be more useful in real-world applications without compromising accuracy.
Crystal structure of 4‐diphosphocytidyl‐2‐C‐methyl‐D‐erythritol kinase (IspE) from Mycobacterium tuberculosis

Isoprenoid precursors, which are a large group of natural products and play key roles in many biological pathways, can only be biosynthesized by the 2‐C‐methyl‐D‐erythritol 4‐phosphate pathway in Mycobacterium tuberculosis. The 4‐diphosphocytidyl‐2‐C‐methyl‐D‐erythritol kinase (IspE), which is an essential enzyme in the isoprenoid precursor biosynthesis pathway, catalyzes ATP‐dependent phosphorylation of 4‐diphospho‐cytidyl‐2‐C‐methyl‐D‐erythritol (CDP‐ME) to 4‐diphos‐phocytidyl‐2C‐methyl‐D‐erythritol‐2‐phosphate and plays a crucial role in M. tuberculosis survival. Therefore, IspE is characterized as an attractive and potential target for antimicrobial drug discovery. However, no experimental structure of M. tuberculosis IspE has been reported, which has hindered our understanding of its structural details and mechanism of action. Here, we report the expression and purification of fully active full‐length M. tuberculosis IspE and solve the high‐resolution crystal structures of IspE alone and in complex with either the substrate CDP‐ME or nonhydrolyzable ATP analog or ADP. The structures present a characteristic galactose/homoserine/mevalonate/phosphomevalonate kinase superfamily α/β‐fold with a catalytic center located in a cleft between 2 domains and display clear substrate and ATP binding pockets. Our results also indicate distinct differences in ligand binding of M. tuberculosis IspE with other reported IspEs. Combined with the results of mutagenesis and enzymatic studies, our results provide useful information on the structural basis of IspE for future anti‐M. tuberculosis drug discovery targeting this kinase. —Shan, S. Chen, X. , Liu, T. , Zhao, H. , Rao, Z. , Lou, Z. Crystal structure of 4‐diphosphocytidyl‐2‐C‐methyl‐d‐erythritol kinase (IspE) from Mycobacterium tuberculosis. FASEB J. 25, 1577–1584 (2011). www.fasebj. org
Word Sense Disambiguation for Acquisition of Selectional Preferences

The selectional preferences of verbal predicates are an important component of lexical information useful for a number of NLP tasks including disambigliation of word senses. Approaches to selectional preference acquisition without word sense disambiguation are reported to be prone to errors arising from erroneous word senses. Large scale automatic semantic tagging of texts in sufficient quantity for preference acquisition has received little attention as most research in word sense disambiguation has concentrated on quality word sense disambiguation of a handful of target words. The work described here concentrates on adapting semantic tagging methods that do not require a massive overhead of manual semantic tagging and that strike a reasonable compromise between accuracy and cost so that large amounts of text can be tagged relatively quickly. The results of some of these adaptations are described here along with a comparison of the selectional preferences acquired with and without one of these methods. Results of a bootstrapping approach are also outlined in which the preferences obtained are used for coarse grained sense disambiguation and then the partially disambiguated data is fed back into the preference acquisition system. 1 1This work was supported by CEC Telematics Applications Programme project LE1-2111 "SPARKLE: Shallow PARsing and Knowledge extraction for Language Engineering".
Dopamine Innervation in the Thalamus: Monkey versus Rat

We recently identified the thalamic dopaminergic system in the human and macaque monkey brains, and, based on earlier reports on the paucity of dopamine in the rat thalamus, hypothesized that this dopaminergic system was particularly developed in primates. Here we test this hypothesis using immunohistochemistry against the dopamine transporter (DAT) in adult macaque and rat brains. The extent and density of DAT-immunoreactive (-ir) axons were remarkably greater in the macaque dorsal thalamus, where the mediodorsal association nucleus and the ventral motor nuclei held the densest immunolabeling. In contrast, sparse DAT immunolabeling was present in the rat dorsal thalamus; it was mainly located in the mediodorsal, paraventricular, ventral medial, and ventral lateral nuclei. The reticular nucleus, zona incerta, and lateral habenular nucleus held numerous DAT-ir axons in both species. Ultrastructural analysis in the macaque mediodorsal nucleus revealed that thalamic interneurons are a main postsynaptic target of DAT-ir axons; this suggests that the marked expansion of the dopamine innervation in the primate in comparison to the rodent thalamus may be related to the presence of a sizable interneuron population in primates. We remark that it is important to be aware of brain species differences when using animal models of human brain disease.
Kar 3 interaction with Cik 1 alters motor structure and function

Kar3, a kinesin-14 motor of Saccharomyces cerevisiae required for mitosis and karyogamy, reportedly interacts with Cik1, a nonmotor protein, via its central, predicted coiled coil. Despite this, neither Kar3 nor Cik1 homodimers have been observed in vivo. Here we show that Kar3 is a dimer in vitro by analytical ultracentrifugation. The motor domains appear as paired particles by rotaryshadow electron microscopy (EM) and circular dichroism (CD) spectroscopy of the nonmotor region shows characteristics of helical structure, typical of coiled coils. Remarkably, the Kar3/Cik1 nonmotor region shows greater helicity by CD analysis and rotary-shadow EM reveals a stalk joined to one large or two smaller particles. The highly helical Kar3/Cik1 nonmotor region and visible stalk indicate that dimerization with Cik1 causes structural changes in Kar3. The Cik1 and Kar3 stalk regions preferentially associate with one another rather than forming homodimers. Kar3/Cik1 moves on microtubules at 2–2.4 lmmin , 2–5-fold faster than Kar3, and destabilizes microtubules at the lagging ends. Thus, structural changes in Kar3 upon dimerization with Cik1 alter the motor velocity and likely regulate Kar3 activity in vivo. The EMBO Journal (2005) 24, 3214–3223. doi:10.1038/ sj.emboj. 7600790; Published online 18 August 2005 Subject Categories: structural biology; membranes & transport
Tenocytes from Ruptured and Tendinopathic Achilles Tendons Produce Greater Quantities of Type III Collagen than Tenocytes from Normal Achilles Tendons: An in Vitro Model of Human Tendon Healing

Type I collagen is the main collagen in tendons; type III collagen is present in small amounts. Ruptured Achilles tendons contain a significantly greater proportion of type III collagen, which predisposes them to rupture. We used an in vitro model to determine whether tenocytes from Achilles tendons that were ruptured (N 22), nonruptured (N 7), tendinopathic (N 12), and fetal (N 8) show different behavior. Samples of Achilles tendon were digested with collagenase and the released tenocytes were collected. Primary tenocyte cultures were established and subsequently cultured onto glass coverslips. Once a confluent monolayer was obtained, the cell populations were “wounded” by scraping a pipette tip along the surface. The cultures were further incubated for either 1, 4, 8, 12, 16, or 24 hours, and production of types I and II collagen was assessed by immunostaining. In cultures from ruptured and tendinopathic tendons, there was increased production of type III collagen. Athletic participation places excess stress on the Achilles tendon, which could potentially lead to areas of microtrauma within the tendon. These areas may heal by the production of type III collagen, which is an abnormal healing response. Accumulation of such episodes of microtrauma could result in a critical point where the resistance of the tissue to tensile forces is compromised and tendon rupture occurs.
Face pose estimating system based on eigenspace analysis

In this paper, we propose a new system for estimating face pose from a facial image. In this system, an input facial image is compared with a database of images of various face pose, then the matched image provides the face pose. The database of images includes not only various face poses but also various illumination conditions, so that the face pose estimation system can be used under various illumination conditions. For collecting such various facial images, they are generated by computer, rather than using real images. The eigenspace method is used for searching a matched image with an input facial image. Since various illumination images are collected in the database of facial images, the extracted principle eigenvectors mostly depend on the face pose. By performing the matching process in the eigenspace, a matched image with the input facial image can be found. The pose of the matched image is closest to the input face. The matching process is also fast because it is performed in small dimensional space spanned by selected eigenvectors only. The proposed pose estimation system can continuously track the face pose of different persons under different light conditions.
Endometrial Adenocarcinoma in Situ in Complex Atypical Hyperplasia: Correlation with Findings in Subsequent Hysterectomy Specimen

Well-differentiated endometrial adenocarcinoma can be difficult to distinguish from complex atypical hyperplasia (CAH) in a curettage or biopsy specimen. When a focus of back-to-back glands or cribriforming smaller than 2.1 mm is seen in a biopsy, we make a diagnosis of adenocarcinoma in situ (AIS). Whether this diagnosis translates into a more frequent diagnosis of carcinoma on the hysterectomy specimen is unknown. The objective of this study was to compare follow-up hysterectomy findings in biopsies showing AIS in CAH with biopsies showing only CAH without AIS. Twelve biopsy/curettage cases diagnosed as endometrial AIS in CAH and 12 biopsy/curettage cases diagnosed as CAH only were reviewed and correlated with corresponding hysterectomy material. A diagnosis of AIS was designated on biopsy/curettings when a focus of back-to-back glands or cribriforming less than 2.1 mm was present. Hysterectomy specimens showed endometrial carcinoma in 6 (50%) of 12 cases of CAH with AIS, and in 2 (17%) of 12 cases diagnosed as CAH only. Endometrial carcinoma with myometrial invasion was identified in 5 (42%) of the cases showing AIS on biopsy, but in none of the 12 cases diagnosed as CAH only on biopsy. Identification of AIS in CAH cases provides useful prognostic information.
XGuide-Concurrent Web Development with Contracts

In this dissertation we propose the XGuide Web development method. XGuide focuses on the timely development of Web applications while guaranteeing high-quality designs and reusable implementation artifacts. It supports the whole life-cycle of a Web application and covers the analysis, design, implementation and maintenance phases. The central idea in XGuide is to bring the well-established software engineering concepts of interfaces and contracts to the Web engineering domain. Contracts clearly state the requirements and internal dependencies of Web pages and act as specifications for a subsequent implementation. To support multiple activities being carried out in parallel by different people, XGuide introduces multi-dimensional contracts that enable the concurrent development of implementation concerns such as the content, the graphical appearance and the application logic. In addition to the parallel implementation phase, contracts also enable the definition of Web components—reusable page fragments that get assembled to form the final Web page. A Web component is fully specified by its contract and contract composition defines the rules for embedding components into pages. The short innovation cycles on the Web further require a Web development methodology to constantly cope with new requirements. In XGuide, a formal definition of contracts and their composition is the foundation for an open contract model that can integrate new concerns such as access control, meta-data or device independence as separate modules. The XGuide process applies a model-driven approach to Web development that iteratively refines initial requirements into design diagrams, contracts and implementation components. After the initial deployment, XGuide directly maps maintenance and evolution tasks to updates of the design models (i.e., diagrams and contracts). Model updates trigger a new iteration of the XGuide process, i.e., follow the same contract-based, parallel implementation paradigm. This round-trip engineering ensures that models remain consistent with the implementation and guarantees well-structured and easy to trace projects. In order to support the application of XGuide in real-world Web projects, we implemented the XSuite Web development environment. The purpose of the XSuite IDE is to support the developer in all phases of the XGuide process. Visual design models are automatically transcoded into contracts and wizards assist in creating pages, composing contracts and deploying the application. XSuite is built on top of the generic Eclipse framework and integrates a Java IDE, a version control system and a Web server into the actual Web development environment. The practicality of the XGuide method and the XSuite tool suite is demonstrated in the implementation of the Vienna International Festival 2003 (VIF) case study.
Use of Bacteriophage MS2 as an Internal Control in Viral Reverse Transcription-PCR Assays

ABSTRACT Diagnostic systems based on reverse transcription (RT)-PCR are widely used for the detection of viral genomes in different human specimens. The application of internal controls (IC) to monitor each step of nucleic acid amplification is necessary to prevent false-negative results due to inhibition or human error. In this study, we designed various real-time RT-PCRs utilizing the coliphage MS2 replicase gene, which differ in detection format, amplicon size, and efficiency of amplification. These noncompetitive IC assays, using TaqMan, hybridization probe, or duplex scorpion probe techniques, were tested on the LightCycler and Rotorgene systems. In our approach, clinical specimens were spiked with the control virus to monitor the efficiency of extraction, reverse transcription, and amplification steps. The MS2 RT-PCR assays were applied for internal control when using a second target hepatitis C virus RNA in duplex PCR in blood donor screening. The 95% detection limit was calculated by probit analysis to 44.9 copies per PCR (range, 38.4 to 73.4). As demonstrated routinely, application of MS2 IC assays exhibits low variability and can be applied in various RT-PCR assays. MS2 phage lysates were obtained under standard laboratory conditions. The quantification of phage and template RNA was performed by plating assays to determine PFU or via real-time RT-PCR. High stability of the MS2 phage preparations stored at −20°C, 4°C, and room temperature was demonstrated.
Valuing the environment in developing countries: modelling the impact of distrust in public authorities' ability to deliver public services on the citizens' willingness to pay for improved environmental quality

In this paper, we employ the choice experiment method to estimate citizens' valuation of an intervention that proposes to improve the quality of the wastewater deposited in the Ganges River, India. We interviewed 150 randomly selected citizens of Chandernagore, along the banks of the Ganges River, to elicit their willingness to pay (WTP) for this intervention, measured in terms of higher municipality taxes. The findings reveal that almost all of the citizens value wastewater quality, though majority protested the intervention, and stated that they donot trust the authorities for effective management of funds. These protest responses were controlled for with the nested logit model. The results reveal that the citizens are willing to pay significant amounts for improved wastewater quality. Municipalities could rely to some extent on their citizens' WTP higher taxes but municipalities' performance, trustworthiness, accountability, as well as the citizens' perceptions of these, should be improved.
Experimental Comparison of Nonlinear Controllers for Flexible Joint Manipulators

In this paper, the authors present an experimental comparison of several nonlinear controllers for flexible joint manipulators. The experimental setup is a 2-DOF manipulator with an elasticity at the second joint. This work follows and confirms a previous com parative study based on theoretical and numerical investigations. The main conclusions of the study are as follows. (1) Some non linear controllers may behave quite differently when applied to a particular device, despite their apparent theoretical resemblance. (2) The compensation of nonlinearities (Coriolis and centrifugal torques), as well as joint flexibilities, may improve the closed-loop performance for certain desired trajectories, despite a rather high joint stiffness. (3) However, when the joint stiffness is sufficiently large, the controllers that do not take into account the joint flexi bility in the design can, in certain cases, behave as well as those that incorporate it. Thus, future experimental work with a smaller joint stiffness is needed. (4) Finally, the complex structure of cer tain nonlinear controllers for flexible joint robots (backstepping and energy-shaping schemes) may be an obstacle to their closed-loop behavior enhancement. The experimental results clearly show that the inputs of such schemes chatter and have a magnitude larger than those of simpler controllers (like singular perturbation-based or Slotine and Li controllers).
Antidepressants for generalized anxiety disorder.

As a group, antidepressants are an effective short-term treatment for GAD. Compared with placebo, about five to six patients must be treated to get one additional patient who responds to therapy. Side effects occur more frequently with antidepressants than with placebo, but they are not severe enough to require discontinuation of treatment.
Segmentation of Nerve Fibers by Introducing Intensity Priority in Level Set

The segmentation of the optic nerve fibers is important for the morphometry study of optic nerve. However, such studies are hampered by the thousands of fibers involved when manual segmentation has to be used. We have developed an automatic segmentation method which is principally based on improved Chan-Vese level set model which integrating myelin sheath intensity priority. Next, identify the axon candidates by labeling closed region based on marker. Our results indicate that this approach for segmenting nerve fiber images is efficient, and advisable compared to manual segmentation.
Improving I/O performance in web browser engine of smart TV platform

Smart TV applications use a web browser to execute xml, html, css, javascripts, images, and videos, which are stored in NAND flash, and load them into memory. The applications also convert resources into a tree data structure. This converted data structure is placed in the heap area and is removed from memory when the application is ended. Therefore, when the application is restarted, this converting process is performed again which slows the speed of a web browser. This paper suggests a technique called fast IO to add persistency to the data tree so that it can be saved and reused when the application is restarted. With fast IO, a persistency area is called an object. It is created the object file and the data file is saved and reused. Storing a tree-data structure in an object adds persistency to the data structure which means it can be reused when the application is restarted after being ended. Applying fast IO in the web browser reduced the time it took to open web pages by up to 68% by omitting the processing of re-forming the tree data structure.