Miracle-dz/UniFAR-FTUs huggingface dataset:
Antigenic variation among Pasteurella multocida isolates from diseased buffaloes by protein profiling and cluster analysis.

Hemorrhagic septicemia is an acute bacterial disease of buffaloes and cattle caused by Pasteurella multocida. In the present study, P. multocida (n=11) were isolated from healthy carrier (04/200 ) and diseased buffaloes (07/200) from Sargodha division, Punjab. Pasteurella multocida were identified by culture characteristics and biochemical profile index (API) Kit. Isolates were confirmed by serological and molecular characterization by PCR. Antigenic variation among P. multocida (11 isolates) and one vaccine strain was revealed by sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS-PAGE). Although SDS-PAGE revealed that five major proteins were present in all the isolates as well as in vaccine strain o f P. multocida but isolates had variations in minor protein bands . Relatedness among the isolates was assessed by cluster analysis using fingerprint analysis of missing data (FAMD) and principal coordinate analysis (PCA) of 11 isolates and one vaccine strain. All isolates were clustered into 5 different groups namely I, II, III, IV and V on the basis of their electrophoretic profile . Group I, II, III, IV and V contained 1 (8.33%), 1(8.33%), 2 (16.67%), 6 (50%) and 2 (16.67%) isolates of P. multocida, respectively. Vaccine strain had high relatedness with group IV (S3, S6, S7, S8, and S9). It is concluded that distinct polypeptide variation is present among P. multocida isolates which insinuate for detailed proteomic and genomic analysis for the development of effective vaccines and cont rol of hemorrhagic septicemia.
Guidelines for the Choice of Visualization Techniques Applied in the Process of Knowledge Extraction

Visualization techniques are tools that can improve analyst's insight into the results of knowledge discovery process or to directly explore and analyze data. They allows analysts to interact with the graphical representation to get new knowledge. The choice of visualization techniques must follow some criteria to guarantee a consistent data representation. This paper presents a study based on Grounded Theory that indicates parameters for select visualization techniques, which are: data type, task type, data volume, data dimension and position of the attributes in the display. These parameters are analyzed in the context of visualization technique categories: standard 1D 3D graphics, iconographic techniques, geometric techniques, pixel-oriented techniques and graph-based or hierarchical techniques. The analysis over the association among these parameters and visualization techniques culminated in guidelines establishment to choose the most appropriate techniques according to the data characteristics and the objective of the knowledge discovery process.
Biphasic Regulation of Yes-associated Protein (YAP) Cellular Localization, Phosphorylation, and Activity by G Protein-coupled Receptor Agonists in Intestinal Epithelial Cells

We examined the regulation of Yes-associated protein (YAP) localization, phosphorylation, and transcriptional activity in intestinal epithelial cells. Our results show that stimulation of intestinal epithelial IEC-18 cells with the G protein-coupled receptor (GPCR) agonist angiotensin II, a potent mitogen for these cells, induced rapid translocation of YAP from the nucleus to the cytoplasm (within 15 min) and a concomitant increase in YAP phosphorylation at Ser127 and Ser397. Angiotensin II elicited YAP phosphorylation and cytoplasmic accumulation in a dose-dependent manner (ED50 = 0.3 nm). Similar YAP responses were provoked by stimulation with vasopressin or serum. Treatment of the cells with the protein kinase D (PKD) family inhibitors CRT0066101 and kb NB 142-70 prevented the increase in YAP phosphorylation on Ser127 and Ser397 via Lats2, YAP cytoplasmic accumulation, and increase in the mRNA levels of YAP/TEAD-regulated genes (Ctgf and Areg). Furthermore, siRNA-mediated knockdown of PKD1, PKD2, and PKD3 markedly attenuated YAP nuclear-cytoplasmic shuttling, phosphorylation at Ser127, and induction of Ctgf and Areg expression in response to GPCR activation. These results identify a novel role for the PKD family in the control of biphasic localization, phosphorylation, and transcriptional activity of YAP in intestinal epithelial cells. In turn, YAP and TAZ are necessary for the stimulation of the proliferative response of intestinal epithelial cells to GPCR agonists that act via PKD. The discovery of interaction between YAP and PKD pathways identifies a novel cross-talk in signal transduction and demonstrates, for the first time, that the PKDs feed into the YAP pathway.
Micromachining along a curve: Femtosecond laser micromachining of curved profiles in diamond and silicon using accelerating beams

We report femtosecond laser micromachining of micron-size curved structures using tailored accelerating beams. We report surface curvatures as small as 70 μm in both diamond and silicon, which demonstrates the wide applicability of the technique to materials that are optically transparent or opaque at the pump laser wavelength. We also report the machining of curved trenches in silicon. Our results are consistent with an ablation-threshold model based on calculated local beam intensity, and we also observe asymmetric debris deposition which is interpreted in terms of the optical properties of the incident accelerating beam.
The CD16+ Monocyte Subset Is More Permissive to Infection and Preferentially Harbors HIV-1 In Vivo1

HIV-1 persists in peripheral blood monocytes in individuals receiving highly active antiretroviral therapy (HAART) with viral suppression, despite these cells being poorly susceptible to infection in vitro. Because very few monocytes harbor HIV-1 in vivo, we considered whether a subset of monocytes might be more permissive to infection. We show that a minor CD16+ monocyte subset preferentially harbors HIV-1 in infected individuals on HAART when compared with the majority of monocytes (CD14highCD16−). We confirmed this by in vitro experiments showing that CD16+ monocytes were more susceptible to CCR5-using strains of HIV-1, a finding that is associated with higher CCR5 expression on these cells. CD16+ monocytes were also more permissive to infection with a vesicular stomatitis virus G protein-pseudotyped reporter strain of HIV-1 than the majority of monocytes, suggesting that they are better able to support HIV-1 replication after entry. Consistent with this observation, high molecular mass complexes of apolipoprotein B mRNA-editing enzyme, catalytic polypeptide-like 3G (APOBEC3G) were observed in CD16+ monocytes that were similar to those observed in highly permissive T cells. In contrast, CD14highCD16− monocytes contained low molecular mass active APOBEC3G, suggesting this is a mechanism of resistance to HIV-1 infection in these cells. Collectively, these data show that CD16+ monocytes are preferentially susceptible to HIV-1 entry, more permissive for replication, and constitute a continuing source of viral persistence during HAART.
Interdependence between International Stock Returns--News or Contagion Effect?

Does the increasing trend of the globalization of equity markets increase price volatility and correlations of international stock returns by propagating a mistake in one market to another market? This paper provides new insights into this issue by examining whether such a transmission of international stock returns has any link to economic news. A one-period model of a competitive security market with heterogeneous information is set up to explain how domestic investors process foreign economic announcements and foreign price changes. The relative importance of U.S. economic announcements and price changes on Japanese stock returns is empirically tested to examine the implications of the model. Empirical results show that U.S. economic announcements-- money supply, wholesale and consumer price indices, and industrial production--have an effect on Japanese stock returns and trading volume. The results suggest that the market perception of Federal Reserves policy is globally communicable across borders.
Topband Queries in Time Series Data

Top-k queries have been extensively studied in various snapshot databases and data streams for applications where the state of an object is static with respect to time. We observe that decision-makers are often interested in a set of objects that exhibit a certain degree of consistent performance over time. In this paper, we introduce a new class of queries called dke-topband that is able to retrieve objects that are within top k at every time point over a specified time interval. Topband queries can be processed using standard SQL and existing top-k methods. However, the SQL method requires the nested loops to compute the top-k result, while the top-k approach leads to large intermediate results and wasted computations. We design a rank-based approach to address these shortcomings. Experiment results on both synthetic and real world datasets indicate that the proposed approach is efficient and scalable, and has direct applications in real world scenarios.
Caspase Inhibition Increases Embryonic Striatal Graft Survival

In transplants of embryonic striatal cells placed into the excitotoxically lesioned rat striatum (a model of Huntington's disease), as many as 60 to 90% of the grafted cells are believed to die. Caspase activation is part of a cascade of events that can lead to apoptosis. We investigated the effect of the caspase inhibitor acetyl-tyrosinyl-valyl-alanyl-aspartyl-chloromethylketone (Ac-YVAD-cmk) on grafted embryonic striatal cells in the excitotoxically lesioned or intact rat striatum. Female Sprague-Dawley rats were subjected to unilateral intrastriatal injection of quinolinic acid. After 10 days, rats received bilateral intrastriatal grafts from embryonic day 14 rat lateral ganglionic eminence. Rats were divided into the following groups: Ac-YVAD-cmk, pretreatment of the graft tissue with the caspase inhibitor (500 microM); and control, untreated control grafts. Rats were perfused 10 days or 5 weeks postgrafting. Brain sections were processed immunohistochemically using an antibody against the striatal neuron marker dopamine- and adenosine 3',5'-monophosphate-regulated phosphoprotein with a molecular weight of 32 kDa (DARPP-32). Adjacent sections were stained for acetylcholinesterase/cresyl violet cytochemistry and Fluoro-Jade cytochemistry, a marker for degenerating neurons. Total graft volume, P-zone volume, total number of neuron-like cells, and number of DARPP-32-positive cells were increased, compared to control, in the group receiving Ac-YVAD-cmk-treated graft tissue. Moreover, transplants injected into the intact striatum were found to be significantly smaller compared to transplants placed into the excitotoxically lesioned striatum. The Fluoro-Jade staining revealed ongoing cell death in transplants 10 days after intrastriatal implantation and that cell death was significantly reduced 5 weeks after grafting.
Expression of regeneration and tolerance factor on B cell chronic lymphocytic leukemias: A possible mechanism for escaping immune surveillance

Regeneration and tolerance factor (RTF) is a protein expressed on developing tissue such as the thymus and the placenta. RTF has been reported to down‐regulate cell‐mediated immune responses. To examine the potential role of tumor‐derived RTF to suppressing antitumor responses, we analyzed a panel of seven B cell tumor lines for the membrane RTF using a fluorescein isothiocyanate (FITC) conjugated monoclonal antibody, which reacts with membrane RTF. All the B cell tumor lines we examined express RTF on the cell surface. We also tested conditioned media from these B cell lines for their ability to suppress IL‐2R expression on activated cells. Conditioned media from each B cell line suppressed IL‐2R expression on activated Jurkat T cells and activated peripheral blood mononuclear cells. A monoclonal antibody to the biologically active portion of RTF reversed this suppressive activity. Finally, the tumor cell population from patients with chronic lymphocytic leukemia was found to express cell surface RTF. Thus, RTF expression could be a new mechanism used by tumor cells to escape immune surveillance. Am. J. Hematol. 61:46–52, 1999. © 1999 Wiley‐Liss, Inc.
Listeria monocytogenes exploits cystic fibrosis transmembrane conductance regulator (CFTR) to escape the phagosome

Virulence of the intracellular pathogen Listeria monocytogenes (Listeria) requires escape from the phagosome into the host cytosol, where the bacteria replicate. Phagosomal escape is a multistep process characterized by perforation, which is dependent on the pore-forming toxin listeriolysin O (LLO), followed by rupture. The contribution of host factors to Listeria phagosomal escape is incompletely defined. Here we show that the cystic fibrosis transmembrane conductance regulator (CFTR) facilitates Listeria cytosolic entry. CFTR inhibition or mutation suppressed Listeria vacuolar escape in culture, and inhibition of CFTR in wild-type mice before oral inoculation of Listeria markedly decreased systemic infection. We provide evidence that high chloride concentrations may facilitate Listeria vacuolar escape by enhancing LLO oligomerization and lytic activity. We propose that CFTR transiently increases phagosomal chloride concentration after infection, potentiating LLO pore formation and vacuole lysis. Our studies suggest that Listeria exploits mechanisms of cellular ion homeostasis to escape the phagosome and emphasize host ion-channel function as a key parameter of bacterial virulence.
Endosidin 7 Speci fi cally Arrests Late Cytokinesis and Inhibits Callose Biosynthesis , Revealing Distinct Traf fi cking Events during Cell Plate Maturation 1 [ W ] [ OPEN ]

Although cytokinesis is vital for plant growth and development, our mechanistic understanding of the highly regulated membrane and cargo transport mechanisms in relation to polysaccharide deposition during this process is limited. Here, we present an in-depth characterization of the small molecule endosidin 7 (ES7) inhibiting callose synthase activity and arresting late cytokinesis both in vitro and in vivo in Arabidopsis (Arabidopsis thaliana). ES7 is a specific inhibitor for plant callose deposition during cytokinesis that does not affect endomembrane trafficking during interphase or cytoskeletal organization. The specificity of ES7 was demonstrated (1) by comparing its action with that of known inhibitors such as caffeine, flufenacet, and concanamycin A and (2) across kingdoms with a comparison in yeast. The interplay between cell plate-specific post-Golgi vesicle traffic and callose accumulation was analyzed using ES7, and it revealed unique and temporal contributions of secretory and endosomal vesicles in cell plate maturation. While RABA2A-labeled vesicles, which accumulate at the early stage of cell plate formation, were not affected by ES7, KNOLLE was differentially altered by the small molecule. In addition, the presence of clathrin-coated vesicles in cells containing elevated levels of callose and their reduction under ES7 treatment further support the role of endocytic membrane remodeling in the maturing cell plate while the plate is stabilized by callose. Taken together, these data show the essential role of callose during the late stages of cell plate maturation and establish the temporal relationship between vesicles and regulatory proteins at the cell plate assembly matrix during polysaccharide deposition.
Farmer-Processor Relationships in the CIS Dairy Sector: Key Findings from the Sidcisa Research Project

The dairy sector is an important component of rural economies in the Commonwealth of Independent States (CIS), providing vital employment and income, in an environment of weak social security and scarce job opportunities. Dairy farming in the CIS encompasses a wide diversity of farms: from 1 and 2 cow units, selling via village collecting stations, which provide an important subsidiary income for vulnerable groups, particularly the elderly, up to ‘super-large’ corporate farms, some of which have witnessed significant recent investment and control thousands of hectares. The Supporting the International Development of CIS Agriculture (SIDCISA) project has sought to understand the Supply Chain Relationships (SCR) of this diverse range of commercial milk producers. In particular we seek to analyse the degree of satisfaction with SCR and analyse the linkages between procurement practices and satisfaction, growth and investment. As far as we are aware this is the first comprehensive, cross-national survey of dairy farming in the CIS. This paper presents an overview of key findings from survey work conducted in Armenia, Moldova and the Dnepropetrovsk region of Ukraine. A more detailed presentation of the context of the study and results are available elsewhere.
Bone age in 116 untreated patients with Turner's syndrome rated by a computer‐assisted method (CASAS)

Bone age maturation in 116 untreated patients with Turner's syndrome was evaluated in a cross‐sectional and longitudinal analysis. A total of 265 radiographs were rated using the TW2‐RUS method on the computer‐assisted skeletal age score (CASAS) system. Bone age was found to be retarded from the chronological age of 3 to 6y. Between the ages of 7 and 12y bone age almost equalled chronological age and progressed normally at a rate of 1 y y−1. Bone maturation slowed down thereafter and epiphyseal closure was not reached before the age of 17 y. Reference data are presented on bone age and a bone age maturation curve for untreated patients with Turner's syndrome to be used in clinical practice. In the assessment of bone age and bone age velocity in Turner's syndrome the CASAS system produced reliable and valid results. The absolute difference between repeated bone age ratings was 0.26“y”(median) with a range of 0.00‐0.56“y”. Future studies evaluating the effect of growth‐promoting treatment in Turner's syndrome should use a computerized method for the determination of bone age.
Interference Aware Routing Game for Cognitive Radio Multi-Hop Networks

In this paper, we introduce a distributed dynamic routing algorithm in multi-hop cognitive radio (CR) networks, in which secondary users (SUs) want to minimize their interference to the primary users (PUs) while keeping the delay along the route low. We employ a cognitive pilot channel (CPC) for SUs to be able to access the information about PUs, including PUs' locations and channel conditions. Medial axis with a relaxation factor is used as a reference path for the routing, along which we develop a hierarchical structure for multiple sources to reach their destinations. We introduce a temporal and spatial dynamic non-cooperative game to model the interactions among the SUs as well as their influences on the PUs, and obtain by backward induction a set of mixed (behavioral) Nash equilibrium strategies. We also employ a multi-stage fictitious play learning algorithm for distributed routing, which minimizes the overall interference from the SUs to the PUs, as well as the average packet delay along the route from the SU nodes to their destinations. Simulation results show that our proposed algorithm can avoid congestion in the CR network and minimize delay while keeping the interference level low.
Mergers, concurrent marketing mechanisms and the performance of sequential auctions

We analyze the effects of mergers and the introduction of concurrent marketing mechanisms on the seller’s revenue, price trend and efficiency in sequential auctions under complete information with asymmetric bidders. First, we provide conditions for bidders to be strategic when the number of objects is less or greater than the number of bidders as this impacts upon the set of possible mergers. Second, we show that mergers may simultaneously increase the seller’s revenue and improve efficiency. Third, we show that having a marketing mechanism working alongside the auction can increase or decrease the average auction price. We use weekly data about Quebec’s daily hog auction to ascertain the effects of a merger and of changes in the weights of concurrent marketing mechanisms on daily auction prices. Our empirical analysis relies on an endogenous structural change test which detected three breaks corresponding to: i) the introduction of a new concurrent mechanism, ii) a joint-venture partnership of the two largest hog processing firms and iii) an announcement by Canada’s Competition Bureau authorizing the full merger of the same two firms.
Distributed Josephson junction arrays as local oscillators

The power and linewidth of the radiation, near 250 GHz, of small distributed Josephson junction array sources have been measured using a single-chip integrated source and receiver. The intermediate frequency (IF), coupled off the chip to a room-temperature spectrum analyzer, permitted a direct measurement of the oscillator linewidth. The one-dimensional arrays were of a novel design with junctions placed in 1/4 wavelength lumps separated by one half wavelength. The measured power ( approximately=2 mu W) and linewidth ( approximately=10 MHz) for the 10 junction sources were in reasonable agreement with those obtained from computer simulations. <<ETX>>
Privacy-enhancing methods for e-health applications: how to prevent statistical analyses and attacks

This paper investigates the privacy issues in the context of e-health and will especially consider e-health portals which provide patients access to Electronic Health Records (EHRs). Since e-health portals can be accessed via the internet, security and privacy issues arise that have to be considered carefully. Besides the traditional security properties, we focus mainly on additional threats, namely the disclosure attack, the anonymity set attack and statistical analysis of metadata. A disclosure attack takes place if a person 'motivates' or even forces another one to present her EHR. We propose so-called multiple identities, which help to eliminate this attack. In the context of anonymous authentication, we will point out weaknesses regarding the choice of anonymity sets. Additionally, by applying statistical analysis on the metadata of an e-health portal, it is possible to determine relevant information which could have negative effects on the patient. We present a concept that includes pseudonymisation of e-health portals, multiple identities, obfuscation of metadata and anonymity methods to prevent the above-mentioned attacks and make statistical analysis difficult. Furthermore, all privacy-enhancing methods do not rely on application-layer mechanisms (which in general can easily be bypassed by insiders), but are based on cryptographic primitives which are state of the art.
MAGNETOPHORETIC MANIPULATION IN MICROSYSTEM USING I-PDMS MICROSTRUCTURES

This paper reports the use of a recent composite material, i-PDMS, made of carbonyl iron microparticles mixed in a PolyDiMethylSiloxane (PDMS) matrix, for magnetophoretic functions such as capture and separation. Indeed, we demonstrated that this composite can locally generate high magnetic field gradients when placed between two permanent magnets. We first investigated the molding resolution offered by i-PDMS to obtain microstructures of various sizes and shapes. Then, we implemented 500 μm i-PDMS microstructures in a microfluidic channel and studied the influence of flow rate on the trapping and deviation of paramagnetic beads flowing at the neighborhood of the composite material.