Miracle-dz/UniFAR-FTUs huggingface dataset:
Lipooligosaccharide‐independent alteration of cellular homeostasis in Neisseria meningitidis‐infected epithelial cells

Neisseria meningitidis (MC) is an important cause of meningitis and septic shock. Primary loose attachment of MC to host epithelial cells is mediated by type IV pili. Lipooligosaccharide (LOS), opacity (Opa) proteins and glycolipid adhesins facilitate subsequent tight attachment. MC infection causes numerous changes in host epithelial cell homeostasis. These include cortical plaque formation, increased expression of proinflammatory cytokines and alterations in host iron homeostasis. Using both biochemical and genetic approaches, we examined the role of LOS in mediating these events. We first examined specific cellular iron homeostasis changes that occur following addition of purified MC LOS to epithelial cells. Using an MC mutant that completely lacks LOS (MC lps tbp), we examined pili‐mediated attachment and cortical plaque formation in human endocervical epithelial cells (A431). We also tested whether the lack of LOS alters cellular homeostasis, including changes in the levels of host stress response factors and proinflammatory cytokines. MC lps tbp elicited the formation of cortical plaques in A431 cells. However, the plaques were less pronounced than those formed by the MC parent. Surprisingly, the proinflammatory cytokine TNFα was upregulated during infection in MC lps tbp‐infected cells. Furthermore, alterations in iron homeostasis, including lower transferrin receptor 1 (TfR‐1) levels, altered TfR‐1 trafficking, an ‘iron‐starvation’ gene expression profile and low iron regulatory protein (IRP) binding activity are independent of LOS. Our results demonstrate that LOS is partially involved in both the attachment to host cells and formation of cortical plaques. However, TNFα induction and changes in iron homeostasis observed in MC‐infected epithelial cells are independent of LOS.
Analysis and visualization of temporal variations in video

Our world is constantly changing, and it is important for us to understand how our environment changes and evolves over time. A common method for capturing and communicating such changes is imagery – whether captured by consumer cameras, microscopes or satellites, images and videos provide an invaluable source of information about the time-varying nature of our world. Due to the great progress in digital photography, such images and videos are now widespread and easy to capture, yet computational models and tools for understanding and analyzing time-varying processes and trends in visual data are scarce and undeveloped. In this dissertation, we propose new computational techniques to efficiently represent, analyze and visualize both short-term and long-term temporal variation in videos and image sequences. Small-amplitude changes that are difficult or impossible to see with the naked eye, such as variation in human skin color due to blood circulation and small mechanical movements, can be extracted for further analysis, or exaggerated to become visible to an observer. Our techniques can also attenuate motions and changes to remove variation that distracts from the main temporal events of interest. The main contribution of this thesis is in advancing our knowledge on how to process spatiotemporal imagery and extract information that may not be immediately seen, so as to better understand our dynamic world through images and videos. Thesis Supervisor: William T. Freeman Title: Professor of Electrical Engineering and Computer Science
Automating Supply Chains

A recent study found that supply-chain problems cost companies between 9 and 20 percent of their value over a six-month period (T.J. Becker, 2000). The problems range from part shortages to poorly utilized plant capacity. When you place this in the context of the overall business-to-business (B2B) market expected to reach US$7 trillion by 2004 (37 percent of which is projected to be e-commerce sales), it is easy to see that effective supply-chain management (SCM) tools could save companies billions of dollars. Attempts to automate solutions to these problems are complicated by the need for the different companies in a supply chain to maintain the integrity and confidentiality of their information systems and operations. The modeling technologies currently used within the manufacturing business-to-business standards communities, such as the Open Applications Group (http://www.openapplications.org) and RosettaNet (http://www.rosettanet.org) do a good job of capturing user requirements. Unfortunately, current technologies do not explicitly link the requirements to formal process models. This missing link is crucial to efficient SCM implementations.
Cadmium selenide and zinc sulfide nanoparticles - challenges in synthesis revealed through optical properties

Semiconductor nanoparticles, also called quantum dots (QDs), are emerging as the new class of fluorescent labeling materials in biological applications. In comparison with fluorescent dyes, QDs have unique optical and electronic properties: size-tunable light emission, high brightness, broad excitation with possible simultaneous excitation of multiple fluorescent colors. One of the key challenges for synthesis chemistry is to produce small size and monodisperse (single color) QDs with high reproducibility. In this report we describe synthesis and characterization of CdSe and ZnS QDs using two different synthesis approaches. The first is carried out at high temperature in trioctyl-phosphine oxide (TOPO) as a coordinating solvent, while the second synthesis is carried out at lower temperature in ethylene glycol. We present the challenges in nanoparticle synthesis and show ways, in which these could be overcome
Invasive validation of the Complior Analyse in the assessment of central artery pressure curves: a methodological study

IntroductionArteries are the target, the place, and the common denominator of cardiovascular diseases; hence, study of arterial function is of greatest importance in clinical practice. The aim of this study was to evaluate the accuracy of carotid pulse wave analysis using the new version of the Complior device – the Complior Analyse. Methods and resultsThis was a cross-sectional study that included 15 patients (seven women), mean age 62.07±10.59 years, referenced for cardiac catheterization. Pressure curves were obtained simultaneously in the ascending aorta (invasively) and in the right common carotid artery (using the Complior Analyse). Mean central arterial pressures, augmentation indexes, and wave morphology obtained using both methods were compared. A good concordance between methods was obtained for all the parameters measured, with intraclass correlation coefficients above 0.9. Bland–Altman analysis also indicated a good accuracy profile of the Complior device, with small mean differences observed for all parameters and most values confined within 2 SD of the mean difference. This was further confirmed by the strong Pearson correlation coefficients, with r2 coefficients above 0.92 for all the variables studied. The correlations observed were independent of sex, age, arterial pressure, and BMI. ConclusionThe results presented and available research clearly indicate that the Complior Analyse device measures carotid pressure waves accurately; therefore, it is a simple and reliable noninvasive alternative for pressure wave analysis.
Convergence of Petviashvili's Iteration Method for Numerical Approximation of Stationary Solutions of Nonlinear Wave Equations

We analyze a heuristic numerical method suggested by V. I. Petviashvili in 1976 for approximation of stationary solutions of nonlinear wave equations. The method is used to construct numerically the solitary wave solutions, such as solitons, lumps, and vortices, in a space of one and higher dimensions. Assuming that the stationary solution exists, we find conditions when the iteration method converges to the stationary solution and when the rate of convergence is the fastest. The theory is illustrated with examples of physical interest such as generalized Korteweg--de Vries, Benjamin--Ono, Zakharov--Kuznetsov, Kadomtsev--Petviashvili, and Klein--Gordon equations.
Protein–protein interactions in actin–myosin binding and structural effects of R405Q mutation: A molecular dynamics study

Detailed residue‐wise interactions involved in the binding of myosin to actin in the rigor conformation without nucleotides have been examined using molecular dynamics simulations of the chicken skeletal myosin head complexed with two actin monomers, based on the cryo‐microscopic model of Holmes et al. (Nature 2003;425:423–427). The overall interaction is largely electrostatic in nature, because of the charged residues in the four loops surrounding the central primary binding site. The 50k/20k loop, disordered in crystal structures and in simulations of free myosin in solution, was found to be in a conformation stabilized with 1∼2 internal salt bridges. The cardiomyopathy loop forms 2∼3 interprotein salt bridges with actin monomers upon binding, whereas its Arg405 residue, the mutation site associated with the hypertrophic cardiomyopathy, forms a strong salt bridge with Glu605 in the neighboring helix away from actin in the actin‐bound myosin. The myopathy loop of the R405Q mutant maintains a high degree of two‐strand β‐sheet character when bound to actin with the corresponding salt bridges broken. Proteins 2006. © 2006 Wiley‐Liss, Inc.
Declining Influence of Race on the Outcome of Living‐Donor Renal Transplantation

A racial disparity in graft survival for renal transplant recipients has been documented for both cadaveric and living‐donor transplants. In the present single‐center study we analyzed graft survival by race for recipients of living‐donor kidney transplants in three eras: 1985–89, 1990–94, and 1995–2000. There was an intensification of the immunosuppressant regimen beginning in 1996, such that all patients received cyclosporine or tacrolimus with mycophenolate and prednisone. Graft survival was analyzed using the Cox proportional hazards model. There were 79 black recipients and 210 white recipients with no difference in mean age, degree of HLA matching, or proportion of recipients with diabetes as the cause of end‐stage renal disease. Using all data from 1985 to 2000, graft survival was significantly better for whites vs. blacks adjusted for age, gender, diabetes, era of the transplant, and haplotype match (p = 0.05). However, when analyzed by era, there was a temporal trend for a progressive decrease in the racial disparity in graft survival. In confirmation of this effect, there was a significant race–era interaction (p = 0.01) on multivariable Cox proportional hazards analysis. The most recent data from the United States Renal Data System (USRDS) show a similar decrease in the racial difference in 1‐year graft survival. We conclude that the influence of race on living‐donor graft survival is diminishing over time.
Design and implementation of a 9-bit 8MHz DPWM with AMI06 process

This paper presents one solution to a question what is the maximum switching frequency of a hybrid digital pulse width modulator (DPWM) if semiconductor process is given and resolution bit number is set high. This paper also proposes a hybrid DPWM structure where voltage controlled oscillator (VCO) and delay line are separated so as to enhance design flexibility and decrease power consumption. And, a phase locked loop is included in the DPWM providing wide-frequency range signal synchronization as well as process, voltage and temperature (PVT) insensitivity facilitating accurate switching frequency control. Taking low cost two metal layers 0.6¿m AMI06 process and 9-bits resolution bit requirement as an example, a 8MHz switching frequency DPWM is designed and implemented in 0.703mm2 die via MOSIS educational program. Chip test result showed that the maximal switching frequency approaches 7.4MHz when DPWM performance is guaranteed, the power consumption is 144¿A/MHzand the synchronization switching frequency range is from 1.8MHz to 7.4MHz.
Mechanical Properties Of The Support Tripod In Running Insects : The Role Of Preflexes In Dynamic Stabilization

Despite variations ranging from leg number and shape to type of skeleton employed, terrestrial runners from mammals to arthropods produce ground reaction forces that can be modeled as a spring-mass system with the same dimensionless stiffness (Blickhan and Full, 1993). There are two major beneficial consequences of bouncing while running: 1) the ability to use springs to store and return elastic strain energy (Alexander, 1988) and 2) passive selfstabilization resulting from a well tuned mechanical (musculo-skeletal) system (Seyfarth et al, 2002; Schmitt et al, 2002).
Analyzing Covert Channels on Mobile Devices Master Thesis

In this work we investigate the problem of stealthy communication between colluding applications on smartphones running the popular Android operating system. Through collusion, applications can cooperatively perform operations they would not be able to perform separately, thus escalating their privileges. This can result in privacy infringements and user data leakage. In order to collude, the two applications must communicate in a way that can bypass the application isolation put in place by the operating system. Throughout this thesis we present different ways to bypass the isolation and thereby allow application collusion. As covert channels are by definition harder to implement but also harder to detect, we use them to create a circumvention that is harder to defeat. To understand the full extent of this problem, we implement very different overt and covert channels and analyse them by testing their throughput, bit-error percentage and synchronisation time. Using our implemented channels we analyse some previously existing countermeasures, in particular TaintDroid and XManDroid, and comment on the countermeasures strengths and limitations. Finally we use the lessons learned from implementing these channels and propose individual countermeasures, which can reduce the feasibility of creating such channels. In this scenario preventing hidden communication channels remains an open problem that we believe the research community should put more focus on.
Two-stage fuzzy navigation control of a vision-based intelligent shopping service robot

The paper describes a two-stage fuzzy navigation controller for a vision-based intelligent shopping service robot (ISSR). The navigation strategy of the robot merges two distinct situations. The global navigation strategy concludes the traveling path from the information such as the task styles assigned to the ISSR and the people distribution in the supermarket. The local navigation control consists of two stages. The obstacle avoidance stage is based on visual feedback and sonar sensory information to detect obstacles, in which, an integrated fuzzy controller is designed to offer a smoother navigation. The guiding control stage provides objective guidance to avoid that the robot travels adrift in the supermarket. The simulation results show the feasibility of the proposed navigation control system.
Exemplar-Based Learning Classifier System with Dynamic Matching Range for Imbalanced Data

In this paper, we propose a method to improve ECSDMR which enables appropriate output for imbalanced data sets. In order to control generalization of LCS in imbalanced data set, we propose a method of applying imbalance ratio of data set to a sigmoid function, and then, appropriately update the matching range. In comparison with our previous work (ECSDMR), the proposed method can control the generalization of the appropriate matching range automatically to extract the exemplars that cover the given problem space, wchich consists of imbalanced data set. From the experimental results, it is suggested that the proposed method provides stable performance to imbalanced data set. The effect of the proposed method using the sigmoid function considering the data balance is shown.
The time dependence of chemical modification reveals slow steps in the folding of a group I ribozyme.

L-21 ScaI ribozyme is a linear form of the self-splicing intron from the precursor of the Tetrahymena thermophila LSU intron. The time scales for tertiary folding of L-21 ScaI were investigated in two ways after bringing it from a partially denatured state at 60 degrees C and 1 mM Mg2+ to a renatured state of 15 degrees C and 10 mM Mg2+. First, formation of a catalytically active structure was monitored by measuring the kinetics of the reaction: p*CUCUA3 + G<==>p*CUCU + GA3. This reaction mimics the first step of splicing. After 1 min of folding time, the catalytic rate is roughly 10% of the rate attained after 8 h of folding. This indicates that much of the structure refolds quickly. Also, at least two time scales of folding are observed, separated by a lag time of about 30 min. To define the regions folding on various time scales, all the guanosines of L-21 ScaI were probed with kethoxal at 15 degrees C while folding was in progress. Based on folding time scales, the guanosines can be placed into at least four classes. These are guanosines that (1) are already protected at 60 degrees C in 1 mM Mg2+ or which fold immediately, (2) fold during the lag time, (3) continue to fold after 1 h, and (4) never fold. These results give insight into the folding pathway of a group I ribozyme at nucleotide resolution. This provides useful information on the regions whose foldings are important for catalytic function of the ribozyme. The method may also provide a general way to suggest regions of an RNA that may interact with each other to form tertiary structure.
Reliability and Validity of the Kiddie Mach Scale in Chinese Children

The present study examined the psychometric properties of a translated Chinese version of the Kiddie Mach Scale in a sample of Chinese students (N = 787) ages 9 to 13 years (416 boys, 371 girls; M age = 11.3 yr., SD = 1.3). Results of confirmatory factor analysis showed a three-factor structure to be the most adequate model: Distrust, Lack of faith in human nature, and Dishonesty. These results are similar to the English version, but not the Greek version. The Chinese version exhibited weak internal consistency, but acceptable 4-week test-retest reliability. The Chinese version of the Kiddie Mach Scale was significantly associated with the Basic Empathy Scale. There was a sex effect on Kiddie Mach Scale scores with boys scoring higher on the Total scale and the Distrust subscale. Some items did not seem to function well in Chinese culture. More research will be needed to find items that represent, especially, distrust in Chinese settings.
Comparison of Efficacy of Intraoperative Indocyanine Green Videoangiography in Clipping of Anterior Circulation Aneurysms with Postoperative Digital Subtraction Angiography

ABSTRACT Introduction: The aim of this study is to assess the efficacy of intraoperative indocyanine green videoangiography (ICG-VA) using postoperative digital subtraction angiography (DSA) in clipped anterior circulation aneurysms. Materials and Methods: A prospective study was conducted for 1 year which included thirty patients of anterior circulation aneurysm treated by clipping of aneurysm. Intraoperative ICG-VA was performed on all the patients. Postoperative DSA was performed to assess the efficacy of ICG-VA. Results: Intraoperative ICG-VA revealed the occlusion of aneurysm in all the thirty patients. Postoperative DSA revealed aneurysm neck remnant in two patients and demonstrated no branch occlusion. Conclusions: Intraoperative ICG-VA is useful in assessing the completeness of clipping of cerebral aneurysms and ensures patency of branch vessels, thus providing a better postoperative outcome. It replaces the need for invasive postoperative angiographic imaging in a selected group of patients and is also cost effective.
Anti-inflammatory and Anti-arthritis Activity of Flavonoids Fractions Isolated from Centipeda minima Leaves Extracts in Rats

Centipeda minima has been used since centuries as a traditional medicinal plant in treating a number of disease conditions, the bioactive components responsible for its anti-inflammatory and anti-arthritis activity have not been identified. The present study was planned to isolate flavonoids fractions from Centipeda minima leaves extracts, and assessed anti-inflammatory and anti-arthritis activity in rats. The hydroalcoholic and aqueous extracts of Centipeda minima leaves were prepared and evaluated for in vitro antioxidant activity namely DPPH, total polyphenol content, total flavonol content and reducing power assay. The different fractions were isolated from hydroalcoholic extracts by using column chromatography. The Flavonoids fractions were investigated for anti-inflammatory and anti-arthritis activity in carrageenan rat induced paw oedema, cotton pellet-induced granuloma model and adjuvant induced chronic arthritis in rats. The findings of in vitro antioxidant activity confirmed that hydroalcoholic extracts expressed higher antioxidant activity compared to aqueous extract, and hence hydroalcoholic extracts was further selected for the isolation of various fractions. The results of phytochemical study suggest that FCM6, FCM7 and FCM8 exposed the presence of polyphenol and flavonoids. The fraction FCM6, FCM7 and FCM8 (25 mg/kg) exhibits significant antiinflammatory and anti-arthritis activity. The outcomes suggest that the anti-inflammatory and anti-arthritis activity of isolated fraction was due to presence of flavonoids and polyphenols.
Performance and behaviour of calves reared in groups or individually following an enhanced-growth feeding programme

Nineteen calves were reared in individual pens (IP), and twenty calves were grouped in four pens of five calves each (GP) to study the effects of grouping on behaviour and performance. All calves were on an enhanced-growth feeding programme and had unlimited access to starter. Total dry matter intake (DMI) body weight (BW), serum urea, non-esterified fatty acid (NEFA), cortisol, insulin, and glucose concentrations, and immune response to vaccination were measured. Behaviour patterns categorized as: non-nutritive oral behaviour, cross-sucking, inter-sucking, and self-grooming, were monitored 20 min following the morning and afternoon milk replacer consumption, and at the same times after weaning. There were no differences in final BW and starter DMI between treatments. The decrease of average daily gain (ADG) during the week following weaning was more pronounced in GP than in IP calves. Serum NEFA concentration increased at the beginning of the study in IP calves but serum urea concentrations were greater in GP than in IP calves the week after weaning. Self-grooming increased in both treatments throughout the study but GP calves increased non-nutritive oral behaviour and decreased cross-sucking and inter-sucking behaviours throughout the study. Rearing calves in groups following an enhanced-growth feeding programme did not increase starter intake. Furthermore, cross-sucking and inter-sucking behaviours in calves reared in groups did not seem to cause increased metabolic or immunological distress.
Development and characterization of microsatellite loci in the pantropical fern Hypolepis punctata (Dennstaedtiaceae)

Premise of the study: Microsatellite loci were isolated in Hypolepis punctata (Dennstaedtiaceae) to further study the reproductive ecology of this species. Methods and Results: We developed 16 microsatellite loci from one sample of H. punctata using an enriched genomic library. These loci were characterized in 28 individuals. The number of alleles per locus ranged from two to 10, and the expected heterozygosity ranged from 0.036 to 0.845. Conclusions: The results indicate that the microsatellite markers can facilitate further studies on inferring the phylogeography and population genetics of H. punctata and related species.