Miracle-dz/UniFAR-FTUs huggingface dataset:
Lipopolysaccharide smooth-rough phase variation in bacteria of the genus Chlamydia

In two strains of Chlamydia psittaci and in Chlamydia trachomatis serotype L1, we have detected a so-far-unknown antigen which (i) is resistant to heat and proteolytic digestion, (ii) can be extracted with phenol-water into the water phase, (iii) gives a ladder-like banding pattern in sodium dodecyl sulfate-polyacrylamide gel electrophoresis, (iv) is immunogenic in rabbits and mice, and (v) contains immunoreactivity of lipid A, a common and characteristic component of gram-negative lipopolysaccharides (LPS). Thus, chlamydiae contain, in addition to the known rough-type LPS, another LPS type which is phenotypically smooth (S-LPS). S-LPS was observed preferentially in chlamydiae grown in the yolk sac of embryonated eggs; it was, however, also detected by immunofluorescence in tissue culture-grown chlamydiae with a monoclonal antibody against S-LPS.
Two Adjacent Trimeric Fas Ligands Are Required for Fas Signaling and Formation of a Death-Inducing Signaling Complex

ABSTRACT The membrane-bound form of Fas ligand (FasL) signals apoptosis in target cells through engagement of the death receptor Fas, whereas the proteolytically processed, soluble form of FasL does not induce cell death. However, soluble FasL can be rendered active upon cross-linking. Since the minimal extent of oligomerization of FasL that exerts cytotoxicity is unknown, we engineered hexameric proteins containing two trimers of FasL within the same molecule. This was achieved by fusing FasL to the Fc portion of immunoglobulin G1 or to the collagen domain of ACRP30/adiponectin. Trimeric FasL and hexameric FasL both bound to Fas, but only the hexameric forms were highly cytotoxic and competent to signal apoptosis via formation of a death-inducing signaling complex. Three sequential early events in Fas-mediated apoptosis could be dissected, namely, receptor binding, receptor activation, and recruitment of intracellular signaling molecules, each of which occurred independently of the subsequent one. These results demonstrate that the limited oligomerization of FasL, and most likely of some other tumor necrosis factor family ligands such as CD40L, is required for triggering of the signaling pathways.
Reverse engineering of source code to sequence diagram using abstract syntax tree

Reverse engineering from a source code to a sequence diagram can be very important in the software maintenance process. On the process of reverse engineering, there are a lot of models/approaches that can be used. Extract-abstract-present model is one model that can be applied because every stage in the model can represent reverse engineering process. On stages in the model, the extracted source code is converted into a specific structure for easy analyzed in the next process. AST (abstract syntax tree) is one of the structures that can be used in the extraction process. AST is commonly used as a data structure in the compiler. This research focus on the process of reverse engineering of source code to sequence diagrams. AST is used to generate the sequence diagram. We have implemented this idea in an application called REVUML. REVUML has helped in the process of understanding the flow of the source code in a software application. Our research concludes that the structure of AST has been able to assist in the reverse engineering process. Additionally our implementation has shown that AST can reveal sequences of statements in the source code which can help developers in the reverse engineering process.
Regulated recruitment of DC‐SIGN to cell–cell contact regions during zymosan‐induced human dendritic cell aggregation

Zymosan is a β‐glucan, mannan‐rich yeast particle widely used to activate the inflammatory response of immune cells. We studied the zymosan‐binding potential of human dendritic cells (hDCs) by using specific carbohydrate inhibitors and blocking monoclonal antibodies. We show that DC‐specific intercellular adhesion molecule‐grabbing nonintegrin (DC‐SIGN) is a major nonopsonic recognition receptor for zymosan on hDCs. Indeed, blocking of DC‐SIGN inhibited the inflammatory response of DCs to zymosan. We compared the zymosan‐binding capacity of hDC‐SIGN to that of Dectin‐1 and complement receptor 3 (CR3), which are receptors involved in the nonopsonic recognition of these yeast‐derived particles. Dectin‐1‐ and DC‐SIGN‐K562 cells bound to zymosan particles, whereas CR3‐K562 cells did not. DC‐SIGN and Dectin‐1 were also expressed in COS cells to compare their ability to trigger particle internalization in a nonphagocytic cell line. DC‐SIGN transfectants were unable to internalize bound particles, indicating that DC‐SIGN is primarily involved in recognition but not in particle internalization. Zymosan induced a rapid DC aggregation that was accompanied by a dramatic change of DC‐SIGN distribution in the plasma membrane. Under resting conditions, DC‐SIGN was diffusely distributed through the cell surface, displaying clusters at the free leading edge. Upon zymosan treatment, DC‐SIGN was markedly redistributed to cell–cell contacts, supporting an adhesion role in DC–DC interactions. The mechanism(s) supporting DC‐SIGN‐mediated intercellular adhesion were further investigated by using DC‐SIGN‐K562 aggregation. DC‐SIGN was highly concentrated at points of cell–cell contact, suggesting a role for enhanced avidity during DC‐SIGN‐mediated intercellular adhesion.
Effects of Lipopolysaccharide Biosynthesis Mutations on K1 Polysaccharide Association with the Escherichia coli Cell Surface

ABSTRACT The presence of cell-bound K1 capsule and K1 polysaccharide in culture supernatants was determined in a series of in-frame nonpolar core biosynthetic mutants from Escherichia coli KT1094 (K1, R1 core lipopolysaccharide [LPS] type) for which the major core oligosaccharide structures were determined. Cell-bound K1 capsule was absent from mutants devoid of phosphoryl modifications on l-glycero-d-manno-heptose residues (HepI and HepII) of the inner-core LPS and reduced in mutants devoid of phosphoryl modification on HepII or devoid of HepIII. In contrast, in all of the mutants, K1 polysaccharide was found in culture supernatants. These results were confirmed by using a mutant with a deletion spanning from the hldD to waaQ genes of the waa gene cluster to which individual genes were reintroduced. A nuclear magnetic resonance (NMR) analysis of core LPS from HepIII-deficient mutants showed an alteration in the pattern of phosphoryl modifications. A cell extract containing both K1 capsule polysaccharide and LPS obtained from an O-antigen-deficient mutant could be resolved into K1 polysaccharide and core LPS by column chromatography only when EDTA and deoxycholate (DOC) buffer were used. These results suggest that the K1 polysaccharide remains cell associated by ionically interacting with the phosphate-negative charges of the core LPS.
Ensemble of Gaussian mixture localized neural networks with application to phone recognition

In this paper we present Ensemble of Gaussian Mixture Localized Neural Networks (EGMLNNs), a model for the joint probability density of input as well as output variables of any general mapping to be estimated. The model aims at identifying clusters in the input data, thereby replacing one complex classiﬁer with an ensemble of relatively simpler classiﬁers, each of which is localized to operate within its associated cluster. We present an algorithm for maximum likelihood parameter estimation for this model using Expectation Maximization (EM). The reported results on phone recognition task on TIMIT database show that the model is able to obtain performance improvement over a single complex classiﬁer while also reducing the computational complexity required for testing.
Hidden understanding models for statistical sentence understanding

We describe the first sentence understanding system that is completely based on learned methods both for understanding individual sentences, and determining their meaning in the context of preceding sentences. We divide the problem into three stages: semantic parsing, semantic classification, and discourse modeling. Each of these stages requires a different model. When we ran this system on the last test (December, 1994) of the ARPA Air Travel Information System (ATIS) task, we achieved a 13.7% error rate. The error rate for those sentences that are context-independent (class A) was 9.7%.
Adaptive fault identification for a class of nonlinear dynamic systems

This paper is concerned with the diagnosis problem of actuator faults for a class of nonlinear systems. It is assumed that the upper bound of the Lipschtiz constant of the nonlinearity in the faulty system is unknown. Then, a new nonlinear observer for fault diagnosis based on an adaptive estimator is proposed. Moreover, by making use of the designed adaptive observer with on-line update control law without σ-modification condition to approximate the faulty system, it is proved that the estimate error of the adaptive control parameter, the output observation error and the error between the system fault and the corresponding estimate value are uniformly ultimately bounded via Lyapunov stability analysis. Finally, simulation examples are provided to illustrate the efficiency of the proposed fault identification approach.
Model reduction studies in LQG optimal control design for high-speed tilting railway carriages

The paper studies the utilisation of model reduction techniques, both physical-based and mathematical-based, in designing simplified LQG optimal tilt controllers to improve the curving performance of railway coaches at increased running speed. The schemes make exclusive use of local practical signal measurements, i.e. sensors mounted on the current passenger coach. The fundamental problem related with straightforward classical nulling-feedback control is presented, while the commercially-used command-driven with precedence scheme is introduced. A combination of simulation results and, a recently proposed, tilt control system assessment method are employed for assessing the performance of the designed LQG controller
The Urokinase/PAI-2 Complex

The efficient inactivation of urokinase plasminogen activator (uPA) by plasminogen activator inhibitor type 2 (PAI-2) at the surface of carcinoma cells is followed by rapid endocytosis of the uPA-PAI-2 complex. We now show that one pathway of this receptor-mediated endocytosis is mediated via the low density lipoprotein receptor-related protein (LRP) in prostate cancer cells. Detailed biochemical analyses using ligand binding assays and surface plasmon resonance revealed a novel and distinct interaction mechanism between native, human LRP and uPA-PAI-2. As reported previously for PAI-1, inhibition of uPA by PAI-2 significantly increased the affinity of the complex for LRP (KD of 36 nm for uPA-PAI-2 versus 200 nm for uPA). This interaction was maintained in the presence of uPAR, confirming the validity of this interaction at the cell surface. However, unlike PAI-1, no interaction was observed between LRP and PAI-2 in either the stressed or the relaxed conformation. This suggests that the uPA-PAI-2-LRP interaction is mediated by site(s) within the uPA molecule alone. Thus, as inhibition of uPA by PAI-2 resulted in accelerated clearance of uPA from the cell surface possibly via its increased affinity for LRP, this represents a mechanism through which PAI-2 can clear proteolytic activity from the cell surface. Furthermore, lack of a direct interaction between PAI-2 and LRP implies that downstream signaling events initiated by PAI-1 may not be activated by PAI-2.
Predicting GFR in children and adults: a comparison of the Cockcroft-Gault, Schwartz, and modification of diet in renal disease formulas.

BACKGROUND A rapid prediction of glomerular filtration rate (GFR) is often needed in clinics. Formulas based on plasma creatinine level are being increasingly used, Schwartz for children, supposed to give GFR; Cockcroft-Gault for adults, supposed to indicate the creatinine clearance; and a recent formula introduced by the Modification of Diet in Renal Disease (MDRD) group. Our objective was to test whether one single formula could suffice and which one gives the best estimation of GFR. METHODS In 198 children (with two kidneys, single kidney, or renal transplant) and 116 adults (single kidney and transplanted), we measured inulin clearance and creatinine clearance and calculated Cockcroft-Gault, MDRD and, in children only, Schwartz. Data were compared with analysis of variance (ANOVA), regression statistics, and concordance studies. RESULTS In patients over 12 years of age, Cockcroft-Gault was almost similar to GFR corrected for body surface and creatinine clearance exceeded GFR by more than 20%; Schwartz was above creatinine clearance excepted for transplanted children. In younger children, no prediction approached GFR. Predictions were well correlated with GFR, but concordance studies showed Schwartz with dispersed results and GFR overestimated (20 mL/min/1.73 m2); Cockcroft-Gault was close to GFR and results were dispersed; MDRD in children gave a large overestimation and badly dispersed results; in transplanted adults its prediction was good. CONCLUSION Cockcroft-Gault prediction could be used for children over 12 years of age and adults; it should not be considered as creatinine clearance but as GFR corrected for body surface, it is merely a prediction, 95% of the results are between +/-40 mL/min/1.73 m(2) in children and +/-30 mL/min/1.72 m(2) in adults. In younger children no formula is satisfying.
The Effect of Interference in Vehicular Communications on Safety Factors

This paper studies how the interference of vehicular communications affects the safety of vehicles in a vehicular ad hoc network. Different signal propagation models with and without carrier sensing are considered for the dissemination of periodic safety messages. Then, by employing the results for different packet success probability of the vehicles, we compare the expected collision probability of vehicles for different signal fading models. Our results show how the collision probabilities of vehicles in the network vary with respect to different models and designs.
Nanoparticle detection of respiratory infection

Abstract Respiratory viruses are a constant concern for all demographics. Examples include established viruses such as respiratory syncytial virus (RSV), the leading cause of respiratory infection in infants and young children, and emerging viruses such as severe acute respiratory syndrome (SARS), which reached near pandemic levels in 2003, or H1N1 (swine) influenza. Despite this prevalence, traditional methods of virus detection are typically labor intensive and require several days to successfully confirm infection. Recently, however, nanoparticle‐based detection strategies have been employed in an effort to develop detection assays that are both sensitive and expedient. Each of these platforms capitalizes on the unique properties of nanoparticles for the detection of respiratory viruses. In this article, several nanoparticle‐based scaffolds are discussed.Gold nanoparticles (AuNPs) have been functionalized with virus specific antibodies or oligonucleotides. In each of these constructs, AuNPs act as both an easily conjugated scaffolding system for biological molecules and a powerful fluorescence quencher. AuNPs have also been immobilized and used as electrochemical transducers. They efficiently serve as a conducting interface of electrocatalyic activity making them a powerful tool in this application. Quantum dots (QDs) posses unique fluorescence properties that have also been explored for their application to virus detection when combined with direct antibody conjugation or streptavidin‐biotin binding systems. QDs have an advantage over many traditional fluorophores because their fluorescence properties can be finely tuned and they are resistant to photobleaching. The development of these nanoparticle‐based detection strategies holds the potential to be a powerful method to quickly and easily confirm respiratory virus infection. WIREs Nanomed Nanobiotechnol 2010 2 277–290 This article is categorized under: 1 Diagnostic Tools > In Vitro Nanoparticle-Based Sensing2 Therapeutic Approaches and Drug Discovery > Nanomedicine for Respiratory Disease
The influence of semi-magnetic wedges on the electromagnetic variables and the harmonic content in induction motors

In this work the influence of semi-magnetic stator wedges on the electromagnetic characteristics and the behavior of the induction motor is investigated. The study will be carried out using FEM analysis. The spatial and time-dependant electromagnetic variables of the motors will be studied. The analysis will reveal that the application of wedges decreases the higher harmonic content of the electromagnetic torque, stator current and magnetic flux density, leading to higher efficiency at nominal speed.
Prevention of Atelectasis in Morbidly Obese Patients during General Anesthesia and Paralysis: A Computerized Tomography Study

Background:Morbidly obese patients show impaired pulmonary function during anesthesia and paralysis, partly due to formation of atelectasis. This study analyzed the effect of general anesthesia and three different ventilatory strategies to reduce the amount of atelectasis and improve respiratory function. Methods:Thirty patients (body mass index 45 ± 4 kg/m2) scheduled for gastric bypass surgery were prospectively randomized into three groups: (1) positive end-expiratory pressure of 10 cm H2O (PEEP), (2) a recruitment maneuver with 55 cm H2O for 10 s followed by zero end-expiratory pressure, (3) a recruitment maneuver followed by PEEP. Transverse lung computerized tomography scans and blood gas analysis were recorded: awake, 5 min after induction of anesthesia and paralysis at zero end-expiratory pressure, and 5 min and 20 min after intervention. In addition, spiral computerized tomography scans were performed at two occasions in 23 of the patients. Results:After induction of anesthesia, atelectasis increased from 1 ± 0.5% to 11 ± 6% of total lung volume (P < 0.0001). End-expiratory lung volume decreased from 1,387 ± 581 ml to 697 ± 157 ml (P = 0.0014). A recruitment maneuver + PEEP reduced atelectasis to 3 ± 4% (P = 0.0002), increased end-expiratory lung volume and increased Pao2/Fio2 from 266 ± 70 mmHg to 412 ± 99 mmHg (P < 0.0001). PEEP alone did not reduce the amount of atelectasis or improve oxygenation. A recruitment maneuver + zero end-expiratory pressure had a transient positive effect on respiratory function. All values are presented as mean ± SD. Conclusions:A recruitment maneuver followed by PEEP reduced atelectasis and improved oxygenation in morbidly obese patients, whereas PEEP or a recruitment maneuver alone did not.
Engineered Muscle: A Tool for Studying Muscle Physiology and Function

Recent advances in skeletal muscle tissue engineering have resulted in an in vitro tissue model that can be used for studying the effects of genetic alterations, pharmacological interventions, and exercise on muscle physiology and function. Here, we present applications for this technology to further our understanding of the molecular mechanisms underlying skeletal muscle adaptation in response to exercise.
Integrating object-oriented requirements specifications with formal notations

We propose an integration of an extension of Bailin's object-oriented requirements specification (OOS) (1989) with a formal notation (Z), called OOSZ. The OOS is used to guide the derivation of Z specifications. In OOSZ a function process is converted into an operation schema. An entity process is manifested through a state schema, an instance creation operation schema and an abstract operation schema. Correctness conjectures are generated for verifying the consistency of intralevel and interlevel specifications. These are illustrated using the problem domain of Auto Banking Systems. The bringing together of diagrammatical and text elements of OOS specifications in Z notations offers three major benefits. First, the relationship, between ERD and EDFD is tightly coupled compared with Yourdon's SA approach. Second, OOS specifications can be seen both as a structuring mechanism that helps in deriving Z specifications, and as a preliminary that assists in ascertaining the clients requirements. Third, Z specifications make it easier to identify omissions or errors.
Naked singularities and other features of self-similar general-relativistic gravitational collapse.

Self-similar solutions are commonly used to describe Newtonian gravitational collapse. We examine, here, the structure of general-relativistic spherical collapse solutions for a perfect fluid with a barotropic equation of state. We find that these solutions are quite different from the homogeneous Oppenheimer-Snyder dust collapse solution on which our intuition is so heavily based. The most amazing feature that we find is the generic appearance of naked singularities in these solutions.
Evolution of the RADARSAT Program

The RADARSAT program takes its origin in the seventies when the Canadian Government was seeking a reliable technology to ensure safe navigation through sea ice. At that time there was an expectation that it would be necessary for large tanker to navigate through the Beaufort Sea to transport oil extracted from drilling platforms. During the same period the Canadian Center for Remote Sensing was developing SAR applications using an airborne SAR instrument on a Convair 580. One of these applications of great interest for the Canadian Ice Service was ice discrimination provided by the C-band SAR data to support the development of ice map to guide navigation in winter in the Gulf of Saint-Lawrence Seaway. With the combination of both, interest for oil transportation in the Beaufort Sea and the need for accurate and frequent ice map the business case for RADARSAT- 1 was born. This paper provides an overview on the RADARSAT program since its beginning and is partially based on a presentation delivered in October 2013 at the Canadian Space Agency on the motivation and evolution of the RADARSAT program [1].
Growth Rate and Cell Size Modulate the Synthesis of, and Requirement for, G1-Phase Cyclins at Start

ABSTRACT In Saccharomyces cerevisiae, commitment to cell cycle progression occurs at Start. Progression past Start requires cell growth and protein synthesis, a minimum cell size, and G1-phase cyclins. We examined the relationships among these factors. Rapidly growing cells expressed, and required, dramatically more Cln protein than did slowly growing cells. To clarify the role of cell size, we expressed defined amounts of CLN mRNA in cells of different sizes. When Cln was expressed at nearly physiological levels, a critical threshold of Cln expression was required for cell cycle progression, and this critical threshold varied with both cell size and growth rate: as cells grew larger, they needed less CLN mRNA, but as cells grew faster, they needed more Cln protein. At least in part, large cells had a reduced requirement for CLN mRNA because large cells generated more Cln protein per unit of mRNA than did small cells. When Cln was overexpressed, it was capable of promoting Start rapidly, regardless of cell size or growth rate. In summary, the amount of Cln required for Start depends dramatically on both cell size and growth rate. Large cells generate more Cln1 or Cln2 protein for a given amount of CLN mRNA, suggesting the existence of a novel posttranscriptional size control mechanism.