Miracle-dz/UniFAR-FTUs huggingface dataset:
Flagellin genes of Yersiniaenterocolitica biotype 1A:playground of evolutiontowards novel flagellin functions

Yersinia enterocolitica strain 8081, representing the high-pathogenic biotype 1B, harbours three flagellin genes arranged in tandem in the order fliC3, fliC, fliC2. The genes are organized monocistronic but coordinately expressed under the control of the flagellar sigma factor. No sequence data is available on flagellins of low-pathogenic Y. enterocolitica biotypes 2-5 and of biotype 1A strains, appearing non-pathogenic in the mouse infection model. We sequenced the flagellin genes of ten biotype 1A and biotype 4 isolates, respectively. While we could not identify any sequence polymorphism among flagellin genes of biotype 4 isolates, we found that biotype 1A strains harbour three variable flagellin genes. Moreover, three biotype 1A isolates exhibited a rearranged flagellin gene order and at least one rearranged flagellin gene was apparently acquired by horizontal gene transfer. The variability of flagellin genes seems to mirror evolution towards novel flagellin functions. By contrast, strictly conserved flagellins of biotype 4 isolates point at a strong selection pressure such as expected to be imposed by an important function in the context of infection.
Conceptual foundations of metamorphosis and regeneration: from historical links to common mechanisms

Metamorphosis and regeneration represent two familiar examples of developmental processes. In Western thought, their conceptual link with broader issues of generation or animal reproduction, including “spontaneous generation,” began with the ancient Greeks. Their ideas dominated scientific discourse on these topics until William Harvey, in the mid‐17th century, redefined and distinguished between epigenesis and metamorphosis as fundamentally different modes of reproduction. However, preformation theories, formulated in response to perceived threats of epigenetic concepts to religious doctrine, eclipsed epigenesis for much of the 18th century. Abraham Trembley's 1740 discovery of hydra regeneration helped to fuel the “epigenesis‐preformation debate” at that time. During that period, an exchange between C.F. Wolff, a young epigenesist, and A. von Haller, the reformed preformationist, saw robust models erected to comprehend generation, metamorphosis, and regeneration under each world view. Subsequent elaboration of experimental zoology and the incremental advance of biological knowledge saw the birth of divergent research traditions in pursuit of specialized problems. Embryology, regeneration, and metamorphosis, like genetics, identified independent study topics and elaborated new techniques, thereby creating their own research trajectories. Conceptual reintegration has slowly emerged with the evolution of current biotechnology. We have now begun to discern common molecular mechanisms underlying and reuniting metamorphosis and regeneration, as revealed in the accompanying symposium papers.
Modeling Multi-factor Financial Derivatives by a Partial Differential Equation Approach with Efficient Implementation on Graphics Processing Units

Modeling multi-factor financial derivatives by a Partial Differential Equation approach with efficient implementation on Graphics Processing Units Duy Minh Dang Doctor of Philosophy Graduate Department of Computer Science University of Toronto 2011 This thesis develops efficient modeling frameworks via a Partial Differential Equation (PDE) approach for multi-factor financial derivatives, with emphasis on three-factor models, and studies highly efficient implementations of the numerical methods on novel high-performance computer architectures, with particular focus on Graphics Processing Units (GPUs) and multi-GPU platforms/clusters of GPUs. Two important classes of multi-factor financial instruments are considered: cross-currency/foreign exchange (FX) interest rate derivatives and multi-asset options. For cross-currency interest rate derivatives, the focus of the thesis is on Power Reverse Dual Currency (PRDC) swaps with three of the most popular exotic features, namely Bermudan cancelability, knockout, and FX Target Redemption. The modeling of PRDC swaps using one-factor Gaussian models for the domestic and foreign interest short rates, and a one-factor skew model for the spot FX rate results in a time-dependent parabolic PDE in three space dimensions. Our proposed PDE pricing framework is based on partitioning the pricing problem into several independent pricing subproblems over each time period of the swap’s tenor structure, with possible communication at the end of the time period. Each of these subproblems requires a solution of the model PDE. We
Lung Injury and Bronchopulmonary Dysplasia in Newborn Infants

Bronchopulmonary dysplasia is the most common morbidity among surviving premature infants. Injury to the developing lung is the result of the interaction between a susceptible host and a number of contributing factors such as mechanical ventilation and infection. The resulting persistent impairment of pulmonary function and need for ongoing therapy are the underlying characteristics of bronchopulmonary dysplasia. Important insights into the pathogenesis of bronchopulmonary dysplasia have led to numerous therapies and preventive approaches. Although significant progress has been made, in order to further affect the incidence and severity of the disease, we need to further study (a) the genetically determined predisposing factors, (b) the relative contribution of the various pathogenetic pathways, and, most important, (c) how to best translate the knowledge gained from these studies into effective clinical approaches.
IFIT 2 define a novel innate immune effector pathway against West Nile virus infection

Background: IFN activates JAK-STAT signaling, where STAT1 phosphorylation is crucial for ISG induction and expression of IFIT2 to limit West Nile virus infection. Results: IKKɛ mediates STAT1 serine 708 phosphorylation exclusive of tyrosine phosphorylation but dependent on nuclear export and ISG synthesis. Conclusion: IKKɛ-mediated STAT1 S708 phosphorylation is crucial for IFIT2 expression to control WNV. Significance: We define a novel anti-WNV innate immune effector pathway.
A Conductance Ring Coupled Cone Meter for Oil-Water Two-Phase Flow Measurement

Simultaneous measurement on the phase fraction and flow rate of oil-water two-phase flow is of significance in process industries. A compact flow meter conductance ring coupled cone meter (CRCC) is presented to measure these two parameters by combining a long-waist cone meter (LWC) for flow rate measurement and a pair of conductance rings at the annular channel of the LWC for phase fraction measurement. The CRCC utilizes the spatial characteristics of LWC and conductance rings to achieve more reliable estimations on flow rate and phase fraction. The sizes of the LWC (diameter ratio β and waist length L) and conductance rings (separation Le between electrodes) are jointly optimized considering the overall pressure drop and sensitivity of electrical sensing field. A CRCC of β = 0.65, L=50 mm, and Le=15 mm is fabricated for static calibration and dynamic oil-water two-phase flow measurement tests. The dynamic experimental results demonstrate that the proposed CRCC is capable of delivering inferences on phase fraction and individual flow rate with an associated average relative error below 5% after easy calibration.
Glycosylate and move! The glycosyltransferase Maf is involved in bacterial flagella formation

The flagella of various Gram-negative bacteria are decorated with diverse glycan structures, amongst them nonulosonic acids related to the sialic acid family. Although nonulosonic sugar biosynthesis pathways have been dissected in various pathogens, the enzymes transferring the sugars onto flagellin are still poorly characterized. The deletion of genes coding for motility associated factors (Mafs) found in many pathogenic strains systematically gives rise to nonflagellated bacteria lacking specific nonulosonic sugars on the flagellins, therefore, relating Maf function to flagellin glycosylation and bacterial motility. We investigated the role of Maf from our model organism, Magnetospirillum magneticum AMB-1, in the glycosylation and formation of the flagellum. Deletion of the gene amb0685 coding for Maf produced a nonflagellated bacterium where the flagellin was still produced but no longer glycosylated. Our X-ray structure analysis revealed that the central domain of Maf exhibits similarity to sialyltransferases from Campylobacter jejuni. Glycan analysis suggested that the nonulosonic carbohydrate structure transferred is pseudaminic acid or a very close derivative. This work describes the importance of glycosylation in the formation of the bacterial flagellum and provides the first structural model for a member of a new bacterial glycosyltransferase family involved in nonulosonic acids transfer onto flagellins.
Risk Assessment by Myocardial Perfusion Imaging for Coronary Revascularization, Medical Therapy, and Noncardiac Surgery

Stress myocardial perfusion imaging (MPI) has become an important tool in risk stratification of patients with known coronary artery disease. A normal myocardial perfusion scan has a high negative predictive value and is associated with low annual mortality rate (< 1%). Patients with extensive ischemia (> 20% of the left ventricle), defects in more than 1 coronary vascular territory, transient or persistent left ventricular cavity dilation, and ejection fraction less than 45% have a high annual mortality rate (> 3%). Those patients should undergo coronary revascularization whenever feasible, as the cardiac event rate increases in proportion to the magnitude of the jeopardized myocardium. Stress MPI can be used to demonstrate ischemia in patients with symptoms early after coronary artery bypass surgery (< 5 years) or in those without symptoms late (≥ 5 years) after coronary artery bypass surgery. With respect to patients who underwent percutaneous interventions, stress MPI can help detect in-stent restenosis early after the intervention (3–6 months) or assess the progression of native coronary disease afterward. Since preliminary data suggest that a reduction in the perfusion defect size may translate to a reduction of coronary events, stress MPI can help assess the efficacy of medical management of coronary disease. Finally, stress MPI is indicated for perioperative cardiac risk stratification for noncardiac surgery in patients with intermediate risk predictors (mild angina, prior myocardial infarction or heart failure symptoms, diabetes mellitus, renal insufficiency) and poor functional capacity or in those who undergo high-risk surgery with significant implications in further preoperative management.
Genetics of familial amyotrophic lateral sclerosis

The completion of the Human Genome Project, together with a better understanding of some of the emerging genetic patterns of human disease, has enabled a thorough examination of the most appropriate genetic models for amyotrophic lateral sclerosis (ALS). The pathology and epidemiology of ALS have been intensively studied since Adar, Charcot, and Duchenne first described the disease in the 1860s. Results of genetic studies that have emerged over the past two decades have led to the identification of SOD1 as a well-established causative gene for ALS. However, the identification of SOD1 has not been followed up by the identification of other genes responsible for classic ALS. This leads to the speculation that more complex genetic mechanisms are involved than initially assumed. While mutations in single genes are still likely to constitute a small proportion of ALS cases, the genes responsible for ALS in families with clusters of two or three affected individuals, and more particularly in sporadic cases, are far from being determined. Multigenic, somatic mutation, and gene–environment models may all contribute to the genetic etiology of ALS. The challenge now lies in determining which models are the most appropriate to dissect out the genetic components involved. This research will ultimately aid in identifying the cumulative risk of developing ALS. GLOSSARY: ALS = amyotrophic lateral sclerosis; FALS = familial ALS; FTD = frontotemporal dementia; HSP = hereditary spastic paraplegia; PDC = Parkinson-dementia complex; PLS = primary lateral sclerosis; PON = paraoxonase; SALS = sporadic ALS; SBMA = spinal and bulbar muscular atrophy; SMA = spinal muscular atrophy; SNP = single nucleotide polymorphism.
Comparison of two control approaches for stability enhancement using STATCOM with active power injection capability

The application of two control strategies for shunt-connected FACTS devices to enhance the transient stability of a power system will be discussed in this paper. The main focus will be on the use of active power in the FACTS device and therefore a STATCOM with active power injection capability will be considered. The first approach represents the classical cascade controller that consists of an inner vector-current controller and various outer-control loops. The alternative approach controls the converter in a similar fashion as a synchronous generator, where the mechanical behavior of the machine is emulated in the control structure using the active power injection capability of the device. Using various simulation and experimental tests, the two methods will be compared in terms of their advantages and disadvantages, and a recommendation will be made on the use of the methods for transient stability enhancement.
Dynamic Cerebral Autoregulation Is Compromised Acutely following Mild Ischaemic Stroke but Not Transient Ischaemic Attack

Background: Dynamic cerebral autoregulation (dCA), the process by which the cerebral blood flow (CBF) is normally maintained relatively constant despite fluctuations in beat-to-beat blood pressure (BP), is impaired acutely following major ischaemic stroke. It is uncertain if dCA is impaired acutely after mild ischaemic stroke or transient ischaemic attack (TIA). We assessed dCA in patients acutely and sub-acutely following TIA or mild ischaemic stroke. Methods: Nineteen consecutive mild ischaemic stroke patients and 17 consecutive TIA patients underwent recordings of beat-to-beat BP, cerebral blood flow velocity (bilateral transcranial Doppler insonation of the middle cerebral artery) and heart rate a median of 36 h from onset and again a median of 96 h from onset. Dynamic autoregulatory indices (ARI) were then calculated from these data and the results compared to 22 age-, BP- and gender-matched controls. Results: ARI was significantly reduced in affected hemispheres of mild stroke patients at baseline compared to controls (4.0 ± 1.7 vs. 5.6 ± 1.1, p < 0.01) and remained so after adjustment for significant covariates. ARI was significantly reduced in both affected (4.0 ± 2.7 vs. 5.6 ± 1.1, p = 0.03) and unaffected hemispheres (4.2 ± 1.8 vs. 5.6 ± 1.1, p = 0.01) of mild stroke patients at follow-up compared to controls. However, after adjustment for significant covariates including ipsilateral carotid stenosis these results were not significant. No reduction in ARI was seen in TIA patients. Conclusions: The impairment of cerebrovascular haemodynamic control that was observed acutely following mild ischaemic stroke may have implications for the appropriate timing of anti-hypertensive therapy acutely following mild ischaemic stroke. No impairment of cerebrovascular haemodynamic control was seen following TIA.
PRE-DISCOVERY 2007 IMAGE OF THE HR 8799 PLANETARY SYSTEM

We present a pre-discovery H-band image of the HR 8799 planetary system that reveals all three planets in 2007 August. The data were obtained with the Keck adaptive optics system, using angular differential imaging and a coronagraph. We confirm the physical association of all three planets, including HR 8799d, which had only been detected in 2008 images taken two months apart, and whose association with HR 8799 was least secure until now. We confirm that the planets are 2–3 mag fainter than field brown dwarfs of comparable near-infrared colors. We note that similar underluminosity is characteristic of young substellar objects at the L/T spectral type transition, and is likely due to enhanced dust content and non-equilibrium CO/CH4 chemistry in their atmospheres. Finally, we place an upper limit of ≳18 mag arcsec−2 on the >120 AU H-band dust-scattered light from the HR 8799 debris disk. The corresponding integrated scattered light flux is <10−4 times the photospheric level, 24 times fainter than for the debris ring around HR 4796A.
Tolerogenic Antigen‐Presenting Cells

The ultimate goal of transplant immunology is to create a state of stable tolerance toward graft-associated antigens, without causing global immunosuppression in the host. T cells provoke antigen-specific graft rejection by recognizing foreign antigens derived from graft-associated proteins. However, in order for T cells to initiate rejection, the antigens must first be presented to them by other cells—the “professional” antigen-presenting cells, macrophages, and dendritic cells. Antigen-presenting cells are thus in a unique position to regulate the process of rejection or tolerance.1 Until recently, macrophages and dendritic cells have been viewed as “accessory” cells, with the sole function of assisting T-cell activation. Now, however, it has become evident that antigen-presenting cells can inhibit T-cell responses and promote tolerance, thus serving as a negative-regulatory element.2 Under physiologic conditions, inhibitory antigen-presenting cells are thought to help maintain tolerance toward self and innocuous environmental antigens. But these endogenous immunoregulatory pathways are also of interest for transplant immunology, because they are more specific and less toxic than the global immunosuppressive agents currently in use. A number of reports have shown that macrophages can suppress T-cell activation in vitro and in vivo (reviewed in Ref. 3). However, the study of immunosuppressive macrophages has been complicated by the fact that there are many types of macrophages (e.g., isolated from different tissues, or derived in vitro under different culture conditions), and a variety of putative mechanisms for suppression (nitric oxide, prostaglandins, reactive oxygen species, etc.). It is not clear which of these are of biologic relevance in vivo. Moreover, macrophages reside in the tissues and do not transport graft antigens to the draining lymph nodes, which is where T-cell immune responses must be initiated. Thus, the real role of macrophages in regulating primary immune responses remains unclear. In contrast, dendritic cells are highly migratory and readily transport tissue antigens to lymph nodes, where they are responsible for initiating primary T-cell responses.4 Recently, it has been recognized that certain subsets of dendritic cells can induce tolerance to the antigens that they present.1,2,5,6 In mice, tolerogenic den-
Characterizing System-Level Vulnerability for Instruction Caches against Soft Errors

With continuous scaling down of the semiconductor technology, the soft errors induced by energetic particles have become an increasing challenge in designing current and next-generation reliable microprocessors. Due to their large share of the transistor budget and die area, cache memories suffer from an increasing vulnerability against soft errors. Previous work based on the vulnerability factor (VF) analysis proposed analytical models to evaluate the reliability of on-chip data and instruction caches. However, we have no possession of a system-level study on the vulnerability of instruction caches. In this paper, we propose a new analytical model to estimate the system-level vulnerability factor for on-chip instruction caches. In our model, the error masking/detection effects in instructions based on the Instruction Set Architecture (ISA) are studied. Our experimental results using SPEC benchmark suite show that the self-error-masking/detection in instructions will reduce the VF of the instruction caches compared to the previous study. We also conduct an evaluation on the effectiveness of the reliability optimization techniques for instruction caches under our system-level VF characterization. Our proposed vulnerability model can provide an insightful guidance for the reliable instruction cache and ISA design.
Landslides analysis in western moutainous areas of China using Distributed Scatterers based InSAR

Multiple InSAR techniques are increasingly being developed for earth observation. However, among them, persistent scatterers-based InSAR (PSI) techniques fail to obtain enough measurement points (MPs) in rural mountainous area due to the lack of persistent scatterers (PSs), such as ma-made structures, rocks, and outcrops, etc. In this paper, Distributed Scatterers-based InSAR (DS-InSAR) algorithm, exploiting both persistent scatterers and distributed scatterers (DSs) widely spreading in rural areas, is proposed to make up the limitation of persistent scatterers-based technique when monitoring mountainous landslides. There are two key steps to preprocess DSs in DS-InSAR algorithm: selecting DS candidates and estimating optimal interferometric phases. The selected DSs and PSs are combined for further processing using traditional PSI procedure. A qualitative and quantitative simulation analysis was operated to validate the DS-InSAR algorithm. Then, both PSI and DS-InSAR were implemented to monitor Xishan landslide in western mountainous region of Sichuan province, based on high-resolution TerraSAR-X images. The obtained results demonstrate that DS-InSAR could detect much more MPs and provide more reliable deformation information.