Miracle-dz/UniFAR-FTUs huggingface dataset:
Dysregulation through the NF-κB Enhancer and TATA Box of the Human Immunodeficiency Virus Type 1 Subtype E Promoter

ABSTRACT The global diversity of human immunodeficiency virus type 1 (HIV-1) genotypes, termed subtypes A to J, is considerable and growing. However, relatively few studies have provided evidence for an associated phenotypic divergence. Recently, we demonstrated subtype-specific functional differences within the long terminal repeat (LTR) region of expanding subtypes (M. A. Montano, V. A. Novitsky, J. T. Blackard, N. L. Cho, D. A. Katzenstein, and M. Essex, J. Virol. 71:8657–8665, 1997). Notably, all HIV-1E isolates were observed to contain a defective upstream NF-κB site and a unique TATA-TAR region. In this study, we demonstrate that tumor necrosis factor alpha (TNF-α) stimulation of the HIV-1E LTR was also impaired, consistent with a defective upstream NF-κB site. Furthermore, repair of the upstream NF-κB site within HIV-1E partially restored TNF-α responsiveness. We also show, in gel shift assays, that oligonucleotides spanning the HIV-1E TATA box displayed a reduced efficiency in the assembly of the TBP-TFIIB-TATA complex, relative to an HIV-1B TATA oligonucleotide. In transfection assays, the HIV-1E TATA, when changed to the canonical HIV-1B TATA sequence (ATAAAA→ATATAA) unexpectedly reduces both heterologous HIV-1B Tat and cognate HIV-1E Tat activation of an HIV-1E LTR-driven reporter gene. However, Tat activation, irrespective of subtype, could be rescued by introducing a cognate HIV-1B TAR. Collectively, these observations suggest that the expanding HIV-1E genotype has likely evolved an alternative promoter configuration with altered NF-κB and TATA regulatory signals in contradistinction with HIV-1B.
Quantity and quality of engrafting cells in cord blood and autologous mobilized peripheral blood.

Cord blood (CB) and autologous mobilized peripheral blood stem/progenitor cells (PBSC) are now used widely for clinical transplantation. We characterized the short-term (<8 weeks) and long-term (>8 weeks) engraftment in NOD/SCID mice resulting from transplanted CD34+ cells from these two sources. We also quantified the frequency of long-term engrafting cells, and the average proliferative capacity of individual engrafting cells by a competitive repopulation assay with binomial variance-covariance modeling. We found that 0.5 million CD34+ CB cells were able to generate sustained, high-level, multilineage human hematopoiesis, whereas a sixfold higher number of CD34+ PBSC (3 million) from cancer patients undergoing chemotherapy generated comparable short-term, but much lower sustained multilineage human hematopoiesis after transplantation. In comparison to CD34+ cells from PBSC from cancer patients, long-term engrafting cells were approximately eightfold enriched in CB CD34+ cells, and each CB long-term engrafting cell had an approximately 15-fold higher multilineage proliferative capacity. Thus, the number and function of transplantable hematopoietic cells were remarkably different between these two sources of stem/progenitor cells.
Evolvable Hardware, a Fundamental Technology for Homeostasis

Maintaining electronic systems in a steady (homeo-static) state of operation so that they perform their tasks when under stress is non-trivial. In order to achieve this we propose an extensible architecture, inspired by the natural immune system. We believe that evolvable and adaptive hardware is a critical underlying technology for homeostasis, and maintenance of homeostasis in electronic systems will be one of the application where evolvable hardware could make a significant impact
3-D Object Recognition Based on Integration of Range Image and Gray-scale Image

In this paper, we propose a practical object recognition system which consists of two functional modules. The first is object extraction module using a range image, and the second is a precise position measurement module using a grayscale intensity image. Both high-reliability and high-accuracy can be achieved by effective image integration. We also propose an idea of stereo vision with random-dot pattern projection as an effective way to obtain a range image. This method enables reliable stereo matching, even for objects with no texture. Through an experiment with real images, we have demonstrated that our system has 99.8% recognition reliability and processing time is approximately 5 seconds per image; as a result, the system can be applied to practical industrial robot vision.
FDI based on WD combined With PEM and RBF networks : Application to the diagnosis of TECP reactor

The objective of our work is to detect and isolate the faults that occur in large scale systems with many measurements. An advanced fault detection and isolation (FDI) method is proposed based on wavelet decomposition, Parameters Elimination Method (PEM) and Radial Basis Function (RBF) networks. Input signals are decomposed into approximations (low frequencies) and details (high frequencies). The extracted statistical parameters from approximation and detail signals pass through Parameters Elimination Method (PEM) to get rid from parameters that are useless for accurate classification. The selected parameters are used to classify the faults using a supervised RBF network. The performance of our algorithm is compared with a usual method based on classification without decomposition technique and parameters selection. The two methods are compared on the simulator of a chemical reactor: the Tennessee Eastman Challenge Process that is a well known benchmark for large scale systems.
Distribution of molecular size within an unfolded state ensemble using small-angle X-ray scattering and pulse field gradient NMR techniques.

The size distribution of molecules within an unfolded state of the N-terminal SH3 domain of drk (drkN SH3) has been studied by small-angle X-ray scattering (SAXS) and pulsed-field-gradient NMR (PFG-NMR) methods. An empirical model to describe this distribution in the unfolded state ensemble has been proposed based on (i) the ensemble-averaged radius of gyration and hydrodynamic radius derived from the SAXS and PFG-NMR data, respectively, and (ii) a histogram of the size distribution of structures obtained from preliminary analyses of structural parameters recorded on the unfolded state. Results show that this unfolded state, U(exch), which exists in equilibrium with the folded state, F(exch), under non-denaturing conditions, is relatively compact, with the average size of conformers within the unfolded state ensemble only 30-40% larger than the folded state structure. In addition, the model predicts a significant overlap in the size range of structures comprising the U(exch) state with those in a denatured state obtained by addition of 2 M guanidinium chloride.
The Linkage of Innate to Adaptive Immunity via Maturing Dendritic Cells In Vivo Requires CD40 Ligation in Addition to Antigen Presentation and CD80/86 Costimulation

Dendritic cell (DC) maturation is an innate response that leads to adaptive immunity to coadministered proteins. To begin to identify underlying mechanisms in intact lymphoid tissues, we studied α-galactosylceramide. This glycolipid activates innate Vα14+ natural killer T cell (NKT) lymphocytes, which drive DC maturation and T cell responses to ovalbumin antigen. Hours after giving glycolipid i.v. , tumor necrosis factor (TNF)–α and interferon (IFN)-γ were released primarily by DCs. These cytokines induced rapid surface remodeling of DCs, including increased CD80/86 costimulatory molecules. Surprisingly, DCs from CD40−/− and CD40L−/− mice did not elicit CD4+ and CD8+ T cell immunity, even though the DCs exhibited presented ovalbumin on major histocompatibility complex class I and II products and expressed high levels of CD80/86. Likewise, an injection of TNF-α up-regulated CD80/86 on DCs, but CD40 was required for immunity. CD40 was needed for DC interleukin (IL)-12 production, but IL-12p40−/− mice generated normal ovalbumin-specific responses. Therefore, the link between innate and adaptive immunity via splenic DCs and innate NKT cells has several components under distinct controls: antigen presentation in the steady state, increases in costimulatory molecules dependent on inflammatory cytokines, and a distinct CD40/CD40L signal that functions together with antigen presentation (“signal one”) and costimulation (“signal two”) to generate functioning CD4+ T helper cell 1 and CD8+ cytolytic T lymphocytes.
Part I: Direct Skinning Methods and Deformation Primitives

Skinning is the process of controlling deformations of a given object using a set of deformation primitives. A typical example of an object often subjected to skinning is the body of a virtual character. In this case, the deformation primitives are rigid transformations associated with bones of an animation skeleton. Later we will see that this is not the only possibility. Also, skinning can be well defined even without any skeleton. At a high level, the landscape of skinning algorithms can be divided into two main streams: direct and variational methods. Variational methods pose the task as an optimization problem, minimizing an objective function (deformation energy). Variational methods are rooted in continuum mechanics and the theory of elasticity and typically require iterative solvers. The focus of this part is on direct skinning methods, which have been developed in order to sidestep the high computational requirements of variational methods. Direct methods compute the resulting deformations using closed-form expressions, i.e., without any numerical optimization. Direct methods are often very fast and embarrassingly parallel, which makes them particularly attractive for interactive, real-time applications and GPU implementations.
Trajectory Tracking Control and Contouring Performance of Three-Dimensional CNC

A three-axes portal-type computer numerical control (CNC) manipulator is analyzed, in this study. In order to improve the trajectory tracking ability of the manipulator for both linear and circular trajectories different controllers are examined. To compare the effectiveness of different control approaches on the improvement of tracking and contouring performance of the examined three-axes portal-type CNC, proportional-integral-derivative (PID), observer-based PID, and feedforward computed torque (FFCT) control approaches are applied. It is observed that not only overshoot in tracking and contour errors but also transient and steady-state errors are reduced using the proposed FFCT controller. Although computing time increases, the FFCT control method is found as the best solution for the considered cases to improve the trajectory tracking ability of the manipulator for both linear and circular trajectories.
Every property of hyperfinite graphs is testable

A property testing algorithm for a property Π in the bounded degree graph model[7] is an algorithm that, given access to the adjacency list representation of a graph G=(V,E) with maximum degree at most d, accepts G with probability at least 2/3 if G has property Π, and rejects G with probability at least 2/3, if it differs on more than ε dn edges from every d-degree bounded graph with property Π. A property is testable, if for every ε,d and n, there is a property testing algorithm Aε,n,d that makes at most q(ε,d) queries to an input graph of n vertices, that is, a non-uniform algorithm that makes a number of queries that is independent of the graph size. A k-disc around a vertex v of a graph G=(V,E) is the subgraph induced by all vertices of distance at most k from v. We show that the structure of a planar graph on large enough number of vertices, n, and with constant maximum degree d, is determined, up to the modification (insertion or deletion) of at most ε d n edges, by the frequency of k-discs for certain k=k(ε,d) that is independent of the size of the graph. We can replace planar graphs by any hyperfinite class of graphs, which includes, for example, every graph class that does not contain a set of forbidden minors. We use this result to obtain new results and improve upon existing results in the area of property testing. In particular, we prove that graph isomorphism is testable for every class of hyperfinite graphs, every graph property is testable for every class of hyperfinite graphs, every hyperfinite graph property is testable in the bounded degree graph model, A large class of graph parameters is approximable for hyperfinite graphs. Our results also give a partial explanation of the success of motifs in the analysis of complex networks.
Induction of Cell-Cell Fusion by Ebola Virus Glycoprotein: Low pH Is Not a Trigger

Ebola virus (EBOV) is a highly pathogenic filovirus that causes hemorrhagic fever in humans and animals. Currently, how EBOV fuses its envelope membrane within an endosomal membrane to cause infection is poorly understood. We successfully measure cell-cell fusion mediated by the EBOV fusion protein, GP, assayed by the transfer of both cytoplasmic and membrane dyes. A small molecule fusion inhibitor, a neutralizing antibody, as well as mutations in EBOV GP known to reduce viral infection, all greatly reduce fusion. By monitoring redistribution of small aqueous dyes between cells and by electrical capacitance measurements, we discovered that EBOV GP-mediated fusion pores do not readily enlarge—a marked difference from the behavior of other viral fusion proteins. EBOV GP must be cleaved by late endosome-resident cathepsins B or L in order to become fusion-competent. Cleavage of cell surface-expressed GP appears to occur in endosomes, as evidenced by the fusion block imposed by cathepsin inhibitors, agents that raise endosomal pH, or an inhibitor of anterograde trafficking. Treating effector cells with a recombinant soluble cathepsin B or thermolysin, which cleaves GP into an active form, increases the extent of fusion, suggesting that a fraction of surface-expressed GP is not cleaved. Whereas the rate of fusion is increased by a brief exposure to acidic pH, fusion does occur at neutral pH. Importantly, the extent of fusion is independent of external pH in experiments in which cathepsin activity is blocked and EBOV GP is cleaved by thermolysin. These results imply that low pH promotes fusion through the well-known pH-dependent activity of cathepsins; fusion induced by cleaved EBOV GP is a process that is fundamentally independent of pH. The cell-cell fusion system has revealed some previously unappreciated features of EBOV entry, which could not be readily elucidated in the context of endosomal entry.
A bi-modal function of Wnt signalling directs an FGF activity gradient to spatially regulate neuronal differentiation in the midbrain

FGFs and Wnts are important morphogens during midbrain development, but their importance and potential interactions during neurogenesis are poorly understood. We have employed a combination of genetic and pharmacological manipulations in zebrafish to show that during neurogenesis FGF activity occurs as a gradient along the anterior-posterior axis of the dorsal midbrain and directs spatially dynamic expression of the Hairy gene her5. As FGF activity diminishes during development, Her5 is lost and differentiation of neuronal progenitors occurs in an anterior-posterior manner. We generated mathematical models to explain how Wnt and FGFs direct the spatial differentiation of neurons in the midbrain through Wnt regulation of FGF signalling. These models suggested that a negative-feedback loop controlled by Wnt is crucial for regulating FGF activity. We tested Sprouty genes as mediators of this regulatory loop using conditional mouse knockouts and pharmacological manipulations in zebrafish. These reveal that Sprouty genes direct the positioning of early midbrain neurons and are Wnt responsive in the midbrain. We propose a model in which Wnt regulates FGF activity at the isthmus by driving both FGF and Sprouty gene expression. This controls a dynamic, posteriorly retracting expression of her5 that directs neuronal differentiation in a precise spatiotemporal manner in the midbrain.
Memory self-efficacy in cognitively normal older adults and older adults with mild cognitive impairment

Although there are ample studies confirming that memory self-efficacy (MSE) declines with age, less is known about what factors account for the variation in MSE among older adults. The purpose of this study was to examine the relationship between MSE, diagnostic and clinical characteristics, and subsequent episodic memory performance in older adults. A nonprobability sample of 200 cognitively normal and older adults with mild cognitive impairment (MCI) participating in a longitudinal population-based study investigating the incidence, prevalence and risk factors for MCI completed a questionnaire about self-referent beliefs of MSE. Bandura’s (1989) selfefficacy theory and the Integration Model (Whittemore, 2005) informed the descriptive study. Pearson product-moment correlations, a general linear model and a multiple linear regression analysis were conducted. The difference in MSE ratings between the cognitively normal group and the MCI group tested as a whole was significant when adjusting for age, gender and educational attainment (p < .001; ES= 0.585). The overall regression model explained 17 % of the variance of MSE (p < .001) and included age, gender, educational attainment, APOE 4 genotype, family history of dementia, cognitive diagnosis and depressive symptoms. After controlling for age and the other variables of interest, cognitive classification and depression were significant predictors of MSE. Higher MSE ratings were correlated with better episodic memory performance for both groups (r = .273, p < .001). Memory training that capitalizes on the benefits accruing from higher MSE is needed for cognitively normal older adults and older adults with MCI. Abstract Approved: ____________________________________ Thesis Supervisor ____________________________________ Title and Department ____________________________________ DateApproved: ____________________________________ Thesis Supervisor ____________________________________ Title and Department ____________________________________ Date
The Corporate Objective Revisited

The stock market convulsions and corporate scandals of 2001 and 2002 have reignited debate on the purposes of the corporation and, in particular, the goal of shareholder value maximization. We revisit the debate, re-examine the traditional rationales, and develop a set of new arguments for why the preferred objective function for the corporation must unambiguously continue to be the one that says "maximize shareholder value. " We trace the origins of the debates from the late nineteenth century, their implications for accepted law and practice of corporate governance in the United States, and their reflection in shareholder versus stakeholder views in the organization studies literature and contractarian versus communitarian views in the legal literature. We address in detail possible critiques of the shareholder value maximization view. Although we recognize certain boundary constraints to our arguments, we conclude that the issues raised by such critiques and constraints are not unique to the shareholder value maximization view, but will exist even if the firm is managed on behalf of nonshareowning stakeholders.
Diagonal Stability for a Class of Cyclic Systems and Applications

We consider a class of systems with a cyclic structure that arises, among other examples, in dynamic models for certain biochemical reactions. We first show that a criterion for local stability, derived earlier in the literature, is in fact a necessary and sufficient condition for diagonal stability of the corresponding class of matrices. We then revisit a recent generalization of this criterion to output strictly passive systems, and recover the same stability condition using our diagonal stability result as a tool for constructing a Lyapunov function. Using this procedure for Lyapunov construction we exhibit classes of cyclic systems with sector nonlinearities and characterize their global stability properties.
Novel node pair selection algorithms for sum-rate enhancement in MIMO interference channel

In multiple-input multiple-output(MIMO) interference channel, multiple transmitters and receivers communicate simultaneously as a pair. We establish the metric for node pair selection algorithm to maximize the sum rate in MIMO interference channel. In this paper, by adjusting node pairs properly, we show that the sum rate can be enhanced. We propose two different node pair selection algorithms to improve the sum rate of MIMO interference channel. Firstly, we propose an optimum node pair selection algorithm by formulating a node pair selection metric to select the best node pairs among all possible node pairs. Then we propose a sub-optimum node pair selection algorithm to lower computational complexity. We confirm from some numerical simulations that the proposed algorithms offer significant sum rate enhancement compared to the case when node pair selection is not considered.
A minimum squared-error framework for generalized sampling

We treat the problem of reconstructing a signal from its nonideal samples where the sampling and reconstruction spaces as well as the class of input signals can be arbitrary subspaces of a Hilbert space. Our formulation is general, and includes as special cases reconstruction from finitely many samples as well as uniform-sampling of continuous-time signals, which are not necessarily bandlimited. To obtain a good approximation of the signal in the reconstruction space from its samples, we suggest two design strategies that attempt to minimize the squared-norm error between the signal and its reconstruction. The approaches we propose differ in their assumptions on the input signal: If the signal is known to lie in an appropriately chosen subspace, then we propose a method that achieves the minimal squared error. On the other hand, when the signal is not restricted, we show that the minimal-norm reconstruction cannot generally be obtained. Instead, we suggest minimizing the worst-case squared error between the reconstructed signal, and the best possible (but usually unattainable) approximation of the signal within the reconstruction space. We demonstrate both theoretically and through simulations that the suggested methods can outperform the consistent reconstruction approach previously proposed for this problem.