Miracle-dz/UniFAR-FTUs huggingface dataset:
A type I interferon autocrine–paracrine loop is involved in Toll-like receptor-induced interleukin-12p70 secretion by dendritic cells

Dendritic cells (DC) produce interleukin-12 (IL-12) in response to Toll-like receptor (TLR) activation. Two major TLR signaling pathways participate in the response to pathogens: the nuclear factor-κB (NF-κB)–dependent pathway leading to inflammatory cytokine secretion including IL-12 and the interferon (IFN)-dependent pathway inducing type I IFN and IFN-regulated genes. Here we show that the two pathways cooperate and are likely both necessary for inducing an optimal response to pathogens. R-848/Resiquimod (TLR7 ligand in the mouse and TLR7/8 ligand in human) synergized with poly(I:C) (TLR3 ligand) or lipopolysaccharide (LPS; TLR4 ligand) in inducing high levels of bioactive IL-12p70 secretion and IFN-β mRNA accumulation by mouse bone marrow–derived DC (BM-DC). Strikingly, IL-12p70 but not IL-12p40 secretion was strongly reduced in BM-DC from STAT1−/− and IFNAR−/− mice. STAT1 tyrosine-phosphorylation, IL-12p35, and IFN-β mRNA accumulation were strongly inhibited in IFNAR−/− BM-DC activated with the TLR ligand combinations. Similar observation were obtained in human TLR8-expressing monocyte-derived DC (moDC) using neutralizing anti-IFNAR2 antibodies, although results also pointed to a possible involvement of IFN-λ1 (also known as IL-29). This suggests that TLR engagement on DC induces endogenous IFNs that further synergize with the NF-κB pathway for optimal IL-12p70 secretion. Moreover, analysis of interferon regulatory factors (IRF) regulation in moDC suggests a role for IRF7/8 in mediating IRF3-independent type I IFN and possibly IL-12p35 synthesis in response to TLR7/8.
Learning graph matching with GNCCP

To improve the accuracy of graph matching problem, two strategies are frequently used, i.e., investigating more accurate optimization methods and constructing more accurate pairwise affinity functions. However, traditional methods have placed emphasizes on one of them. Here, we consider both. More specifically, we combine the graduated nonconvexity concavity relaxation procedure with the learning graph matching method. The former one is robust in dealing with graph matching problem, the latter one can construct the pairwise affinity functions by a supervised learning procedure. Experimental results show that the method perform better on CMU house/hotel data set, and competitively on synthetic noisy data set with the state of the art.
A Hierarchical Evaluation Methodology in Speech Recognition

In speech recognition vast hypothesis spaces are generated, so the search methods used and their speedup techniques are both of great importance. One way of getting a speedup gain is to search in multiple steps. In this multipass search technique the first steps use only a rough estimate, while the latter steps apply the results of the previous ones. To construct these raw tests we use simplified phoneme groups which are based on some distance function defined over phonemes. The tests we performed show that this technique could significantly speed up the recognition process.
Static reuse distances for locality-based optimizations in MATLAB

The problem of modeling memory locality of applications to guide compiler optimizations in a systematic manner is an important unsolved problem, made even more significant with the advent of multi-core and many-core architectures. We describe an approach based on a novel source-level metric, called static reuse distance, to model the memory behavior of applications written in matlab. We use matlab as a representative language that lets end-users express their algorithms precisely, but at a relatively high level. Matlab's "high-level" characteristics allow the static analysis to focus on large objects, such as arrays, without losing accuracy due to processor-specific layout of scalar values in memory. We present an efficient algorithm to compute static reuse distances using an extended version of dependence graphs. Our approach differs from earlier similar attempts in three important aspects: it targets high-level programming systems characterized by heavy use of libraries; it works on full programs, instead of being confined to loops; and it integrates practical mechanisms to handle separately compiled procedures as well as pre-compiled library procedures that are only available in binary form. We study matlab code, taken from real programs, to demonstrate the effectiveness of our model. Finally, we present some applications of our approach to program transformations that are known to be important in matlab, but are expected to be relevant to other similar high level languages as well.
Imprints of mass accretion on properties of galaxy clusters

A large-scale smoothed particle hydrodynamics (SPH) plus N-body simulation (GADGET) of the concordance A cold dark matter (CDM) universe is used to investigate orientation and angular momentum of galaxy clusters at z = 0 in connection with their recent accretion histories. The basic cluster sample comprises the 3000 most massive friends-of-friends (FoF) haloes found in the 500 h -1 Mpc simulation box. Two disjoint subsamples are constructed, using the mass ratio of the two most massive progenitors at z = 0.5 m 2 /m 1 [m 1 ≥ m 2 ), namely a recent major merger sample and a steady accretion mode sample. The mass of clusters in the merger sample is on average ∼43 per cent larger than the mass of the two progenitors (m + m 2 ), whereas in the steady accretion mode sample a smaller increase of ∼25 per cent is found. The separation vector connecting the two most massive progenitor haloes at z = 0.5 is strongly correlated with the orientation of the cluster at z = 0. The angular momentum of the clusters in the recent major merger sample tends to be parallel to orbital angular momentum of the two progenitors, whereas the angular momentum of the steady accretion mode sample is mainly determined by the angular momentum of the most massive progenitor. The long-range correlations for the major and the minor principal axes of cluster pairs extend to distances of ∼100 h -1 Mpc. Weak angular momentum correlations are found for distances ≤20 h -1 Mpc. Within these ranges, the major axes tend to be aligned with the connecting line of the cluster pairs, whereas minor axes and angular momenta tend to be perpendicular to this line. A separate analysis of the two subsamples reveals that the long-range correlations are independent of the mass accretion mode. Thus, orientation and angular momentum of galaxy clusters is mainly determined by the accretion along the filaments independently of the particular accretion mode.
Interactions Between Evolution and Learning

In this thesis, I report on a study of the interactions between evolution and learning. The methodology used is to build an abstract computational model of these processes, and study them from an Artificial Life perspective. Restrictions imposed by biology as we know it are relaxed, and experiments are carried out in the spirit of exploring life as it could be. Also included is a study of the inheritance of acquired characteristics, or Lamarckism. The Baldwin effect was revisited. Experiments were carried out to explore the factors that affect the evolution of the rate of learning. I show how the rate of change of environment, the costs associated with learning, the different selection pressures and the rate of mutation affect the evolution of learning. Interesting features such as cycling in the rate of learning were observed. Lamarckism was explored in a similar vein. Its advantage in stationary and slowly changing environments was shown; at the same time it was found that if there were any costs associated with Lamarckism, the degree of Lamarckism always evolved to zero. This leads to an interesting explanation of why Lamarckism will never be favoured by evolution by natural selection. I round off with a few experiments that explore the dynamics of mixed populations of individuals in competition with each other; to determine the best evolutionary strategy for a given combination of costs and environmental dynamics. Finally I tie together all these threads, and present through the outcomes, a unified picture of the interactions between evolution and learning.
Constraint Fluids

We present a fluid simulation method based on Smoothed Particle Hydrodynamics (SPH) in which incompressibility and boundary conditions are enforced using holonomic kinematic constraints on the density. This formulation enables systematic multiphysics integration in which interactions are modeled via similar constraints between the fluid pseudoparticles and impenetrable surfaces of other bodies. These conditions embody Archimede's principle for solids and thus buoyancy results as a direct consequence. We use a variational time stepping scheme suitable for general constrained multibody systems we call SPOOK. Each step requires the solution of only one Mixed Linear Complementarity Problem (MLCP) with very few inequalities, corresponding to solid boundary conditions. We solve this MLCP with a fast iterative method. Overall stability is vastly improved in comparison to the unconstrained version of SPH, and this allows much larger time steps, and an increase in overall performance by two orders of magnitude. Proof of concept is given for computer graphics applications and interactive simulations.
Inference of transition probabilities between the attractors in Boolean networks with perturbation

This paper investigates the inference of Boolean networks with perturbation (BNp) from simulated data and observed data. We interpret the discretised gene expression levels as attractor states of the underlying network and use the sequence of attractor states to determine the model. We consider the case where a complete sequence of attractors is known and the case where the known attractor states are arrived at by sampling from an underlying sequence of attractors. We apply the resulting algorithm to the interferon regulatory network using gene expression data taken from murine bone-derived macrophage cells infected with cytomegalovirus.
Dopamine Pathology in Schizophrenia: Analysis of Total and Phosphorylated Tyrosine Hydroxylase in the Substantia Nigra

Introduction: Despite the importance of dopamine neurotransmission in schizophrenia, very few studies have addressed anomalies in the mesencephalic dopaminergic neurons of the substantia nigra/ventral tegmental area (SN/VTA). Tyrosine hydroxylase (TH) is the rate-limiting enzyme for the production of dopamine, and a possible contributor to the anomalies in the dopaminergic neurotransmission observed in schizophrenia. Objectives: In this study, we had three objectives: (1) Compare TH expression (mRNA and protein) in the SN/VTA of schizophrenia and control postmortem samples. (2) Assess the effect of antipsychotic medications on the expression of TH in the SN/VTA. (3) Examine possible regional differences in TH expression anomalies within the SN/VTA. Methods: To achieve these objectives three independent studies were conducted: (1) A pilot study to compare TH mRNA and TH protein levels in the SN/VTA of postmortem samples from schizophrenia and controls. (2) A chronic treatment study was performed in rodents to assess the effect of antipsychotic medications in TH protein levels in the SN/VTA. (3) A second postmortem study was performed to assess TH and phosphorylated TH protein levels in two types of samples: schizophrenia and control samples containing the entire rostro-caudal extent of the SN/VTA, and schizophrenia and control samples containing only mid-caudal regions of the SN/VTA. Results and Conclusion: Our studies showed impairment in the dopaminergic system in schizophrenia that could be mainly (or exclusively) located in the rostral region of the SN/VTA. Our studies also showed that TH protein levels were significantly abnormal in schizophrenia, while mRNA expression levels were not affected, indicating that TH pathology in this region may occur posttranscriptionally. Lastly, our antipsychotic animal treatment study showed that TH protein levels were not significantly affected by antipsychotic treatment, indicating that these anomalies are an intrinsic pathology rather than a treatment effect.
Evaluating enterprise resource planning (ERP) systems using an interpretive approach

Enterprise Resource Planning (ERP) systems involve the purchase of pre-written software modules from third party suppliers, rather than bespoke (i.e. specially tailored) production of software requirements, and are often described as a buy rather than build approach to information systems development. Current research has shown that there has been a notable decrease in the satisfaction levels of ERP implementations over the period 1998-2000. The environment in which such software is selected, implemented and used may be viewed as a social activity system, which consists of a variety of stakeholders e.g. users, developers, managers, suppliers and consultants. In such a context, an interpretive research approach (Walsham, 1995) is appropriate in order to understand the influences at work. This paper reports on an interpretive study that attempts to understand the reasons for this apparent lack of success by analyzing issues raised by representatives of key stakeholder groups. Resulting critical success factors are then compared with those found in the literature, most notably those of Bancroft et al (1998). Conclusions are drawn on a wide range of organizational, management and political issues that relate to the multiplicity of stakeholder perceptions.
Analysis by X-ray diffraction of the mechanical behaviour of austenitic and ferritic phases of a duplex stainless steel

This paper deals with the X-ray diffraction characterisation of the mechanical behavior of a cast duplex stainless steel, containing 30% ferrite and 70% austenite. The structure of solidification leads a coarse grain material with grain size of the order of millimeters. The aim of the study is to identify the mechanical behavior for both phases by X-ray diffraction and to correlate it to the microstructure. The classical sin2w method for stress determination can not be applied to this material because of the large grains single size. The stresses are determined using a method resulting from an adaptation of the single crystal measurement method to large grains materials. So stress are determined using a method resulting Corn an adaptation of the single crystal measurement method to coarse grain materials. The measurement in each phase has successfully be applied to follow the stress state evolution during an in-situ tensile test. Three grains, with different crystallographic orientations were studied. For each one, the stress tensor was determined in the two phases under different macroscopic loading in elastic and plastic domains. For all grains, stress state in the ferritic phase is higher than the applied macroscopic stress and compared to the austenitic one where the stress is lower. This can be explained by ageing embrittlement of the ferrite which makes it much harder than the austenite. The important heterogeneity stress level is getting worse because of the crystallographic orientation of each grain. At each loading, micrographic observation are made to correlate the mechanical state determined by X-ray diffraction with the microstructure. Visible glides and cracks are noted and related to the stress state. This coupling of methods has been applied to identify the yield stress of each phase and the critical stress that leads to cracking of ferrite. The yield stresses so determined are in agreement with those deduced from the 8-28 peak broadening analysis.
Mobile indoor location based on fractional differentiation

While the static indoor location of a mobile terminal (MT) has been extensively studied on last decade, the prediction of the trajectory of a MT still is the major problem for building mobile location (tracking) systems (TSs). This problem is solved for outdoor TSs using global positioning system (GPS), however, it remains an essential obstacle to construct reliable indoor TSs. Different approaches were proposed in the literature, the most used is that based on prediction filters, such as linear filters (LF), Kalman filters (KF) and particle filters (PF). In this paper, we propose to enhance the performance of the predictors using digital fractional differentiation (DFD) to predict a MT trajectory. To illustrate the obtained results, three indoor trajectory scenarios inspired from real daily promenades are simulated (museum visit, hospital doctor walking and shopping in the market). Experimental results show a significant improvement of the performance of the classical predictors, particularly in noisy cases.
Hypotension, hypoxia, and head injury: frequency, duration, and consequences.

BACKGROUND Retrospective studies have suggested an association between systemic hypotension and hypoxia and worsened outcome from traumatic brain injury. Little is known, however, about the frequency and duration of these potentially preventable causes of secondary brain injury. HYPOTHESIS Early episodes of hypoxia and hypotension occurring during initial resuscitation will have a significant impact on outcome following traumatic brain injury. DESIGN Prospective cohort study. SETTING Urban level I trauma center. PATIENTS Patients with a traumatic brain injury who had a Glasgow Coma Score of 12 or less within the first 24 hours of admission to the hospital and computed tomographic scan results demonstrating intracranial pathologic features. Patients who died in the emergency department were excluded from the study. MAIN OUTCOME MEASURES Automated blood pressure and pulse oximetry readings were collected prospectively from the time of arrival through initial resuscitation. The number and duration of hypotensive (systolic blood pressure, < or =90 mm Hg) and hypoxic (oxygen saturation, < or =92%) events were analyzed for their association with mortality and neurological outcome. RESULTS One hundred seven patients met the enrollment criteria (median Glasgow Coma Score, 7). Overall mortality was 43%. Twenty-six patients (24%) had hypotension while in the emergency department, with an average of 1.5 episodes per patient (mean duration, 9.1 minutes). Of these 26 patients with hypotension, 17 (65%) died (P =.01). When the number of hypotensive episodes increased from 1 to 2 or more, the odds ratio for death increased from 2.1 to 8.1. Forty-one patients (38%) had hypoxia, with an average of 2.1 episodes per patient (mean duration, 8.7 minutes). Of these 41 patients with hypoxia, 18 (44%) died (P =.68). CONCLUSIONS Hypotension, but not hypoxia, occurring in the initial phase of resuscitation is significantly (P =.009) associated with increased mortality following brain injury, even when episodes are relatively short. These prospective data reinforce the need for early continuous monitoring and improved treatment of hypotension in brain-injured patients.
A relationship between emotional intelligence and Myer Briggs Big Five personality model

Emotional intelligence is the ability to understand the emotions of self and others and react accordingly. Emotional intelligence plays a crucial role in an individual's life. Each individual is unique and personality type of every person differs from one another. Personality types and emotional intelligence are essentially correlated and individuals tend to exhibit differences in their emotional intelligences owing to their personality types. This is a very important concept to be studied especially in present day life to cope up with everyday hurdles. This study focuses on trait EI and Big Five personality traits of individuals. The present study was done to find out the relation between the personality types as per the Myer Briggs Big Five model and the emotional intelligence. The target respondents for this study are students of a well reputed private university in India.
Pax-6 interactions with TATA-box-binding protein and retinoblastoma protein.

PURPOSE To identify proteins that physically interact with Pax-6, a paired domain- and homeodomain (HD)-containing transcription factor that is a key regulator of eye development. METHODS Protein-protein interactions involving Pax-6, TATA-box-binding protein (TPB), and retinoblastoma protein were studied using affinity chromatography with Pax-6 as ligand, glutathione-S-transferase (GST) pull-down assays, and immunoprecipitations. RESULTS The authors have shown that Pax-6 is a sequence-specific activator of many crystallin genes, all containing a TATA box, in the lens. Others have shown that lens fiber cell differentiation, characterized by temporally and spatially regulated crystallin gene expression, depends on retinoblastoma protein. In the present study it was shown that Pax-6 interacted with the TBP, the DNA-binding subunit of general transcription complex TFIID. GST pull-down assays indicated that this interaction was mediated by the Pax-6 HD, with a substantial role for its N-terminal arm and first two alpha-helices. The experiments also indicated a binding role for the C-terminal-activation domain of the protein. In addition, the present study showed that the HD of Pax-6 interacted with retinoblastoma protein. Immunoprecipitation experiments confirmed retinoblastoma protein/Pax-6 complexes in lens nuclear extracts. CONCLUSIONS Blending the present results with those in the literature suggests that Pax-6 and retinoblastoma protein participate in overlapping regulatory pathways controlling epithelial cell division, fiber cell elongation, and crystallin gene expression during lens development.
Multiversioning in the Store Queue Is the Root of All Store-forwarding Evil

As semiconductor technologies have continued to scale according to Moore's Law, complexity , power consumption, and energy dissipation have become first-order considerations in microprocessor design. In processors that issue instructions out-of-order, store-load forwarding is a source of significant complexity and energy dissipation. To decrease the complexity and improve the energy efficiency of store-load forwarding, this thesis proposes the forwarding cache (FC), an address-indexed, set-associative alternative to the age-indexed, fully associative store queue (SQ). The SQ is a content-addressable memory (CAM) that holds in-flight stores in program order. Because the SQ is age-indexed, a load's address may match one or more stores located anywhere in the SQ. Thus, the SQ search is fully associative and priority-encoded. In today's wide-issue processors, the SQ is large (24 to 32 entries), multiported (to accommodate the issue of multiple loads in a single cycle), and fast (no slower than an L1 data cache hit). The energy and complexity required to perform a fast search in a highly associative, multiported CAM are substantial. The contributions of this work are as follows. First, this thesis shows empirically that address multiversioning and the accompanying age-ordered, priority-encoded search are rarely necessary to perform store-load forwarding correctly. While others have observed the same empirical result on a particular processor configuration using a particular load speculation policy , this thesis extends the analysis to a broad variety of processors using several load speculation policies. Second, this thesis proposes the forwarding cache (FC), an address-indexed, set-associative cache that performs store-load forwarding. Third, this thesis investigates the sensitivity of the FC's performance and energy dissipation to several design parameters, including size, associativity, number of banks, and number of ports. The results show that a small, simple, set-associative FC performs comparably to the complex, fully associative SQ on both control-intensive and scientific workloads, while dissipating nearly ten times less energy than the SQ. iii To my parents, Harry and Mary Ann, who have always encouraged and supported me, and to Chip Coulter, the very best computer science teacher any student could hope to find. iv ACKNOWLEDGMENTS