Miracle-dz/UniFAR-FTUs huggingface dataset:
TIM 3 Mediates T Cell Exhaustion during Mycobacterium tuberculosis Infection

While T cell immunity initially limitsMycobacterium tuberculosis infection, why T cell immunity fails to sterilize the infection and allows recrudescence is not clear. One hypothesis is that T cell exhaustion impairs immunity and is detrimental to the outcome ofM. tuberculosis infection. Here we provide functional evidence for the development T cell exhaustion during chronic TB. Second, we evaluate the role of the inhibitory receptor T cell immunoglobulin and mucin domain–containing-3 (TIM3) during chronicM. tuberculosis infection. We find that TIM3 expressing T cells accumulate during chronic infection, co-express other inhibitory receptors including PD1, produce less IL-2 and TNF but more IL-10, and are functionally exhausted. Finally, we show that TIM3 blockade restores T cell function and improves bacterial control, particularly in chronically infected susceptible mice. These data show that T cell immunity is suboptimal during chronicM. tuberculosis infection due to T cell exhaustion. Moreover, in chronically infected mice, treatment with anti-TIM3 mAb is an effective therapeutic strategy against tuberculosis.
Design trade-offs in high-throughput coherence controllers

Recent research shows that the high occupancy of coherence controllers (CCs) is a major performance bottleneck in scalable shared-memory multiprocessors. We propose to take microarchitectural enhancements used for microprocessors and apply them to improve the throughput of hardwired CCs. These enhancements are CC support for nonblocking execution, early fetches of directory and L3 information, and superpipelining. Nonblocking execution in the CC reduces stalls by processing subsequent coherence transactions in the presence of misses in the directory cache and tag cache. Early fetching in the CC hides misses in the directory and tag caches and, therefore, also removes stalls. Finally, superpipelining in the CC increases its processing bandwidth. These supports all serve to increase the overall throughput of CCs and improve overall system performance. Using both SPLASH-2 and parallelized SPEC95 applications on detailed simulation models, we show that CCs that support nonblocking execution and superpipelining boost the performance of machines substantially. With these CCs, a 64-processor machine with four nodes of four SMPs per node runs on average 3.56 times faster than if it used conventional CCs. In addition, the machine runs about as fast as a more costly 64-processor machine with sixteen nodes of one SMP per node and the same advanced CCs. This is despite using much less network, chassis, and node hardware. Consequently, with our proposed advanced CCs, we can reduce the system cost significantly without affecting performance.
User-motivated topology formation for green communication networks

The energy consumption in communication networks has attracted increasing attentions. However, the survey shows that the network is still idle at some time due to the redundant deployment of networks and varying traffic requirements. Sleeping in the network is an efficient way to save energy since the network in idle state consumes almost 90% of that in busy state. Considering that a centralized sleeping scheduling in communication networks is complicated for implementation, we propose a user-motivated topology formation scheme for green communication networks. Furthermore, we model and analyze our proposal using a potential game. The equilibrium topology formation is proved to exist and the performance of our proposal in terms of price of stability are discussed in the paper. Simulations are also conducted to show the performance of the equilibrium solution, comparing with the optimal sleeping scheduling solution.
Prophylactic effect of topical silica nanoparticles as a novel antineovascularization agent for inhibiting corneal neovascularization following chemical burn

Background: Angiogenesis-related corneal blindness includes the spectrum of corneal diseases that are caused by pathological angiogenesis, leading to untoward visual impairment. The purpose of this study was to investigate the antineovascularization effect of topical silica nanoparticles (SiNPs) in inhibiting chemical-burn-induced corneal neovascularization. Materials and Methods: A total number of 20 corneas of 10 Wistar Albino rats were included in this study. Silver nitrate cauterization was pressed to the central cornea for 5 s to induce corneal neovascularization. They were randomly allocated to case and control groups (ten eyes in each group). SiNPs were synthesized by the reverse microemulsion method. SiNPs drop 1 mg/ml was started in ten eyes and artificial tear drop was started in the control group (ten eyes) immediately after chemical cauterization. Video-based photography was performed before and after treatment. Corneal image analysis was performed on each cornea using an image analysis software program. All rats were euthanized and the eyes were sent for histopathologic examinations14 days after chemical cauterization. Results: Scanning electron microscopy (SEM) images showed spherical-shaped particles. The mean size and polydispersity index of prepared SiNPs were 30.1 ± 5.6 nm and 0.254 ± 0.11, respectively. Fourteen days after chemical cauterization, the mean vascularized corneal area was 21% of total corneal area in the case group and 85% in the control group (P < 0.05). The control group revealed more extensive intrastromal vascularization compared with the case group in histopathologic examinations (P < 0.05). Conclusions: SiNPs is an effective modality for inhibiting corneal neovascularization following chemical burn in an experimental model. Further investigations are suggested for evaluation of its safety and efficacy in human eyes.
Vilya, a component of the recombination nodule, is required for meiotic double-strand break formation in Drosophila

Meiotic recombination begins with the induction of programmed double-strand breaks (DSBs). In most organisms only a fraction of DSBs become crossovers. Here we report a novel meiotic gene, vilya, which encodes a protein with homology to Zip3-like proteins shown to determine DSB fate in other organisms. Vilya is required for meiotic DSB formation, perhaps as a consequence of its interaction with the DSB accessory protein Mei-P22, and localizes to those DSB sites that will mature into crossovers. In early pachytene Vilya localizes along the central region of the synaptonemal complex and to discrete foci. The accumulation of Vilya at foci is dependent on DSB formation. Immuno-electron microscopy demonstrates that Vilya is a component of recombination nodules, which mark the sites of crossover formation. Thus Vilya links the mechanism of DSB formation to either the selection of those DSBs that will become crossovers or to the actual process of crossing over. DOI: http://dx.doi. org/10.7554/eLife.08287. 001
Pdxscholar Social Work Faculty Publications and Presentations School of Social Work Getting Performance Metrics Right: a Qualitative Study of Staff Experiences Implementing and Measuring Practice Transformation Getting Performance Metrics Right: a Qualitative Study of Staff Experiences Implementing 

qualitative study of staff experiences implementing and measuring practice transformation. Journal of general internal medicine, 29(2), 607-613. BACKGROUND: Quality improvement is a central goal of the patient-centered medical home (PCMH) model, and requires the use of relevant performance measures that can effectively guide comprehensive care improvements. Existing literature suggests performance measurement can lead to improvements in care quality, but may also promote practices that are detrimental to patient care. Staff perceptions of performance metric implementation have not been well-researched in medical home settings. OBJECTIVE: To describe primary care staff (clinicians and other staff) experiences with the use of performance metrics during the implementation of the Veterans Health Administration's (VHA) Patient Aligned Care Team (PACT) model of care. DESIGN: Observational qualitative study; data collection using role-stratified focus groups and semi-struc-tured interviews. PARTICIPANTS: Two hundred and forty-one of 337 (72 %) identified primary care clinic staff in PACT team and clinic administrative/other roles, from 15 VHA clinics in Oregon and Washington. APPROACH: Data coded and analyzed using conventional content analysis techniques. KEY RESULTS: Primary care staff perceived that performance metrics: 1) led to delivery changes that were not always aligned with PACT principles, 2) did not accurately reflect patient-priorities, 3) represented an opportunity cost, 4) were imposed with little communication or transparency, and 5) were not well-adapted to team-based care. CONCLUSIONS: Primary care staff perceived responding to performance metrics as time-consuming and not consistently aligned with PACT principles of care. The gaps between the theory and reality of performance metric implementation highlighted by PACT team members are important to consider as the medical home model is more widely implemented.
A Modified Johnson–Cook Model to Predict Stress-strain Curves of Boron Steel Sheets at Elevated and Cooling Temperatures

Abstract In order to predict correctly stress-strain curve for tensile tests at elevated and cooling temperatures, a modification of a Johnson–Cook (J-C) model and a new method to determine (J-C) material parameters are proposed. A MATLAB tool is used to determine material parameters by fitting a curve to follow Ludwick and Voce's hardening law at various elevated temperatures. Those hardening law parameters are then utilized to determine modified (J-C) model material parameters. The modified (J-C) model shows the better prediction compared to the conventional one. An FEM tensile test simulation based on the isotropic hardening model for metal sheet at elevated temperatures was carried out via a user-material subroutine, using an explicit finite element code. The simulation results at elevated temperatures were firstly presented and then compared with the measurements. The temperature decrease of all elements due to the air cooling process was then calculated when considering the modified (J-C) model and coded to VUMAT subroutine for tensile test simulation. The modified (J-C) model showed the good comparability between the simulation results and the corresponding experiments.
On the Design of Cognitive-Radio-Inspired Asymmetric Network Coding Transmissions in MIMO Systems

In this paper, a cognitive-radio-inspired asymmetric network coding (CR-AsNC) scheme is proposed for multiple-input-multiple-output (MIMO) cellular transmissions, where information exchange among users and base-station (BS) broadcasting can be accomplished simultaneously. The key idea is to apply the concept of cognitive radio (CR) in network coding transmissions, where the BS tries sending new information while helping users' transmissions as a relay. In particular, we design an asymmetric network coding method for information exchange between the BS and the users, although many existing works consider the design of network coding in symmetric scenarios. To approach the optimal performance, an iterative precoding design for CR-AsNC is first developed. Then, a channel-diagonalization-based precoding design with low complexity is proposed, to which power allocation can be optimized with a closed-form solution. The simulation results show that the proposed CR-AsNC scheme with precoding optimization can significantly improve system transmission performance.
Regression-based approaches for the decomposition of income inequality in Italy, 1998-2008

Because of the high unemployment rate and the low chances to get a permanent job, young people in Italy face major problems in entering the labour market. In this paper, we address the issue of the labour market entry of young Italian workers by using a sample dataset of the new Compulsory Communication data for the period 2008 - 2010. We ask whether there are some individual characteristics which are more favourable for openended contracts. Then, we analyse how different types of temporary jobs have different probability of transforming into permanent ones. Finally, we estimate a survival model on the duration of temporary jobs.
MTP -493G/T gene polymorphism is associated with steatosis in hepatitis C-infected patients

The reduction of hepatic microsomal transfer protein (MTP) activity results in fatty liver, worsening hepatic steatosis and fibrosis in chronic hepatitis C (CHC). The G allele of the MTP gene promoter, -493G/T, has been associated with lower transcriptional activity than the T allele. We investigated this association with metabolic and histological variables in patients with CHC. A total of 174 untreated patients with CHC were genotyped for MTP -493G/T by direct sequencing using PCR. All patients were negative for markers of Wilson's disease, hemochromatosis and autoimmune diseases and had current and past daily alcohol intake lower than 100 g/week. The sample distribution was in Hardy-Weinberg equilibrium. Among subjects with genotype 1, 56.8% of the patients with fibrosis grade 3+4 presented at least one G allele versus 34.3% of the patients with fibrosis grade 1+2 (OR = 1.8; 95%CI = 1.3-2.3). Logistic regression analysis with steatosis as the dependent variable identified genotypes GG+GT as independent protective factors against steatosis (OR = 0.4, 95%CI = 0.2-0.8; P = 0.01). The results suggest that the presence of the G allele of MTP -493G/T associated with lower hepatic MTP expression protects against steatosis in our CHC patients.
An Evaluation of SMT-Based Schedule Synthesis for Time-Triggered Multi-hop Networks

Networks for real-time systems have stringent end-to-end latency and jitter requirements. One cost-efficient way to meet these requirements is the time-triggered communication paradigm which plans the transmission points in time of the frames off-line. This plan prevents contentions of frames on the network and is called a time-triggered schedule (tt-schedule). In general the tt-scheduling is a bin-packing problem, known to be NP-complete, where the complexity is mostly driven by the freedom in topology of the network, its associated hardware restrictions, and application-imposed constraints. Multi-hop networks, in particular, require the synthesis of path-dependent tt-schedules to maintain full determinism of time-triggered communication from sender to receiver. Our experiments using the YICES SMT solver show that the scheduling problem can be solved by YICES out-of-the-box for a few hundred random frame instances on the network. A customized tt-scheduler using YICES as a back-end solver allows to increase this number of frame instances up to tens of thousands. In terms of scheduling quality, the synthesis produces up to ninety percent maximum utilization on a communication link with schedule synthesis times of about half an hour for the biggest examples we have studied. As a nice side-effect the YICES out-of-the-box approach is immediately applicable for the verification of existing (even large-scale) tt-schedules and for debugging more sophisticated tt-schedulers.
Spatial Evolution of Water Surface Waves: Numerical Simulation and Experiment of Bichromatic Waves

The modified nonlinear Schr6dinger (MNLS) equation for spatial evolution of weakly nonlinear water surface waves is shown to yield good comparisons with experimental measurements of bichromatic waves in a long tank. While linear theory does not predict neither the phase velocity nor the evolution of the envelope well, the cubic nonlinear Schr6dinger (NLS) equation improves the prediction of the phase velocity but not the modulation of the envelope. The MNLS equation predicts both the evolution of individual wave crests and the modulation of the envelope over longer fetch, and thus permits accurate forecasting of individual ocean wave crests over a fetch of several tens of wavelengths.
A Bayesian Approach to Policy Recognition and State Representation Learning

Learning from demonstration (LfD) is the process of building behavioral models of a task from demonstrations provided by an expert. These models can be used, e.g., for system control by generalizing the expert demonstrations to previously unencountered situations. Most LfD methods, however, make strong assumptions about the expert behavior, e.g., they assume the existence of a deterministic optimal ground truth policy or require direct monitoring of the expert's controls, which limits their practical use as part of a general system identification framework. In this work, we consider the LfD problem in a more general setting where we allow for arbitrary stochastic expert policies, without reasoning about the optimality of the demonstrations. Following a Bayesian methodology, we model the full posterior distribution of possible expert controllers that explain the provided demonstration data. Moreover, we show that our methodology can be applied in a nonparametric context to infer the complexity of the state representation used by the expert, and to learn task-appropriate partitionings of the system state space.
Neuro-Genetic System for DAX Index Prediction

The task of stock index prediction is presented in this paper. The data is gathered at the target stock market (DAX) and two other markets (KOSPI and DJIA). The data contains not only raw numerical values from the markets but also indicators pre-processed in terms of technical analysis, i.e. oscillators and patterns. Statistical analysis and the genetic algorithm are used to create the proper sequence of inputs from all available variables. Selected data is input to a neural network trained with backpropagation with momentum. The prediction goal is the next day’s closing value of German stock market index DAX with consideration of Korean and USA stock markets’ indexes. The prediction is performed within a tight time-window in order to protect the model against changing relationships between variables. For each time-window the best neural network is evolved and applied. The evaluation is repeated for every time-window in order to discover a new set of proper
g Signaling by IFN-Reprogramming of IL-10 Activity and

One important mechanism of cross-regulation by opposing cytokines is inhibition of signal transduction, including inhibition of Janus kinase-STAT signaling by suppressors of cytokine signaling. We investigated whether IFN- (cid:1) , a major activator of macrophages, inhibited the activity of IL-10, an important deactivator. Preactivation of macrophages with IFN- (cid:1) inhibited two key anti-inﬂammatory functions of IL-10, the suppression of cytokine production and of MHC class II expression. Gene expression proﬁling showed that IFN- (cid:1) broadly suppressed the ability of IL-10 to induce or repress gene expression. Although IFN- (cid:1) induced expression of suppressor of cytokine signaling proteins, IL-10 signal transduction was not suppressed and IL-10 activation of Janus kinases and Stat3 was preserved. Instead, IFN- (cid:1) switched the balance of IL-10 STAT activation from Stat3 to Stat1, with concomitant activation of inﬂammatory gene expression. IL-10 activation of Stat1 required the simultaneous presence of IFN- (cid:1) . These results demonstrate that IFN- (cid:1) operates a switch that rapidly regulates STAT activation by IL-10 and alters macrophage responses to IL-10. Dynamic regulation of the activation of different STATs by the same cytokine provides a mechanism by which cells can integrate and balance signals delivered by opposing cytokines, and extends our understanding of cross-regulation by opposing cytokines to include reprogramming of signaling and alteration of function. The Journal of Immunology, 2003, 171: 5034–5041. fusion receptor was constructed by amplifying the IL-10R1 cytoplasmic domain using PCR and fusing it with the extracellular and transmembrane domains of IL-22R1 (21). Clon- ing junctions and the sequence of the IL-10R1 intracellular domain were conﬁrmed by DNA sequencing. 293T cells were transfected in duplicate in six-well plates using Lipofectamine (Life Technologies) and a total of 12 (cid:3) g of plasmid DNA per well. Cells were cotransfected with plasmids en- coding IL-22R1-IL-10R1, either Stat1, Stat3, or an empty control expression vector, and (cid:4) -galactosidase. Cells were split 18 h after transfection, and then stimulated with cytokines after an additional 24 h of culture. Transfection efﬁciency was monitored by assaying for (cid:4) -galactosidase ac- tivity. A total of ﬁve transfection experiments were performed.
Based Appearance Model with Approximate Nearest Neigbour Search

Visual Object Tracking is an important module in a variety of applications, such as: surveillance, human computer interaction, and visual servoing. The main goal is to compute the trajectory of the object of interest given an initial bounding box for the object. 2D tracking is when the trajectory of the object is computed in terms of camera coordinates.It has been heavily investigated in the past decades, but in this project the main focus is on one of the techniques devised in[1] that is Approximate Nearest Neighbour Tracking.
Preparation and interaction characteristics of exfoliated ABS/organoclay nanocomposite

A series of poly(acrylonitrile-co-butadiene-co-styrene) (ABS)/organoclays (Cloisite10A, Cloisite25A, and Cloisite30B) nanocomposites are prepared via two different methods: one is a solution blending and the other is a two-step process where the solution blended mixture is subsequently compounded in the melt state using a torque rheometer (SOAM method). The effect of surfactants on the surface of three different organoclays that are modified with alkylammonium salts in polymer/ organoclay nanocomposites is investigated by focusing on two major aspects; Flory-Huggins interaction parameters and physical (thermal and mechanical) properties. The d-spacing of both neat organoclays and intercalated/exfoliated organoclays is examined by X-ray diffraction analysis, and the microstructure of these nanocomposites is examined by FE-TEM. Solubility parameters of both polymer and organoclays of interest are calculated according to the group contribution method. Viscoelastic behavior of the nanocomposites is also investigated by measuring rheological properties under an oscillatory shear. The increase in the onset temperature of the thermal degradation indicates the enhancement of thermal stability of ABS due to intercalation or partial exfoliation. Mechanical properties, such as, tensile strength, tensile modulus, and elongation at break of the nanocomposites are measured. POLYM. ENG. SCI., 50:504–512, 2010. a 2009 Society of Plastics Engineers
Single Step Preparation of Novel Hydrophobic Composite Films for Low‐k Applications

Composite films with low dielectric constants (k) containing micro‐ and mesopores are synthesized from precursor solutions for the preparation of mesoporous silica and ethanolic suspensions of silicalite‐1 nanoparticles. The material contains silicalite‐1 nanoparticles (include nanocrystals and nanoslabs/intermediates) embedded in a randomly oriented matrix of highly porous mesoporous silica. Micropores result from the incorporated silicalite‐1 nanoparticles, while decomposition of the porogen F127 leads to additional mesopores. The porosity of the composite films increases from 9 to 60% with the increase in porogen loading, while in parallel the elastic modulus and hardness decrease. The elastic moduli of the films are in the range of 13–20 GPa. Hydrophobic surfaces of the composite films are obtained by introducing methyl triethoxysilane during the preparation of both precursor solutions, leading to the incorporation of CH3 groups in the final composite films. These methyl groups are stable up to at least 500 °C. A low k value of approximately 2 is observed for films cured at 400 °C in N2 flow, which is ideal for removing templates without decomposing methyl groups. Due to the intrinsic hydrophobicity of the material, post‐silylation is not required rendering the composite films attractive candidates for future low k materials.