Miracle-dz/UniFAR-FTUs huggingface dataset:
Low-cost soft error resilience with unified data verification and fine-grained recovery for acoustic sensor based detection

This paper presents Turnstile, a hardware/software cooperative technique for low-cost soft error resilience. Leveraging the recent advance of acoustic sensor based soft error detection, Turnstile achieves guaranteed recovery by taking into account the bounded detection latency. The compiler forms verifiable regions and selectively inserts store instructions to checkpoint their register inputs so that Turnstile can verify the register/memory states with regard to a region boundary in a unified way without expensive register file protection. At runtime, for each region, Turnstile regards any stores (to both memory and register checkpoints) as unverified, and thus holds them in a store queue until the region ends and spends the time of the error detection latency. If no error is detected during the time, the verified stores are merged into memory systems, and registers are checkpointed. When all the stores including checkpointing stores prior to a region boundary are verified, the architectural and memory states with regard to the boundary are verified, thus it can serve as a recovery point. In this way, Turnstile contains the errors within the core without extra memory buffering. When an error is detected, Turnstile invalidates unverified entries in the store queue and restores the checkpointed register values to get the architectural and memory states back to what they were at the most recently verified region boundary. Then, Turnstile simply redirects program control to the verified region boundary and continues execution. The experimental results demonstrate that Turnstile can offer guaranteed soft error recovery with low performance overhead (<;8% on average).
FOXO1 plays an essential role in apoptosis of retinal pericytes

Purpose An early and significant event in diabetic retinopathy is the loss of retinal microvascular pericytes. Studies were performed to investigate pathways through which an advanced glycation endproduct and tumor necrosis factor (TNF)-α stimulate apoptosis in retinal pericytes through the activation of the pro-apoptotic transcription factor Forkhead box O1 (FOXO1). Methods Human retinal pericytes were stimulated by carboxymethyllysine (CML)-collagen, an advanced glycation endproduct, or TNF-α in vitro. Apoptosis was assessed by measuring cytoplasmic histone-associated DNA. The role of FOXO1 was examined by RNA interference (RNAi), and specific inhibitors were used to investigate the role of p38 and Jun N-terminal kinase mitogen-activated protein kinase (JNK MAP) kinases, Akt, and nuclear factor kappa B (NF-κB). Caspase-3 activity was measured with a luminescent substrate, and FOXO1 DNA-binding activity was measured by electrophoretic mobility shift assay (EMSA). Results TNF-α and CML-collagen but not control collagen stimulated apoptosis, caspase-3 activity, and FOXO1 DNA-binding activity in pericytes. Silencing FOXO1 by small interfering RNA prevented apoptosis of pericytes in response to both TNF-α and CML-collagen. By use of specific inhibitors, we demonstrated that both FOXO1 activation and subsequent apoptosis was mediated, in part, by p38 and JNK MAP kinases. In contrast Akt and NF-κB inhibitors had the opposite effect on pericyte apoptosis. Conclusions The results demonstrate pathways through which two different mediators, TNF-α and an advanced glycation endproduct, can induce pericyte apoptosis through activation of the transcription factor FOXO1.
Direct role of interrod spacing in mediating cell adhesion on Sr-HA nanorod-patterned coatings

The process in which nanostructured surfaces mediate cell adhesion is not well understood, and may be indirect (via protein adsorption) or direct. We prepared Sr-doped hydroxyapatite (Sr1-HA) 3D nanorods (with interrod spacing of 67.3±3.8, 95.7±4.2, and 136.8±8.7 nm) and 2D nanogranulate patterned coatings on titanium. Employing the coatings under the same surface chemistry and roughness, we investigated the indirect/direct role of Sr1-HA nanotopographies in the regulation of osteoblast adhesion in both serum-free and serum-containing Dulbecco’s Modified Eagle/Ham’s Medium. The results reveal that the number of adherent cells, cell-secreted anchoring proteins (fibronectin, vitronectin, and collagen), vinculin and focal adhesion kinase (FAK) denoted focal adhesion (FA) contact, and gene expression of vinculin, FAK, and integrin subunits (α2, α5, αv, β1, and β3), undergo significant changes in the inter-nanorod spacing and dimensionality of Sr1-HA nanotopographies in the absence of serum; they are significantly enhanced on the <96 nm spaced nanorods and more pronounced with decreasing interrod spacing. However, they are inhibited on the >96 nm spaced nanorods compared to nanogranulated 2D topography. Although the adsorption of fibronectin and vitronectin from serum are higher on 136.8±8.7 nm spaced nanorod patterned topography than nanogranulated topography, cell adhesion is inhibited on the former compared to the latter in the presence of serum, further suggesting that reduced cell adhesion is independent of protein adsorption. It is clearly indicated that 3D nanotopography can directly modulate cell adhesion by regulating integrins, which subsequently mediate anchoring proteins’ secretion and FA formation rather than via protein adsorption.
Identification and Estimation of Causal Mechanisms and Net Effects of a Treatment Under Unconfoundedness

An important goal when analyzing the causal effect of a treatment on an outcome is to understand the mechanisms through which the treatment causally works. We define a causal mechanism effect of a treatment and the causal effect net of that mechanism using the potential outcomes framework. These effects provide an intuitive decomposition of the total effect that is useful for policy purposes. We offer identification conditions based on an unconfoundedness assumption to estimate them, within a heterogeneous effect environment, and for the cases of a randomly assigned treatment and when selection into the treatment is based on observables. Two empirical applications illustrate the concepts and methods.
The Protein Kinase Double-Stranded RNA-Dependent (PKR) Enhances Protection against Disease Cause by a Non-Viral Pathogen

PKR is well characterized for its function in antiviral immunity. Using Toxoplasma gondii, we examined if PKR promotes resistance to disease caused by a non-viral pathogen. PKR−/− mice infected with T. gondii exhibited higher parasite load and worsened histopathology in the eye and brain compared to wild-type controls. Susceptibility to toxoplasmosis was not due to defective expression of IFN-γ, TNF-α, NOS2 or IL-6 in the retina and brain, differences in IL-10 expression in these organs or to impaired induction of T. gondii-reactive T cells. While macrophages/microglia with defective PKR signaling exhibited unimpaired anti-T. gondii activity in response to IFN-γ/TNF-α, these cells were unable to kill the parasite in response to CD40 stimulation. The TRAF6 binding site of CD40, but not the TRAF2,3 binding sites, was required for PKR phosphorylation in response to CD40 ligation in macrophages. TRAF6 co-immunoprecipitated with PKR upon CD40 ligation. TRAF6-PKR interaction appeared to be indirect, since TRAF6 co-immunoprecipitated with TRAF2 and TRAF2 co-immunoprecipitated with PKR, and deficiency of TRAF2 inhibited TRAF6-PKR co-immunoprecipitation as well as PKR phosphorylation induced by CD40 ligation. PKR was required for stimulation of autophagy, accumulation the autophagy molecule LC3 around the parasite, vacuole-lysosomal fusion and killing of T. gondii in CD40-activated macrophages and microglia. Thus, our findings identified PKR as a mediator of anti-microbial activity and promoter of protection against disease caused by a non-viral pathogen, revealed that PKR is activated by CD40 via TRAF6 and TRAF2, and positioned PKR as a link between CD40-TRAF signaling and stimulation of the autophagy pathway.
Tuning the defect configurations in nematic and smectic liquid crystalline shells

Thin liquid crystalline shells surrounding and surrounded by aqueous phases can be conveniently produced using a nested capillary microfluidic system, as was first demonstrated by Fernandez-Nieves et al. in 2007. By choosing particular combinations of stabilizers in the internal and external phases, different types of alignment, uniform or hybrid, can be ensured within the shell. Here, we investigate shells in the nematic and smectic phases under varying boundary conditions, focusing in particular on textural transformations during phase transitions, on the interaction between topological defects in the director field and inclusions in the liquid crystal (LC), and on the possibility to relocate defects within the shell by rotating the shell in the gravitational field. We demonstrate that inclusions in a shell can seed defects that cannot form in a pristine shell, adding a further means of tuning the defect configuration, and that shells in which the internal aqueous phase is not density matched with the LC will gently rearrange the internal structure upon a rotation that changes the influence of gravity. Because the defects can act as anchor points for added linker molecules, allowing self-assembly of adjacent shells, the various arrangements of defects developing in these shells and the possibility of tuning the result by modifying boundary conditions, LC phase, thickness and diameter of the shell or applying external forces make this new LC configuration very attractive.
Close dependence of fibroblast proliferation on collagen scaffold matrix stiffness

Human dermal fibroblasts (HDFs) in free‐floating collagen matrices show minimal proliferation, although this may increase when the matrix is ‘under tension’. We have investigated the detailed mechanics underlying one of the possible controls of this important cell behaviour, in particular the hypothesis that this is a response to substrate stiffness. Hyperhydrated collagen gels were plastic‐compressed (PC) to give a predetermined collagen density and stiffness. Mechanical properties were tested using a dynamic mechanical analyser; cell number by Alamar blue assay. In the stiffest PC matrices, cell proliferation was rapid and seeding density‐dependent, with a population doubling time of 2 days. In contrast, compliant attached matrices showed a 4 day lag period and a doubling time of 6 days. HDF growth was directly related to matrix stiffness, such that increasing stiffness using a range of compression levels (0–75% fluid removal) supported increasing proliferation rate, doubling times and matrix elastic modulus. HDF quiescence in compliant matrices was reversible, such that increasing stiffness in situ by compression at 1 and 5 days initiated proliferation. We conclude that collagen matrix stiffness regulates proliferation of fibroblasts (a duro‐response), with important implications for understanding fibroblast–matrix feedback controls during wound healing and the design and regulation of engineered connective tissues based on collagen and other hydrogel‐based scaffolds. Copyright © 2008 John Wiley & Sons, Ltd.
Perturbation of the T Lymphocyte Lineage In Transgenic Mice Expressing a Constitutive Repressor of Nuclear Factor (NF)-κB

Members of the nuclear factor (NF)-κB/Rel family transcription factors are induced during thymic selection and in mature T lymphocytes after ligation of the T cell antigen receptor (TCR). Despite these findings, disruption of individual NF-κB/Rel genes has revealed no intrinsic defect in the development of mature T cells, perhaps reflecting functional redundancy. To circumvent this possibility, the T cell lineage was targeted to express a trans-dominant form of IκBα that constitutively represses the activity of multiple NF-κB/Rel proteins. Transgenic cells expressing this inhibitor exhibit a significant proliferative defect, which is not reversed by the addition of exogenous interleukin-2. Moreover, mitogenic stimulation of splenocytes leads to increased apoptosis of transgenic T cells as compared with controls. In addition to deregulated T cell growth and survival, transgene expression impairs the development of normal T cell populations as evidenced by diminished numbers of TCRhi CD8 single-positive thymocytes. This defect was significantly amplified in the periphery and was accompanied by a decrease in CD4+ T cells. Taken together, these in vivo findings indicate that the NF-κB/Rel signaling pathway contains compensatory components that are essential for the establishment of normal T cell subsets.
Identifying and Screening Patients at Risk of Second Cancers

Background: The average age of the U.S. population is increasing, and cancer incidence increases with age. Both improved early detection of first malignancies and effective primary oncologic therapy have led to prolonged survival, and the risk of secondary malignancies has consequently increased. A few anatomic sites are at increased risk for second malignancies within the same organ: breast, colon and rectum, lung, head and neck (or upper aerodigestive malignancies), prostate, and the uterine cervix. Some of the cancers also incur a risk for a second malignancy at another anatomic site. In addition, there are well-described clinical genetic syndromes that, as unique clinical entities, predispose to second malignant tumors. Methods/Results: In this review, we focus on issues related to the risk of second malignancies among patients with primary breast, colon, lung and head and neck, prostate, and cervical cancers that comprise the most common sites of primary malignancy among patients in the United States. We review recent data related to both established and new screening strategies at these sites. Conclusions: There is some evidence that screening will improve outcomes among patients who may develop second malignancies, although the data are limited. The optimal screening modalities and strategies to reduce mortality from second malignancies remain to be defined for most tumor sites. (Cancer Epidemiol Biomarkers Prev 2006;15(11):2027–32)
Zinc and Lead in Aquatic Plants and Bottom Sediments of Anthropogenic Rivers

Abstract The aim of the study was to assess contamination of bottom sediments with heavy metals (lead and zinc) and its influence on the dominant macrophytes in selected four Polish anthropogenic rivers. Due to metal concentration, the sediments were classified in terms of their purity by three criteria: geochemical criterion, LAWA classification and ecotoxicological criterion. The studies revealed that tested macrophytes (Common Reed and Yellow Iris) were characterized by low and very low accumulation coefficient translocation factors of heavy metals. Common Reed was the plant which, to the greatest extent, accumulated heavy metals and therefore it was proposed as an indicator of lead and zinc contamination of river sediments. Heavy metals were mainly accumulated in roots and were not transported to their shoots as evidenced by very low translocation factors. Yellow Iris accumulated heavy metals to a lesser extent than Common Reed, however, it showed higher translocation factors of these metals. Zinc was preferentially collected by both plants in comparison with lead, as confirmed by higher translocation factors for zinc. Streszczenie Celem pracy była ocena stopnia zanieczyszczenia osadów dennych metalami ciężkimi (ołowiem i cynkiem) oraz ich wpływu na dominujące makrofity w wybranych czterech przekształconych antropogenicznie rzekach w Polsce. Ze względu na stężenie metali osady rzeczne zostały sklasyfikowane pod kątem ich czystości według trzech kryteriów: kryterium geochemicznego, klasyfikacji LAWA i kryterium ekotoksykologicznego. Badania wykazały, że badane makrofity (trzcina pospolita i kosaciec żółty) charakteryzowały się niskimi i bardzo niskimi współczynnikami akumulacji i translokacji metali ciężkich. Trzcina pospolita to roślina, która w największym stopniu akumulowała metale ciężkie i dlatego została zaproponowana, jako wskaźnik stopnia skażenia osadów rzecznych ołowiem i cynkiem. Metale ciężkie gromadziły się głównie w korzeniach i nie były transportowane do pędów, o czym świadczą bardzo niskie wartości współczynników translokacji. Kosaciec żółty akumulował metale ciężkie w mniejszym stopniu niż trzcina pospolita, jednakże w tym przypadku zaobserwowano wyższe współczynniki translokacji metali. Cynk był preferencyjnie pobierany przez obie rośliny w porównaniu do ołowiu, co potwierdzono wyższymi wartościami współczynników translokacji.
Creativity as action: findings from five creative domains

The present paper outlines an action theory of creativity and substantiates this approach by investigating creative expression in five different domains. We propose an action framework for the analysis of creative acts built on the assumption that creativity is a relational, inter-subjective phenomenon. This framework, drawing extensively from the work of Dewey (1934) on art as experience, is used to derive a coding frame for the analysis of interview material. The article reports findings from the analysis of 60 interviews with recognized French creators in five creative domains: art, design, science, scriptwriting, and music. Results point to complex models of action and inter-action specific for each domain and also to interesting patterns of similarity and differences between domains. These findings highlight the fact that creative action takes place not “inside” individual creators but “in between” actors and their environment. Implications for the field of educational psychology are discussed.
Do adrenal metastases from lung cancer develop by lymphogenous or hematogenous route?

In order to analyse the possible mode and pathways of adrenal metastases from lung cancer, the frequency of adrenal metastases ipsilateral and contralateral to the site of the primary cancer was investigated based on autopsied lung cancer cases. In 405 of 1,607 such cases, adrenal metastases could be found: on both sides, 234; ipsilateral only, 105: contralateral only, 66 cases. In the early stages of tumor progression, a striking difference can be seen between the two sides. Ipsilateral metastases were of significantly higher incidence in early metastatic tumor stages, but later, in cases having six or more involved organs, the ipsilateral/contralateral quotient reaches 1. It is postulated that in the early stages adrenal metastases from lung cancer probably develop mainly by lymphogenous, but later mainly by hematogenous routes.
Genetic and Environmental Contributions to Stability in Adult Obsessive Compulsive Behavior

This study investigates the relative contribution of genetic and environmental factors to the stability of obsessive-compulsive (OC) symptoms in an adult population-based sample. We collected data from twin pairs and their siblings, using the Padua Inventory Revised Abbreviated, from the population-based Netherlands Twin Register (NTR) in 2002 (n = 10.134) and 2008 (n = 15.720). Multivariate twin analyses were used to estimate the stability of OC symptoms as a function of genetic and environmental components. OC symptoms were found to be highly stable, with a longitudinal phenotypic correlation of 0.63. Longitudinal broad sense heritability was found to be 56.0%. Longitudinal correlations for genetic (r = 0.58 for additive, r = 1 for non-additive genetic factors) and non-shared environment (r = 0.46) reflected stable effects, indicating that both genes and environment are influencing the stability of OC symptoms in adults. For the first time, evidence is reported for non-additive genetic effects on the stability of OC symptoms. In conclusion, this study showed that OC symptoms are highly stable across time in adults, and that genetic effects contribute mostly to this stability, both in an additive and non-additive way, besides non-shared environmental factors. These data are informative with respect to adult sample selection for future genetic studies, and suggest that gene–gene interaction studies are needed to further understand the dominance effect found in this study.
Down‐regulation of human RNA/DNA helicase SUV3 induces apoptosis by a caspase‐ and AIF‐dependent pathway

Background information. The nuclear gene hSUV3 (human SUV3) encodes an ATP‐dependent DNA/RNA helicase. In the yeast Saccharomyces cerevisiae the orthologous Suv3 protein is localized in mitochondria, and is a subunit of the degradosome complex which regulates RNA surveillance and turnover. In contrast, the functions of human SUV3 are not known to date.
Area deprivation predicts lung function independently of education and social class

The cross-sectional association between socioeconomic status (at both the individual and area-based level) and lung function, as measured by forced expiratory volume in one second, in a large population-based cohort was investigated. The study population consisted of 22,675 males and females aged 39–79 yrs. They were recruited from the general community in Norfolk, UK using general practice age/sex registers, as part of the European Prospective Investigation into Cancer (EPIC-Norfolk). It was found that being in a manual occupational social class, having no educational qualifications and living in a deprived area all independently predicted significantly lower lung function, even after controlling for smoking habit. The influence of area-deprivation on lung function, independent of individual socioeconomic status and of individual smoking habit, suggests that apart from targeting individuals who are at high-risk, such as smokers, environmental determinants also need to be examined when considering measures to improve respiratory health.
The ACL Anthology Reference Corpus: A Reference Dataset for Bibliographic Research in Computational Linguistics

The ACL Anthology is a digital archive of conference and journal papers in natural language processing and computational linguistics. Its primary purpose is to serve as a reference repository of research results, but we believe that it can also be an object of study and a platform for research in its own right. We describe an enriched and standardized reference corpus derived from the ACL Anthology that can be used for research in scholarly document processing. This corpus, which we call the ACL Anthology Reference Corpus (ACL ARC), brings together the recent activities of a number of research groups around the world. Our goal is to make the corpus widely available, and to encourage other researchers to use it as a standard testbed for experiments in both bibliographic and bibliometric research.
Statistical amplitude scale estimation for quantization-based watermarking

Quantization-based watermarking schemes are vulnerable to amplitude scaling. Therefore the scaling factor has to be accounted for either at the encoder, or at the decoder, prior to watermark decoding. In this paper we derive the marginal probability density model for the watermarked and attacked data, when the attack channel consists of amplitude scaling followed by additive noise. The encoder is Quantization Index Modulation with Distortion Compensation. Based on this model we obtain two estimation procedures for the scale parameter. The first approach is based on Fourier Analysis of the probability density function. The estimation of the scaling parameter relies on the structure of the received data. The second approach that we obtain is the Maximum Likelihood estimator of the scaling factor. We study the performance of the estimation procedures theoretically and experimentally with real audio signals, and compare them to other well known approaches for amplitude scale estimation in the literature.