Miracle-dz/UniFAR-FTUs huggingface dataset:
Dynamically Translating x86 to LLVM using QEMU

QEMU [1] is a system emulator that can run unmodiﬁedguest operating systems on a host OS, where the guestand host CPU architecture can be different. For exam-ple, QEMU can run x86 guest OSes on a MIPS host, oreven x86 on x86 (e.g., a Windows guest on a Linuxhost). QEMU emulates a complete system including proces-sors, devices, and chipsets. More implementation detailsregarding QEMU are available in [1]. In this paper, we focus on the design and implemen-tation of the LLVM backend for QEMU. LLVM [5]is a compiler framework which can optimize programsacross their entire lifetime, including compile-time andrun-time. It also performs ofﬂine optimizations. TheLLVM backend converts the guest instruction set toLLVM bitcode, optimizes this bitcode, and turns it backto x86, using the JIT capabilities of the LLVM run-time.We build upon an existing attempt to write an LLVMbackend for QEMU [6]. The LLVM backend can be used for several purposes.We interfaced QEMU with the KLEE symbolic exe-cution engine to test OS kernel, drivers, and applica-tions [3]; we also use the LLVM backend for devicedriver testing [4] and reverse engineering [2]. The paper is structured as follows. First, we explainhow QEMU runs unmodiﬁed guest OSes (§2), then wedescribethe speciﬁcities of theLLVM backend(§3),howit is implemented (§4), evaluate its performance (§5),discuss the limitations (§6), and conclude (§7).
Self-Confidence and Reactions to Subjective Performance Evaluations

Subjective performance evaluations are commonly used to provide feedback and incentives to workers. However, such evaluations can generate significant disagreements and conflicts, the severity of which may be driven by many factors. In this paper we show that a workers' level of self-confidence plays a central role in shaping reactions to subjective evaluations - overconfident agents engage in costly punishment when they receive evaluations below their own, but provide limited rewards to principals when evaluations exceed their own. In contrast, underconfident agents do not significantly react to evaluations below their own, but reward significantly evaluations exceeding their own. Our analysis exploits data from a principal-agent experiment run with a large sample of the Danish working age population, varying the financial consequences associated with the evaluations workers receive. In contrast to existing economic models of reciprocal behavior, reactions to evaluations are weakly related to the financial consequences of the evaluations. These results point towards a behavioral model of reciprocity that intertwines the desire to protect self-perceptions with over-/underconfidence.
Dietary fatty acids and pancreatic cancer in the NIH-AARP diet and health study.

BACKGROUND Previous research relating dietary fat, a modifiable risk factor, to pancreatic cancer has been inconclusive. METHODS We prospectively analyzed the association between intakes of fat, fat subtypes, and fat food sources and exocrine pancreatic cancer in the National Institutes of Health-AARP Diet and Health Study, a US cohort of 308 736 men and 216 737 women who completed a 124-item food frequency questionnaire in 1995-1996. Hazard ratios (HRs) and 95% confidence intervals (CIs) were calculated using Cox proportional hazards regression models, with adjustment for energy intake, smoking history, body mass index, and diabetes. Statistical tests were two-sided. RESULTS Over an average follow-up of 6.3 years, 865 men and 472 women were diagnosed with exocrine pancreatic cancer (45.0 and 34.5 cases per 100 000 person-years, respectively). After multivariable adjustment and combination of data for men and women, pancreatic cancer risk was directly related to the intakes of total fat (highest vs lowest quintile, 46.8 vs 33.2 cases per 100 000 person-years, HR = 1.23, 95% CI = 1.03 to 1.46; P(trend) = . 03), saturated fat (51.5 vs 33.1 cases per 100 000 person-years, HR = 1.36, 95% CI = 1.14 to 1.62; P(trend) < . 001), and monounsaturated fat (46.2 vs 32.9 cases per 100 000 person-years, HR = 1.22, 95% CI = 1.02 to 1.46; P(trend) = . 05) but not polyunsaturated fat. The associations were strongest for saturated fat from animal food sources (52.0 vs 32.2 cases per 100 000 person-years, HR = 1.43, 95% CI = 1.20 to 1.70; P(trend) < . 001); specifically, intakes from red meat and dairy products were both statistically significantly associated with increased pancreatic cancer risk (HR = 1.27 and 1.19, respectively). CONCLUSION In this large prospective cohort with a wide range of intakes, dietary fat of animal origin was associated with increased pancreatic cancer risk.
Inhibition of fibroblast growth factor receptor 3-dependent lung adenocarcinoma with a human monoclonal antibody

ABSTRACT Activating mutations in fibroblast growth factor receptor 3 (FGFR3) have been identified in multiple types of human cancer and in congenital birth defects. In human lung cancer, fibroblast growth factor 9 (FGF9), a high-affinity ligand for FGFR3, is overexpressed in 10% of primary resected non-small cell lung cancer (NSCLC) specimens. Furthermore, in a mouse model where FGF9 can be induced in lung epithelial cells, epithelial proliferation and ensuing tumorigenesis is dependent on FGFR3. To develop new customized therapies for cancers that are dependent on FGFR3 activation, we have used this mouse model to evaluate a human monoclonal antibody (D11) with specificity for the extracellular ligand-binding domain of FGFR3, that recognizes both human and mouse forms of the receptor. Here, we show that D11 effectively inhibits signaling through FGFR3 in vitro, inhibits the growth of FGFR3-dependent FGF9-induced lung adenocarcinoma in mice, and reduces tumor-associated morbidity. Given the potency of FGF9 in this mouse model and the absolute requirement for signaling through FGFR3, this study validates the D11 antibody as a potentially useful and effective reagent for treating human cancers or other pathologies that are dependent on activation of FGFR3. Summary: This study validates the FGF9 lung adenocarcinoma mouse model as a tool to screen and evaluate potential therapeutics that are designed to inhibit FGF9 or its target receptor, FGFR3.
P70S6 Kinase Phosphorylation: A New Site to Assess Pharmacodynamy of Sirolimus

Background: The phosphorylation of p70S6 kinase (p70S6K) represents an important target for sensitive detection on pharmacodynamic effects of sirolimus, but the methods of assessing p70S6K phosphorylation are still unclear. The aim of this study was to investigate p70S6K phosphorylation located down-stream of the mammalian target of rapamycin (mTOR) pathway in peripheral blood mononuclear cells (PBMCs) of liver transplant patients through different methods. Methods: Seventy-five liver transplant recipients from Beijing Chaoyang Hospital of the Capital Medical University were analyzed in this study. Patients were divided into three groups, patient treated with sirolimus (n = 22), patient treated with tacrolimus (n = 30), patient treated with cyclosporine (n = 23). The p70S6K phosphorylation of PBMCs in patients and healthy control (HC, n = 12) were analyzed by phospho-flow cytometry and Western blotting. A correlation analysis of data from phospho-flow cytometry and Western blotting was performed. Intra-assay variability of p70S6K phosphorylation in HC and different patients were measured. Results: Intra-assay variability of p70S6K phosphorylation in phospho-flow cytometry was from 4.1% to 8.4% and in Western blotting was from 8.2% to 18%. The p70S6K phosphorylation in patients receiving a sirolimus (19.5 ± 7.7) was significantly lower than in HC (50.1 ± 11.3, P < 0.001), tacrolimus (37.7 ± 15.7, P < 0.001) or cyclosporine treated patients (41.7 ± 11.7, P < 0.001). The p70S6K phosphorylation in HC (50.1 ± 11.3) was significantly higher than in tacrolimus (37.7 ± 15.7, P < 0.01) or cyclosporine-treated patients (41.7 ± 11.7, P < 0.01). There was correlation between data from phospho-flow cytometry and data from Western blotting (r = 0.88, P < 0.001). Conclusions: The degree of mTOR inhibition by assessing p70S6K phosphorylation was established by phospho-flow cytometry and Western blotting. Assessment of p70S6K phosphorylation may play an adjunct role to on pharmacodynamically guide and individualize sirolimus based on immunosuppression.
INFLUENCE OF ERYTHROMYCIN ON THE PHARMACOKINETICS OF XIMELAGATRAN MAY INVOLVE INHIBITION OF P-GLYCOPROTEIN-MEDIATED EXCRETION

A pharmacokinetic interaction between erythromycin and ximelagatran, an oral direct thrombin inhibitor, was demonstrated in this study in healthy volunteers. To investigate possible interaction mechanisms, the effects of erythromycin on active transport mediated by P-glycoprotein (P-gp) in vitro in Caco-2 and P-gp-over-expressing Madin-Darby canine kidney-human multidrug resistance-1 cell preparations and on biliary excretion of melagatran in rats were studied. In healthy volunteers (seven males and nine females; mean age 24 years) receiving a single dose of ximelagatran 36 mg on day 1, erythromycin 500 mg t.i. d. on days 2 to 5, and a single dose of ximelagatran 36 mg plus erythromycin 500 mg on day 6, the least-squares mean estimates (90% confidence intervals) for the ratio of ximelagatran with erythromycin to ximelagatran given alone were 1.82 (1.64–2.01) for the area under the concentration-time curve and 1.74 (1.52–2.00) for the maximum plasma concentration of melagatran, the active form of ximelagatran. Neither the slope nor the intercept of the melagatran plasma concentration-effect relationship for activated partial thromboplastin time statistically significantly differed as a function of whether or not erythromycin was administered with ximelagatran. Ximelagatran was well tolerated regardless of whether it was administered with erythromycin. Erythromycin inhibited P-gp-mediated transport of both ximelagatran and melagatran in vitro and decreased the biliary excretion of melagatran in the rat. These results indicate that the mechanism of the pharmacokinetic interaction between oral ximelagatran and erythromycin may involve inhibition of transport proteins, possibly P-gp, resulting in decreased melagatran biliary excretion and increased bioavailability of melagatran.
Meta-analysis on Methane Mitigating Properties of Saponin-rich Sources in the Rumen: Influence of Addition Levels and Plant Sources

Saponins have been considered as promising natural substances for mitigating methane emissions from ruminants. However, studies reported that addition of saponin-rich sources often arrived at contrasting results, i.e. either it decreased methane or it did not. The aim of the present study was to assess ruminal methane emissions through a meta-analytical approach of integrating related studies from published papers which described various levels of different saponin-rich sources being added to ruminant feed. A database was constructed from published literature reporting the addition of saponin-rich sources at various levels and then monitoring ruminal methane emissions in vitro. Accordingly, levels of saponin-rich source additions as well as different saponin sources were specified in the database. Apart from methane, other related rumen fermentation parameters were also included in the database, i.e. organic matter digestibility, gas production, pH, ammonia concentration, short-chain fatty acid profiles and protozoal count. A total of 23 studies comprised of 89 data points met the inclusion criteria. The data obtained were subsequently subjected to a statistical meta-analysis based on mixed model methodology. Accordingly, different studies were treated as random effects whereas levels of saponin-rich source additions or different saponin sources were considered as fixed effects. Model statistics used were p-value and root mean square error. Results showed that an addition of increasing levels of a saponin-rich source decreased methane emission per unit of substrate incubated as well as per unit of total gas produced (p<0.05). There was a decrease in acetate proportion (linear pattern; p<0.001) and an increase in propionate proportion (linear pattern; p<0.001) with increasing levels of saponin. Log protozoal count decreased (p<0.05) at higher saponin levels. Comparing between different saponin-rich sources, all saponin sources, i.e. quillaja, tea and yucca saponins produced less methane per unit of total gas than that of control (p<0.05). Although numerically the order of effectiveness of saponin-rich sources in mitigating methane was yucca>tea>quillaja, statistically they did not differ each other. It can be concluded that methane mitigating properties of saponins in the rumen are level- and source-dependent.
Application of Pseudo Strain-hardening Cementitious Composites to Shear Resistant Structural Elements

This article describes design concept and material characteristics of a new ductile fiber reinforced cementitious composite referred to as ECC (Engineered Cementitious Composite). This particular ECC contains Polyvinyl Alcohol fiber and exhibits remarkably ductile tensile property with over 1% of tensile strain capacity. The high tensile strain performance of the ECC was found successfully utilized to improve the performance of structural elements via two demonstrative examples. First, it was found that ECC significantly enhanced shear performance of short span beam under cyclic loading. Second, ECC enables one to realize simple dry joint connecting panels with remarkably high shear load capacity for structural wall assembly. As conclusion, a strong potential of the ECC has been established to enhance the structural performance of seismic resistant elements.
Discriminating Selection on Lateral Plate Phenotype and Its Underlying Gene, Ectodysplasin, in Threespine Stickleback

When a signature of natural selection is discovered on a gene that is pleiotropic or in tight linkage with other genes, it is challenging to determine which of the affected phenotypes is under selection. One way to make progress is to employ methods for analyzing natural selection on correlated traits, including both genotype and phenotype. We used this approach in threespine stickleback to estimate selection on a rapidly evolving trait, lateral armor plates, while controlling for variation at its major underlying gene, Ectodysplasin (Eda), and vice versa. This allowed for independent estimates of selection on lateral plates and on Eda via other traits. Previously, we demonstrated allele frequency changes at Eda in a pond experiment. Here we show that this resulted from selection on both plates and on Eda, implying additional selection on other phenotypic traits affected by the same gene. This represents the first evidence for direct selection on lateral plates independent of selection on the Eda locus and highlights the value of measuring selection on both phenotypes and genotypes in studies of adaptation.
Convergence Properties of Evolution Strategies with the Derandomized Covariance Matrix Adaptation: T

The intermediate (center of mass) recombination of object parameters is introduced in the evolution strategy with derandomized covariance matrix adaptation (CMA-ES). On various (unimodal) real space tness functions convergence properties and robustness against distorted selection are tested for diierent parent numbers. Introducing (== I ;)-selection signiicantly improves robustness and has comparatively minor innuence on the convergence speed of the CMA-ES.
Characterization of the UGA-recoding and SECIS-binding activities of SECIS-binding protein 2

Selenium, a micronutrient, is primarily incorporated into human physiology as selenocysteine (Sec). The 25 Sec-containing proteins in humans are known as selenoproteins. Their synthesis depends on the translational recoding of the UGA stop codon to allow Sec insertion. This requires a stem-loop structure in the 3’ untranslated region of eukaryotic mRNAs known as the Selenocysteine Insertion Sequence (SECIS). The SECIS is recognized by SECIS-binding protein 2 (SBP2) and this RNA:protein interaction is essential for UGA recoding to occur. Genetic mutations cause SBP2 deficiency in humans, resulting in a broad set of symptoms due to differential effects on individual selenoproteins. Progress on understanding the different phenotypes requires developing robust tools to investigate SBP2 structure and function. In this study we demonstrate that SBP2 protein produced by in vitro translation discriminates among SECIS elements in a competitive UGA recoding assay and has a much higher specific activity than bacterially expressed protein. We also show that a purified recombinant protein encompassing amino acids 517-777 of SBP2 binds to SECIS elements with high affinity and selectivity. The affinity of the SBP2:SECIS interaction correlated with the ability of a SECIS to compete for UGA recoding activity in vitro. The identification of a 250 amino acid sequence that mediates specific, selective SECIS-binding will facilitate future structural studies of the SBP2:SECIS complex. Finally, we identify an evolutionarily conserved core cysteine signature in SBP2 sequences from the vertebrate lineage. Mutation of multiple, but not single, cysteines impaired SECIS-binding but did not affect protein localization in cells.
Shape Bottlenecks and Conservative Flow Systems

This paper proposes an alternative to mathematical morphology to analyze complex shapes. This approach aims mainly at the detection of shape bottlenecks which are often of interest in medical imaging because of their anatomical meaning. The detection idea consists in simulating the steady state of an information transmission process between two parts of a complex object in order to highlight bottlenecks as areas of high information flow. This information transmission process is supposed to have a conservative flow which leads to the well-known Dirichlet-Neumann problem. This problem is solved using finite differences, over-relaxation and a raw to fine implementation. The method is applied to the detection of main bottlenecks of brain white matter network, namely corpus callosum, anterior commissure and brain stem.
Part Ii: Why Is Civil War so Common

In Part I we saw that civil war is a major impediment to development and has spillovers that make it a problem of global concern. We now turn to what fuels civil war. An understanding of the factors that make civil war more or less likely is a helpful input into the formulation of policy responses, which is the subject of Part III. In Chapter 3 we analyze what makes a country more or less prone to civil war – both the risk that a war will ignite, and the factors that tend to sustain it once it has started. Although civil war is intensely political, some of the most important factors affecting proneness to conflict turn out to be closely associated with economic development: risks are much higher for the poorest countries. Further, far from war resolving political struggle, there is a 'conflict trap': one civil war tends to lead to another. In Chapter 4 we scale this analysis up to the global level, trying to understand what has determined the global incidence of conflict, and how it might change.
GHGT-12 Energetics of electrochemically-mediated amine regeneration

Cost-effective, large-scale carbon dioxide capture is a critical technology for mitigating greenhouse gas emissions, and current capture technologies are energy intensive and difficult to deploy in existing power plants. We have previously introduced a novel electrochemically-mediated process for amine regeneration, and demonstrated its feasibility with a proof-of-concept system that can efficiently modulate amine affinity to carbon dioxide under the effect of redox-responsive molecules. The electrochemical process is simple to install, obviating the need for expensive retrofits. In addition, due to its targeted nature, the process has the potential for lower energy consumption as compared with the thermal amine capture process. In this work, we analyze the energy consumption of the electrochemical process, building from thermodynamic lower bounds, and addressing electrochemical kinetics, transport requirements as well compression and pumping energy. The analysis suggests that the electrochemical process can generate carbon dioxide at the conditions required for transportation with an electrical energy consumption of less than 50 kJ per mole of carbon dioxide captured and compressed. The electrochemical process efficiency can be further improved by optimizing flow design and utilizing additives to reduce activation overpotentials. © 2013 The Authors. Published by Elsevier Ltd. Selection and peer-review under responsibility of GHGT.
LAG IDENTIFICATION FOR VECTOR NONLINEAR TIME SERIES

Exploratory methods for determining appropriate lagged variables in a vector nonlinear time series model are investigated. The rst is a multivariate extension of the R statistic considered by Granger and Lin (1994), which is based on an estimate of the mutual information criterion. The second method uses Kendall's and partial statistics for lag determination. Both methods provide nonlinear analogs of the autocorrelation and partial autocorrelation matrices for a vector time series. Simulation studies indicate the methods reliably identify appropriate lags for many types of vector nonlinear time series. For illustration, the methods are applied to set of annual temperature and tree ring measurements at Campito Mountain in California.
From quasi-entropy to skew information

This paper gives an overview about particular quasi-entropies, generalized quantum covariances, quantum Fisher informations, skew-informations and their relations. The point is the dependence on operator monotone functions. It is proven that a skew-information is the Hessian of a quasi-entropy. The skew-information and some inequalities are extended to a von Neumann algebra setting.
A hypothetical neurological association between dehumanization and human rights abuses

Dehumanization is anecdotally and historically associated with reduced empathy for the pain of dehumanized individuals and groups and with psychological and legal denial of their human rights and extreme violence against them. We hypothesize that ‘empathy’ for the pain and suffering of dehumanized social groups is automatically reduced because, as the research we review suggests, an individual's neural mechanisms of pain empathy best respond to (or produce empathy for) the pain of people whom the individual automatically or implicitly associates with her or his own species. This theory has implications for the philosophical conception of ‘human’ and of ‘legal personhood’ in human rights jurisprudence. It further has implications for First Amendment free speech jurisprudence, including the doctrine of ‘corporate personhood’ and consideration of the potential harm caused by dehumanizing hate speech. We suggest that the new, social neuroscience of empathy provides evidence that both the vagaries of the legal definition or legal fiction of ‘personhood’ and hate speech that explicitly and implicitly dehumanizes may (in their respective capacities to artificially humanize or dehumanize) manipulate the neural mechanisms of pain empathy in ways that could pose more of a true threat to human rights and rights-based democracy than previously appreciated.