Miracle-dz/UniFAR-FTUs huggingface dataset:
A Survey on Tools for Binary Code Analysis

Different strategies for binary analysis are widely used in systems dealing with software maintenance and system security. Binary code is self-contained; though it is easy to execute, it is not easy to read and understand. Binary analysis tools are useful in software maintenance because the binary of software has all the information necessary to recover the source code. It is also incredibly important and sensitive in the domain of security. Malicious binary code can infect other applications, hide in their binary code, contaminate the whole system or travel through Internet and attack other systems. This makes it imperative for security personnel to scan and analyze binary codes with the aid of the binary code analysis tools. On the other hand, crackers can reverse engineer the binary code to assembly code in order to break the secrets embedded in the binary code, such as registration number, password or secret algorithms. This motivates researches to prevent malicious monitoring by binary code analysis tools. Evidently, binary analysis tools play an important doublesided role in security. This paper surveys binary code analysis from the most fundamental perspective views: the binary code formats, several of the most basic analysis tools, such as disassembler, debugger and the instrumentation tools based on them. The previous research on binary analysis are investigated and summarized and a new approach of analysis, disasembler-based binary interpreter, is proposed and discussed.
Mutational Interference and the Progression of Muller's Ratchet When Mutations Have a Broad Range of Deleterious Effects

Deleterious mutations can accumulate in asexual haploid genomes through the process known as Muller's ratchet. This process has been described in the literature mostly for the case where all mutations are assumed to have the same effect on fitness. In the more realistic situation, deleterious mutations will affect fitness with a wide range of effects, from almost neutral to lethal. To elucidate the behavior of the ratchet in this more realistic case, simulations were carried out in a number of models, one where all mutations have the same effect on selection [one-dimensional (1D) model], one where the deleterious mutations can be divided into two groups with different selective effects [two-dimensional (2D) model], and finally one where the deleterious effects are distributed. The behavior of these models suggests that deleterious mutations can be classified into three different categories, such that the behavior of each can be described in a straightforward way. This makes it possible to predict the ratchet rate for an arbitrary distribution of fitness effects using the results for the well-studied 1D model with a single selection coefficient. The description was tested and shown to work well in simulations where selection coefficients are derived from an exponential distribution.
p53 Expression in a Malignant Mesothelioma Patient during Seven-Year Follow-up

Malignant mesothelioma (MM) is the aggressive tumor of serosal surfaces. There are crude pathogenetic results regarding the biology of MM. Coordinated upregulations of p53 gene expression are shown in malignancies. We believed that there are changes in the p53 expression with transformation from reactive hyperplasia to MM. A 65-year-old male was admitted the hospital because of left pleuritic chest pains in 2004. Chest computed tomography (CT) results showed left pleural effusions with loculation and pleural thickening. Pathologic findings revealed reactive mesothelial hyperplasia. In 2008, the patient again felt left pleuritic chest pains. Chest CT showed progressive thickening of the left pleura. Pathologic diagnosis was atypical mesothelial hyperplasia. In 2011, chest CT showed progressive thickening of his left pleura. He was diagnosed with well-differentiated papillary mesothelioma. Serial change was analyzed by immunohistochemical staining for p53 of pleural tissues. There were no remarkable changes in p53 expressions during the transformation to MM.
Autonomy and Normativity: Investigations of Truth, Right and Beauty

Part I Truth: chapter I - freedom from foundations, the normativity of autonomy in theory and practice chapter II - Hegel's remedy for the impasse of contemporary philosophy chapter III - philosophy without foundations? chapter IV - concept, individuality and truth chapter V - space, time and matter, conceiving nature without foundations. Part II Right: chapter VI - ethical community without communitarianism chapter VII - the immanent critique of natural ethical community chapter VIII - with what must ethics begin? reflections on property and contract chapter IX - unity in the common law? chapter X - friendship, family and ethical community chapter XI - the unfinished revolution in family law chapter XII - should the economy be democratized? chapter XIII - relativism and democracy chapter XIV - post-colonialism and right. Part III Beauty: chapter XV - the individuality of art and the collapse of metaphysical aesthetics chapter XVI - romaticism and modernity chapter XVII - the challenge of architecture to systematic aesthetics conclusion - modernity and the recovery of truth, right and beauty.
The Adherence of Open Source Java Programmers to Standard Coding Practices

The use of agreed-upon coding practices is believed to enhance program comprehension, which directly affects reuse and maintainability. This paper describes a controlled small-scale experiment that tries to determine how well open source Java programmers adhere to a set of well publicized coding practices. The experiment evaluated 100 arbitrarily selected open source Java classes from different programmers with respect to 16 standard coding practices. The results of this experiment indicate that open source Java programmers do not always adhere to standard coding practices. It was found that only 4% of the subject classes have no violations to any of the 16 standard coding practices and there were only 5 of 16 coding practices that all subjects followed. It was also found that there are positive correlations between the number of violations found in a class and its lines-of-code, number of methods, and number of attributes.
Hydrogen Sensors and Switches from Electrodeposited Palladium Mesowire Arrays

Hydrogen sensors and hydrogen-activated switches were fabricated from arrays of mesoscopic palladium wires. These palladium “mesowire” arrays were prepared by electrodeposition onto graphite surfaces and were transferred onto a cyanoacrylate film. Exposure to hydrogen gas caused a rapid (less than 75 milliseconds) reversible decrease in the resistance of the array that correlated with the hydrogen concentration over a range from 2 to 10%. The sensor response appears to involve the closing of nanoscopic gaps or “break junctions” in wires caused by the dilation of palladium grains undergoing hydrogen absorption. Wire arrays in which all wires possessed nanoscopic gaps reverted to open circuits in the absence of hydrogen gas.
A massive planet to the young disc star HD 81040

We report the discovery of a massive planetary companion orbiting the young disc star HD 81040. Based on five years of precise radial-velocity measurements with the HIRES and ELODIE spectrographs, we derive a spectroscopic orbit with a period $P =1001.0$ days and eccentricity $e = 0.53$. The inferred minimum mass for the companion of $m_2\sin i = 6.86$ $M_\mathrm{Jup}$ places it in the high-mass tail of the extrasolar planet mass distribution. From the ELODIE spectra we derive a Lithium abundance of $\log\epsilon{\rm (Li)} = 1.90$, and from the HIRES spectra of the cores of the Ca II H and K lines we derive an activity index of $\langle \log R^\prime_\mathrm{HK}\rangle = -4.48$, suggesting an age of about 0.8 Gyr. The radial-velocity residuals exhibit a scatter significantly larger than the typical internal measurement precision of the instruments. We attribute this excess velocity jitter to activity on the surface of the moderately young host star. However, the amplitude of the jitter is much too small and the expected period of rotation is much too short to explain the observed orbital motion, which we conclude is due to a massive planetary companion.
Auspicious Compounds *

This paper provides additional support for the widely held view that the first member of a synthetic compound cannot correspond to the external argument of the (verb within the) head. Apparent counter-examples of the form city-employee from Lieber (2001) are re-examined and contrasted with minimally different examples; the conclusion is that there is a subtle, yet I believe secure, contrast in meaning between the acceptable and unacceptable cases, and that the acceptable cases do not involve a true external argument.
Clustered genetic semantic graph approach for multi-document abstractive summarization

Multi-document summarization aims to produce a compressed version of numerous online text documents and preserves the salient information. A particular challenge for multi-document summarization is that there is an inevitable overlap in the information stored in different documents. Thus, effective summarization methods that merge similar information across the documents are desirable. This paper introduces a clustered genetic semantic graph approach for multi-document abstractive summarization. The semantic graph from the document set is constructed in such a way that the graph vertices represent the predicate argument structures (PASs), extracted automatically by employing semantic role labeling (SRL); and the edges of graph correspond to semantic similarity weight determined from PAS-to-PAS semantic similarity, and PAS-to-document relationship. The PAS-to-document relationship is expressed by different features, weighted and optimized by genetic algorithm. The salient graph nodes (PASs) are ranked based on modified weighted graph based ranking algorithm. The clustering algorithm is performed to eliminate redundancy in such a way that representative PAS with the highest salience score from each cluster is chosen, and fed to language generation to generate summary sentences. Experiment of this study is performed using DUC-2002, a standard corpus for text summarization. Experimental results indicate that the proposed approach outperforms other summarization systems.
Moving Beyond the Rhetoric of Pluralism: Suggestions for an “Inside-the-Mainstream” Heterodoxy

David Colander has been writing about economic methodology for over 30 years, but he goes out of his way to emphasize that he does not see himself as a methodologist. His pragmatic methodology is applicable to what economists are doing and attempts to answer questions that all economists face as they go about their work. The articles collected in this volume are divided, with the first part providing a framework underlying Colanderâ€™s methodology and introducing Colanderâ€™s methodology for economic policy within that framework. Part two presents Colanderâ€™s view on the methodology for microeconomics, while part three looks at Colanderâ€™s methodology for macroeconomics. The book closes with discussions of broader issues.
The Immunobiology of Inductive Anti‐CD40L Therapy in Transplantation: Allograft Acceptance is Not Dependent Upon the Deletion of Graft‐Reactive T Cells

CD40–CD40L costimulatory interactions are crucial for allograft rejection, in that treatment with anti‐CD40L mAb markedly prolongs allograft survival in several systems. Recent reports indicate that costimulatory blockade results in deletion of graft‐reactive cells, which leads to allograft tolerance. To assess immunologic parameters that were influenced by inductive CD40–CD40L blockade, cardiac allograft recipients were treated with multiple doses of the anti‐CD40L mAb MR1, which was remarkably effective at prolonging allograft survival. Acute allograft rejection responses such as IL‐2 producing helper cell priming, Th1 priming, and alloantibody production were abrogated by anti‐CD40L treatment. Interestingly, the spleens of mice bearing long‐term cardiac allografts following inductive anti‐CD40L treatment retained precursor donor alloantigen‐reactive CTL, IL‐2 producing helper cells, and Th1 in numbers comparable to those observed in naïve mice. These mice retained the ability to reject donor‐strain skin allografts, but were incapable of rejecting the original cardiac allograft, or a second donor‐strain cardiac allograft. Further, differentiated effector cells were incapable of mediating rejection following adoptive transfer into mice bearing long‐term allografts, suggesting that regulatory cell function, rather than effector cell deletion was responsible for long‐term graft acceptance. Collectively, these data demonstrate that inductive CD40–CD40L blockade does not result in the deletion of graft‐reactive T cells, but induces the maintenance of these cells in a quiescent precursor state. They further point to a tissue specificity of this hyporesponsiveness, suggesting that not all donor alloantigen‐reactive cells are subject to this regulation.
Real-world Polymorphic Attack Detection

As state-of-the-art attack detection technology becomes more prevalent, attackers have started to employ evasion techniques such as code obfuscation and polymorphism to defeat existing defenses. We have recently proposed network-level emulation, a heuristic detection method that scans network traffic to detect polymorphic attacks. Our approach uses a CPU emulator to dynamically analyze every potential instruction sequence in the inspected traffic, aiming to identify the execution behavior of certain malicious code classes, such as self-decrypting polymorphic shellcode. In this paper, we present results and experiences from deployments of network-level emulation in production networks. After more than a year of continuous operation, our prototype implementation has captured more than a million attacks against real systems, while so far has not resulted to any false positives. The observed attacks employ a highly diverse set of exploits, often against less widely used vulnerable services, and in some cases, sophisticated obfuscation schemes.
Quantitation of Regional Cardiac Function by Two–dimensional Echocardiography: I. Patterns of Contraction in the Normal Left Ventricle

Regional differences in wall motion and wall thickening were quantitated in the normal left ventricle using two-dimensional echocardiography (2-D echo). Using a computer-aided system, the left ventricle was subdivided in a standardized manner into 40 segments of five 2-D echo short-axis cross sections from the mitral valve level to the low left ventricle or apex. Measurements of sectional and segmental cavity areas, muscle areas and endocardial as well as epicardial peritneters, allowed assessment of contractile function using such indexes as endocardial systolic fractional area change (FAC), wall thickening (WTh), and circumferential fiber shortening (shortening). In 50 normal anesthetized, closed-chest dogs (including 10 studies in the conscious state) and in 32 normal humans, left ventricular contractile function increased significantly from base to apex. Thus, in anesthetized dogs, sectional FAC, WTh and shortening increased from left ventricular base to apex as follows: 39.4 ± 5.1% to 61.6 ± 7.2%, 20.5 ± 6.6% to 46.7 11.5% and 22.7 ± 3.4% to 35.4 5.9%, respectively. Similar trends were noted in conscious dogs. In man, sectional FAC, WTh and shortening also increased from the mitral valve to the low left ventricular level: 38.8 3.3% to 60.7 4.5%, 23.9 ± 5.6% to 28.9 ± 7.6% and 21.4 ± 5.0% to 30.6 ± 5.6%, respectively. Detailed segmental analysis in individual cross sections also revealed regional differences in contraction. Generally, contraction was most vigorous in posterior regions of the left ventricle. The septal regions exhibited lowest contraction at the base, but also the greatest increase from base to apex, both in the canine and human. Lateral regions did not show significant changes along the length of the left ventricle. Diastolic wall thickness also varied. We conclude that contraction in the normal left ventricle cannot be assumed to be uniform or symmetrical. These normal regional differences in function should be taken into account when evaluating altered physiologic states and in studying effects of therapeutic interventions.
Methanobactin and the Link between Copper and Bacterial Methane Oxidation

SUMMARY Methanobactins (mbs) are low-molecular-mass (<1,200 Da) copper-binding peptides, or chalkophores, produced by many methane-oxidizing bacteria (methanotrophs). These molecules exhibit similarities to certain iron-binding siderophores but are expressed and secreted in response to copper limitation. Structurally, mbs are characterized by a pair of heterocyclic rings with associated thioamide groups that form the copper coordination site. One of the rings is always an oxazolone and the second ring an oxazolone, an imidazolone, or a pyrazinedione moiety. The mb molecule originates from a peptide precursor that undergoes a series of posttranslational modifications, including (i) ring formation, (ii) cleavage of a leader peptide sequence, and (iii) in some cases, addition of a sulfate group. Functionally, mbs represent the extracellular component of a copper acquisition system. Consistent with this role in copper acquisition, mbs have a high affinity for copper ions. Following binding, mbs rapidly reduce Cu2+ to Cu1+. In addition to binding copper, mbs will bind most transition metals and near-transition metals and protect the host methanotroph as well as other bacteria from toxic metals. Several other physiological functions have been assigned to mbs, based primarily on their redox and metal-binding properties. In this review, we examine the current state of knowledge of this novel type of metal-binding peptide. We also explore its potential applications, how mbs may alter the bioavailability of multiple metals, and the many roles mbs may play in the physiology of methanotrophs.
Significant hepatic histopathology in chronic hepatitis B patients with serum ALT less than twice ULN and high HBV‐DNA levels in Indonesia

OBJECTIVE: To study the prevalence of significant hepatic histopathology in chronic hepatitis B (CHB) patients with alanine aminotransferase (ALT) ≤ twice upper limit of normal (ULN) and its association with age, HBeAg status, hepatitis B virus (HBV)‐DNA level and viral genotype.
Molecular basis of proton block of L-type Ca2+ channels

Hydrogen ions are important regulators of ion flux through voltage- gated Ca2+ channels but their site of action has been controversial. To identify molecular determinants of proton block of L-type Ca2+ channels, we combined site-directed mutagenesis and unitary current recordings from wild-type (WT) and mutant L-type Ca2+ channels expressed in Xenopus oocytes. WT channels in 150 mM K+ displayed two conductance states, deprotonated (140 pS) and protonated (45 pS), as found previously in native L-type Ca2+ channels. Proton block was altered in a unique fashion by mutation of each of the four P-region glutamates (EI-EIV) that form the locus of high affinity Ca2+ interaction. Glu(E)-->Gln(Q) substitution in either repeats I or III abolished the high-conductance state, as if the titration site had become permanently protonated. While the EIQ mutant displayed only an approximately 40 pS conductance, the EIIIQ mutant showed the approximately 40 pS conductance plus additional pH-sensitive transitions to an even lower conductance level. The EIVQ mutant exhibited the same deprotonated and protonated conductance states as WT, but with an accelerated rate of deprotonation. The EIIQ mutant was unusual in exhibiting three conductance states (approximately 145, 102, 50 pS, respectively). Occupancy of the low conductance state increased with external acidification, albeit much higher proton concentration was required than for WT. In contrast, the equilibrium between medium and high conductance levels was apparently pH-insensitive. We concluded that the protonation site in L-type Ca2+ channels lies within the pore and is formed by a combination of conserved P-region glutamates in repeats I, II, and III, acting in concert. EIV lies to the cytoplasmic side of the site but exerts an additional stabilizing influence on protonation, most likely via electrostatic interaction. These findings are likely to hold for all voltage-gated Ca2+ channels and provide a simple molecular explanation for the modulatory effect of H+ ions on open channel flux and the competition between H+ ions and permeant divalent cations. The characteristics of H+ interactions advanced our picture of the functional interplay between P-region glutamates, with important implications for the mechanism of Ca2+ selectivity and permeation.
Accuracy of Craniofacial Measurements: Computed Tomography and Three-Dimensional Computed Tomography Compared With Stereolithographic Models

In a retrospective study, distance measurements of nine children with craniofacial malformation were analyzed. The accuracy of measurements was compared when measured on a workstation using a 16-slice multidetector spiral computed tomography and on a stereolithographic model. Three different methods of defining distances were investigated: 1) on the stereolithographic plastic models, 14 distances connecting landmarks were identified with a digitizer (Polaris Tracker); 2) the same distances were defined at axial, coronal, and sagittal reformats of the computed tomography data set and measured using a Philips MX View workstation; and 3) the same 14 distances were defined at three-dimensional virtual reality models of the skulls at the same workstation. All measurements were performed with all three methods by three different readers. The following conclusions could be drawn: stereolithographic models provide a highly exact reproduction of the skull in children with craniofacial malformations. They are a reliable basis for all analytic and probatory endeavors preparing complicated surgical corrections. Three-dimensional virtual reality display modes serve significantly better for exact distance measurements on the complex surface of the human skull than planar reformats of the same computed tomography data sets.
Adaptive Divergence in Experimental Populations of Pseudomonas fluorescens. IV. Genetic Constraints Guide Evolutionary Trajectories in a Parallel Adaptive Radiation

The capacity for phenotypic evolution is dependent upon complex webs of functional interactions that connect genotype and phenotype. Wrinkly spreader (WS) genotypes arise repeatedly during the course of a model Pseudomonas adaptive radiation. Previous work showed that the evolution of WS variation was explained in part by spontaneous mutations in wspF, a component of the Wsp-signaling module, but also drew attention to the existence of unknown mutational causes. Here, we identify two new mutational pathways (Aws and Mws) that allow realization of the WS phenotype: in common with the Wsp module these pathways contain a di-guanylate cyclase-encoding gene subject to negative regulation. Together, mutations in the Wsp, Aws, and Mws regulatory modules account for the spectrum of WS phenotype-generating mutations found among a collection of 26 spontaneously arising WS genotypes obtained from independent adaptive radiations. Despite a large number of potential mutational pathways, the repeated discovery of mutations in a small number of loci (parallel evolution) prompted the construction of an ancestral genotype devoid of known (Wsp, Aws, and Mws) regulatory modules to see whether the types derived from this genotype could converge upon the WS phenotype via a novel route. Such types—with equivalent fitness effects—did emerge, although they took significantly longer to do so. Together our data provide an explanation for why WS evolution follows a limited number of mutational pathways and show how genetic architecture can bias the molecular variation presented to selection.