Miracle-dz/UniFAR-FTUs huggingface dataset:
Practical Verification Condition Generation for a Bytecode Language

Automatic program verifiers typically generate verification conditions from the program and discharge them with an automated theorem prover. An important consideration is the manner in which program code and invariants are expressed. We have developed a bytecode language (similar, in spirit, to Java bytecode) on which verification is performed. This serves as both an intermediate language for use within the compiler, and a binary format with which dependencies (e.g. for libraries) can be resolved. Our bytecode language is a three-address code with semi-structured control-flow. Program code and invariants are represented uniformly to ensure bytecode programs are compact. In this paper, we present our bytecode language and outline a verification condition generator based on a path-sensitive forward-propagation algorithm.
Executing Compressed Programs On An Embedded RISC Architecture

The difference in code size between RISC and CISC processors appears to be a significant factor limiting the use of RISC architectures in embedded systems. Fortunately, RISC programs can be effectively compressed. An ideal solution is to design a RISC system that can directly execute compressed programs. A new RISC system architecture called a Compressed Code RISC Processor is presented. This processor depends on a code-expanding instruction cache to manage compressed programs. The compression is transparent to the processor since all instructions are executed from cache. Experimental simulations show that a significant degree of compression can be achieved from a fixed encoding scheme. The impact on system performance is slight and for some memory implementations the reduced memory bandwidth actually increases performance.
RNA interference for antiviral therapy

Silencing gene expression through a process known as RNA interference (RNAi) has been known in the plant world for many years. In recent years, knowledge of the prevalence of RNAi and the mechanism of gene silencing through RNAi has started to unfold. It is now believed that RNAi serves in part as an innate response against invading viral pathogens and, indeed, counter silencing mechanisms aimed at neutralizing RNAi have been found in various viral pathogens. During the past few years, it has been demonstrated that RNAi, induced by specifically designed double‐stranded RNA (dsRNA) molecules, can silence gene expression of human viral pathogens both in acute and chronic viral infections. Furthermore, it is now apparent that in in vitro and in some in vivo models, the prospects for this technology in developing therapeutic applications are robust. However, many key questions and obstacles in the translation of RNAi into a potential therapeutic platform still remain, including the specificity and longevity of the silencing effect, and, most importantly, the delivery of the dsRNA that induces the system. It is expected that for the specific examples in which the delivery issue could be circumvented or resolved, RNAi may hold promise for the development of gene‐specific therapeutics. Copyright © 2006 John Wiley & Sons, Ltd.
Interferons can upregulate the expression of the tumor associated antigen G250-MN/CA IX, a potential target for (radio)immunotherapy of renal cell carcinoma.

BACKGROUND Interleukin-2 (IL-2) and interferon-alpha (IFN-alpha) can induce therapeutic responses in a minority (5-25%) of patients with metastatic renal cell carcinoma (RCC). G250-MN/CA IX, a tumor-associated antigen expressed on the majority of clear cell RCCs, is a potential (radio)immunotherapeutic target for G250-antibody based (radio)immunotherapy. We investigated the effect of the biological response modifiers (BRMs) IL-2, IFN-alpha, and IFN-gamma on the expression of the G250 antigen on RCC cells. METHODS In vitro, the expression of the G250 antigen was measured by flow cytometry (FCM) after culturing RCC cells in the presence of various concentrations of the BRMs. Additionally, the number of G250 epitopes per cell was determined quantitatively by Scatchard analysis. RESULTS Upregulation of G250 expression was observed on RCC cells cultured in the presence of IFN-alpha or IFN-gamma, whereas the addition of IL-2 had no effect. For both IFNs a clear dose-response relation between G250 antigen expression and IFN dose was observed, with IFN-gamma being the more potent agent. G250 expression could be upregulated four-fold. Interestingly, the effect of combining IFN-alpha and IFN-gamma revealed a more pronounced upregulation of G250 expression than either one of the IFNs alone. CONCLUSIONS On the basis of in vitro experiments, G250 expression can be upregulated by IFN-alpha and IFN-gamma. In vivo studies are warranted to investigate whether due to IFN treatment increased G250 expression occurs, and whether increased G250 expression can enhance the therapeutic efficacy of G250-antibody based (radio)immunotherapy.
The application of Ag/AgCl electrodes as chloride sensors in cementitious materials

Determination of the chloride content in a reinforced concrete structure is important for evaluation of the risk of chloride-induced corrosion of reinforcement. The traditional techniques for chloride determination in concrete are laborious, time-consuming and cannot be used for continuous monitoring of the chloride content. The investigation on the use of Ag/AgCl electrodes as chloride sensors in cement-based materials dates back to 1990s. Interpretation of the sensor’s response in cementitious materials requires the knowledge of chloride sensor’s characteristics and the interaction between the sensor and the surrounding medium. Hence, the stability of the chloride sensor’s response in cementitious materials depends on the properties of Ag/AgCl interface, AgCl/cement paste interface and the pore solution composition of cementitious materials. The influence of these factors on the stability of the sensor’s response was studied in this thesis. In Chapter 1 the background and motivation for the thesis were presented. In Chapter 2 the advantages and drawbacks of available test methods for determination of the chloride content in cementitious materials were explained.
Tuning-Free Heterogeneity Pursuit in Massive Networks

Heterogeneity is often natural in many contemporary applications involving massive data. While posing new challenges to effective learning, it can play a crucial role in powering meaningful scientific discoveries through the understanding of important differences among subpopulations of interest. In this paper, we exploit multiple networks with Gaussian graphs to encode the connectivity patterns of a large number of features on the subpopulations. To uncover the heterogeneity of these structures across subpopulations, we suggest a new framework of tuning-free heterogeneity pursuit (THP) via large-scale inference, where the number of networks is allowed to diverge. In particular, two new tests, the chi-based test and the linear functional-based test, are introduced and their asymptotic null distributions are established. Under mild regularity conditions, we establish that both tests are optimal in achieving the testable region boundary and the sample size requirement for the latter test is minimal. Both theoretical guarantees and the tuning-free feature stem from efficient multiple-network estimation by our newly suggested approach of heterogeneous group square-root Lasso (HGSL) for high-dimensional multi-response regression with heterogeneous noises. To solve this convex program, we further introduce a tuning-free algorithm that is scalable and enjoys provable convergence to the global optimum. Both computational and theoretical advantages of our procedure are elucidated through simulation and real data examples.
Idiopathic Progressive Subglottic Stenosis: Findings and Treatment in 52 Patients

Rarely, patients develop severe idiopathic subglottic stenosis. In 34 years, we have observed this disorder in 52 patients. All but 1 of the patients were female — a finding that suggests a hormonal cause. Without treatment, the airway progressively narrows — in some cases, until the patient requires tracheotomy. Laser submucosal resection and rotation mucosal flaps open and stabilize the airway and provide effective palliation. However, unlike traumatic subglottic stenosis, which has been cured with this technique, the idiopathic form causes submucosal fibrosis that regenerates spontaneously. Thus, treatment helps, but does not cure, the patient. The characteristic pathological finding is of submucosal dense fibrotic tissue with evidence of chronic inflammation. The clinical findings and treatment are here discussed.
Fundamental limitations on DRAM storage capacitors

The evolution of the silicon dynamic RAM toward higher levels of integration has occurred primarily as a result of decreasing the size of the area in which a single bit is stored. This has been accomplished by reducing the thickness of the storage capacitor insulator, introducing higher dielectric constant materials, and increasing the silicon doping levels. Existing published data are used to explore the consequences and requirements of continuing existing density trends into the 1-4 Mb range. The results indicate that the stored charge density requirement for planar capacitors will be limited by the resultant electric field both in the insulator and silicon. These limitations are imposed by insulator conduction, tunneling, and silicon impact ionization. It is evident that for the projected stored charge density of 30 fc/μm2 for a 4-Mb DRAM, new concepts of cell design or operation must be introduced.
The Parsec-Scale Structure and Jet Motions of the TeV Blazars 1ES 1959+650, PKS 2155–304, and 1ES 2344+514

As part of our study of the VLBI properties of TeV blazar jets, we present here a series of high-resolution 15 GHz Very Long Baseline Array (VLBA) images of the parsec-scale jets of the TeV blazars 1ES 1959+650, PKS 2155-304, and 1ES 2344+514, with linear resolutions of ~0.5 pc. Each of these sources was observed with the VLBA at three or four epochs during 1999 and 2000. There is a notable lack of any strong moving components on the VLBI images (in contrast to the rapid superluminal motions seen in EGRET blazars), and the structure of the VLBI jet can be modeled either as a series of stationary Gaussian components or as a smooth power law for two of the sources (PKS 2155-304 and 1ES 2344+514). The low apparent speeds, together with beaming indicators such as the brightness temperature of the VLBI core, imply only modest Doppler boosting of the VLBI radio emission and only modest bulk Lorentz factors (δ and Γ ≈ a few), in contrast to the more extreme values of these parameters invoked to explain the high-energy emission. The fact that no moving shocks or plasmoids are seen on the parsec scale suggests that the shocks or plasmoids that are assumed to be responsible for the high-energy flares must dissipate before they separate from the core on the VLBI images. This requires the loss of a substantial amount of bulk kinetic energy on parsec scales and implies a higher efficiency than is typically assumed for internal shock scenarios.
Bacterial Strategies to Maintain Zinc Metallostasis at the Host-Pathogen Interface*

Among the biologically required first row, late d-block metals from MnII to ZnII, the catalytic and structural reach of ZnII ensures that this essential micronutrient touches nearly every major metabolic process or pathway in the cell. Zn is also toxic in excess, primarily because it is a highly competitive divalent metal and will displace more weakly bound transition metals in the active sites of metalloenzymes if left unregulated. The vertebrate innate immune system uses several strategies to exploit this “Achilles heel” of microbial physiology, but bacterial evolution has responded in kind. This review highlights recent insights into transcriptional, transport, and trafficking mechanisms that pathogens use to “win the fight” over zinc and thrive in an otherwise hostile environment.
Visualization and clustering of crowd video content in MPCA subspace

This paper presents a novel approach for the visualization and clustering of crowd video contents by using multilinear principal component analysis (MPCA). In contrast to feature-point-based approach and frame-based dimensionality reduction approach, the proposed method maps each short video segment to a point in MPCA subspace to take temporal information into account naturally through tensorial representations. Specifically, MPCA projects each short segment of a video to a low-dimensional tensor first. A few MPCA features are then selected according to the variance captured as the final representation. Thus, a video is visualized as a trajectory in MPCA subspace. The trajectory generated enables visual interpretation of video content in a compact space as well as visual clustering of video events. The proposed method is evaluated on the PETS 2009 datasets through comparison with three existing methods for video visualization. The MPCA visualization shows superior performance in clustering segments of the same event as well as identifying the transitions between events.
A Plasma Anti-Contaminator for Imbedded Applications in SEMs and FIBs

XEI Scientific invented a practical plasma anticontamination system for Scanning Electron Microscopes (SEMs) in 1999 [1]. Now called the Evactron® Anti-Contaminator, this system has been found to quickly and effectively remove hydrocarbons from both EM chambers and specimens. By removing hydrocarbons, contamination artifacts such as black squares and scan deposits are prevented and controlled. The Evactron unit uses a unique plasma generator to create a low temperature RF plasma in a low vacuum that is able to make oxygen radicals from air. These radicals (oxygen atoms) gently ash hydrocarbons in the vacuum chamber to form CO and H2O gases that are removed by viscous flow to the vacuum pump.
Identification of Veillonella Species in the Tongue Biofilm by Using a Novel One-Step Polymerase Chain Reaction Method

Six Veillonella species have been frequently isolated from human oral cavities including infectious sites. Recently, it was reported that diet, smoking, and possibly socioeconomic status can influence the bacterial profile in oral cavities. In addition, oral hygiene habits may also influence oral microbiota in terms of both numbers and diversity of microorganisms. In this study, the identification of Veillonella species in tongue biofilms of Thai children, divided into three groups dependent on their status of oral hygiene. For this, we used a novel one-step PCR method with species-specific primer sets based on sequences of the rpoB gene. As shown in the results, the number of isolates of Veillonella species was 101 strains from only 10 of 89 subjects. However, the total number of bacteria was high for all subjects. Since it was reported in previous studies that Veillonella species were easy to isolate in human tongue biofilms at high numbers, the results obtained in this study may suggest country- or age-specific differences. Moreover, Veillonella species were detected predominantly in subjects who had poor oral hygiene compared to those with good or moderate oral hygiene. From these results, there is a possibility that Veillonella species may be an index of oral hygiene status. Furthermore, V. rogosae was a predominant species in tongue biofilms of Thai children, whereas V. parvula and V. denticariosi were not isolated at all. These characteristics of the distribution and frequency of Veillonella species are similar to those reported in previous studies. Although further studies are needed in other countries, in this study, a successful novel one-step PCR method was established to detect Veillonella species in human oral cavities easily and effectively. Furthermore, this is the first report investigating the distribution and frequency of Veillonella species in tongue biofilms of Thai children.
Predicting Helical Topologies in RNA Junctions as Tree Graphs

RNA molecules are important cellular components involved in many fundamental biological processes. Understanding the mechanisms behind their functions requires knowledge of their tertiary structures. Though computational RNA folding approaches exist, they often require manual manipulation and expert intuition; predicting global long-range tertiary contacts remains challenging. Here we develop a computational approach and associated program module (RNAJAG) to predict helical arrangements/topologies in RNA junctions. Our method has two components: junction topology prediction and graph modeling. First, junction topologies are determined by a data mining approach from a given secondary structure of the target RNAs; second, the predicted topology is used to construct a tree graph consistent with geometric preferences analyzed from solved RNAs. The predicted graphs, which model the helical arrangements of RNA junctions for a large set of 200 junctions using a cross validation procedure, yield fairly good representations compared to the helical configurations in native RNAs, and can be further used to develop all-atom models as we show for two examples. Because junctions are among the most complex structural elements in RNA, this work advances folding structure prediction methods of large RNAs. The RNAJAG module is available to academic users upon request.
Evaluation of Bond Strength of Reinforcement in Concrete Containing Fibers, Micro-silica and Nano-silica

The present study analyzes the bond stress in steel reinforcements embedded in concrete containing polymer fibers, micro- and nano-silica particles. For this purpose, 36 cylindrical (with a diameter of 10cm and height of 15cm) and36 cubic (10 × 10 × 10cm) specimens containing different contents of additives and three types of cement strength grade (i.e. 32.5, 42.5 and 52.5MPa) were constructed and subjected to pull-out and compressive strength tests, respectively. The experimental observations were then compared to previously proposed models available in the literature. The results indicated that microand nano-silica particles, compared to fibers, had more impacts on improving the reinforcement-concrete bond strength. Moreover, the highest bond strength was observed for the specimen containing equal content of microand nano-silica particles. An acceptable agreement was also obtained between the results of current study and previous models, highlighting the capability of the proposed models in prediction of the actual behavior of such specimens.
Respiratory dysfunction after coronary artery bypass grafting employing bilateral internal mammary arteries: the inﬂuence of intact pleura

Objective : To evaluate the role of intact pleurae regarding the postoperative respiratory functional status in patients undergoing coronary revascularization employing both internal mammary arteries (IMAs), according to the pedunculated or skeletonized technique (SKT) with opened or intact pleurae. Materials and methods : Using both IMAs, 299 patients underwent elective coronary revascularization. They were randomized and divided into group I ( n (cid:136) 82, undergoing IMA harvesting according to the SKT without opening the pleurae); group II ( n (cid:136) 186, undergoing IMA harvesting according the pedunculated technique with open pleurae); and group III ( n (cid:136) 31, undergoing IMA harvesting according the SKT with incidentally opened pleurae). There were no differences regarding the preoperative patient characteristics and the anaesthetic and surgical management. Results : There were two deaths in group I versus seven in group II and one in group III ( P (cid:136) ns). The number of total arterial myocardial revascularization and arterial composite grafts was signiﬁcantly higher in groups I and III than in group II, ( P , 0 : 001 and P , 0 : 005, respectively). The incidence of postoperative complications was similar between groups. Blood loss of . 1000 ml was signiﬁcantly higher in group II than group I ( P , 0 : 028); but the incidence of re-thoracotomy and blood transfusion was similar between groups. The mechanical ventilation time was signiﬁcantly higher in groups II and III versus group I ( P , 0 : 018 and P , 0 : 02, respectively). The incidence of prolonged ventilation ( . 24 h), pleural effusion, thoracocentesis and atelectasis, resulted in being signiﬁcantly higher in group II than group I. The incidence of thoracocentesis was signiﬁcantly higher in group III than group I. The pain score and analgesic requirements at 1–12 h after awakening were signiﬁcantly higher in groups II and III versus group I, becoming similar after the chest tubes were removed. PaO 2 was signiﬁcantly higher, and PaCO 2 and FiO 2 were signiﬁcantly lower in group I than groups II and III at 1 and 4 h before extubation and at 1 and 4 h after extubation. PaO 2 and PaCO 2 became similar between groups at the 5th postoperative day. Conclusions : According to our results, we may conclude that pleural integrity has beneﬁcial effects on the respiratory functional status after coronary revascularization using both IMAs. A meticulous and more careful IMA harvesting approach signiﬁcantly reduces the postoperative morbidity regarding the pulmonary functional status, and as a consequence, reduces the hospital costs. q 2001 Elsevier Science B.V. All rights reserved.
Myosin XI Is Essential for Tip Growth in Physcomitrella patens[W]

Class XI myosins are unique to plants and known to function in cytoplasmic streaming. This study demonstrates that the two myosin XI genes present in the moss Physcomitrella patens are functionally redundant, localize to the apical region of actively growing protonemal cells, and play a key role in tip growth. Class XI myosins are plant specific and responsible for cytoplasmic streaming. Because of the large number of myosin XI genes in angiosperms, it has been difficult to determine their precise role, particularly with respect to tip growth. The moss Physcomitrella patens provides an ideal system to study myosin XI function. P. patens has only two myosin XI genes, and these genes encode proteins that are 94% identical to each other. To determine their role in tip growth, we used RNA interference to specifically silence each myosin XI gene using 5′ untranslated region sequences. We discovered that the two myosin XI genes are functionally redundant, since silencing of either gene does not affect growth or polarity. However, simultaneous silencing of both myosin XIs results in severely stunted plants composed of small rounded cells. Although similar to the phenotype resulting from silencing of other actin-associated proteins, we show that this phenotype is not due to altered actin dynamics. Consistent with a role in tip growth, we show that a functional, full-length fusion of monomeric enhanced green fluorescent protein (mEGFP) to myosin XI accumulates at a subcortical, apical region of actively growing protonemal cells.