gebhart/patrepeval huggingface dataset:
Raksha (2007)

High-level semantic vulnerabilities such as SQL injection and crosssite scripting have surpassed buffer overflows as the most prevalent security exploits. The breadth and diversity of software vulnerabilities demand new security solutions that combine the speed and practicality of hardware approaches with the flexibility and robustness of software systems. This paper proposes Raksha, an architecture for software security based on dynamic information flow tracking (DIFT). Raksha provides three novel features that allow for a flexible hardware/software approach to security. First, it supports flexible and programmable security policies that enable software to direct hardware analysis towards a wide range of high-level and low-level attacks. Second, it supports multiple active security policies that can protect the system against concurrent attacks. Third, it supports low-overhead security handlers that allow software to correct, complement, or extend the hardware-based analysis without the overhead associated with operating system traps. We present an FPGA prototype for Raksha that provides a full featured Linux workstation for security analysis. Using unmodified binaries for real-world applications, we demonstrate that Raksha can detect high-level attacks such as directory traversal, command injection, SQL injection, and cross-site scripting as well as low-level attacks such as buffer overflows. We also show that low overhead exception handling is critical for analyses such as memory corruption protection in order to address false positives that occur due to the diverse code patterns in frequently used software.
Nanoscale p-MOS Thin-Film Transistor With TiN Gate Electrode Fabricated by Low-Temperature Microwave Dopant Activation (2010)

In this letter, nanoscale p-MOS TFTs with a TiN gate electrode were realized using a novel microwave (MW) dopant-activation technique. We compared both low-temperature MW annealing and rapid thermal annealing. We successfully activated the source/drain region and suppressed the short-channel effects using low-temperature MW annealing. This technique is promising from the viewpoint of realizing high-performance and low-cost upper layer nanoscale transistors required for low-temperature 3-D integrated circuit fabrication.
The Peptidyl-Prolyl Isomerase Pin1 Regulates Granulocyte-Macrophage Colony-Stimulating Factor mRNA Stability in T Lymphocytes (2006)

Abstract Cytokine production is associated with both the normal and pathologic inflammatory response to injury. Previous studies have shown that the immunosuppressants cyclosporin A or FK506, which interact with the peptidyl-propyl isomerases cyclophilin A and FK506-binding protein (FKBP12), respectively, block cytokine expression. A third member of the peptidyl-propyl isomerase family, Pin1 is expressed by immune and other cells. Pin1 has been implicated in cell cycle progression, is overexpressed in human tumors, and may rescue neurons from τ-associated degeneration. However, the role of Pin1 in the immune system remains largely unknown. In this study, we analyze the role of Pin1 in GM-CSF expression by human PBMC and CD4+ lymphocytes. We show that Pin1 isomerase activity is necessary for activation-dependent, GM-CSF mRNA stabilization, accumulation, and protein secretion, but not non-AU-rich elements containing cytokine mRNAs, including TGF-β and IL-4. Mechanistically, Pin1 mediated the association of the AU-rich element-binding protein, AUF1, with GM-CSF mRNA, which determined the rate of decay by the exosome.
Pathogenesis of calcium crystal deposition in the ligamentum flavum correlates with lumbar spinal canal stenosis. (2005)

We believe that rupture of elastic fibre bundles is the first change to occur in degeneration of the ligamentum favum. Calcium crystal deposition was seen within these fibrous and chondrometaplastic areas. Hypertrophic chondrocytes regulate crystal formation and tissue reconstruction by secreting cytokines.
Superprecipitation Is a Model for in Vitro Contraction Superior to ATPase Activity (1986)

We investigated which activity of myosin B (natural actomyosin), superprecipitation or ATPase, is better suited as a parameter for measuring in vitro contraction with emphasis on the response of myosin B to Sr2+. The Sr2+ concentration giving half-maximum (KSr2+) binding of Sr2+ to cardiac troponin was not different from that to skeletal troponin, whether the troponins were contained in the actomyosin system or in the isolated state. However, KSr2+ for the ATPase activity of cardiac myosin B is slightly smaller than that of skeletal myosin B. This difference in KSr2+ is more marked when superprecipitation was used as the indication for in vitro contraction. If the above results were compared with those of Kitazawa (1976) using glycerinated fibers of cardiac and skeletal muscle, the differences in KSr2+ between cardiac and skeletal muscle increased in the order: Sr-binding to troponin<ATPase activity<superprecipitation<contraction of glycerinated fibers. The increase in the effect of pH on Ca2+-related properties is also in the order: Ca-binding to troponin<ATPase activity<superprecipitation<contraction of glycerinated fibers. All the results coincide with one another that the results with superprecipitation are invariably more akin to those with glycerinated fibers than to those with the ATPase activity. It is concluded that superprecipitation is a better parameter for representing in vitro contraction than ATPase activity.
Length variation in short tandem repeats affects gene expression in natural populations of Arabidopsis thaliana (2021)

The genetic basis for the fine-tuned regulation of gene expression is complex and ultimately influences the phenotype and thus the local adaptation of natural populations. Short tandem repeats (STRs) consisting of repetitive DNA motifs have been shown to regulate gene expression. STRs are variable in length within a population and serve as a heritable, but semi-reversible, reservoir of standing genetic variation. For sessile organisms, such as plants, STRs could be of major importance in fine-tuning gene expression as a response to a shifting local environment. Here, we used a transcriptome dataset from natural accessions of Arabidopsis thaliana to investigate population-wide gene expression patterns in light of genome-wide STR variation. We empirically modeled gene expression as a response to the STR length within and around the gene and demonstrated that an association between gene expression and STR length variation is unequivocally present in the sampled population. To support our model, we explored the promoter activity in a transcriptional regulator involved in root hair formation and provided experimentally determined causality between coding sequence length variation and promoter activity. Our results support a general link between gene expression variation and STR length variation in A. thaliana.
Judging distance by motion-based visually mediated odometry (2004)

Inspired by the abilities of both the praying mantis and the pigeon to judge distance by use of motion-based visually mediated odometry, we create miniature models for depth estimation that are similar to the head movements of these animals. We develop mathematical models of the praying mantis and pigeon visual behavior and describe our implementation and experimental environment. We investigate structure from motion problems when images are taken from a camera whose focal point is translating the first case is reminiscent of a praying mantis peering its head left and right, apparently to obtain depth perception, hence the moniker "mantis head camera." In the second case this motion is reminiscent of a pigeon bobbing its head back and forth, also apparently to obtain depth perception, hence the moniker " pigeon head camera." We present the performance of the mantis head camera and pigeon head camera models and provide experimental results of the algorithms. We provide the comparison of the definitiveness of the results obtained by both models. The precision of our mathematical model and its implementation is consistent with the experimental facts obtained from various biological experiments.
Closed-Loop Control of Force During Electrical Stimulation of Muscle (1980)

The control of contractions elicited by electrical stimulation of muscle could be improved if there was a linear repeatable input-output relationship. The input is the command to the controlled stimulator and the output is the evoked contraction. Systems employing closed-loop force feedback to provide regulation of contractions were investigated in these studies. Force was modulated by both recruitment and temporal summation during intramuscular stimulation. Closed-loop systems with combined proportional and integral control were found to be stable and linear and to have good compensation for variations in muscle properties. A low proportional loop gain (approximately unity) was found necessary to prevent oscillation when modulating recruitment. Ratios of integral to proportional gain of about 10 gave the fastest response without compromising stability. The response time of the closed-loop system was as fast as or faster than the open-loop system.
Further development of learning techniques (2011)

The CONNECT Integrated Project aims at enabling continuous composition of networked systems, by developing techniques for synthesizing connectors. A prerequisite for synthesis is to learn about the interaction behavior of networked peers. The role of WP4 is to develop techniques for learning models of networked peers and middleware through exploratory interaction. During Y1 of CONNECT, exploratory work was performed to understand the requirements for learning techniques in the CONNECT process, and to develop concepts for using a priori knowledge about component interfaces as a basis for learning. During Y2, a major goal has been to develop techniques for automatically learning models of networked peers and middleware, based on the concepts developed during Y1 (cf. D4.1). This deliverable surveys the significant progress made on problems that are important for realizing this goal. We have developed techniques for drastically improving the efficiency of active learning, meaning to explore significantly larger parts of component behavior within a given time. We verified the power of our approaches by winning the ZULU challenge in competition with several very strong groups in the language learning community. We have also made significant breakthroughs for learning of rich models with data. We have developed a novel compact and intuitive automaton model for representing learned behavior in a canonical way. Canonicity is very helpful for organizing the resuls of exploratory interactions, since it allows the extension of stable techniques for learning classical finite-state automata (such as L ) to richer models with data. We confirm this by using the new automaton as a basis for an extension of L to richer automaton models. During Y1, we have identified abstractions as an important concept in the process of learning behavioral models of realistic systems: we introduce a method for refining a given abstraction when needed during the learning process. We also present a specialization of learning, which does not generate complete models of behavior, but concentrates on aspects that are relevant in a specific context. Finally, the deliverable reports on our efforts to learn non-functional properties, the development of a monitoring infrastructure, and further development of the learning tool infrastructure, based on LearnLib.
Cardiac Expression of Neutrophil Gelatinase-Associated Lipocalin in a Model of Cancer Cachexia-Induced Cardiomyopathy (2018)

Cancer cachexia induced increased levels of aldosterone and NGAL, contributing to worsening cardiac damage in cancer cachexia-induced cardiomyopathy. Spironolactone treatment may greatly attenuate cardiac dysfunction and lean mass atrophy associated with cancer cachexia.
Mechanism for the formation of [M–1]+ in flavones (1984)

Abstract The electron impact induced fragmentations of flavone have been studied with the aid of high resolution measurements, metastable decompositions and deuterium labelling. Based on the obtained data a mechanism for the formation of the [MH] + ion is proposed and further substantiated from the study of substituted flavones.
Autologous Tenocyte Therapy Using Porcine-Derived Bioscaffolds for Massive Rotator Cuff Defect in Rabbits (2007)

Large and retracted rotator cuff tendon tears fail to repair or retear after surgical intervention. This study attempted to develop novel tissue-engineering approaches using tenocyte-seeded bioscaffolds for tendon reconstruction of massive rotator cuff tendon defect in rabbits. Porcine small intestine submucosa (Restore) and type I/III collagen bioscaffold (ACI-Maix) were chosen as bioscaffold carriers for autologous tenocytes. Biological characterization of autologous tenocytes was conducted before the implantation. The tenocyte-seeded bioscaffolds were implanted as interposition grafts to reconstruct massive rotator cuff tendon defects in rabbits. In situ reimplantation of the autologous rotator cuff tendon, excised during defect creation, served as a positive control. Histological outcomes were analyzed and semi-quantitatively graded at 4 and 8 weeks after surgery. At 4 weeks, both tenocyte-seeded bioscaffolds displayed inflammatory reaction similar to bioscaffold-only cuff reconstruction, and the histological grading were inferior to control repair. However, at 8 weeks, inflammatory reaction of both tenocyte-seeded bioscaffolds were dramatically less than with bioscaffold alone. In addition, bioscaffolds seeded with tenocytes generated a histological appearance similar to that of the positive control. The implantation of autologous tenocytes on collagen-based bioscaffolds results in better rotator cuff tendon healing and remodeling than with the implantation of bioscaffold alone.
Estimation of Power Extinction Factor in Presence of Brillouin Precursor Formation Through Dispersive Media (2011)

In this paper, we analyze the advantages of the Brillouin precursor formation through dispersive media for a given modulated monopulse signal. The algebraic power extinction factor associated with the formation of Brillouin precursor appears to be in charge of the optimized propagation distance within the dispersive media. The analysis has been done in UHF band for rectangular and Gaussian pulses for three different dispersive media, namely, triple distilled water, vegetation and soil. It appears that Brillouin precursors will form given a suitable pulse configuration within a proper frequency window that is related to the dielectric model of the underlying media.
Interactive lakes in the Canadian Regional Climate Model, version 5: the role of lakes in the regional climate of North America (2012)

Two one-dimensional (1-D) column lake models have been coupled interactively with a developmental version of the Canadian Regional Climate Model. Multidecadal reanalyses-driven simulations with and without lakes revealed the systematic biases of the model and the impact of lakes on the simulated North American climate. The presence of lakes strongly influences the climate of the lake-rich region of the Canadian Shield. Due to their large thermal inertia, lakes act to dampen the diurnal and seasonal cycle of low-level air temperature. In late autumn and winter, ice-free lakes induce large sensible and latent heat fluxes, resulting in a strong enhancement of precipitation downstream of the Laurentian Great Lakes, which is referred to as the snow belt. The FLake (FL) and Hostetler (HL) lake models perform adequately for small subgrid-scale lakes and for large resolved lakes with shallow depth, located in temperate or warm climatic regions. Both lake models exhibit specific strengths and weaknesses. For example, HL simulates too rapid spring warming and too warm surface temperature, especially in large and deep lakes; FL tends to damp the diurnal cycle of surface temperature. An adaptation of 1-D lake models might be required for an adequate simulation of large and deep lakes.
Cytotoxic Immune Response to a Xenogeneic Bioartificial Liver (2004)

Prior studies have suggested the possibility of immune-mediated death of xenogeneic hepatocytes in a bioartificial liver (BAL) during hemoperfusion. This study was designed to elucidate how immunity may cause death of xenogeneic hepatocytes in the BAL. Healthy dogs were treated with a BAL containing hollow fiber membranes with large pores (200 nm) or small pores (400 kDa). The immune response of recipient dogs to BAL therapy was monitored over 3 h of treatment. We observed significantly greater loss of viability of hepatocytes in the 200 nm group compared with the 400 kDa group (p &lt; 0.001). Low viability after treatment with the large pore membrane was associated with positive staining for dog IgG, dog IgM, and dog complement on dead hepatocytes. Significant levels of dog antibody were detected in samples of BAL medium from the 200 nm group. These canine antibodies were cytotoxic to porcine hepatocytes. In contrast, medium from the 400 kDa group contained only trace levels of dog IgG and were noncytotoxic. We conclude that antibody-mediated cytotoxicity contributed to the death of hepatocytes during treatment with a xenogeneic BAL. Immune-mediated death of hepatocytes was reduced by increasing selectivity of the BAL membrane.
Trasiocation affects normalc-mycpromoter usage and activates fifteen crypticc-myctranscription starts in plasmacytoma M603 (1984)

Plasmacytoma M603 contains one normal, nontranslocated c-myc gene and one translocated c-myc gene in which c-myc exon 1 is juxtaposed with the immunoglobulin heavy chain enhancer and c-myc exons 2 and 3 are juxtaposed with C alpha. We find that steady-state c-myc RNA levels are 2-4 fold elevated in M603 relative to normal liver or spleen and that these transcripts originate predominantly if not exclusively from the translocated c-myc gene. Although both promoters on the nontranslocated c-myc gene are repressed, the proximal promoter, P1, is active on the translocated 5' c-myc region which is juxtaposed with the immunoglobulin heavy chain enhancer. The 3' portion of the translocated c-myc gene is transcribed from fifteen cryptic start sites and spliced at aberrant donor and acceptor splice sites, thereby generating a mixture of transcripts with different, abnormal 5' untranslated regions. Although the reason that translocation activates the cryptic c-myc starts in M603 is not completely understood, we show that truncation of the c-myc gene is not sufficient to activate cryptic transcription sites.
Twenty-Fold Enhancement of Molecular Fluorescence by Coupling to a J-Aggregate Critically Coupled Resonator (2011)

We report a 20-fold enhancement in the fluorescence of the organic dye DCM when resonantly coupled to a strongly optically absorbing structure of a thin film of spin-deposited molecular J-aggregates in a critically coupled resonator (JCCR) geometry. A submonolayer equivalent of DCM molecules is shown to absorb and re-emit 2.2% of the incident resonant photons when coupled to the JCCR enhancement structure, compared to 0.1% for the bare film of same thickness on quartz. Such a JCCR structure is a general energy focusing platform that localizes over 90% of incident light energy within a 15 nm thin film layer in the form of excitons that can subsequently be transferred to colocated lumophores. Applications of the exciton-mediated concentration of optical energy are discussed in the context of solid-state lighting, photodetection, and single photon optics.
Context-aware communication for severely disabled users (2002)

Even with assistive communication technology, interactive conversation is extremely difficult for users with severely limited mobility and loss of speech. Input to such devices is painfully slow and subject to high error rates with the resulting output not reliably reflecting the true intentions of the user. Conversational prediction has been incorporated into assistive systems to help speed up communication but could be further improved by considering the contextual interaction between the user and conversant. Contextual information applied to user profiles can greatly enhance conversational prediction and increase a severely disabled user's control over his or her complex world. We present a framework that integrates a rich profile of the user, a model of the user's environment, and actors on that environment. To test the validity of the framework, we develop a set of profiles and apply them in two different scenarios. Initial results show that the context-aware user profiles can increase both the accuracy and speed of the communication.
The Role of General and Metal-Specific Cellular Responses in Protection and Repair of Metal-Induced Damage: Stress Proteins and Metallothioneins (2023)

This chapter discusses our current knowledge of the mechanisms by which organisms protect themselves from metal-induced damage at the molecular and cellular levels. Initially we discuss the mechanisms of metal toxicity, both direct and indirect, and the nature of the potential molecular damage. We then focus on two cellular strategies in which exposure to metals induces the synthesis of proteins that act to protect and repair macromolecules from damage. One system, the cellular stress response, functions to repair and protect macromolecules from many types of environmentally induced damage, including metal toxicity. It acts to provide cellular protection through the protection and repair of proteins and protein complexes. In addition, another strategy which entails the metal-specific induction of metallothionein synthesis is also often brought online to alter metal metabolism in a specific manner. Each of these protective strategies is discussed from the perspective of what is known regarding their function in cell physiology under both normal and stressful conditions, the ways in which each system provides protection from metal toxicity, and interrelationships between the two responses. In addition, the induction of the cellular stress response and metallothionein by specific metals is reviewed.