gebhart/patrepeval huggingface dataset:
A framework for building type-safe configurations for JVM using code generation techniques (2017)

One of the common errors in software development is a configuration mistake. This type of error can have a wide range of severity levels. Consequences of a wrong configuration can be small and insignificant such as a website showing an incorrect font type, or large and consequential such as deleting customer data, incorrect price calculation, or charging a fee twice. In addition, an incorrect configuration may introduce subtle and lurking vulnerabilities into a system. Statically typed programming languages generally can mitigate these kinds of problems to some extent. At compile time, a compiler can detect incorrect types as well as other common mistakes such as some typographical errors, invalid type coercions, and invalid object references. It goes without saying that developers need to correct all compile-time errors before a project can be built. However, hardcoded configurations are not desirable since the input data cannot be changed without rebuilding a project. Due to this inflexibility, external configuration files are needed, but they bring back some thorny issues since the compiler cannot validate the types in those files. Adding validation logic does not substantially mitigate this problem because it is activated at runtime, and errors may not be discovered until a project is deployed to production servers. An external configuration file somewhat lessens the benefit of static type-checking that a compiler provides. Furthermore, string keys are needed for linking the variables in the source code to the values in configuration files. If a key is required to be renamed, it should be renamed in both configuration file and source code. Otherwise, the link will be broken. We propose a new framework that can generate source code from configuration files during development. Many configuration file formats support basic data types and nested object structure which can be mapped to Java types and the Java static nested class. The configuration library that we used is config by typesafehub. The library supports the Human-Optimized Config Object Notation (HOCON) file format which is a superset of the JavaScript Object Notation (JSON). The library's objects are encapsulated in the generated configuration object, which cannot be directly accessed by developers. We discovered that this method can prevent some types of human errors, and it also takes advantage of the validation provided by a compiler. The configuration key is no longer a string, rather a chain of methods or attributes, which is more flexible and type-safe. The configuration objects and their values are immutable. The complexity of how mutable values are converted to immutable ones is hidden from the developers. There are a number of other subtle details that are addressed in the paper, as well as some limitations and enhancements.
Noise analysis of a 1 MHz–3 GHz magnetic thin film permeance meter (1999)

We analyzed the permeability measurement error of a low permeance thin film. We clarified that the noise voltage was excited by a current loop which is composed of the coaxial cable and the ground plane. The current loop should be removed for high sensitivity of the permeameter. The permeability of a high electrical resistivity film (CoFeHfO) has been demonstrated 1 MHz–3.5 GHz.
Treatment of Depression (2013)

Chapter 4 covers the treatment of depression, and discusses popular myths regarding depression, its frequency, characteristics and diagnosis, and includes case studies, assessment, case conceptualization, intervention development and course of treatment, problems that may arise in therapy, ethical considerations, common mistakes in the course of treatment, relapse prevention, and cultural factors.
Epidemiology of acute lung injury (2005)

Recent epidemiologic studies of the incidence of acute lung injury and acute respiratory distress syndrome have indicated a similar incidence in developed societies, and they confirm that mortality is falling in comparison with a decade ago. The awaited publication of new consensus guidelines for the definition of acute lung injury and acute respiratory distress syndrome may render new studies necessary.
An artificial metalloenzyme with the kinetics of native enzymes (2016)

Natural enzymes contain highly evolved active sites that lead to fast rates and high selectivities. Although artificial metalloenzymes have been developed that catalyze abiological transformations with high stereoselectivity, the activities of these artificial enzymes are much lower than those of natural enzymes. Here, we report a reconstituted artificial metalloenzyme containing an iridium porphyrin that exhibits kinetic parameters similar to those of natural enzymes. In particular, variants of the P450 enzyme CYP119 containing iridium in place of iron catalyze insertions of carbenes into C-H bonds with up to 98% enantiomeric excess, 35,000 turnovers, and 2550 hours<sup>-1</sup> turnover frequency. This activity leads to intramolecular carbene insertions into unactivated C-H bonds and intermolecular carbene insertions into C-H bonds. These results lift the restrictions on merging chemical catalysis and biocatalysis to create highly active, productive, and selective metalloenzymes for abiological reactions.
Scalable and fault-tolerant support for variable bit-rate data in the exedra streaming server (2005)

We describe the design and implementation of the Exedra continuous media server, and experimentally evaluate alternative resource management policies using a prototype system that we built. Exedra has been designed to provide scalable and efficient support for variable bit-rate media streams whose compression efficiency leads to reduced storage space and bandwidth requirements in comparison to constant bit-rate streams of equivalent quality. We examine alternative disk striping policies, and quantify the benefits of innovative techniques for storage space allocation, buffer management, and resource reservation, which we developed to achieve both predictability and high-performance in handling disk and network data transfers of variable size. Additionally, we investigate the differences between diverse data replication schemes over disk arrays, and compare methods for disk access time reservation that enable tolerance of disk failures at minimal cost. Overall, we demonstrate the feasibility of building network media servers that exploit the latest advances in media compression technology towards reducing the cost of wide-scale streaming services for stored data.
Positive Correlation between H,K-Adenosine Triphosphatase Autoantibodies and Helicobacter pylori Antibodies in Patients with Pernicious Anemia (1994)

There was a positive correlation and a high incidence of antibodies against H,K-ATPase and H. pylori in sera from patients with pernicious anemia. These antibodies recognized different epitopes.
StreetGAN: towards road network synthesis with generative adversarial networks (2017)

We propose a novel example-based approach for road network synthesis relying on Generative Adversarial Networks\n(GANs), a recently introduced deep learning technique. In a pre-processing step, we first convert a given\nrepresentation of a road network patch into a binary image where pixel intensities encode the presence or absence\nof streets. We then train a GAN that is able to automatically synthesize a multitude of arbitrary sized street networks\nthat faithfully reproduce the style of the original patch. In a post-processing step, we extract a graph-based\nrepresentation from the generated images. In contrast to other methods, our approach does neither require domainspecific\nexpert knowledge, nor is it restricted to a limited number of street network templates. We demonstrate the\ngeneral feasibility of our approach by synthesizing street networks of largely varying style and evaluate the results\nin terms of visual similarity as well as statistical similarity based on road network similarity measures.
Recent Advances in Topical Ocular Drug Delivery (2015)

Topical ocular drug delivery has been considered to be an ideal route of administration for treatment of ocular diseases related to the anterior segment of the eye. However, topical ocular delivery is a challenging task because of barriers such as nasolacrimal drainage, corneal epithelium, blood-ocular barriers, and metabolism in the eye. Approaches to improve ocular bioavailability include physical approaches such as formulations of drugs as solutions (Zymaxid(™)), suspensions (Zigran(®)), gels (Akten(®)) and chemical approaches such as prodrugs (Xalatan(™)), chemical delivery systems, and soft drugs. The purpose of this review article is to summarize recent advances in topical drug delivery to the anterior segment of the eye. Functional transporters in the corneal epithelium were also discussed as they provide prospects in topical ocular delivery. In addition to conventional delivery systems, novel delivery systems involving nanocarriers were also investigated for topical ocular delivery. Furthermore, due to increased interest, gene therapy applications of topical ocular delivery of genes to the anterior segment of the eye were also discussed. Research in topical ocular delivery is active for more than 50 years and proven to be advantageous for the treatment of many ocular diseases. However, there is scope for innovation in topical drug delivery to develop delivery systems with a high patient safety profile and compliance for effective clinical usefulness.
Is hydrogen peroxide a second messenger of salicylic acid in systemic acquired resistance? (1995)

Elevated levels of salicylic acid (SA) are required for the induction of systemic acquired resistance (SAR) in plants. Recently, a salicylic acid‐binding protein (SABP) isolated from tobacco was shown to have catalase activity. Based on this finding elevated levels of hydrogen peroxide (H 2 O 2 ) were postulated to act as a second messenger of SA in the SAR signal transduction pathway. A series of experiments have been carried out to clarify the role of H 2 O 2 in SAR‐signaling. No increase of H 2 O 2 was found during the onset of SAR. Induction of the SAR gene, PR‐1, by H 2 O 2 and H 2 O 2 ‐inducing chemicals is strongly suppressed in transgenic tobacco plants that express the bacterial salicylate hydroxylase gene, indicating that H 2 O 2 induction of SAR genes is dependent on SA accumulation. Following treatment of plants with increasing concentrations of H 2 O 2 , a dose‐dependent accumulation of total SA species was found, suggesting that H 2 O 2 may induce PR‐1 gene expression through SA accumulation. While the results do not support a role for H 2 O 2 in SAR signaling, it is suggested that SA inhibition of catalase activity may be important in tissues undergoing a hypersensitive response.
Duplex ultrasound scanning of the carotid arteries with velocity spectrum analysis. (1983)

Duplex ultrasound examination of the carotid arteries using high-resolution realtime imaging and pulsed Doppler flow measurements with velocity spectrum analysis was performed on a series of 50 consecutive patients (100 vessels), and findings were compared with findings of conventional carotid arteriography. The criteria for an abnormal duplex examination included: a velocity ratio of 1.5 or more (ratio of the maximum internal carotid artery [ICA] flow velocity to the maximum common carotid artery flow velocity); turbulence, as indicated by an ICA velocity spectral width of 40 cm per second or more; visible plaque that produced an ICA stenosis of 50% or more; a maximum ICA velocity of 100 cm per second or more; and inability to detect ICA flow. A flow-limiting stenosis was defined arteriographically as a 50% or greater stenosis of the diameter of the arterial lumen. The velocity ratio was the best single duplex criterion, with an overall accuracy of 88%. The sensitivity or specificity of the duplex examination was as high as 97%, depending on the number of duplex criteria that were abnormal.
PPARγ Ligand Inhibits Osteopontin Gene Expression Through Interference With Binding of Nuclear Factors to A/T-Rich Sequence in THP-1 Cells (2002)

Peroxisome proliferator-activated receptor gamma (PPARgamma) is a member of the nuclear receptor superfamily that acts as a key player in adipocyte differentiation, glucose metabolism, and macrophage differentiation. Osteopontin (OPN), a component of extracellular matrix, is elevated during neointimal formation in the vessel wall and is synthesized by macrophages in atherosclerotic plaques. In the present study, we investigated the molecular mechanisms regulating OPN gene expression by PPARgamma in THP-1 cells, a cell line derived from human monocytic leukemia cells. Northern and Western blot analyses showed that exposure of THP-1 cells to PMA (phorbol 12-myristate 13-acetate) increases OPN mRNA and protein levels in a time-dependent manner. PMA-induced OPN expression was significantly decreased by troglitazone (Tro) and other PPARgamma ligands. Transient transfection assays of the human OPN promoter/luciferase construct showed that PPARgamma represses OPN promoter activity, and the PPARgamma-responsive region within the OPN promoter lies between -1000 and -970 relative to the transcription start site. Site-specific mutation analysis and electrophoretic mobility shift assays indicated that a homeobox-like A/T-rich sequence between -990 and -981, which functions as a binding site for PMA-induced nuclear factors other than PPARgamma, mediates the repression of OPN expression by Tro. Furthermore, concatenated A/T-rich sequences conferred the PPARgamma responsiveness on the heterologous promoter. Taken together, these data suggest that PPARgamma ligand inhibits OPN gene expression through the interference with the binding of nuclear factors to A/T-rich sequence in THP-1 cells.
An inflatable carpet to reduce the loading of the lower extremities: evaluation by a new sled test method with toepan intrusion (1998)

The unprecedented spread of the highly pathogenic avian influenza type A H5N1 is a threat to veterinary public health. However, the virus does not in its present form constitute a major threat to human public health. Only if the virus mutates to spread effectively from person to person will there be a risk of a new pandemic. It is not possible to predict if this will happen, when it may happen or how serious it may be. At present, seasonal influenza represents the greatest burden of illness among the three types of influenza A illness: seasonal, avian, and pandemic influenza.
The molecular context of determinants within the priming antigen establishes a hierarchy of T cell induction: T cell specificities induced by peptides of β‐galactosidase <i>vs.</i> the whole antigen (1989)

The antibody response following priming with a macromolecule or a peptide will depend on the regulatory T cells that become activated by the antigenic determinants available. In this report, activation of T helper (Th) and T suppressor (Ts) cells by determinants on beta-galactosidase (GZ) was examined by comparing native GZ [1023 amino acid (a.a.) residues per monomer] with peptides from the immunodominant region encompassing residues 3 to 187. Each immunogen established its characteristic hierarchy of dominance of determinants within it: in particular, GZ and CB-2-3 (a.a. 3-187) each induced immunodominant Th cells which could not be induced by T8 (a.a. 60-140). Hierarchies of suppressor determinant are also created: T8-Ts suppresses all Th specificities and therefore can be deemed immunodominant: T8-2-Ts and T8-3-Ts have a more selective suppressor activity and can be considered subdominant. We conclude that the outcome of immunization shifts with a change in the nature of the immunogen and the context within which the determinant lies will crucially influence its expression. A particular "context" presumably determines the likely order of processing of that molecule which leads to a characteristic relationship among the Ts, Th and B cell determinants involved.
Detecting Driver Distraction Using Smartphones (2015)

Cell phone usage while driving is a major distraction. Due to the number of accidents that are related to cell phone use while driving, laws have been introduced making the use of a cell phone while driving illegal in several jurisdictions. In this paper, we address a fundamental problem of distinguishing the driver from passengers using ubiquitous camera feature of cell phones to determine the position of the camera (hence, cell phone) in a vehicle. Compared with the state of-the-art solutions, a key property of our solution is non-intrusiveness, i.e., Enabling driver phone detection without relying on any particular situations, events, and dedicated hardware devices. Our system only utilizes the camera functionality of a smart phone. Images captured from a camera are compared with reference images by applying image registration methods, making a comparison. Through extensive experimental results and analysis, we demonstrate that our methodology can provide accurate localization of a smart phone, thus effectively distinguishing driver from passengers.
Soft substrates normalize nuclear morphology and prevent nuclear rupture in fibroblasts from a laminopathy patient with compound heterozygous LMNA mutations (2013)

Laminopathies, mainly caused by mutations in the LMNA gene, are a group of inherited diseases with a highly variable penetrance; i.e., the disease spectrum in persons with identical LMNA mutations range from symptom-free conditions to severe cardiomyopathy and progeria, leading to early death. LMNA mutations cause nuclear abnormalities and cellular fragility in response to cellular mechanical stress, but the genotype/phenotype correlations in these diseases remain unclear. Consequently, tools such as mutation analysis are not adequate for predicting the course of the disease. Here, we employ growth substrate stiffness to probe nuclear fragility in cultured dermal fibroblasts from a laminopathy patient with compound progeroid syndrome. We show that culturing of these cells on substrates with stiffness higher than 10 kPa results in malformations and even rupture of the nuclei, while culture on a soft substrate (3 kPa) protects the nuclei from morphological alterations and ruptures. No malformations were seen in healthy control cells at any substrate stiffness. In addition, analysis of the actin cytoskeleton organization in this laminopathy cells demonstrates that the onset of nuclear abnormalities correlates to an increase in cytoskeletal tension. Together, these data indicate that culturing of these LMNA mutated cells on substrates with a range of different stiffnesses can be used to probe the degree of nuclear fragility. This assay may be useful in predicting patient-specific phenotypic development and in investigations on the underlying mechanisms of nuclear and cellular fragility in laminopathies.
Stepwise Refinement Process With Modularity: An Algebraic Approach (2005)

Stepwise refinement method can be formalised algebraically, using specification morphism. Algebraic schemes also offer a natural way, like that we have adopted, to modularise speci- fications in the shape of distinct sort sets. Our definition of stepwise refinement with modularity is a faithful rendition of system development processes, as is shown by the example of designing an editor. We propose a concrete environment implementing our approach, based on OBJ2.
Sol and gel states in peptide hydrogels visualized by Gd(III)‐enhanced magnetic resonance imaging (2011)

The hydrogels assembled from a pair of self-repulsive but mutually attractive decapeptides are visualized by magnetic resonance imaging (MRI). It is found that in the absence of Gd(III)-chelate, gelation has little effect on MRI signal intensity. In the presence of Gd(III)-chelate, gelation leads to significant changes in water relaxation and MR signal intensity. The sol to gel transition is best visualized by T2-weighted imaging using large echo time with the sol producing a bright spot and the gel producing a dark spot. MRI studies point to high local Gd(III)-chelate concentration. Small-angle X-ray scattering study indicates that this local enrichment of Gd(III)-chelate has two contributing processes: first, the aggregation of peptides into fibers; second, within peptide fibers, Gd(III)-chelate further aggregate into clusters. This work demonstrates that the status of peptide-based hydrogels can be visualized by MRI with the aid of covalently linked Gd(III)-chelates. This result has implications for monitoring peptide scaffolds in vivo.
A Historical Comparison of Resource-Based Theory and Five Schools of Thought Within Industrial Organization Economics: Do We Have a New Theory of the Firm? (1991)

A resource-based approach to strategic management focuses on costly-to-copy attributes of the firm as sources of economic rents and, therefore, as the fundamental drivers of performance and competitive advantage. Interest presently exists in whether explicit acknowledgement of the resource-based view may form the kernel of a unifying paradigm for strategy research. This article addresses the degree to which a resource-based view represents a fundamentally different approach from theories used in industrial organization (10) economics. The central thesis is that, put informal terms, the resource-based approach is reaching for a theory of the firm. To determine its distinctiveness in comparison to IO, therefore, an appropriate comparison is with other theories of the firm developed within that tradition. Section I summarizes and analyzes five theories that have been significant in the historical evolution of IO. These are neoclassical theory's perfect competition model, Bain-type IO, the Schumpeterian and Chicago responses, and transaction cost theory. The first part of Section II analyzes the resource-based approach in terms of similarities to and differencesfrom these IO-related theories. The conclusion is that resource-based theory both incorporates and rejects at least one major element from each of them; thus resource-based theory reflects a strong IO heritage, but at the same time incorporates fundamental differences from any one of these theories. The second part of Section II analyzes resource-based theory as a new theory of the firm.
Attack Surface Metrics and Automated Compile-Time OS Kernel Tailoring. (2013)

The economy of mechanism security principle states that program design should be kept as small and simple as possible. In practice, this principle is often disregarded to maximize user satisfaction, resulting in systems supporting a vast number of features by default, which in turn offers attackers a large code base to exploit. The Linux kernel exemplifies this problem: distributors include a large num-ber of features, such as support for exotic filesystems and socket types, and attackers often take advantage of those. A simple approach to produce a smaller kernel is to manually configure a tailored Linux kernel. However, the more than 11,000 configuration options available in recent Linux versions make this a time-consuming and non-trivial task. We design and implement an automated approach to produce a kernel configuration that is adapted to a particular workload and hardware, and present an attack surface evaluation framework for evaluating security im-provements for the different kernels obtained. Our results show that, for real-world server use cases, the attack surface reduction obtained by tailoring the kernel ranges from about 50 % to 85%. Therefore, kernel tailoring is an attractive approach to improve the security of the Linux kernel in practice.