gebhart/patrepeval huggingface dataset:
Fault injection techniques and tools (1997)

Fault injection is important to evaluating the dependability of computer systems. Researchers and engineers have created many novel methods to inject faults, which can be implemented in both hardware and software. The contrast between the hardware and software methods lies mainly in the fault injection points they can access, the cost and the level of perturbation. Hardware methods can inject faults into chip pins and internal components, such as combinational circuits and registers that are not software-addressable. On the other hand, software methods are convenient for directly producing changes at the software-state level. Thus, we use hardware methods to evaluate low-level error detection and masking mechanisms, and software methods to test higher level mechanisms. Software methods are less expensive, but they also incur a higher perturbation overhead because they execute software on the target system.
Biomass for energy (2006)

Abstract Bio‐energy is now accepted as having the potential to provide the major part of the projected renewable energy provisions of the future as biofuels in the form of gas, liquid or solid fuels or electricity and heat. There are three main routes to providing these biofuels—thermal conversion, biological conversion and physical conversion—all of which employ a range of chemical reactor configurations and designs. This review focuses on thermochemical conversion processes for their higher efficiencies, lower costs and greater versatility in providing a wide range of energy, fuel and chemical options. The technologies of gasification and fast pyrolysis are described, particularly the reactors that have been developed to provide the necessary conditions to optimise performance. The primary products that can be derived as gas, liquid and solid fuels are characterised, as well as the secondary products of electricity and/or heat, liquid fuels and a considerable number of chemicals. Copyright © 2006 Society of Chemical Industry
Rapid identification of Escherichia coli by Fluorocult media and positive indole reaction (1988)

To assess the specificity and sensitivity of Fluorocult media for the identification of Escherichia coli, the beta-glucuronidase activities of 1,258 bacterial strains, as well as 20 strains of Candida spp., were investigated. Fluorescence of colonies combined with positive indole reaction resulted in specificities of 99.6 to 99.8%. Sensitivities were 59.1% (MacConkey agar), 69.9% (brolacin agar), 85.5% (Columbia agar), and 85.8% (ECD agar).
Twenty Years of SynGAP Research: From Synapses to Cognition (2020)

SynGAP is a potent regulator of biochemical signaling in neurons and plays critical roles in neuronal function. It was first identified in 1998, and has since been extensively characterized as a mediator of synaptic plasticity. Because of its involvement in synaptic plasticity, SynGAP has emerged as a critical protein for normal cognitive function. In recent years, mutations in the <i>SYNGAP1</i> gene have been shown to cause intellectual disability in humans and have been linked to other neurodevelopmental disorders, such as autism spectrum disorders and schizophrenia. While the structure and biochemical function of SynGAP have been well characterized, a unified understanding of the various roles of SynGAP at the synapse and its contributions to neuronal function remains to be achieved. In this review, we summarize and discuss the current understanding of the multifactorial role of SynGAP in regulating neuronal function gathered over the last two decades.
A More Effective Method for Image Representation: Topic Model Based on Latent Dirichlet Allocation (2015)

Nowadays, the Bag-of-words (BoW) representation is well applied to recent state-of-the-art image retrieval works. However, with the rapid growth in the number of images, the dimension of the dictionary increases substantially which leads to great storage and CPU cost. Besides, the local features do not convey any semantic information which is very important in image retrieval. In this paper, we propose to use "topics" instead of "visual words" as the image representation by topic model to reduce the feature dimension and mine more high level semantic information. We call this as Bag-of-Topics (BoT) which is a type of statistical model for discovering the abstract "topics" from the words. We extract the topics by Latent Dirichlet Allocation (LDA) and calculate the similarity between the images using BoT model instead of BoW directly. The results show that the dimension of the image representation has been reduced significantly, while the retrieval performance is improved.
Entropy Based Data Hiding For Document Images (2007)

In this paper we present a novel technique for data hiding in binary document images. We use the concept of entropy in order to identify document specific least distortive areas throughout the binary document image. The document image is treated as any other image and the proposed method utilizes the standard document characteristics for the embedding process. Proposed method minimizes perceptual distortion due to embedding and allows watermark extraction without the requirement of any side information at the decoder end.
Issues on the Design of a Variable Power LINC Amplifier System in SiGe Operating at 2.4 GHz (2006)

An increasing number of wireless communication systems require linear transmitters that can achieve high efficiency. Good linearity is necessary for bandwidth efficient modulation while poor efficiency directly affects operational costs and causes thermal losses in the base station. This paper examines the implementation of the outphasing technique, also known as Linear Amplification with Nonlinear Components (LINC) using a 0.25 μm SiGe BICMOS process. Adaptation of the amplifier in order to achieve different power levels, via the use of Class-F amplifying sections working in parallel is also examined. The effects of the input and output mismatch introduced when changing the power level are discussed and possible solutions presented. Furthermore, specific problems which arise when using a bipolar technology are addressed. This work also discusses the adaptation of a tunable phase shifter for a 1V supply and wide-linear range. The 2.4GHz amplifier system presented in this work achieved a 3-level power control with a maximum PAE in the range of 58-73%.
Enhancing program comprehension with recovered state models (2003)

State transition machines are high-level behavior descriptions often used as modeling tools for the design and implementation of a large class of software systems. Some of the state transition machine implementation approaches are such that the static structure of the resulting code closely matches that of the original state transition machines. Therefore, having a representation of the original state transition machines is likely to improve the corresponding code understandability. We present an approach supported by a prototype tool, to extract state transition machines by static analysis of source code. An objective of this work is to enhance program comprehension with visual representations of the behavior of the programs being analyzed.
The Interaction Between Dietary Fructose and Magnesium Adversely Affects Macromineral Homeostasis in Men (2000)

These findings indicate that dietary fructose adversely affects macromineral homeostasis in humans and suggest further studies to see if a high fructose diet coupled with low dietary magnesium and marginal calcium leads to bone loss.
<i>prpR</i> , <i>ntrA</i> , and <i>ihf</i> Functions Are Required for Expression of the <i>prpBCDE</i> Operon, Encoding Enzymes That Catabolize Propionate in <i>Salmonella enterica</i> Serovar Typhimurium LT2 (2000)

ABSTRACT The genes required for the catabolism of propionate in Salmonella enterica serovar Typhimurium are organized as two transcriptional units ( prpR and prpBCDE ) that are divergently transcribed from one another. Sequence homology to genes encoding members of the sigma-54 family of transcriptional activators and the identification of a consensus sigma-54 promoter 5′ to the prpBCDE operon suggested that PrpR was required to activate expression of this operon. We isolated insertions in prpR and showed that prpR function was needed for growth on propionate as a carbon and energy source. A medium-copy-number plasmid carrying the lacZ gene under the control of the native sigma-54 promoter of prpBCDE was used to study prpBCDE operon expression. Transcription of the lacZ reporter in prpR , ntrA , and ihfB mutants was 85-, 83-, and 15-fold lower than the level of transcription measured in strains carrying the wild-type allele of the gene tested. These data indicated that PrpR, IHF, and transcription sigma factor RpoN were required for the expression of the prpBCDE operon. Further analysis of the involvement of the integration host factor (IHF) protein in the expression of this operon is required due to the well-documented pleiotropic effect the lack of this global regulator has on gene expression. Deletion of the 5′ 615-bp portion of the prpR gene resulted in a PrpR c mutant protein that activated prpBCDE transcription regardless of the ability of the strain to synthesize 2-methylcitrate, the putative coactivator of PrpR. These results indicate that the N terminus of PrpR is the coactivator-sensing domain of the protein. When placed under the control of the arabinose-inducible promoter P araBAD , expression of prpR c allele by arabinose had a strong negative effect on growth of the cell. It is proposed that this deleterious effect of PrpR c may be due to an uncontrolled ATPase activity of PrpR or to cross-activation of genes whose functions negatively affect cell growth under the conditions tested.
A novel method for the multiplexed target enrichment of MinION next generation sequencing libraries using PCR-generated baits (2015)

The enrichment of targeted regions within complex next generation sequencing libraries commonly uses biotinylated baits to capture the desired sequences. This method results in high read coverage over the targets and their flanking regions. Oxford Nanopore Technologies recently released an USB3.0-interfaced sequencer, the MinION. To date no particular method for enriching MinION libraries has been standardized. Here, using biotinylated PCR-generated baits in a novel approach, we describe a simple and efficient way for multiplexed enrichment of MinION libraries, overcoming technical limitations related with the chemistry of the sequencing-adapters and the length of the DNA fragments. Using Phage Lambda and Escherichia coli as models we selectively enrich for specific targets, significantly increasing the corresponding read-coverage, eliminating unwanted regions. We show that by capturing genomic fragments, which contain the target sequences, we recover reads extending targeted regions and thus can be used for the determination of potentially unknown flanking sequences. By pooling enriched libraries derived from two distinct E. coli strains and analyzing them in parallel, we demonstrate the efficiency of this method in multiplexed format. Crucially we evaluated the optimal bait size for large fragment libraries and we describe for the first time a standardized method for target enrichment in MinION platform.
Sketch Based Mesh Extrusion With Remeshing Techniques (2001)

Abstract In this paper, we proposed a useful 3D mesh extrusion method for intuitive, efficient geometric modeling of free-form polygonal models. With our method, the user can sketch two strokes to extrude a polygonal mesh surface. Two remeshing techniques: partial mesh re-triangulation and mesh optimization are described in this paper first. After that, the extrusion algorithm with the remeshing techniques is introduced in detail. The method can be widely used in the modeling of free-form polygonal objects. And at the end of this paper, several examples are given.
Atomic-resolution STM study of a structural phase transition of steps on vicinal As/Ge(100) (1999)

Scanning tunneling microscope images of arsenic-exposed vicinal Ge(100) surfaces show that most As/Ge steps are reconstructed and that a variety of different step structures exist. The entire family of reconstructed As/Ge steps can be divided into two types, which we have chosen to call ``single-row'' (SR) steps and ``double-row'' (DR) steps. By changing the sample preparation conditions, we are able to consistently change the ratio of SR/DR steps. In other words, we have observed a structural phase transition in the reconstruction of As/Ge steps at atomic resolution.
Anxioselective Compounds Acting at the GABAA Receptor Benzodiazepine Binding Site (2003)

With the exception of obsessive compulsive disorder, benzodiazepines (BZs) remain a major first line treatment for anxiety disorders. However, as well as being anxiolytic, BZs also cause sedation acutely, related to the fact that BZs are also used as hypnotics, and chronically may have abuse potential as well as cause physical dependence which manifests itself as the demonstration of a number of adverse events upon discontinuation. The molecular mechanisms of BZs are now well defined in that they enhance the actions of the inhibitory neurotransmitter GABA by binding to a specific recognition site on GABA(A) receptors containing alpha1, alpha2, alpha3 and alpha5 subunits. Compounds that bind at this modulatory site and enhance the inhibitory actions of GABA are classified as agonists, those that decrease the actions of GABA are termed inverse agonists whereas compounds which bind but have no effect on GABA inhibition are termed antagonists. The clinically used BZs are full agonists and between the opposite ends of the spectrum, i.e. full agonist and full inverse agonist, are a range of compounds with differing degrees of efficacy, such as partial agonists and partial inverse agonists. Attempts have been made to develop compounds which are anxioselective in that they retain the anxiolytic properties of the full agonist BZs but have reduced sedation and dependence (withdrawal) liabilities. Such compounds may interact with all four (i.e. alpha1-, alpha2-, alpha3- and alpha5-containing) GABA(A) receptor subtypes and have partial rather than full agonist efficacies. Examples of nonselective partial agonists include bretazenil, imidazenil, FG 8205, abecarnil, NS 2710, pagoclone, RWJ-51204 and (S)-desmethylzopiclone. Alternatively, a compound might have comparable binding affinity but different efficacies at the various subtypes, thereby preferentially exerting its effects at subtypes thought to be associated with anxiety (alpha2- and/or alpha3-containing receptors) rather than the subtype associated with sedation (alpha1-containing receptors). Examples of efficacy selective compounds include L-838417, NGD 91-3 and SL651498. For each compound, preclinical and where available clinical data will be reviewed. Emerging themes include the lack of definitive intrinsic efficacy data for certain compounds (e.g. abecarnil, ocinaplon, pagoclone) and the difficulty in translating robust anxiolysis and a separation between anxiolytic and sedative doses of non-selective partial agonists in preclinical species into consistent clinical benefit in man (e.g. bretazenil, abecarnil, pagoclone). With respect to efficacy selective compounds, NGD 91-3 was not anxiolytic in man but in the absence of efficacy data, these results are difficult to interpret. Nevertheless, efficacy selective compounds represent a novel approach to targeting specific subtypes of the GABA(A) receptor, the ultimate test of which will be evaluation in the clinic.
CREB binding protein is a required coactivator for Smad-dependent, transforming growth factor β transcriptional responses in endothelial cells (1998)

The transforming growth factor-beta (TGF-beta) superfamily of growth factors and cytokines has been implicated in a variety of physiological and developmental processes within the cardiovascular system. Smad proteins are a recently described family of intracellular signaling proteins that transduce signals in response to TGF-beta superfamily ligands. We demonstrate by both a mammalian two-hybrid and a biochemical approach that human Smad2 and Smad4, two essential Smad proteins involved in mediating TGF-beta transcriptional responses in endothelial and other cell types, can functionally interact with the transcriptional coactivator CREB binding protein (CBP). This interaction is specific in that it requires ligand (TGF-beta) activation and is mediated by the transcriptional activation domains of the Smad proteins. A closely related, but distinct endothelial-expressed Smad protein, Smad7, which does not activate transcription in endothelial cells, does not interact with CBP. Furthermore, Smad2,4-CBP interactions involve the COOH terminus of CBP, a region that interacts with other regulated transcription factors such as certain signal transduction and transcription proteins and nuclear receptors. Smad-CBP interactions are required for Smad-dependent TGF-beta-induced transcriptional responses in endothelial cells, as evidenced by inhibition with overexpressed 12S E1A protein and reversal of this inhibition with exogenous CBP. This report demonstrates a functional interaction between Smad proteins and an essential component of the mammalian transcriptional apparatus (CBP) and extends our insight into how Smad proteins may regulate transcriptional responses in many cell types. Thus, functional Smad-coactivator interactions may be an important locus of signal integration in endothelial cells.
The CHOICE Network: Dynamic Host Configuration for Managing Mobility Between Public and Private Networks (2000)

The usage and service options of a public network generally differ from a private (enterprise and home) network and consequently, the two networks are often configured differently. The existence of such networks motivates our need to improve support and management of nomadic users who frequently roam between them. Using a real-world public network as a case study, we discuss this problem in detail and describe a solution that allows client devices to dynamically configure themselves to adapt to the local network configuration. In addition to supporting mobility, we describe how our solution also provides fail-over mechanisms for providing a highly available service; load balancing and location services. Furthermore, our solution can be used to scale networks that are deployed in a large setting. We discuss in detail the various issues that need to be dealt with for achieving true device-level mobility; pointing out several unsolved problems in this area. The algorithms and software proposed in this paper have been implemented, are deployed, and are currently being used in a real-world public network that is operational at the Crossroads Mall in Bellevue, Washington.
Zone-based shortest positioning time first scheduling for MEMS-based storage devices (2004)

Access latency to secondary storage devices is frequently a limiting factor in computer system performance. New storage technologies promise to provide greater storage densities at lower latencies than is currently obtainable with hard disk drives. MEMS-based storage devices use orthogonal magnetic or physical recording techniques and thousands of simultaneously active MEMS-based read-write tips to provide high-density low-latency nonvolatile storage. These devices promise seek times 10-20 times faster than hard drives, storage densities 10 times greater, and power consumption an order of magnitude lower. Previous research has examined data layout and request ordering algorithms that are analogs of those developed for hard drives. We present an analytical model of MEMS device performance that motivates a computationally simple MEMS-based request scheduling algorithm called ZSPTF, which has average response times comparable to shortest positioning time first (SPTF) but with response time variability comparable to circular scan (C-SCAN).
Adaptive B-Snake model using shape and appearance information for object segmentation (2010)

A novel adaptive B-Spline deformable model is presented in this paper for object segmentation. Comparing with other B-Spline models, the proposed model has the following advantages. First, a fully automatic and affine-invariant strategy is proposed for landmark point assignment. Second, contrary to other B-Spline models that rely on predetermined number of control points, an automatic scheme for control point insertion is designed to enhance the adaptivity and the flexibility of B-Spline model for segmenting shapes with high complexity. Thirdly, a statistical framework is embedded for modeling the shape distribution and appearance characteristics of landmark points in the training samples. Fine deformation can be achieved through the minimum mean square error approach that allows the model to accurately adapt to the desired object boundaries in the image. Experiments on medical image segmentation are carried out to validate the performance, and comparison has been made with respect to the traditional Snake and ASM. It turns out that the proposed adaptive B-Spline model can attain more accurate object segmentation. Copyright © 2010 John Wiley & Sons, Ltd.
Improved hematopoietic stem cell transplantation upon inhibition of natural killer cell-derived interferon-gamma (2021)

Hematopoietic stem cell transplantation (HSCT) is a frequent therapeutic approach to restore hematopoiesis in patients with hematologic diseases. Patients receive a hematopoietic stem cell (HSC)-enriched donor cell infusion also containing immune cells, which may have a beneficial effect by eliminating residual neoplastic cells. However, the effect that donor innate immune cells may have on the donor HSCs has not been deeply explored. Here, we evaluate the influence of donor natural killer (NK) cells on HSC fate, concluded that NK cells negatively affect HSC frequency and function, and identified interferon-gamma (IFNγ) as a potential mediator. Interestingly, improved HSC fitness was achieved by NK cell depletion from murine and human donor infusions or by blocking IFNγ activity. Thus, our data suggest that suppression of inflammatory signals generated by donor innate immune cells can enhance engraftment and hematopoietic reconstitution during HSCT, which is particularly critical when limited HSC numbers are available and the risk of engraftment failure is high.