gebhart/patrepeval huggingface dataset:
Simplify: a theorem prover for program checking (2005)

This article provides a detailed description of the automatic theorem prover Simplify, which is the proof engine of the Extended Static Checkers ESC/Java and ESC/Modula-3. Simplify uses the Nelson--Oppen method to combine decision procedures for several important theories, and also employs a matcher to reason about quantifiers. Instead of conventional matching in a term DAG, Simplify matches up to equivalence in an E-graph, which detects many relevant pattern instances that would be missed by the conventional approach. The article describes two techniques, error context reporting and error localization, for helping the user to determine the reason that a false conjecture is false. The article includes detailed performance figures on conjectures derived from realistic program-checking problems.
Alternate Assessments for Students With Disabilities (2001)

Preface Meet Lara Audience Acknowledgments About the Authors 1. Alternate Assessment What and Why 2. Inclusive Standards High Expectations for All Students 3. Alternate Assessment Partners 4. Assessment Participation Decisions 5. Standards-Based IEPs, Transition Plans, and Alternate Assessments 6. The Nuts and Bolts of Alternate Assessment Administration 7. Scoring, Reporting, and Using Alternate Assessment Data 8. Tying It All Together Resource A Legal References Resource B Resources for Information and Assistance References Recommended Reading Index
Adaptation of Bacillus subtilis to oxygen limitation (2006)

Bacillus subtilis grows anaerobically by at least two different pathways, respiration using nitrate as an electron acceptor and fermentation in the absence of electron acceptors. Regulatory mechanisms have evolved allowing cells to shift to these metabolic capabilities in response to changes in oxygen availability. These include transcriptional activation of fnr upon oxygen limitation, a process requiring the ResD-ResE two-component signal transduction system that also regulates aerobic respiration. FNR then activates transcription of other anaerobically induced genes including the narGHJI operon which encodes a respiratory nitrate reductase. Genes involved in fermentative growth are controlled by an unidentified FNR-independent regulatory pathway.
Information Seeking with Social Signals: Anatomy of a Social Tag-based Exploratory Search Browser (2010)

Whereas for the fact-retrieval searches, optimal paths to the documents containing the required information are crucial, learning and investigation activities lead to a more continuous and exploratory process with the knowledge acquired during this “journey ” being essential as well. Therefore, information seeking systems should focus on providing cues that might make these explorations more efficient. One possible solution is in building information seeking systems in which navigation signposts are provided by social cues provided by a large number of other people. One possible source for social cues is all of the social bookmarks on social tagging sites. Social tagging arose out of the need to organize found information that is worth revisiting. The collective behavior of users who tagged contents seems to offer a good basis for exploratory search interfaces, even for users who are not using social bookmarking sites. In this paper, we present the algorithm of a tag-based exploratory system based on this idea.
IP Version 6 Management Information Base for The Multicast Listener Discovery Protocol (2001)

This document defines a portion of the Management Information Base (MIB) for use with network management protocols in Internet Protocol Version 6 internets. Specifically, this document is the MIB module that defines managed objects for implementations of the Multicast Listener Discovery Protocol [RFC2710].
Therapeutic Potential for Bone Morphogenetic Protein 4 in Human Malignant Glioma (2017)

Human glioma, in particular, malignant forms such as glioblastoma exhibit dismal survival rates despite advances in treatment strategies. A population of glioma cells with stem-like features, glioma cancer stem-like cells (GCSCs), contribute to renewal and maintenance of the tumor cell population and appear responsible for chemotherapeutic and radiation resistance. Bone morphogenetic protein 4 (BMP4), drives differentiation of GCSCs and thus improves therapeutic efficacy. Based on this observation it is imperative that the clinical merits of BMP4 in treating human gliomas should be addressed. This article reviews BMP4 signaling in central nervous system development and in glioma tumorigenesis, and the potential of this molecule as a treatment target in human gliomas. Further work needs to be done to determine if distinct lineages of GCSCs, associated with different glioma sub-classifications, proneural, neural, classical and mesenchymal, differ in responsiveness to BMP4 treatment. Additionally, interaction among BMP4 and cell matrix, tumor-vascular molecules and microglial immune cells also needs to be investigated, as this will enhance our knowledge about the role of BMP4 in human glioma and lead to the identification and/or development of novel therapeutic approaches that improve treatment outcomes of these devastating tumors.
Destruktion or Recovery?: Leo Strauss’s Critique of Heidegger (1997)

In systems with strong electron-lattice coupling, such as manganites, orbital degeneracy is lifted, causing a null expectation value of the orbital magnetic moment. Magnetic structure is thus determined by spin-spin superexchange. In titanates, however, with much smaller Jahn-Teller distortions, orbital degeneracy might allow non-zero values of the orbital magnetic moment, and novel forms of ferromagnetic superexchange interaction unique to t(2g) electron systems have been theoretically predicted, although their experimental observation has remained elusive. In this paper, we report a new kind of Ti(3+) ferromagnetism at LaMnO(3)/SrTiO(3) epitaxial interfaces. It results from charge transfer to the empty conduction band of the titanate and has spin and orbital contributions evidencing the role of orbital degeneracy. The possibility of tuning magnetic alignment (ferromagnetic or antiferromagnetic) of Ti and Mn moments by structural parameters is demonstrated. This result will provide important clues for understanding the effects of orbital degeneracy in superexchange coupling.
3D beamforming for wireless data centers (2011)

Contrary to prior assumptions, recent measurements show that data center traffic is not constrained by network bisection bandwidth, but is instead prone to congestion loss caused by short traffic bursts. Compared to the cost and complexity of modifying data center architectures, a much more attractive option is to augment wired links with flexible wireless links in the 60 GHz band. Current proposals, however, are severely constrained by two factors. First, 60 GHz wireless links are limited by line-of-sight, and can be blocked by even small obstacles between the endpoints. Second, even beamforming links leak power, and potential interference will severely limit concurrent transmissions in dense data centers. In this paper, we explore the feasibility of a new wireless primitive for data centers, 3D beamforming. We explore the design space, and show how bouncing 60 GHz wireless links off reflective ceilings can address both link blockage and link interference, thus improving link range and number of current transmissions in the data center.
Anti-Inflammatory Agent Indomethacin Reduces Invasion and Alters Metabolism in a Human Breast Cancer Cell Line (2007)

Hostile physiological environments such as hypoxia and acidic extracellular pH, which exist in solid tumors, may promote invasion and metastasis through inflammatory responses and formation of eicosanoids. Here, we have investigated the effects of the anti-inflammatory agent indomethacin on the invasion and metabolism of the human breast cancer cell line MDA-MB-435 in Dulbecco's Modified Eagles (DME)-based or Roswell Park Memorial Institute (RPMI)-based cell medium, using a magnetic resonance-compatible invasion assay. Indomethacin treatment significantly reduced the invasion of MDA-MB-435 cells independent of the culture and perfusion conditions examined. Significant changes were detected in levels of intracellular choline phospholipid metabolites and in triglyceride (TG) concentrations of these cells, depending on indomethacin treatment and basal cell medium used. Additionally, genetic profiling of breast cancer cells, grown and treated with low-dose indomethacin in cell culture using an RPMI-based medium, revealed the upregulation of several genes implicating cyclooxygenase-independent targets of indomethacin. These data confirm the ability of an anti-inflammatory agent to reduce breast cancer invasion and demonstrate, depending on cell culture and perfusion conditions, that the indomethacin-induced decrease in invasion is associated with changes in choline phospholipid metabolism, TG metabolism, and gene expression.
Improved Sphingolipidomic Approach Based on Ultra-High Performance Liquid Chromatography and Multiple Mass Spectrometries with Application to Cellular Neurotoxicity (2014)

The emerging field of sphingolipidomics calls for accurate quantitative analyses of sphingolipidome. Existing analytical methods for sphingolipid (SPL) profiling often suffer from isotopic/isomeric interference, leading to the low-abundance, but biologically important SPLs being undetected. In the current study, we have developed an improved sphingolipidomic approach for reliable and sensitive quantification of up to 10 subclasses of cellular SPLs. By integratively utilizing high efficiency chromatographic separation, quadrupole time-of-flight (Q-TOF) and triple quadrupole (QQQ) mass spectrometry (MS), our approach facilitated unambiguous identification of several groups of potentially important but low-abundance SPLs that are usually masked by isotopic/isomeric species and hence largely overlooked in many published methods. The methodology, which featured a modified sample preparation and optimized MS parameters, permitted the measurement of 86 individual SPLs in PC12 cells in a single run, demonstrating great potential for high throughput analysis. The improved characterization, along with increased sensitivity for low-abundance SPL species, resulted in the highest number of SPLs being quantified in a single run in PC12 cells. The improved method was fully validated and applied to a lipidomic study of PC12 cell samples with or without amyloid β peptide (Aβ) treatment, which presents a most precise and genuine sphingolipidomic profile of the PC12 cell line. The adoption of the metabolomics protocol, as described in this study, could avoid misidentification and bias in the measurement of the analytically challenging low-abundance endogenous SPLs, hence achieving informative and reliable sphingolipidomics data relevant to discovery of potential SPL biomarkers for Aβ-induced neurotoxicity and neurodegenerative disease.
Design space exploration for early identification of yield limiting patterns (2016)

In order to resolve the causality dilemma of which comes first, accurate design rules or real designs, this paper presents a flow for exploration of the layout design space to early identify problematic patterns that will negatively affect the yield. A new random layout generating method called Layout Schema Generator (LSG) is reported in this paper, this method generates realistic design-like layouts without any design rule violation. Lithography simulation is then used on the generated layout to discover the potentially problematic patterns (hotspots). These hotspot patterns are further explored by randomly inducing feature and context variations to these identified hotspots through a flow called Hotspot variation Flow (HSV). Simulation is then performed on these expanded set of layout clips to further identify more problematic patterns. These patterns are then classified into design forbidden patterns that should be included in the design rule checker and legal patterns that need better handling in the RET recipes and processes.
Three Body Problem and Formation of Binary System (1985)

The singularities of differential Newtonian equation of motion in three body problem cause the loss of accuracy and the considerable increase of the computer time. These singularities could be eliminated during the process of regularization to transform the independent variables and the coordinate of Newtonian equations of motion. In this study, we calculated the positions and velocities of three body along the time scale to find out the unique solution of regularized Newtonian equations of motion with the 5th order Runge-Kutta method by assuming the suitable initial velocities and positions. As the results of these calculations it is shown that the triple stellar system eventually distintegrated, two of them formed a binary, and the last one escaped from this system with a hyperbolic orbit. This may suggest one possible explanation for the binary formation.
Data location aware scheduling for virtual Hadoop cluster deployment on private cloud computing environment (2016)

With the advancements of Internet-of-Things (IoT) and Machine-to-Machine Communications (M2M), the ability to generate massive amount of streaming data from sensory devices in distributed environment is inevitable. A common practice nowadays is to process these data in a high-performance computing infrastructure, such as cloud. Cloud platform has the ability to deploy Hadoop ecosystem on virtual clusters. In cloud configuration with different geographical regions, virtual machines (VMs) that are part of virtual cluster are placed randomly. Prior to processing, data have to be transferred to the regional sites with VMs for data locality purposes. In this paper, a provisioning strategy with data-location aware deployment for virtual cluster will be proposed, as to localize and provision the cluster near to the storage. The proposed mechanism reduces the network distance between virtual cluster and storage, resulting in reduced job completion times.
JC virus persistence following progressive multifocal leukoencephalopathy in multiple sclerosis patients treated with natalizumab (2010)

JC virus (JCV) DNA in the cerebrospinal fluid (CSF) provides the laboratory confirmatory diagnosis of progressive multifocal leukoencephalopathy (PML) in patients whose clinical symptoms and magnetic resonance imaging findings are consistent with PML.The Laboratory of Molecular Medicine and Neuroscience (LMMN), National Institute of Neurological Disorders and Stroke (NINDS), National Institutes of Health (NIH), made the confirmatory laboratory diagnosis in 35 multiple sclerosis (MS) patients treated with natalizumab. Thirteen patients had 3 or more CSF samples taken from weeks to months following PML diagnosis. Seven of the 13 patients demonstrated persistence of JCV DNA in the CSF even though all patients experienced immune reconstitution inflammatory syndrome (IRIS), 11 patients had plasma exchange, and 2 had immunoabsorption. Specific anti-JCV antibody was measured in plasma/sera samples from 25 of the 35 patients. Most of the samples showed moderate to high or rising antibody levels from the time of PML diagnosis. However, plasma from 1 patient at or near the time of PML diagnosis had a titer considered seronegative and 2 other plasma samples from patients had titers considered at baseline for seropositivity. In several PML cases, viral persistence and neurological deficits have continued for several years, indicating that once initiated, JCV infection may not entirely clear, even with IRIS.
Insider Threat Study: Computer System Sabotage in Critical Infrastructure Sectors (2005)

Abstract : Efforts to estimate how often companies face attacks from within are difficult to make. It has been suggested that insider attacks are under-reported to law enforcement and prosecutors. Reasons for such under-reporting include an insufficient level of damage to warrant prosecution, a lack of evidence or insufficient information to prosecute, and concerns about negative publicity. Moreover, statistics vary regarding the prevalence of cases perpetrated by insiders compared to those perpetrated by individuals external to the target organizations. The E-Crime Watch Survey(Trademark), carried out by the United States Secret Service (Secret Service), the CERT(Copyright R) Program of Carnegie Mellon University's Software Engineering Institute (CERT), and CSO Magazine in spring 2004, elicited responses from 500 security and law enforcement executives on issues related to electronic crimes. Among the 70 percent of respondents who were able to identify whether outsiders or insiders were responsible for an e-crime or intrusion committed in 2003, 71% reported that one or more attacks were known or suspected to have come from outsiders compared to 29% from insiders. Respondents identified current or former employees and contractors as the second greatest cyber security threat, preceded only by hackers.
A mobile robot localization using ultrasonic sensors in indoor environment (2002)

This paper proposes a new method for estimating the position and orientation of a mobile robot in an indoor environment. The method is different from previous one in the way that the simply shaped objects, such as walls, corners and edges, called geometric elements, selected from the environment rather than artificial ones are used as landmarks. The mobile robot moves from a starting point to its target point along a designed path relying on its own sensors. When the mobile robot moves in an environment, it measures the distance to the geometric elements, uses the role of triangle geometry to estimate the position and the orientation of itself and corrects its path. The presented algorithm is especially suitable for processing the sonar scan data obtained by ultrasonic sensors with wide beam spread. The validity of the proposed method has been proved by experiments, and its performance investigated.
Relationship between the triacylglycerol composition and foaming of mixed coconut oil under deep-fat frying. (1988)

The characteristic foaming property of coconut oil or palm kernel oil with one of the nonlauric oils under deep-fat frying was investigated. The foaming property of the mixed oil disappeared after random interesterification, by which new molecular species with an intermediate carbon number increased, while the fatty acid composition of the oil remained unchanged. Similar effects of interesterification were found in a model system of monoacid triacylglycerol mixtures having medium (C8-C12) and long (C16-C18) chain fatty acids. The foaming may depend on the disparity of the triacylglycerol molecular size in the mixed oil, regardless of the fatty acid composition.
Bacterial adhesion to intravenous cannulae: influence of implantation in the rabbit and of enzyme treatments (1988)

Comparison was made of the adhesion of Staphylococcus epidermidis, Staphylococcus aureus, Escherichia coli, Klebsiella aerogenes and Pseudomonas aeruginosa to six types of intravascular cannula material. Adhesion to materials removed from rabbit tissues did not differ significantly between types of material or between bacterial species. In contrast, major differences were found when unimplanted materials were examined; the overall rank order of adhesiveness of bacteria to unimplanted materials (S. epidermidis greater than P. aeruginosa greater than S. aureus much greater than K. aerogenes greater than E. coli) was highly significant (F = 13.0, P less than 0.0005), and although no single material was consistently least attractive to all micro-organisms, FEP-Teflon and PTFE-Teflon showed significantly lower overall affinity for bacteria than other materials (P less than 0.001); all species showed a significant preference for a silicone polymer (P less than 0.0005). The nature of the bacterial surface structures responsible for adhesion were investigated by the actions of pronase and mixed glycosidase, which produced significant respective decreases and increases in adhesion of staphylococci to unimplanted materials; their effects on the Gram-negative bacilli were less consistent.
Somatic Hypermutation and Diverse Immunoglobulin Gene Usage in the Human Antibody Response to the Capsular Polysaccharide of S<i>treptococcus pneumoniae</i>Type 6B (2004)

Combinatorial cloning and expression library analysis were used to determine the expressed human antibody repertoire specific for the capsular polysaccharide (PS) of Streptococcus pneumoniae serotype 6B. Sequence analysis of 55 6B-specific antibody Fab fragments isolated from six vaccinated donors reveal that different individuals used a variety of heavy and light chain germ line variable (V) region genes to form pneumococcal capsular PS (PPS) 6B-specific paratopes. Within each donor, however, the response was more restricted, with five of the six donors using at most one or two gene pairs to form combining sites. Analysis also indicated that although the response in each donor was oligoclonal in terms of variable gene usage, the combination of extensive somatic hypermutation, deletion of germ line-encoded residues, insertion of non-germ line-encoded residues, and intraclonal isotype switching generated a surprising degree of paratope diversity within the individuals analyzed. In contrast to previously studied PS-specific responses, we find that the PPS 6B repertoire makes use of a diverse collection of heavy-chain and light-chain V region gene products to form specific paratopes, with no apparent tendency for conservation of immunoglobulin gene usage between individuals.
Abstract 11415: Enhancing Direct Cardiac Reprogramming Efficiency Using Small Molecules (2015)

The ability to directly trans-differentiate fibroblasts into cardiomyocytes through overexpression of three core transcription factors, Gata4, Mef2C &TBX5 (GMT), has been demonstrated by our group and others. Direct cardiac reprogramming has great potential to treat heart failure. However, clinical application remains limited due to inefficiencies in the reprogramming process and immaturity of the differentiated cardiomyocytes. In the current work, using a chemical approach we aim to increase the efficiency and the maturation of these directly reprogrammed cardiomyocytes. We have optimized a high-throughput screening method in 384-well plates using an alpha-MHC-GFP reporter to detect cardiac reprogramming in mouse cardiac fibroblasts. We screened 5500 compounds and identified 20 hits which have increased the reprogramming efficiency by 2-6 fold compared to controls. Among these top hits, 4 TGF-β inhibitors (DS 1-4) and 4 WNT inhibitors (DS 5-8) enhanced direct cardiac reprogramming. Further in depth investigations showed that the combination of the TGF-β inhibitor DS1 and the WNT inhibitor DS5 increased reprogramming efficiency 7 fold when added to the GMT-overexpressing fibroblasts on the first day of reprogramming. This combination of small molecules also enhanced the maturation of the reprogrammed cells, as we observed beating cells after only 1 week of reprogramming compared to 6–8 weeks without the small molecules. Activation of canonical WNT signaling or TGF-β signaling significantly abrogates the improvement in cardiac reprogramming by DS1 and DS5. These results indicate the specificity of the action of these inhibitors through the canonical WNT and TGF-β pathways. In a translational effort, we injected DS1, 2 and 5 intraperitoneally in mice for 2 weeks in combination with GMT following myocardial infarction (MI) and found a significant improvement in cardiac function as represented by an ejection fraction of 39.11% ±1.2% in the GMT + compounds group vs. 28.44% ± 3.98% in the GMT only group (p<0.05), 6 weeks after MI compared to an ejection fraction of 22.72% in the control untreated group. In conclusion, small molecules, especially the TGF-β inhibitors and WNT inhibitors, greatly enhanced direct reprogramming in vitro and in vivo.