gebhart/patrepeval huggingface dataset:
Morse Description and Geometric Encoding of Digital Elevation Maps (2004)

Two complementary geometric structures for the topographic representation of an image are developed in this work. The first one computes a description of the Morse-topological structure of the image, while the second one computes a simplified version of its drainage structure. The topographic significance of the Morse and drainage structures of digital elevation maps (DEMs) suggests that they can been used as the basis of an efficient encoding scheme. As an application, we combine this geometric representation with an interpolation algorithm and lossless data compression schemes to develop a compression scheme for DEMs. This algorithm achieves high compression while controlling the maximum error in the decoded elevation map, a property that is necessary for the majority of applications dealing with DEMs. We present the underlying theory and compression results for standard DEM data.
Current Research and Development of Chemotherapeutic Agents for Melanoma (2010)

Cutaneous malignant melanoma is the most lethal form of skin cancer and an increasingly common disease worldwide. It remains one of the most treatment-refractory malignancies. The current treatment options for patients with metastatic melanoma are limited and in most cases non-curative. This review focuses on conventional chemotherapeutic drugs for melanoma treatment, by a single or combinational agent approach, but also summarizes some potential novel phytoagents discovered from dietary vegetables or traditional herbal medicines as alternative options or future medicine for melanoma prevention. We explore the mode of actions of these natural phytoagents against metastatic melanoma.
Reduction of major and minor hysteresis loops in a piezoelectric actuator (2002)

This paper addresses the compensation of major and minor hysteresis loops using an operator termed a phaser, which shifts the phase of a periodic signal by an amount /spl phi/. For periodic inputs, hysteresis can be approximated by a phaser with a negative phase shift opening the possibility of cascade compensation. Since in actual hysteresis the phase shift varies according to the size of the input, giving rise to minor loops, the possibility exists to handle the compensation of minor loops by using phasors which vary the phase shift according to the magnitude of the input in an inverse fashion. In this paper, this technique is applied to the compensation of a piezoelectric actuator.
Accuracy and Its Determinants in Distributional Assessment (2000)

Abstract Rating accuracy is proposed to consist of 2 components: internal and external accuracy. Internal accuracy is identified as the appropriate basis for evaluating the impact of rating methodology on rating accuracy. Improved indexes of accuracy were used to study the internal accuracy of distributional assessment (DA). DA achieved moderate to high internal accuracy levels in reproducing the entire profiles, means, and standard deviations of true distributions. It also proved to be significantly more internally accurate than a conventional Likert-type rating scale in estimating distributional means. DA proved to be particularly accurate when ratings were elicited in the form of raw count estimates of frequencies obtained under short recall delay conditions. Correlational findings suggested that different cognitive processes and/or memory sources may underlie assessments obtained via distributional and conventional rating methods.
Dendritic cells in chronic myelomonocytic leukaemia (1999)

Blood dendritic cells (DC) differentiate in vitro via two separate pathways: either directly from blood DC precursors (DCp) or from CD14+ monocytes. In chronic myelomonocytic leukaemia (CMML) abnormal bone marrow precursors contribute to blood monocyte development but DC development has not been studied previously. Monocytes comprised 60% of blood MNC in 15 CMML patients studied, compared with 20% in 16 age-matched controls. The increase in blood monocytes was accompanied by a reciprocal decrease in mean blood DC percentage (from 0.42% of MNC in normal individuals to 0.16% of MNC in CMML patients). Absolute blood DC numbers showed a minimal (non-significant) reduction from 9.8 x 10(6)/l in normal individuals to 7.5 x 10(6)/l in CMML patients. The CD14(low) WCD16+ monocyte subpopulation was not found in CMML patients. After culture in GM-CSF/IL-4, CMML CD14+ monocytes acquired the phenotype of immature monocyte derived DC (Mo-DC) with similar yields to normal blood Mo-DC generation. Addition of TNF-alpha or LPS induced both normal and CMML Mo-DC to express prominent dendritic processes, the CMRF44+ and CD83+ antigens and high levels of HLA-DR, CD80 and CD86. Treatment either with TNF-alpha or LPS increased the allostimulatory activity of normal Mo-DC, but had little effect on the allostimulatory activity of CMML Mo-DC, perhaps reflecting the underlying neoplastic changes in monocyte precursors. We conclude that the blood DC numbers are relatively unaffected in CMML, suggesting discrete regulation of monocyte and DC production.
An X-linked channelopathy with cardiomegaly due to a CLIC2 mutation enhancing ryanodine receptor channel activity (2012)

Chloride intracellular channel 2 (CLIC2) protein is a member of the glutathione transferase class of proteins. Its' only known function is the regulation of ryanodine receptor (RyR) intracellular Ca(2+) release channels. These RyR proteins play a major role in the regulation of Ca(2+) signaling in many cells. Utilizing exome capture and deep sequencing of genes on the X-chromosome, we have identified a mutation in CLIC2 (c.303C>G, p.H101Q) which is associated with X-linked intellectual disability (ID), atrial fibrillation, cardiomegaly, congestive heart failure (CHF), some somatic features and seizures. Functional studies of the H101Q variant indicated that it stimulated rather than inhibited the action of RyR channels, with channels remaining open for longer times and potentially amplifying Ca(2+) signals dependent on RyR channel activity. The overly active RyRs in cardiac and skeletal muscle cells and neuronal cells would result in abnormal cardiac function and trigger post-synaptic pathways and neurotransmitter release. The presence of both cardiomegaly and CHF in the two affected males and atrial fibrillation in one are consistent with abnormal RyR2 channel function. Since the dysfunction of RyR2 channels in the brain via 'leaky mutations' can result in mild developmental delay and seizures, our data also suggest a vital role for the CLIC2 protein in maintaining normal cognitive function via its interaction with RyRs in the brain. Therefore, our patients appear to suffer from a new channelopathy comprised of ID, seizures and cardiac problems because of enhanced Ca(2+) release through RyRs in neuronal cells and cardiac muscle cells.
The coil array method for creating a dynamic imaging volume (2016)

Experimental results show the feasibility of a moving imaging region within an MRI with a low number of coils in the array. Magn Reson Med 78:784-793, 2017. © 2016 International Society for Magnetic Resonance in Medicine.
Biomolecular Events in Cancer Revealed by Attractor Metagenes (2013)

Mining gene expression profiles has proven valuable for identifying signatures serving as surrogates of cancer phenotypes. However, the similarities of such signatures across different cancer types have not been strong enough to conclude that they represent a universal biological mechanism shared among multiple cancer types. Here we present a computational method for generating signatures using an iterative process that converges to one of several precise attractors defining signatures representing biomolecular events, such as cell transdifferentiation or the presence of an amplicon. By analyzing rich gene expression datasets from different cancer types, we identified several such biomolecular events, some of which are universally present in all tested cancer types in nearly identical form. Although the method is unsupervised, we show that it often leads to attractors with strong phenotypic associations. We present several such multi-cancer attractors, focusing on three that are prominent and sharply defined in all cases: a mesenchymal transition attractor strongly associated with tumor stage, a mitotic chromosomal instability attractor strongly associated with tumor grade, and a lymphocyte-specific attractor.
Rcs — a system for version control (1985)

Abstract An important problem in program development and maintenance is version control, i.e. the task of keeping a software system consisting of many versions and configurations well organized. The Revision Control System (RCS) is a software tool that assists with that task. RCS manages revisions of text documents, in particular source programs, documentation, and test data. It automates the storing, retrieval, logging and identification of revisions, and it provides selection mechanisms for composing configurations. This paper introduces basic version control concepts and discusses the practice of version control using RCS. For conserving space, RCS stores deltas, i.e. differences between successive revisions. Several delta storage methods are discussed. Usage statistics show that RCS's delta method is space and time efficient. The paper concludes with a detailed survey of version control tools.
Endogenous Type I CRISPR-Cas: From Foreign DNA Defense to Prokaryotic Engineering (2020)

Establishment of production platforms through prokaryotic engineering in microbial organisms would be one of the most efficient means for chemicals, protein, and biofuels production. Despite the fact that CRISPR (clustered regularly interspaced short palindromic repeats)-based technologies have readily emerged as powerful and versatile tools for genetic manipulations, their applications are generally limited in prokaryotes, possibly owing to the large size and severe cytotoxicity of the heterogeneous Cas (CRISPR-associated) effector. Nevertheless, the rich natural occurrence of CRISPR-Cas systems in many bacteria and most archaea holds great potential for endogenous CRISPR-based prokaryotic engineering. The endogenous CRISPR-Cas systems, with type I systems that constitute the most abundant and diverse group, would be repurposed as genetic manipulation tools once they are identified and characterized as functional in their native hosts. This article reviews the major progress made in understanding the mechanisms of invading DNA immunity by type I CRISPR-Cas and summarizes the practical applications of endogenous type I CRISPR-based toolkits for prokaryotic engineering.
RETRACTED: Hypoxia-inducible factors are required for chemotherapy resistance of breast cancer stem cells (2014)

Triple negative breast cancers (TNBCs) are defined by the lack of estrogen receptor (ER), progesterone receptor (PR), and human epidermal growth factor receptor 2 expression, and are treated with cytotoxic chemotherapy such as paclitaxel or gemcitabine, with a durable response rate of less than 20%. TNBCs are enriched for the basal subtype gene expression profile and the presence of breast cancer stem cells, which are endowed with self-renewing and tumor-initiating properties and resistance to chemotherapy. Hypoxia-inducible factors (HIFs) and their target gene products are highly active in TNBCs. Here, we demonstrate that HIF expression and transcriptional activity are induced by treatment of MDA-MB-231, SUM-149, and SUM-159, which are human TNBC cell lines, as well as MCF-7, which is an ER(+)/PR(+) breast cancer line, with paclitaxel or gemcitabine. Chemotherapy-induced HIF activity enriched the breast cancer stem cell population through interleukin-6 and interleukin-8 signaling and increased expression of multidrug resistance 1. Coadministration of HIF inhibitors overcame the resistance of breast cancer stem cells to paclitaxel or gemcitabine, both in vitro and in vivo, leading to tumor eradication. Increased expression of HIF-1α or HIF target genes in breast cancer biopsies was associated with decreased overall survival, particularly in patients with basal subtype tumors and those treated with chemotherapy alone. Based on these results, clinical trials are warranted to test whether treatment of patients with TNBC with a combination of cytotoxic chemotherapy and HIF inhibitors will improve patient survival.
Devign: Effective Vulnerability Identification by Learning Comprehensive Program Semantics via Graph Neural Networks (2019)

Vulnerability identification is crucial to protect the software systems from attacks for cyber security. It is especially important to localize the vulnerable functions among the source code to facilitate the fix. However, it is a challenging and tedious process, and also requires specialized security expertise. Inspired by the work on manually-defined patterns of vulnerabilities from various code representation graphs and the recent advance on graph neural networks, we propose Devign, a general graph neural network based model for graph-level classification through learning on a rich set of code semantic representations. It includes a novel Conv module to efficiently extract useful features in the learned rich node representations for graph-level classification. The model is trained over manually labeled datasets built on 4 diversified large-scale open-source C projects that incorporate high complexity and variety of real source code instead of synthesis code used in previous works. The results of the extensive evaluation on the datasets demonstrate that Devign outperforms the state of the arts significantly with an average of 10.51% higher accuracy and 8.68\% F1 score, increases averagely 4.66% accuracy and 6.37% F1 by the Conv module.
Herpes Simplex Virus Type 1 Origins of DNA Replication Play No Role in the Regulation of Flanking Promoters (2002)

Herpes simplex virus (HSV) exhibits altered gene regulation in neuronal compared to nonneuronal tissues. It has been hypothesized that initiation of DNA synthesis at the viral origins of replication (oriS and oriL) is a critical step in the upregulation of transcriptional activity of flanking divergent promoters, thereby increasing productive gene expression in neurons. Notably, oriS is flanked by the immediate-early (IE) ICP4 and ICP22/47 promoters, and oriL is flanked by the early (E) UL29 and UL30 promoters. To test this hypothesis further, a series of constructs were generated in which these promoters were placed upstream of luciferase genes. In addition, DNA replication origins were deleted in the context of these promoter constructs. All cassettes were recombined into the viral genome of HSV type 1 strain KOS at a site distal to its native origins. Recombinant reporter expression was monitored in vitro and in vivo to determine the role of viral origins of DNA replication in the regulation of their flanking promoters. Reporter gene expression was unaffected by the presence or absence of oriS or oriL, with the exception of a twofold increase in ICP22/47 promoter activity in the absence of oriS. DNA synthesis inhibitors resulted in a decrease of both IE- and E-promoter activity in primary cells but not continuous cell cultures. Reporter activity was readily assayed in vivo during acute infection and reactivation from latency and was also sensitive to DNA synthesis inhibitors. In all assays, reporter gene expression was unaffected by the presence or absence of either oriS or oriL. These data support the requirement of DNA synthesis for full viral gene expression in vivo but suggest that the origin elements play no role in the regulation of their flanking promoters.
Inline ultrafiltration (2010)

Inline ultrafiltration (UF) can significantly increase the recoverable mass of biopharmaceutical products when pool tank volumes are limiting. Using relatively small commercially available ultrafiltration cassettes, a proof-of-concept study demonstrates that inline UF can significantly increase recoverable mass in an antibody purification process. With ever-increasing cell culture titers pushing product masses to higher levels, inline UF offers a relatively easy-to-implement and less disruptive alternative to installing larger pool tanks and enables more cost-effective production utilizing facilities designed for smaller bulk sizes.
Purpose of the Canada/U.S. Law Institute (1999)

The Impact of Technological Change in the Canada/U.S. Context
Research on Roman silver plate (1990)

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Becoming a Fruitful Tree: Christ and the Limits of Legal Thinking (2013)

This essay is adapted from a Spirit of the Law address given at BYU Law School on March 5, 2002.
Keeping Fiduciary Liability within Acceptable Limits (1998)

Fiduciary law now covers a wide range of situations, in the commercial as well as the property areas, that are far removed from its origin in the law of express trusteeship. It is feared for its uncertainty of application, which is in part due to the generalizations in which the law that governs conflict of duty and interest on the part of trustees is couched. A different approach is needed for the variety of fiduciaries which exist in the modern law. It is necessary that the response of fiduciary law to situations which it is dealing with must be proportionate. It will also be suggested that the parties are able to regulate and limit their obligations under it through the law of contract.
45.1: <i>Invited Paper</i> : Future Possibilities of Crystalline Oxide Semiconductor, Especially <i>C</i> ‐Axis‐Aligned Crystalline IGZO (2015)

Through detailed analyses, the structure of c‐axis‐aligned crystalline (CAAC) IGZO, which is a dense, stable crystal morphology, is found to differ from single‐crystal and amorphous structures. We propose a model for determining its film deposition mechanism. CAAC‐IGZO field‐effect transistors find application in displays for use as human‐machine interfaces.
Alkaline Stability of Quaternized Diels–Alder Polyphenylenes (2019)

Alkaline stability of anion exchange membranes (AEMs) is an essential requirement for the practical application of alkaline membrane fuel cells. In this study, we investigate the alkaline stability of Diels–Alder polyphenylenes (DAPPs) under various stability testing conditions. Structural analysis and membrane properties of the DAPPs indicated that different chemical structural changes of quaternized DAPPs occur depending on test conditions. Benzyltrimethylammonium-functionalized DAPPs degraded rapidly via nucleophilic benzyl substitution under a relatively mild condition at 80 °C with 4 M NaOH, whereas DAPPs with hexyltrimethylammonium (HTMA DAPP) exhibited much better alkaline stability under the same condition. While only cross-linking of unreacted alkyl bromides of HTMA DAPP occurred at 80 °C, we observed the degradation of the cations via β elimination after long-term testing. At higher temperature or reduced relative humidity (RH) conditions, for example, 160 °C with 8 M NaOH or RH 10% at 100 °C, the rapid degradation of the cation in HTMA DAPP occurred via nucleophilic methyl substitution. These results suggest that accelerated stress tests may not be a quick and straightforward alternative to prolonged alkaline stability tests of AEMs.
Tuning Selectivity of CO<sub>2</sub> Hydrogenation Reactions at the Metal/Oxide Interface (2017)

The chemical transformation of CO<sub>2</sub> not only mitigates the anthropogenic CO<sub>2</sub> emission into the Earth's atmosphere but also produces carbon compounds that can be used as precursors for the production of chemicals and fuels. The activation and conversion of CO<sub>2</sub> can be achieved on multifunctional catalytic sites available at the metal/oxide interface by taking advantage of the synergy between the metal nanoparticles and oxide support. Herein, we look at the recent progress in mechanistic studies of CO<sub>2</sub> hydrogenation to C1 (CO, CH<sub>3</sub>OH, and CH<sub>4</sub>) compounds on metal/oxide catalysts. On this basis, we are able to provide a better understanding of the complex reaction network, grasp the capability of manipulating structure and combination of metal and oxide at the interface in tuning selectivity, and identify the key descriptors to control the activity and, in particular, the selectivity of catalysts. Finally, we also discuss challenges and future research opportunities for tuning the selective conversion of CO<sub>2</sub> on metal/oxide catalysts.
A comparative study of the self-immolation of para-aminobenzylalcohol and hemithioaminal-based linkers in the context of protease-sensitive fluorogenic probes (2010)

This study focuses on the disassembly-behavior of self-immolative pro-fluorescent linkers under physiological conditions and through an enzyme-initiated domino reaction. The targeted linkers are based on para-aminobenzylalcohol (PABA) or hemithioaminal derivatives of para-carboxybenzaldehyde or glyoxilic acid. We found that a fine tuning of the kinetic properties could be obtained through the modulation of the linker structure, giving either a fast signal response or free-adaptable systems suitable for the design of protease-sensitive fluorogenic probes or prodrug systems.
Postirradiation Morphea in Breast Cancer (2003)

Resumen Se describe el caso de una mujer de 56 anos de edad, que debido a un carcinoma de mama fue sometida a una mastectomia radical izquierda, con tratamiento radio y quimioterapico postoperatorio. La paciente empleo tras la intervencion una protesis externa de silicona. Dos anos despues comenzo a desarrollar una placa esclerodermiforme en el lugar de la cicatriz, confirmandose mediante el estudio histologico que se trataba de una morfea.
Prokineticins: novel mediators of inflammatory and contractile pathways at parturition? (2010)

The onset of labour is associated with inflammatory cascades in the uteroplacental unit, and these are prematurely activated in preterm labour. Infection can induce an inflammatory response, which results in premature onset of the pro-inflammatory parturient cascades and preterm delivery. We have become interested in two proteins called prokineticins and the role they may play in labour and its premature onset. Prokineticin 1 and 2 bind to two G-protein coupled receptors, called prokineticin receptor 1 and 2. Expression of the prokineticins and their receptors is elevated in the uteroplacental unit during labour and they can induce expression of a host of genes known to be important in initiating the inflammatory and contractile events of labour. Prokineticins have also been shown to directly induce contractility of smooth muscles. Analysing the promoter regions of the prokineticins and their receptors highlights their potential regulation by pathways activated by infectious agents. Hence, we propose that infection can result in premature activation of prokineticin expression and signalling in the uteroplacental unit and this initiates a premature inflammatory and contractile cascade leading to preterm birth. Antagonism of prokineticin action may provide a suitable therapy for preterm labour that targets both inflammation and contractile pathways.