gebhart/patrepeval huggingface dataset:
Main Surface Crack Propagation and Crack Initiation and Propagation on Counter Surface under Cyclic Bending (2005)

Cyclic bending is a dominant loading mode in structures sustaining thermal loads. Numerical analysis was performed for the evaluation of the main elliptical crack propagation and crack initiation and propagation on the counter surface under cyclic out-of-plane bending. Inelastic three-dimensional finite element analyses were conducted taking crack opening and closure into account. When the front surface is in tension, the main crack opens and the compressive strain on the counter surface increases. Thus, deeper the main crack, larger the total strain range on the counter surface and this stimulates crack initiation on the counter surface. As the main crack propagates, the J-integral range at the deepest point decreases for deeper than 40% of the plate thickness. These numerical results explain the previous cyclic bending test results; a crack initiates and propagates on the counter surface and meets the main crack near 1/3 of the plate thickness of the specimen while the main crack grows. The J-integral range of the counter surface crack increase rapidly and becomes larger than that of the main crack. The calculated crack propagation rates in both longitudinal and depth directions of the main and the counter surface cracks based on the J-integral ranges were close to the experimental ones.
A facet ensemble approach for evaluation of array performance in ultrasonic NDE (1994)

The use of ultrasonic array systems, in conjunction with a synthetic aperture focusing technique (SAFT) has recognized potential for flaw characterization in nondestructive evaluation (NDE). However, defect type, location, orientation and geometrical constraints imposed by the test specimen can reduce the effectiveness of nonoptimal array systems. To assist with design, a simulation approach for evaluation of array performance for NDE imaging was developed and is described in this paper. In the development of the model, several key factors were identified as being critical in defining the response of a linear ultrasonic transducer array. These include the ultrasonic wavelet generated by each array element, the directivity of the transducers and the interaction of the ultrasonic wave field with the surface which is to be imaged. Following several simplifying assumptions, and employing a linear systems approach, the cumulative response of all these factors was formulated. Thus a low-cost, yet powerful, interactive model for system design evaluation could be implemented. To illustrate the model, a range of simulation results is presented, concerning the imaging of a fatigue crack in a solid medium. The influence of array element spacing and centre frequency is considered, in conjunction with aperture size, defect orientation and surface roughness. In each case, the principal factors governing final image quality are discussed and where possible, recommendations are made concerning array design and imaging strategy.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Expression Analysis of a Ripening-Specific, Auxin-Repressed Endo-1,4-β-Glucanase Gene in Strawberry (1998)

A cDNA (Cel1) encoding an endo-1,4-beta-glucanase (EGase) was isolated from ripe fruit of strawberry (Fragaria x ananassa). The deduced protein of 496 amino acids contains a presumptive signal sequence, a common feature of cell wall-localized EGases, and one potential N-glycosylation site. Southern- blot analysis of genomic DNA from F. x ananassa, an octoploid species, and that from the diploid species Fragaria vesca indicated that the Cel1 gene is a member of a divergent multigene family. In fruit, Cel1 mRNA was first detected at the white stage of development, and at the onset of ripening, coincident with anthocyanin accumulation, Cel1 mRNA abundance increased dramatically and remained high throughout ripening and subsequent fruit deterioration. In all other tissues examined, Cel1 expression was invariably absent. Antibodies raised to Cel1 protein detected a protein of 62 kD only in ripening fruit. Upon deachenation of young white fruit to remove the source of endogenous auxins, ripening, as visualized by anthocyanin accumulation, and Cel1 mRNA accumulation were both accelerated. Conversely, auxin treatment of white fruit repressed accumulation of both Cel1 mRNA and ripening. These results indicate that strawberry Cel1 is a ripening-specific and auxin-repressed EGase, which is regulated during ripening by a decline in auxin levels originating from the achenes.
A multiscale model linking ion-channel molecular dynamics and electrostatics to the cardiac action potential (2009)

Ion-channel function is determined by its gating movement. Yet, molecular dynamics and electrophysiological simulations were never combined to link molecular structure to function. We performed multiscale molecular dynamics and continuum electrostatics calculations to simulate a cardiac K(+) channel (I(Ks)) gating and its alteration by mutations that cause arrhythmias and sudden death. An all-atom model of the I(Ks) alpha-subunit KCNQ1, based on the recent Kv1.2 structure, is used to calculate electrostatic energies during gating. Simulations are compared with experiments where varying degrees of positive charge-added via point mutation-progressively reduce current. Whole-cell simulations show that mutations cause action potential and ECG QT interval prolongation, consistent with clinical phenotypes. This framework allows integration of multiscale observations to study the molecular basis of excitation and its alteration by disease.
Automatic configuration of dynamically alterable object oriented systems (2002)

Customization is a powerful tool, but to be truly useful its application must require a minimum of expertise and effort from the programmer. While many programming languages provide support for modularity and encapsulation, it is object-oriented languages with their associated object constructor/destructor mechanisms which provide the key to automating customizations of complex system specifications. We outline a scheme for such a configuration mechanism in the context of the PEACE system, a dynamically alterable object-oriented parallel operating system. Our mechanism is largely transparent to the user, using the C++ programming language and its associated object constructors and destructors to generate an initial version of system configuration information from a combination of user-specified parameters and system defaults. This initial configuration information is automatically installed at system invocation, and is also dynamically alterable at runtime. The information is used by the PEACE system and its applications to guide dynamic system alterations such as loading and/or garbage-collecting of system components on demand,but the same approach is also applicable in other contexts.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Derivation of a second generation multivariate index assay to improve specificity in pre-surgical evaluation of adnexal masses for risk of ovarian malignancy. (2015)

5561 Background: The FDA cleared in vitro diagnostic multivariate index assay OVA1, with its intended utility to assist in referral of high risk patients to gynecologic oncologists, was by design to have a high sensitivity in assessing risk of malignancy in patients diagnosed with an adnexal mass prior to planned surgery. In this study, we developed and evaluated a second generation multivariate index assay (MIAG2) to improve specificity while maintaining a level of sensitivity similar to OVA1. Methods: CA 125 II, prealbumin, apolipoprotein A-1 (ApoA1), beta 2-microglobulin, transferrin (TRF), follicle-stimulating hormone (FSH), and Human epididymis protein 4 (HE4) were retrospectively analyzed on serum samples from a prospective multicenter study of patients with a documented pelvic mass planned for surgery. The samples were divided by block randomization into a training set (pre-/post-menopausal: 130/150; benign: 174, malignant: 106 including 35 stage I/II and 16 low malignant potential (LMP) cases) and a preliminary validation set (pre-/post-menopausal: 154/151; benign: 233, malignant: 72 including 19 stage I/II and 13 LMP cases). Results: Selected through extensive statistical resampling, the MIAG2 panel consists of CA 125 II, ApoA1, TRF, FSH, and HE4. Its algorithm uses two ensembles of classification models, for pre- and post-menopausal women respectively. However, with the help of FSH, the outputs of the models were integrated into a single-valued index with a cutoff of 5.0 arbitrary units for all patients. The specificity and sensitivity of the MIAG2 for the validation set were 60.1% (140/233) and 88.9% (64/72), respectively, compared to OVA1 which had a specificity of 47.2% (110/233) at a sensitivity of 95.8% (69/72). The improvement in specificity was statistically significant (p < 0.001). It is of interest to note that both the MIAG2 and OVA1 had a high sensitivity in detecting non-LMP ovarian cancer at 96.6% (57/59) and 100.0% (59/59), respectively. Conclusions: The MIAG2 significantly improved specificity over that of OVA1 while maintaining a comparably high sensitivity in pre-surgical assessment of adnexal masses for risk of malignancy.
[A case of clinically diagnosed eosinophilic bronchiolitis]. (2007)

A 71-year-old man was referred to our hospital because of an intractable productive cough. Although he was treated for bronchial asthma, the symptom did not improve. Furthermore, since he developed progressive dyspnea and hypoxemia, he was admitted to our hospital. Marked eosinophilia in a blood test and sputum, poorly defined centrilobular nodules throughout the bilateral lung fields in a chest CT scan, and mixed ventilatory impairment in a spirometric test were revealed. Thoracoscopic lung biopsy and bronchoalveolar lavage were not conducted because of progressive respiratory failure. Therefore, we clinically diagnosed eosinophilic bronchiolitis, and immediately administered oral prednisolone (30 mg daily). His symptoms and examination findings rapidly improved. This case suggests that eosinophilic bronchiolitis should be taken into consideration for differential diagnoses of eosinophilic lung disease and obstructive lung disease, and marked eosinophilia in sputum may be one of the useful tools for diagnosis of this disease when invasive examinations are inadequate.
Effect of Different Environmental Conditions on Durabilities of Polyester- and Vinylester-Based Glass-Fiber-Reinforced Polymer Pultruded Profiles (2022)

This paper presents the results of experimental investigations on the durability of glass-fiber-reinforced polymer (GFRP) pultruded profiles made of unsaturated polyester (UP) and vinylester (VE) resins commonly used in civil engineering. The water absorption, tensile properties, and microstructures of GFRP profiles exposed to several typical accelerated aging environments (e.g., deionized water, salt water, salt fog, and combined hygrothermal cycles) for 12 months were investigated. Moreover, a sustained loading factor was included in the test to reflect the behavior of the GFRP profiles in real structures. A normalization approach based on the controlled specimens was used to assess the effectiveness and relevance of the accelerated exposure. The results indicated that the maximum moisture absorption of both UP and VE GFRP profiles was immersed in deionized water, where the masses increased by 1.03 and 0.53%, respectively, leading to the maximum degradation of tensile strength (24.03%) of UP GFRP profile immersion in deionized water after 360 days of aging. However, the tensile modulus was more sensitive to high temperatures and has the maximum degradation (47.03%) after hygrothermal cycles. Moreover, VE GFRP profiles show superior humidity and temperature endurance. Furthermore, the sustained loading exacerbated the degradation of tensile properties slightly under the same conditions. Finally, by incorporating the cumulative damage caused by the sustained loading and a time-dependent factor into a residual strength model, a revised model was proposed to describe the tensile strength loss of pultruded UP GFRP profiles.
Numerical simulation of two-phase flow pattern of supercritical carbon dioxide with PAG-type lubricating oil in gas cooler. (2012)

It has been reported that lubricating oil has a significant influence on the cooling heat transfer of supercritical carbon dioxide. In this study, numerical analysis of the flow pattern of a carbon dioxide (CO2)-oil mixture in a gas cooler was conducted to analyze the change in oil film thickness and heat transfer coefficient against bulk temperature. Simulations were conducted using FLUENT software, and the volume-of-fluid (VOF) model was applied to capture the interface of the lubricating oil and CO2. The compatibility of lubricants was found to have a dramatic influence on cooling heat transfer. The flow regime changes due to CO2 dissolving into the oil causing changes in viscosity, surface tension, and density of the oil film. The comparison of simulated heat transfer coefficients with experimental results showed that the numerical simulation is an effective approach to analyze the characteristics of the flow and heat transfer of supercritical CO2-oil mixture, and the numerical approach proposed could be further extended to the actual gas cooler design.
Supplementary Table S4 from Cross-Species Genomics Reveals Oncogenic Dependencies in ZFTA/C11orf95 Fusion–Positive Supratentorial Ependymomas (2023)

&lt;p&gt;Suppl. Table S4 - Histopathological evaluation of 25 cases&lt;/p&gt;
Strong Consistency, Graph Laplacians, and the Stochastic Block Model (2020)

Spectral clustering has become one of the most popular algorithms in data clustering and community detection. We study the performance of classical two-step spectral clustering via the graph Laplacian to learn the stochastic block model. Our aim is to answer the following question: when is spectral clustering via the graph Laplacian able to achieve strong consistency, i.e., the exact recovery of the underlying hidden communities? Our work provides an entrywise analysis (an $\ell_{\infty}$-norm perturbation bound) of the Fielder eigenvector of both the unnormalized and the normalized Laplacian associated with the adjacency matrix sampled from the stochastic block model. We prove that spectral clustering is able to achieve exact recovery of the planted community structure under conditions that match the information-theoretic limits.
Solution of the Oldano-Barbero paradox (1996)

The appearance of the splay-bend elastic constant ${\mathit{K}}_{13}$ in the theory of elasticity of nematic liquid crystals causes a serious problem. This problem is known as the Oldano-Barbero paradox. The approaches of Barbero et al., Faetti, and Pergamenshchik for solving this paradox are analyzed in view of two starting points of the continuum theory. The analysis clearly shows the imperfections of their treatments. In order to remedy these imperfections a proposal is made to eliminate the paradox in accordance with the assumptions of the continuum theory. The solution requires a modification of the surface free energy density, namely, the derivatives of the director field normal to the surface must be excluded. \textcopyright{} 1996 The American Physical Society.
RNAPosers: Machine Learning Classifiers for Ribonucleic Acid–Ligand Poses (2020)

Determining the three-dimensional (3D) structures of ribonucleic acid (RNA)-small molecule ligand complexes is critical to understanding molecular recognition in RNA. Computer docking can, in principle, be used to predict the 3D structure of RNA-small molecule complexes. Unfortunately, retrospective analysis has shown that the scoring functions that are typically used for pose prediction tend to misclassify non-native poses as native and vice versa. Here, we use machine learning to train a set of pose classifiers that estimate the relative "nativeness" of a set of RNA-ligand poses. At the heart of our approach is the use of a pose "fingerprint" (FP) that is a composite of a set of atomic FPs, which individually encode the local "RNA environment" around ligand atoms. We found that by ranking poses based on classification scores from our machine learning classifiers, we were able to recover native-like poses better than when we ranked poses based on their docking scores. With a leave-one-out training and testing approach, we found that one of our classifiers could recover poses that were within 2.5 Å of the native poses in ∼80% of the 80 cases we examined, and, on two separate validation sets, we could recover such poses in ∼60% of the cases. Our set of classifiers, which we refer to as RNAPosers, should find utility as a tool to aid in RNA-ligand pose prediction, and so we make RNAPosers open to the academic community via https://github.com/atfrank/RNAPosers.
A folk theorem with codes of conduct and communication (2016)

We study self-referential games in which players have the ability to commit to a code of conduct—a complete description of how they play and their opponents should play. Each player receives a private signal about each others’ code of conduct and their codes of conduct specify how to react to these signals. When only some players receive informative signals, players are allowed to communicate using public messages. Our characterization of the effect of communication on the equilibrium payoffs yields a folk theorem and players share their private information truthfully in equilibrium. We also provide an application of codes of conduct: games that are played through computer programs.
Interfaces to knowledge organization systems in Canadian digital library collections (2005)

Purpose The purpose of this paper is to report an investigation into the ways in which Canadian digital library collections have incorporated knowledge organization systems into their search interfaces. Design/methodology/approach A combination of data‐gathering techniques was used. These were as follows: a review of the literature related to the application of knowledge organization systems, deep scanning of Canadian governmental and academic institutions web sites on the web, identify and contact researchers in the area of knowledge organization, and identify and contact people in the governmental organizations who are involved in knowledge organization and information management. Findings A total of 33 digital collections were identified that have made use of some type of knowledge organization system. Thesauri, subject heading lists and classification schemes were the widely used knowledge organization systems in the surveyed Canadian digital library collections. Research limitations/implications The target population for this research was limited to governmental and academic digital library collections. Practical implications An evaluation of the knowledge organization systems interfaces showed that searching, browsing and navigation facilities as well as bilingual features call for improvements. Originality/value This research contributes to the following areas: digital libraries, knowledge organization systems and services and search interface design.
Ligation of exogenous linear DNA after gene transfer in vitro and in vivo (2003)

These data suggest that linear DNA is efficiently circularized after gene transfer in vitro and in vivo. Secondly, equally high luciferase activities were observed in the mouse after rapid intravenous injection of luciferase expression cassettes, either consisting of linear DNA produced by PCR, or carried by linearized plasmid DNA. These findings encourage the use of linear DNA elements for gene transfer applications in vivo.
Recursive Wang tiles for real-time blue noise (2006)

Well distributed point sets play an important role in a variety of computer graphics contexts, such as anti-aliasing, global illumination, halftoning, non-photorealistic rendering, point-based modeling and rendering, and geometry processing. In this paper, we introduce a novel technique for rapidly generating large point sets possessing a blue noise Fourier spectrum and high visual quality. Our technique generates non-periodic point sets, distributed over arbitrarily large areas. The local density of a point set may be prescribed by an arbitrary target density function, without any preset bound on the maximum density. Our technique is deterministic and tile-based; thus, any local portion of a potentially infinite point set may be consistently regenerated as needed. The memory footprint of the technique is constant, and the cost to generate any local portion of the point set is proportional to the integral over the target density in that area. These properties make our technique highly suitable for a variety of real-time interactive applications, some of which are demonstrated in the paper.Our technique utilizes a set of carefully constructed progressive and recursive blue noise Wang tiles. The use of Wang tiles enables the generation of infinite non-periodic tilings. The progressive point sets inside each tile are able to produce spatially varying point densities. Recursion allows our technique to adaptively subdivide tiles only where high density is required, and makes it possible to zoom into point sets by an arbitrary amount, while maintaining a constant apparent density.
Abstract 14173: Depletion of Neutrophils Ablates Cardiac Ruptures after Treatment with TWEAK (Tumor Necrosis Factor-Like Weak Inducer of Apoptosis) in a Mouse Model of Myocardial Infarction (2012)

Acne RA-1,2 was well tolerated and effective at reducing comedones and sebum production and improving epidermal barrier function. These results suggest that Acne RA-1,2 is useful against acne-prone facial skin, particularly as it targets sebum production, which topical pharmacological acne therapies do not address.
Correlated color temperature as an explicit function of chromaticity coordinates (1992)

Abstract A simple equation to compute correlated color temperature (CCT) from CIE 1931 chromaticity coordinates x and y is given. Over the range of interest in color science, the errors are negligible. It was derived from the fact that the isotemperature lines for CCTs of principle interest nearly converge toward a point on the chromaticity diagram and the assumption that CCT may be represented by a third‐order polynomial function of the reciprocal of the slope of the line from that point to the chromaticity of the light. the equation is useful in designing sources to simulate CIE colorimetric illuminants.
DNA Replication Origin Plasticity and Perturbed Fork Progression in Human Inverted Repeats (2005)

The stability of metazoan genomes during their duplication depends on the spatiotemporal activation of origins and the progression of forks. Human rRNA genes represent a unique challenge to DNA replication since a large proportion of them exist as noncanonical palindromes in addition to canonical tandem repeats. Whether origin usage and/or fork elongation can cope with the variable structure of these genes is unknown. By analyzing single combed DNA molecules from HeLa cells, we studied the rRNA gene replication program according to the organization of canonical versus noncanonical rRNA genes. Origin positioning, spacing, and timing were not affected by the underlying rRNA gene physical structure. Conversely, fork arrest, both temporary and permanent, occurred more frequently when rRNA gene palindromes were encountered. These findings reveal that while initiation mechanisms are flexible enough to adapt to an rRNA gene structure of any arrangement, palindromes represent obstacles to fork progression, which is a likely source of genomic instability.
Contraceptives and cervical carcinoma (1969)

thing ?), for which you condemn prophylactic antibiotics.Our experience of 22 cases of gas gangrene suggests that this condition was unexpected and arose from a variety of orthopaedic operations-only four had had amputations.