gebhart/patrepeval huggingface dataset:
Accessible surface areas as a measure of the thermodynamic parameters of hydration of peptides. (1987)

A method is described for the inclusion of the effects of hydration in empirical conformational energy computations on polypeptides. The free energy of hydration is composed of additive contributions of various functional groups. The hydration of each group is assumed to be proportional to the accessible surface area of the group. The constants of proportionality, representing the free energy of hydration per unit area of accessible surface, have been evaluated for seven classes of groups (occurring in peptides) by least-squares fitting to experimental free energies of solution of small monofunctional aliphatic and aromatic molecules. The same method has also been applied to the modeling of the enthalpy and heat capacity of hydration, each of which is computed from the accessible surface area.
Towards an integrated restoration/forward geomechanical modelling workflow for basin evolution prediction (2018)

Many sedimentary basins host important reserves of exploitable energy resources. Understanding of the present-day state of stresses, porosity, overpressure and geometric configuration is essential in order to minimize production costs and enhance safety in operations. The data that can be measured from the field is, however, limited and at a non-optimal resolution. Structural restoration (inverse modelling of past deformation) is often used to validate structural interpretations from seismic data. In addition, it provides the undeformed state of the basin, which is a pre-requisite to understanding fluid migration or to perform forward simulations. Here, we present a workflow that integrates geomechanical-based structural restoration and forward geomechanical modelling in a finite element framework. The geometry and the boundary kinematics derived from restoration are used to automatically create a forward geomechanical model. Iterative correction may then be performed by either modifying the assumptions of the restoration or modifying the restoration-derived boundary conditions in the forward model. The methodology is applied to two problems; firstly, a sand-box scale benchmark model consisting of sand sediments sliding on silicon leading to the formation of a graben structure; secondly, a field-scale thrust-related anticline from Niger Delta. Two strategies to provide further constraint on fault development in the restoration-derived forward simulation are also presented. It is shown that the workflow reproduces the first order structural features observed in the target geometry. Furthermore, it is demonstrated that the iterative approach provides improved understanding of the evolution and additional information of current-day stress and material state for the Niger Delta Case.
BASP1 Is a Transcriptional Cosuppressor for the Wilms' Tumor Suppressor Protein WT1 (2003)

The Wilms' tumor suppressor protein WT1 is a transcriptional regulator that plays a key role in the development of the kidneys. The transcriptional activation domain of WT1 is subject to regulation by a suppression region within the N terminus of WT1. Using a functional assay, we provide direct evidence that this requires a transcriptional cosuppressor, which we identify as brain acid soluble protein 1 (BASP1). WT1 and BASP1 associate within the nuclei of cells that naturally express both proteins. BASP1 can confer WT1 cosuppressor activity in transfection assays, and elimination of endogenous BASP1 expression augments transcriptional activation by WT1. BASP1 is present in the developing nephron structures of the embryonic kidney and, coincident with that of WT1, its expression is restricted to the highly specialized podocyte cells of the adult kidney. Taken together, our results show that BASP1 is a WT1-associated factor that can regulate WT1 transcriptional activity.
Progress Report of CEFR Project in 2012 (2012)

1 Overview China Experimental Fast Reactor (CEFR), with the thermal power of 65 MW, experimental electrical power of 20 MW, and UO2 as first loading fuel, adopts a pool-type reactor structure and a sodium-sodium-water 3-loop design for heat removal system; it independently launched, for the first time, a passive accident heat removal system.
Germ-line mutations in the von Hippel-Lindau tumor-suppressor gene are similar to somatic von Hippel-Lindau aberrations in sporadic renal cell carcinoma. (1994)

von Hippel-Lindau (VHL) disease is a hereditary tumor syndrome predisposing to multifocal bilateral renal cell carcinomas (RCCs), pheochromocytomas, and pancreatic tumors, as well as angiomas and hemangioblastomas of the CNS. A candidate gene for VHL was recently identified, which led to the isolation of a partial cDNA clone with extended open reading frame, without significant homology to known genes or obvious functional motifs, except for an acidic pentamer repeat domain. To further characterize the functional domains of the VHL gene and assess its involvement in hereditary and nonhereditary tumors, we performed mutation analyses and studied its expression in normal and tumor tissue. We identified germline mutations in 39% of VHL disease families. Moreover, 33% of sporadic RCCs and all (6/6) sporadic RCC cell lines analyzed showed mutations within the VHL gene. Both germ-line and somatic mutations included deletions, insertions, splice-site mutations, and missense and nonsense mutations, all of which clustered at the 3' end of the corresponding partial VHL cDNA open reading frame, including an alternatively spliced exon 123 nt in length, suggesting functionally important domains encoded by the VHL gene in this region. Over 180 sporadic tumors of other types have shown no detectable base changes within the presumed coding sequence of the VHL gene to date. We conclude that the gene causing VHL has an important and specific role in the etiology of sporadic RCCs, acts as a recessive tumor-suppressor gene, and appears to encode important functional domains within the 3' end of the known open reading frame.
Artifact reduction in lenticular multiscopic 3D displays by means of anti-alias filtering (2003)

This paper addresses the issue of artifact visibility in automultiscopic 3-D lenticular displays. A straightforward extension of the two-view lenticular autostereoscopic principle to M views results in an M-fold loss of horizontal resolution due to the subsampling needed to properly multiplex the views. In order to circumvent the imbalance between the horizontal and vertical resolution, a tilt can be applied to the lenticules to orient them at a small angle to the vertical direction, as is done in the <i>SynthaGram</i> display from Stereographics Corp. In either case, to avoid aliasing the subsampling should be preceded by suitable lowpass pre-filtering. Although for purely vertical lenticules a sufficiently narrowband lowpass horizontal filtering suffices, the situation is more complicated for diagonal lenticules; the subsampling of each view is no more orthogonal, and more complex sampling models need to be considered. Based on multidimensional sampling theory, we have studied multiview sampling models based on lattices. These models approximate pixel positions on a lenticular automultiscopic display and lead to optimal anti-alias filters. In this paper, we report results for a separable approximation to non-separable 2-D anti-alias filters based on the assumption that the lenticule slant is small. We have carried out experiments on a variety of images, and different filter bandwidths. We have observed that the theoretically-optimal bandwidth is too restrictive; aliasing artifacts disappear, but some image details are lost as well. Somewhat wider bandwidths result in images with almost no aliasing and largely preserved detail. For subjectively-optimized filters, the improvements, although localized, are clear and enhance the 3-D viewing experience.
Effective ambulatory service capacity management. (1989)

An effective capacity management program can increase operational productivities while reducing patient congestion. A framework for ambulatory care capacity management is presented that includes both demand-smoothing and supply-matching strategies. A case study focuses on analyzing congestion in the patient care delivery process at a medical oncology outpatient clinic. Through the use of a balanced and coordinated set of capacity management strategies, a low-cost approach to improved performance may be designed.
New Weakly Coordinating Anions. III. Useful Silver and Trityl Salt Reagents of Carborane Anions (1994)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTNew Weakly Coordinating Anions. III. Useful Silver and Trityl Salt Reagents of Carborane AnionsZuowei Xie, Tomas Jelinek, Robert Bau, and Christopher A. ReedCite this: J. Am. Chem. Soc. 1994, 116, 5, 1907–1913Publication Date (Print):March 1, 1994Publication History Published online1 May 2002Published inissue 1 March 1994https://pubs.acs.org/doi/10.1021/ja00084a034https://doi.org/10.1021/ja00084a034research-articleACS PublicationsRequest reuse permissionsArticle Views1681Altmetric-Citations136LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-AlertscloseSupporting Info (2)»Supporting Information Supporting Information Get e-Alerts
Effects of local immunization with glucosyltransferase on colonization of hamsters by Streptococcus mutans (1982)

Experiments were performed to study the effect of antibody to Streptococcus mutans glucosyltransferase (GTF) on the implantation of these organisms in hamsters. Salivary (immunoglobulin A) and serum (immunoglobulin G) antibodies to GTF and GTF-inhibiting activity were elicited by injection of GTF in Freund complete adjuvant in the salivary gland region. Sham-immunized and GTF-immunized groups were then orally challenged with approximately 10(7), 10(8), or 10(9) colony-forming units of cariogenic S. mutans 6715. The results were evaluated by systematically swabbing molars 4 days and approximately 4 weeks after challenge. In general, fewer GTF-immunized hamsters became infected with S. mutans after challenge with 10(7) or 10(8) organisms than did identically challenged sham-immunized hamsters. Of the animals that did become infected, fewer S. mutans colony-forming units were recovered from GTF-immunized hamsters. These results indicate that the presence of antibody to GTF can diminish the ability of S. mutans to implant in the oral cavity of immunized hamsters.
Gemini Lite: a non-intrusive debugger for Windows NT (2000)

It is frequently useful to debug a running software system in a production environment with a symbolic debugger without interfering with the operation of the system. The user of such a debugger may want to inspect data or trigger some data collecting operations whenever the running program hits an arbitrary address. Terminating or initiating the debugging session must also be transparent to users of the system. Debuggers available for Windows NT (or any debugger written with the Win32 debugging API) cannot detach from a running process without killing it, so they are unsuitable for debugging live systems. This paper presents the design of Gemini Lite, a debugger written without the Win32 debugger API, which has the capabilities needed to debug running production systems.
Helium bubbles in silicon: Structure and optical properties (1995)

Silicon samples were implanted with 20 keV He at various temperatures. The damage and the size of the He bubbles created during the implantation were measured with Raman spectroscopy and transmission electron microscopy. Room temperature implantation with 2.5×1017 He atoms/ cm2 produced an amorphized layer with a high density of small voids (∼5 nm). After annealing at 923 K the amorphous layer was recrystallized, but still contained extended defects. The He bubbles coalesced forming large bubbles in the implanted region. Implantation at 723 K left the Si essentially crystalline, but with a large number of defects. The He bubbles created at this temperature were larger than after room temperature implantation. Light emitting properties of this porous material are briefly discussed.
Can visual fixation patterns improve image fidelity assessment? (2008)

This paper presents the results of a computational experiment designed to investigate the extent to which metrics of image fidelity can be improved through knowledge of where humans tend to fixate in images. Five common metrics of image fidelity were augmented using two sets of fixation data, one set obtained under task-free viewing conditions and another set obtained when viewers were asked to judge image quality. The augmented metrics were then compared to subjective ratings of the images. The results show that most metrics can be improved using eye fixation data, but a greater improvement was found using fixations obtained in the task-free condition (task-free viewing).
Activity Levels of Tamoxifen Metabolites at the Estrogen Receptor and the Impact of Genetic Polymorphisms of Phase I and II Enzymes on Their Concentration Levels in Plasma (2011)

The therapeutic effect of tamoxifen depends on active metabolites, e.g., cytochrome P450 2D6 (CYP2D6) mediated formation of endoxifen. To test for additional relationships, 236 breast cancer patients were genotyped for CYP2D6, CYP2C9, CYP2B6, CYP2C19, CYP3A5, UGT1A4, UGT2B7, and UGT2B15; also, plasma concentrations of tamoxifen and 22 of its metabolites, including the (E)-, (Z)-, 3-, and 4'-hydroxymetabolites as well as their glucuronides, were quantified using liquid chromatography-tandem mass spectrometry (MS). The activity levels of the metabolites were measured using an estrogen response element reporter assay; the strongest estrogen receptor inhibition was found for (Z)-endoxifen and (Z)-4-hydroxytamoxifen (inhibitory concentration 50 (IC50) 3 and 7 nmol/l, respectively). CYP2D6 genotypes explained 39 and 9% of the variability of steady-state concentrations of (Z)-endoxifen and (Z)-4-hydroxytamoxifen, respectively. Among the poor metabolizers, 93% had (Z)-endoxifen levels below IC90 values, underscoring the role of CYP2D6 deficiency in compromised tamoxifen bioactivation. For other enzymes tested, carriers of reduced-function CYP2C9 (*2, *3) alleles had lower plasma concentrations of active metabolites (P < 0.004), pointing to the role of additional pathways.
Generating Counterfactual Explanations with Natural Language (2018)

Natural language explanations of deep neural network decisions provide an intuitive way for a AI agent to articulate a reasoning process. Current textual explanations learn to discuss class discriminative features in an image. However, it is also helpful to understand which attributes might change a classification decision if present in an image (e.g., "This is not a Scarlet Tanager because it does not have black wings.") We call such textual explanations counterfactual explanations, and propose an intuitive method to generate counterfactual explanations by inspecting which evidence in an input is missing, but might contribute to a different classification decision if present in the image. To demonstrate our method we consider a fine-grained image classification task in which we take as input an image and a counterfactual class and output text which explains why the image does not belong to a counterfactual class. We then analyze our generated counterfactual explanations both qualitatively and quantitatively using proposed automatic metrics.
Auger recombination dynamics of In<sub><i>x</i></sub>Ga<sub>1-<i>x</i></sub>Sb (1999)

The alloy In1-xGaxSb has been identified as potentially an important component in mid-infrared laser diodes which use band structure engineering of quantum structures based on the narrow-gap III-V material InSb. A pump-probe measurement has been made of carrier recombination in bulk In1-xGaxSb, for a range of alloy compositions. Over the range of excited carrier densities (5 × 1016-3 × 1017 cm-3) and at the temperatures (30-300 K) studied experimentally, contributions to the recombination from Auger, Shockley-Read-Hall and radiative mechanisms were calculated using an analytic approximation, with carrier degeneracy included. Excellent agreement with experiment was obtained over the alloy range x = 0.0-0.2 (corresponding to a room-temperature energy gap variation from 0.175 eV to 0.215 eV). Numerically the room-temperature Auger coefficient, C, decreased from the value 1.17 × 1026 cm6 s-1 at x = 0 (i.e. InSb) to 0.98 × 1026 cm6 s-1 at x = 0.2. The fact that C decreases with energy gap increase, in good agreement with theoretical predictions, is important for strained layer quantum well device applications.
Automatic equalization using a successive overrelaxation iterative technique (1975)

The successive overrelaxation iterative technique is used as the algorithm for the iterative adjustment of transversal equalizer tap gains during a training period using isolated pulses for the minimization of the mean-square error. For certain channel models, substantial improvement is demonstrated in the rate of convergence over the commonly used gradient techniques. Numerical simulations indicate that the relaxation algorithm consistently converged much faster than the gradient techniques. The behavior of the algorithm in noise is also investigated and is shown to be no worse than any other equalizer algorithm.
Generation of wavelength tunable gain-switched pulses from FP MQW lasers with external injection seeding (1997)

High-repetition rate (20 GHz), wavelength tunable (40 nm) optical pulses have been generated by gain switching of 1.55-μm Fabry-Perot (FP) multiple-quantum-well (MQW) lasers using continuous-wave (CW) light injection for longitudinal mode selection. After fiber compression, a pulse duration shorter than 5.8 ps was obtained over the entire wavelength tuning range. The pulsewidth, chirping characteristics and side-mode suppression ratio were investigated as functions of the seeding power and wavelength. In addition, we report on the observation of chaos and period doubling for a gain-switched laser without injection seeding, and show that irregular behavior can be suppressed by injection seeding of the laser.
Dense target signal processing (1991)

The problem of determining the density of targets at every range and velocity is addressed. These targets consist of a dense group of reflecting objects moving with different velocities and at different ranges. The problem of how to choose the outgoing signals and process the echoes of those signals from the targets to determine the density function is discussed. The problem is a classical inverse problem. The objective is to reconstruct a function of two variables (range and velocity) from limited information. Two schemes are given. The first of these methods modifies the method of J.R. Klauder et al. (1960) to the case of signals with a large range of frequency components (wideband signals). The second is an improvement on the first that uses a formula of I. Khalil (1974) from affine group theory. Numerical solutions support the conclusions. The method has applications in echocardiography, radar, sonar and fluid flow measurement.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Speckle techniques for material testing (1995)

Material testing is an important task during product design, manufacturing and inspection processes. Speckle techniques are increasingly used as effective tools for this work. In this paper, we discuss the use of speckle interferometric techniques such as electronic speckle pattern interferometry (ESPI) and shearography for non-destructive testing (NDT) of composite materials. Three test coupons of the same composite material with different defects were tested, and the experimental results by using these two methods were compared.
A high speed algorithm for identifying hand gestures for an ATM input system for the blind (2015)

With the evolution in science and technology, a lot has been done over the past few years to make the lives of the differently-abled more comfortable and easy. This paper concentrates on a novel methodology to ease the use of an ATM machine for the blind. It describes an approach wherein both the username and PIN for the ATM machine can be input using British Sign Language. A cost effective setup and also a high speed algorithm for hand gesture recognition has been elaborated. In comparison with previous algorithms, the method explained in this paper is 1.65 times faster thus proving its efficacy and efficiency. All algorithms were first designed and developed in MATLAB 2011b and then later deployed as software using the Java programming language.
Automatic verification technology of software patches for user virtual environments on IaaS cloud (2015)

We propose here a technique for automatic verification of software patches for user virtual environments on Infrastructure as a Service (IaaS) Cloud to reduce the cost of verifying patches. IaaS services have been spreading rapidly, and many users can customize virtual machines on IaaS Cloud like their own private servers. However, users must install and verify software patches of the OS or middleware installed on virtual machines by themselves. This task increases the user’s operation costs. Our proposed method replicates user virtual environments, extracts verification test cases for user virtual environments from a test case database (DB), distributes patches to virtual machines in the replicated environments, and executes the test cases automatically on the replicated environments. To reduce test cases creation efforts, we propose an idea of two-tier abstraction which groups software to software groups and function groups and selects test cases belonging to each group. We applied the proposed method on OpenStack using Jenkins and confirmed its feasibility. We evaluated the effectiveness of test case creation efforts and the automatic verification performance of environment replications, test cases extractions, and test case executions.