gebhart/patrepeval huggingface dataset:
Fitting an inhibitor into the active site of thermolysin: A molecular dynamics case study (1996)

We used molecular dynamics computer simulation to “fly” a small flexible ligand, L-leucine hydroxamic acid, into the active site of thermolysin. The potential, which imposed no constraints between protein and ligand, produced conformations close to the crystallographically determined one. The calculations made use of the combined molecular mechanics/grid method of Luty et al. (J. Comp. Chem. 16:454–464, 1995), in which atoms of the active site are free to move whereas the rest of the protein, assumed to be rigid, is represented as points of a grid, and which also includes an implicit solvation model. The method is sufficiently fast that large sets of simulations could be carried out, enabling statistical sampling and exploration of the effect of initial position and conformation of the ligand on the probability of successful docking. In a charged catalytic Glu/uncharged ligand regime, when the initial position of the ligand was determined by random translations and rotations that kept the center of mass within 8.0 Å of the crystal one, none of the 20 runs placed the ligand correctly. In a second set with uncharged Glu and zwitterionic ligand, 3 of 24 similarly placed random structures flew the ligand in successfully. In a third set with the same protonation scheme as the second the starting positions had randomly determined conformations but kept the hydroxyamate oxygens within 4.0 Å of the zinc; in this case 22 of 25 runs reoriented correctly. A diverse set of energetic, structural, and dynamic criteria was used for evaluation of the calculations. The results indicate the method to be a promising tool for the rational drug design process.
Antibody-affinity purification of novel α-<scp>l</scp>-fucosidase from mouse liver (1987)

Previous studies have documented the presence of a novel alpha-L-fucosidase in mouse liver that contains unique basic isoelectric forms and that is antigenically similar to, but not identical with, human liver alpha-L-fucosidase [Laury-Kleintop, Damjanov & Alhadeff (1985) Biochem. J. 230, 75-82]. In the present investigation, mouse liver alpha-L-fucosidase was purified approx. 26,500-fold in 10% overall yield by antibody-affinity chromatography with the IgG fraction of goat anti-(human alpha-L-fucosidase) antibody coupled to Sepharose 4B. Native polyacrylamide-gel electrophoresis and SDS/polyacrylamide-gel electrophoresis indicated that the mouse fucosidase is highly purified if not homogeneous. Isoelectric focusing demonstrated that all enzymic forms found in crude mouse liver supernatant fluids were purified by the antibody-affinity procedure.
The echolocating phone app (2013)

Acoustic echolocation systems have a multitude of applications including test/measurement, noise cancellation, and object detection. Current smartphone technology possesses the necessary computing power to implement sophisticated echolocation systems on smartphones. This provides the smartphone user with the ability to perform complicated acoustic measurement tasks in any situation and environment. This project implements an active sonar system on an Android smartphone. The sonar system has three main modes of operation: object detection and ranging, object velocity estimation, and joint object range and velocity estimation. Each of these operational modes are accomplished by utilizing one of the phone’s speakers as a transmitter and one or more of the microphones as a receiver. The app employs a simple Graphical User Interface that allows the user to switch between the modes of operation and observe/analyze object data. Additional functionality may include the ability to write object data to various data formats for offline processing and analysis. Because this app employs several modes of operations, there are several potential commercial applications including measuring a room’s acoustic impulse response or a vehicle speed gun as well as many educational apps exploring various acoustic phenomena.
Prospective Memory in Workplace and Everyday Situations (2012)

Forgetting to perform intended actions can have major consequences, including loss of life in some situations. Laboratory research on prospective memory—remembering (and sometimes forgetting) to perform deferred intentions—is growing rapidly, thanks to new laboratory paradigms that are being used to uncover underlying cognitive mechanisms. Everyday situations and workplace situations in fields such as aviation and medicine, which have been studied less extensively, reveal aspects of prospective remembering that have both practical and theoretical implications, which are discussed here. Several types of situations in which individuals are vulnerable to forgetting intentions, but which have not been studied extensively in laboratory research, are described, and ways to reduce vulnerability to forgetting are suggested.
Application of W/O Emulsions to Cosmetic Foundations. (2001)

W/Oエマルション製剤は耐水性に優れているため, 乳化型ファンデーションの製剤に適している。とくに油剤にシリコーン油を用いた場合は使用感も良好である。そこで界面活性剤としてシリコーン鎖にグリセリルエーテル基を導入した誘導体に着目し, シリコーン系W/Oエマルションを安定化するために必要なW/O型乳化剤としての構造条件を得た。さらに最適構造を有するグリセリルエーテル変性シリコーンを用いて, 低粘度W/Oエマルシヨンを調製した。ここではその安定化機構と乳化型ファンデーションヘの応用例について述べる。
Glycomic Analysis Using Glycoprotein Immobilization for Glycan Extraction (2013)

Glycosylation is one of the most common protein modifications and is involved in many functions of glycoproteins. Investigating aberrant protein glycosylation associated with diseases is useful in improving disease diagnostics. Due to the nontemplate nature of glycan biosynthesis, the glycans attached to glycoproteins are enormously complex; thus, a method for comprehensive analysis of glycans from biological or clinical samples is needed. Here, we describe a novel method for glycomic analysis using glycoprotein immobilization for glycan extraction (GIG). Proteins or peptides from complex samples were first immobilized on solid support, and other nonconjugated molecules were removed. Glycans were enzymatically or chemically modified on solid phase before releasing from glycoproteins/glycopeptides for mass spectrometry analysis. The method was applied to the glycomic analysis of both N- and O-glycans.
Monitoring immune modulation by nutrition in the general population: identifying and substantiating effects on human health (2013)

Optimal functioning of the immune system is crucial to human health, and nutrition is one of the major exogenous factors modulating different aspects of immune function. Currently, no single marker is available to predict the effect of a dietary intervention on different aspects of immune function. To provide further guidance on the assessment and interpretation of the modulation of immune functions due to nutrition in the general population, International Life Sciences Institute Europe commissioned a group of experts from academia, government and the food industry to prepare a guidance document. A draft of this paper was refined at a workshop involving additional experts. First, the expert group defined criteria to evaluate the usefulness of immune function markers. Over seventy-five markers were scored within the context of three distinct immune system functions: defence against pathogens; avoidance or mitigation of allergy; control of low-grade (metabolic) inflammation. The most useful markers were subsequently classified depending on whether they by themselves signify clinical relevance and/or involvement of immune function. Next, five theoretical scenarios were drafted describing potential changes in the values of markers compared with a relevant reference range. Finally, all elements were combined, providing a framework to aid the design and interpretation of studies assessing the effects of nutrition on immune function. This stepwise approach offers a clear rationale for selecting markers for future trials and provides a framework for the interpretation of outcomes. A similar stepwise approach may also be useful to rationalise the selection and interpretation of markers for other physiological processes critical to the maintenance of health and well-being.
Modeling of re-entrant coaxial and combline resonators and filters (2002)

The resonant frequency, Q-factor and the slot coupling of the re-entrant coaxial and combline structures have been studied by using rigorous numerical and analytical techniques. The validation and accuracy of the results are verified by experiments. A 6-pole iris coupled coaxial filter is designed and tested. Excellent frequency responses are obtained.
Adaptive Beam Search Decoding for Discrete Keyphrase Generation (2021)

Keyphrase Generation compresses a document into some highly-summative phrases, which is an important task in natural language processing. Most state-of-the-art adopt greedy search or beam search decoding methods. These two decoding methods generate a large number of duplicated keyphrases and are time-consuming. Moreover, beam search only predicts a fixed number of keyphrases for different documents. In this paper, we propose an adaptive generation model-AdaGM, which is mainly inspired by the importance of the first words in keyphrase generation. In AdaGM, a novel reset state training mechanism is proposed to maximize the difference in the predicted first words. To ensure the discreteness and get an appropriate number of keyphrases according to the content of the document adaptively, we equip beam search with a highly effective filter mechanism. Experiments on five public datasets demonstrate the proposed model can generate marginally less duplicated and more accurate keyphrases. The codes of AdaGM are available at: https://github.com/huangxiaolist/adaGM.
PTEN mutation in a family with Cowden syndrome and autism (2001)

We report on a mother and son with Cowden syndrome and a PTEN mutation. The boy also exhibits autistic behavior and mental retardation, while his mother has a normal intelligence and social interaction pattern. We review the scanty literature data on the association of Cowden syndrome and autism and emphasize that the association of progressive macrocephaly and pervasive developmental disorder seems to be an indication for screening for PTEN mutations.
Rule-based tuning for control of flexible-link manipulators (2002)

The authors summarize work on a two-level hierarchical control strategy to achieve accurate end-point position of a planar two-link flexible manipulator. The upper level in the hierarchy consists of a feedforward supervisory controller that incorporates fuzzy logic, whereas the lower level consists of conventional controllers using shaft and endpoint information. This hierarchical control strategy results in an improvement over the performance of current techniques for endpoint position control in the presence of flexure effects.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Blunt and blast head trauma: different entities. (2009)

Mild traumatic brain injury (mTBI) caused by blast-related and blunt head trauma is frequently encountered in clinical practice. Understanding the nuances between these two distinct types of injury leads to a more focused approach by clinicians to develop better treatment strategies for patients. In this study, we evaluated two separate cohorts of mTBI patients to ascertain whether any difference exists in vestibular-ocular reflex (VOR) testing (n = 55 enrolled patients: 34 blunt, 21 blast) and vestibular-spinal reflex (VSR) testing (n = 72 enrolled patients: 33 blunt, 39 blast). The VOR group displayed a preponderance of patients with blunt mTBI, demonstrating normal to high-frequency phase lag on rotational chair testing, whereas patients experiencing mTBI from blast-related causes revealed a trend toward low-frequency phase lag on evaluation. The VSR cohort showed that patients with posttraumatic migraine-associated dizziness tended to test higher on posturography. However, an indepth look at the total patient population in this second cohort reveals that a higher percentage of blast-exposed patients exhibited a significantly increased latency on motor control testing as compared to patients with blunt head injury (p < .02). These experiments identify a distinct difference between blunt-injury and blast-injury mTBI patients and provide evidence that treatment strategies should be individualized on the basis of each mechanism of injury.
Differential Viewpoints for Ground Terrain Material Recognition (2020)

Computational surface modeling that underlies material recognition has transitioned from reflectance modeling using in-lab controlled radiometric measurements to image-based representations based on internet-mined single-view images captured in the scene. We take a middle-ground approach for material recognition that takes advantage of both rich radiometric cues and flexible image capture. A key concept is differential angular imaging, where small angular variations in image capture enables angular-gradient features for an enhanced appearance representation that improves recognition. We build a large-scale material database, Ground Terrain in Outdoor Scenes (GTOS) database, to support ground terrain recognition for applications such as autonomous driving and robot navigation. The database consists of over 30,000 images covering 40 classes of outdoor ground terrain under varying weather and lighting conditions. We develop a novel approach for material recognition called texture-encoded angular network (TEAN) that combines deep encoding pooling of RGB information and differential angular images for angular-gradient features to fully leverage this large dataset. With this novel network architecture, we extract characteristics of materials encoded in the angular and spatial gradients of their appearance. Our results show that TEAN achieves recognition performance that surpasses single view performance and standard (non-differential/large-angle sampling) multiview performance.
Specifying Augmented Virtuality Systems for Creative Architectural Design (2007)

Despite active research in Virtual and Augmented Reality, the emerging new technology of Augmented Virtuality (AV) has rarely been explored in the architecture arena. Augmented Virtuality, where a predominantly virtual environment is enhanced by the addition of real entities, provides a means to merge richly layered, multi-modal, 3D real context and experience acquired from the real world into virtual architectural designs. There are no noted investigations on principles of implementing AV concept in the context of architectural design with the purpose of maximizing its full potentials. This paper discusses issues and approaches in establishing scientific principles for applying AV technology in supporting architectural design comprehension. As an initial effort towards those issues, the paper also formulates a comprehensive taxonomy for specifying A V technology for architectural applications.
Identification of the Capacitating Agent for Bovine Sperm in Egg Yolk-TEST Semen Extender (1989)

Bovine sperm can be capacitated in egg yolk-TEST buffer. To determine what constituent of the buffer was responsible, ejaculated semen was diluted 1:10 at 37 degrees C with the following 20% egg yolk (vol/vol)-containing buffers: TES-Tris, TES-tetramethylammonium hydroxide, taurine-Tris, citric acid-Tris, citrate, egg yolk salts, egg yolk proteins Tris, and citrate-taurine. Buffers were pH 7.6 and 321 to 325 mOsmol/kg. Extended semen was cooled slowly to 4 degrees C and stored 8 h. Sperm taken at 0 and 8 h were washed in pH 7.6 bovine serum albumin-saline and assessed for motility and capacitation using zona-free hamster eggs. Sperm motilities at 0 and 8 h were similar (60 to 73%) in all extenders except citric acid-Tris (54%) and egg yolk proteins Tris (15%). Bull sperm, stored 8 h in egg yolk-TEST, became capacitated. Because sperm storage in egg yolk-citrate did not result in penetration, both egg yolk and citrate were ruled out as capacitating agents. Capacitating activity resided in the TES and Tris molecules. The TES molecule contains a Tris component and this capacitated bull sperm. The TES molecule also contains a taurine component. However, taurine was not a capacitating agent for bull sperm. In conclusion, both TES- and Tris-containing buffers, alone or together (TEST), were equally effective in capacitating bull sperm.
Activin A/Bone Morphogenetic Protein (BMP) Chimeras Exhibit BMP-like Activity and Antagonize Activin and Myostatin (2007)

Activins and bone morphogenetic proteins (BMPs) are members of the transforming growth factor-beta family of growth and differentiation factors that induce signaling in target cells by assembling type II and type I receptors at the cell surface. Ligand residues involved in type II binding are located predominantly in the C-terminal region that forms an extended beta-sheet, whereas residues involved in type I binding are located in the alpha-helical and preceding loop central portion of the molecule. To test whether the central residues are sufficient to determine specificity toward type I receptors, activin A/BMP chimeras were constructed in which the central residues (45-79) of activin A were replaced with corresponding residues of BMP2 and BMP7. The chimeras were assessed for activin type II receptor (Act RII) binding, activin-like bioactivity, and BMP-like activity as well as antagonistic properties toward activin A and myostatin. ActA/BMP7 chimera retained Act RII binding affinity comparable with wild type activin A, whereas ActA/BMP2 chimera showed a slightly reduced affinity toward Act RII. Both the chimeras were devoid of significant activin bioactivity in 293T cells in the A3 Lux reporter assay up to concentrations 10-fold higher than the minimal effective activin A concentration (approximately 4 nM). In contrast, these chimeras showed BMP-like activity in a BRE-Luc assay in HepG2 cells as well as induced osteoblast-like phenotype in C2C12 cells expressing alkaline phosphatase. Furthermore, both the chimeras activated Smad1 but not Smad2 in C2C12 cells. Also, both the chimeras antagonized ligands that signal via activin type II receptor, such as activin A and myostatin. These data indicate that activin residues in the central region determine its specificity toward type I receptors. ActA/BMP chimeras can be useful in the study of receptor specificities and modulation of transforming growth factor-beta members, activins, and BMPs.
Urea-induced inactivation and denaturation of clostridial glutamate dehydrogenase: the absence of stable dimeric or trimeric intermediates (1995)

Urea-induced effects in clostridial glutamate dehydrogenase (GDH, EC 1.4.1.2) were studied by spectrophotometry, circular dichroism, FPLC, affinity chromatography and PAGE. Denaturation of enzyme occurred over a narrow range of urea concentrations (2.5-3.5 M), accompanied by inactivation of enzyme with a similar rate constant. The contribution of instantaneous inhibition by urea was also ascertained. FPLC studies of urea-treated GDH gave no evidence for dissociated oligomeric fragments of the hexamer in the presence of subdenaturing concentrations of urea. Likewise a mixture of fully 5,5'-dithiobis-(2-nitrobenzoic acid)-modified GDH hexamers and unmodified enzyme in 2 M urea failed to give rise to hybrid molecules. Exposure of unmodified GDH to high concentrations of urea led to the dissociation of hexamers to denatured monomers followed by association to form non-specific high-M(r) aggregates. This conclusion was confirmed by native gradient PAGE experiments. Various specific ligands stabilized the enzyme against urea-induced inactivation, succinate and 2-oxoglutarate being particularly effective. This protection of the native state was enhanced in ternary complexes, and the complex most resistant to urea-induced inactivation was the productive ternary complex GDH-NADH-2-oxoglutarate. Native gradient PAGE experiments indicate that these protecting ligands preserve the native hexameric structure of GDH.
I. Shiga toxin B-subunit system: retrograde transport, intracellular vectorization, and more (2002)

Many intracellular transport routes are still little explored. This is particularly true for retrograde transport between the plasma membrane and the endoplasmic reticulum. Shiga toxin B subunit has become a powerful tool to study this pathway, and recent advances on the molecular mechanisms of transport in the retrograde route and on its physiological function(s) are summarized. Furthermore, it is discussed how the study of retrograde transport of Shiga toxin B subunit allows one to design new methods for the intracellular delivery of therapeutic compounds.
A Convenient Synthesis of 4-Hydroxy-3-methyl-2-(2-propynyl)-cyclopent-2-enone, an Alcohol Moiety of a Synthetic Pyrethroid Having Strong Killing and Knockdown Activity (1982)

Journal Article A Convenient Synthesis of 4-Hydroxy-3-methyl-2-(2-propynyl)-cyclopent-2-enone, an Alcohol Moiety of a Synthetic Pyrethroid Having Strong Killing and Knockdown Activity Get access Noritada Matsuo, Noritada Matsuo Institute for Biological Science, Sumitomo Chemical Co. Ltd., Takatsukasa, Takarazuka, Hyogo 665, Japan Search for other works by this author on: Oxford Academic Google Scholar Fumio Fujita, Fumio Fujita Institute for Biological Science, Sumitomo Chemical Co. Ltd., Takatsukasa, Takarazuka, Hyogo 665, Japan Search for other works by this author on: Oxford Academic Google Scholar Osamu Magara, Osamu Magara Institute for Biological Science, Sumitomo Chemical Co. Ltd., Takatsukasa, Takarazuka, Hyogo 665, Japan Search for other works by this author on: Oxford Academic Google Scholar Hiroko Yamazaki, Hiroko Yamazaki Institute for Biological Science, Sumitomo Chemical Co. Ltd., Takatsukasa, Takarazuka, Hyogo 665, Japan Search for other works by this author on: Oxford Academic Google Scholar Koichi Aketa, Koichi Aketa Institute for Biological Science, Sumitomo Chemical Co. Ltd., Takatsukasa, Takarazuka, Hyogo 665, Japan Search for other works by this author on: Oxford Academic Google Scholar Toshio Nishioka, Toshio Nishioka Institute for Biological Science, Sumitomo Chemical Co. Ltd., Takatsukasa, Takarazuka, Hyogo 665, Japan Search for other works by this author on: Oxford Academic Google Scholar Nobushige Itaya Nobushige Itaya Institute for Biological Science, Sumitomo Chemical Co. Ltd., Takatsukasa, Takarazuka, Hyogo 665, Japan Search for other works by this author on: Oxford Academic Google Scholar Agricultural and Biological Chemistry, Volume 46, Issue 7, 1 July 1982, Pages 1911–1912, https://doi.org/10.1080/00021369.1982.10865349 Published: 01 July 1982 Article history Received: 10 April 1981 Published: 01 July 1982
Organizations Non Gratae? The Impact of Unethical Corporate Acts on Interorganizational Networks (2007)

In this study, we examine the effects of illegal/unethical acts on interfirm networks. We hypothesize that the quality of network partners will decline and overall network structure will change after a firm commits an unethical act. More specifically, we posit that the decline in partner quality is primarily driven by higher quality firms leaving the network, and the focal firm being forced to replace them with lower quality ones. We also propose that partner prominence and network cohesion will be affected after these acts, and that the changes in partner quality and network structure will be greater for those acts perceived as more illegitimate. We test these hypotheses using a sample of 200 large firms in the United States and data on unethical acts by these firms. Our results show that the quality of a firm’s network partners declines after the firm’s commission of an unethical act, and that the deterioration in partner quality tends to be greater for acts of greater illegitimacy. Our results also show declines in network prominence and cohesion for firms involved in these activities. We discuss the implications of our results for the literatures on interfirm networks and unethical corporate activities.