gebhart/patrepeval huggingface dataset:
β-Turn and β-Hairpin Mimicry with Tetrasubstituted Alkenes (1999)

Synthesis and conformational analysis are reported for molecules containing the trans-5-amino-3,4-dimethylpent-3-enoic acid residue (ADPA, 1). This amino acid is a glycylglycine mimic, in which the central amide group is replaced with an E-tetrasubstituted alkene. It was anticipated that this isosteric replacement would promote specific local (β-turn) and nonlocal (β-hairpin) conformational preferences. Previous work has shown that the most common β-turn conformations (type I and type II) are not strong inducers of β-hairpin formation, while the rare “mirror image” β-turns (type I‘ and type II‘) promote β-hairpin formation. We therefore sought an achiral unit with a strong turn-forming propensity, since the lack of stereogenic centers within such a unit would eliminate the energetic distinction between common and “mirror image” turn conformations. In, the ADPA unit, avoidance of allylic strain was expected to preorganize the backbone for adoption of folded conformations. A combination of NMR and IR data for di-, tri-, and tetrapeptide analogues containing the ADPA residue reveal that β-turn- and β-hairpin-like folding is promoted in methylene chloride solution.
Identification and simulation of the impact characteristics of the viscous mount (2006)

Hydraulic excavators have many different front attachments, and they are operated in various manners. Accordingly, stationary excitation and excessive impact loads are applied to the operator cabin. In recent years, a variety of mounts, including high viscous oil mounts, have been used to reduce the cabin vibration. Many papers have shown the stationary characteristics of the viscous mount has frequency-and amplitude-dependency, but there are few papers to characterize the impact behaviour of the viscous mount. The objective of this paper is to understand the impact behaviour of viscous mounts, which corresponds to impact loads for the actual machine. First, the reaction force and the response acceleration of the viscous mounts installed on the vehicle are measured during a critical drop impact test. Next, the impact test of the mount is performed to identify its impact characteristics. The test is performed with a shock load equivalent to the load applied during the drop impact test for the actual vehicle. The equivalent mass of the cabin is also applied to the mount during this shock load test. The characteristics are estimated from the measured data of the mount force and displacement at the initial impact by the least square method. Then, the response acceleration on the mount is calculated by the estimated characteristics using the impact load measured on the drop impact test for the actual vehicle. Finally, it is found that the identified characteristics are appropriate to correlate the calculated acceleration with the measured acceleration on the vehicle.
An algorithm for exact super-resolution and phase retrieval (2014)

We explore a fundamental problem of super-resolving a signal of interest from a few measurements of its low-pass magnitudes. We propose a 2-stage tractable algorithm that, in the absence of noise, admits perfect super-resolution of an r-sparse signal from 2r <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> -2r + 2 low-pass magnitude measurements. The spike locations of the signal can assume any value over a continuous disk, without increasing the required sample size. The proposed algorithm first employs a conventional super-resolution algorithm (e.g. the matrix pencil approach) to recover unlabeled sets of signal correlation coefficients, and then applies a simple sorting algorithm to disentangle and retrieve the true parameters in a deterministic manner. Our approach can be adapted to multi-dimensional spike models and random Fourier sampling by replacing its first step with other harmonic retrieval algorithms.
HANS &#x2013; A New Color Separation and Halftoning Paradigm (2010)

Traditionally the choices made by color separation are expressed as amounts of each of the available colorants to use for each of the reproducible colors. Halftoning then deals with the spatial distribution of colorants, which also results in the nature of their overprinting. However, having a colorant space as the way for color separation to communicate with halftoning gives access only to some of the possible printed patterns that a given printing system is capable of and therefore only to a reduced range of print attributes. In the present paper a method &#x2013; HANS &#x2013; is proposed to gain access to all possible, printable patterns by specifying relative area coverages of a printing system's Neugebauer primaries instead of only colorant amounts. This results in delivering prints with more optimal print attributes than were possible using existing methods, allowing for up to 34% less ink use while delivering a 10% greater color gamut on a test printing system using CMYKcm inks.
A Site-specific Indoor Link Model for Realistic Wireless Network Simulations (2011)

Compared to testbeds, the efficiency and accuracy of wireless networking simulations are constantly questioned by the network community. It is widely accepted today that the current network simulators are not able to fully represent the real wireless characteristics, especially at the physical (PHY)
ChemInform Abstract: Synthesis of a Monocyclic Core of the Antifungal Sordarins. (1999)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
Correction to Discovery of Potent and Selective 8-Fluorotriazolopyridine c-Met Inhibitors (2015)

ADVERTISEMENT RETURN TO ISSUEPREVAddition/CorrectionNEXTORIGINAL ARTICLEThis notice is a correctionCorrection to Discovery of Potent and Selective 8-Fluorotriazolopyridine c-Met InhibitorsEmily A. Peterson*, Yohannes Teffera, Brian K. Albrecht, David Bauer, Steven F. Bellon, Alessandro Boezio, Christiane Boezio, Martin A. Broome, Deborah Choquette, Katrina W. Copeland, Isabelle Dussault, Richard Lewis, Min-Hwa Jasmine Lin, Julia Lohman, Jingzhou Liu, Michele Potashman, Karen Rex, Roman Shimanovich, Douglas A. Whittington, Karina R. Vaida, and Jean-Christophe HarmangeCite this: J. Med. Chem. 2015, 58, 9, 4087Publication Date (Web):April 22, 2015Publication History Published online22 April 2015Published inissue 14 May 2015https://doi.org/10.1021/acs.jmedchem.5b00591Copyright © 2015 American Chemical SocietyRIGHTS & PERMISSIONSArticle Views808Altmetric-Citations-LEARN 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 InReddit PDF (498 KB) Get e-Alerts Get e-Alerts
Measurement of Pudendal Evoked Potentials During Feminizing Genitoplasty: Technique and Applications (1995)

We report on 6 patients (average age 13 months) with ambiguous genitalia who underwent stimulation of the dorsal neurovascular bundle of the phallus during feminizing genitoplasty. Three patients had the adrenogenital syndrome, 1 underwent removal of a masculinizing adrenal tumor before genital reconstruction, 1 had mixed gonadal dysgenesis and 1 had male pseudohermaphroditism. Stimulation of the dorsal neurovascular bundle with measurement of electromyographic nerve conduction latencies was performed before and after ligation of the corporeal bodies and excision of the erectile tissue. In all 6 cases electromyographic responses were preserved after phallic reduction. Our study clearly shows that modern techniques of genital reconstruction allow for preservation of nerve conduction in the dorsal neurovascular bundle and may permit normal sexual function in adulthood.
Molecular cloning and sequencing of mRNAs coding for minor adult globin polypeptides of Xenopus laevis (1983)

Globin mRNA was isolated from immature red blood cells of an adult Xenopus laevis female. mRNA/cDNA hybrids were integrated in the Pst I cleavage site of pBR 322 by G/C tailing, and cloned in Escherichia coli strain HB 101. By restriction site analysis as well as hybridization behaviour we identified two clones coding for minor adult alpha and beta globin chains. Nucleotide sequence analysis and derived amino acid sequences are presented.
Approximate state-feedback linearization using spline functions (2005)

This paper presents a algorithm for the construction of a state-feedback linearizing controller. The technique uses part of the state coordinate transformation from the pseudo-linearizing method as an "output function". Spline function interpolation is used to construct the controller, which can be accomplished regardless of the complexity of the nonlinear model. A coplanar two-link robotic manipulator Acrobot is used to illustrate the design technique, and simulation results are presented which support assertions of computational efficiency and high-performance.
An Interpreted Atlas of Biosynthetic Gene Clusters from 1000 Fungal Genomes (2020)

Abstract Fungi are prolific producers of natural products, compounds which have had a large societal impact as pharmaceuticals, mycotoxins, and agrochemicals. Despite the availability of over 1000 fungal genomes and several decades of compound discovery efforts from fungi, the biosynthetic gene clusters (BGCs) encoded by these genomes and the associated chemical space have yet to be analyzed systematically. Here we provide detailed annotation and analyses of fungal biosynthetic and chemical space to enable genome mining and discovery of fungal natural products. Using 1037 genomes from species across the fungal kingdom (e.g., Ascomycota, Basidiomycota, and non-Dikarya taxa), 36,399 predicted BGCs were organized into a network of 12,067 gene cluster families (GCFs). Anchoring these GCFs with reference BGCs enabled automated annotation of 2,026 BGCs with predicted metabolite scaffolds. We performed parallel analyses of the chemical repertoire of Fungi, organizing 15,213 fungal compounds into 2,945 molecular families (MFs). The taxonomic landscape of fungal GCFs is largely species-specific, though select families such as the equisetin GCF are present across vast phylogenetic distances with parallel diversifications in the GCF and MF. We compare these fungal datasets with a set of 5,453 bacterial genomes and their BGCs and 9,382 bacterial compounds, revealing dramatic differences between bacterial and fungal biosynthetic logic and chemical space. These genomics and cheminformatics analyses reveal the large extent to which fungal and bacterial sources represent distinct compound reservoirs. With a &gt;10-fold increase in the number of interpreted strains and annotated BGCs, this work better regularizes the biosynthetic potential of fungi for rational compound discovery. Significance Statement Fungi represent an underexploited resource for new compounds with applications in the pharmaceutical and agriscience industries. Despite the availability of &gt;1000 fungal genomes, our knowledge of the biosynthetic space encoded by these genomes is limited and ad hoc. We present results from systematically organizing the biosynthetic content of 1037 fungal genomes, providing a resource for data-driven genome mining and large-scale comparison of the genetic and molecular repertoires produced in fungi and compare to those present in bacteria.
Food Category Representatives: Extracting Categories from Meal Names in Food Recordings and Recipe Data (2015)

Food Log is a multimedia recording tool for producing food records for many individuals. In one year of operation, Food Log has produced more than one million food records for meals eaten by users. We found nearly 70,000 unique food records among these data. In analyzing them, one of the challenges is to extract meal categories from such a large number of records. In this paper, we propose a method for compressing a meal name into a shorter representation. First, we collect similar meal names using a k-nearest neighbor search. Next, we construct a word graph to model the relationship between the meal names and items in the database. We select representative words by identifying minimal paths in the word graph. Finally, we obtain a few words that represent categorical information about the original meal name. We applied the method to data in food records for both Food Log and the Rakuten Recipe database. Our results show that the method worked effectively for both datasets.
From Denoising to Compressed Sensing (2016)

A denoising algorithm seeks to remove noise, errors, or perturbations from a signal. Extensive research has been devoted to this arena over the last several decades, and as a result, todays denoisers can effectively remove large amounts of additive white Gaussian noise. A compressed sensing (CS) reconstruction algorithm seeks to recover a structured signal acquired using a small number of randomized measurements. Typical CS reconstruction algorithms can be cast as iteratively estimating a signal from a perturbed observation. This paper answers a natural question: How can one effectively employ a generic denoiser in a CS reconstruction algorithm? In response, we develop an extension of the approximate message passing (AMP) framework, called denoising-based AMP (D-AMP), that can integrate a wide class of denoisers within its iterations. We demonstrate that, when used with a high-performance denoiser for natural images, D-AMP offers the state-of-the-art CS recovery performance while operating tens of times faster than competing methods. We explain the exceptional performance of D-AMP by analyzing some of its theoretical features. A key element in D-AMP is the use of an appropriate Onsager correction term in its iterations, which coerces the signal perturbation at each iteration to be very close to the white Gaussian noise that denoisers are typically designed to remove.
Epilogue: A Personal Perspective: Aptamers after 15 Years (2006)

In 1990 Craig Tuerk and I published the first paper The technology described the entirely in vitro combinatorial chemistry method in which the materials in the compound library were single-stranded nucleic acids. While the first experiment used only 65 000 different RNA sequences, it was clear immediately that single-stranded nucleic acid libraries could be larger than any other combinatorial chemistry library (because of nucleic acid amplification techniques). One important lesson from SELEX is that library size can be very important, an idea I will return to at the end of this chapter.
Influence of ASE Noise on the Performance of DWDM Networks Using Low-Power Pumped Raman Amplifiers (2015)

We present the results of investigation of influence of amplified spontaneous emission (ASE) noise, noise figure (NF) and dispersion chromatic on the performance of middle-distance dense-wavelength-division-multiplexing (DWDM) networks using low-power pumped distributed Raman amplifiers (DRAs) in two different pump configurations, i.e., forward and backward pumping. We found that the pumping configurations, ASE noise, and dispersion play an important role for improving the network performance by reduction of NF and bit error rate (BER) of the system. Simulation results show that the lowest BER and low NF were obtained, when using the forward pumping configuration. Moreover, we have also compared ASE noise powers of the simulation with this experiment. These results conclude that DRA with low pump power (<1 W) is the promising key technology for short- and/or middle-distance DWDM transmission networks.
Concurrent segmentation of the prostate on MRI and CT via linked statistical shape models for radiotherapy planning (2012)

The fLSSM provides an accurate alternative to SSMs that require careful expert delineations of the SOI that may be difficult or laborious to obtain. Additionally, the fLSSM has the added benefit of providing concurrent segmentations of the SOI on multiple imaging modalities.
SQL Anywhere: A Holistic Approach to Database Self-management (2007)

In this paper we present an overview of the self-management features of SQL anywhere, a full-function relational database system designed for frontline business environments with minimal administration. SQL Anywhere can serve as a high-performance workgroup server, an embedded database that is installed along with an application, or as a mobile database installed on a handheld device that provides full database services, including two-way synchronization, to applications when the device is disconnected from the corporate intranet. We illustrate how the various self-management features work in concert to provide a robust data management solution in zero-administration environments.
Synthesis of 4-Trifluoromethylated 2-Alkyl- and 2,3-Dialkyl-Substituted Azetidines (2003)

[reaction: see text]. A diastereoselective approach to the synthesis of 4-trifluoromethylated 2-alkyl- and 2,3-dialkylazetidines, including BOC-protected 4-trifluoromethylazetidin-2-ylcarboxylic acid, was developed via Wittig reaction of 4-trifluomethylated beta-lactam followed by alkylation and hydrogenation.
Jasper Jumper versus a one-piece anterior positioning appliance in the treatment of sleep apnea (2012)

Purpose The purpose of this study was to compare theChange of anatomical relationship of the oropharyngealairway space in loud snoring patients by using tworemovable prosthetic appliances for improvement ofsnoring and respiratory disturbance.Materials and Methods Ten completely dentulous orpartially edentulous male patients with Class II AngleClassification were selected. They had a history ofhabitual loud snoring. All the selected patients weresubjected pre-prosthetically to clinical examination andnasal examination. Lateral Cephalometric Radiographwas done while the patient was laying down on hisback (supine position) with cross-table technique.The radiograph was traced, for each patient. Cephalometriclandmarks, linear measurement), and total pharyngeallength were identified. Two different designs ofanterior mandibular positioning device were constructedfor each patient: 1-Jasper Jumper Appliance (A),2- One-piece Appliance (B). Cephalogram was doneafter two months of using the appliance. Matched pairssigned ranks test (wilcoxon) was used for comparison ofthe average pre-prosthetic and post-prosthetic appliance(A) and appliance (B) to study the relation betweenmeasurement, Spearmen’s rank correlation coefficientwas used.Results The superior anterior, superior posterior, middleand inferior airway linear distance showed significantincrease when appliance A was worn. The totalpharyngeal length showed no significant changebetween appliance A and B (Pr0.05). The posteriornasal spine showed no significant changes betweenappliance A and appliance B, The respiratorydisturbance index showed significant decreasewhile the lowest arterial oxygen saturation wassignificant increased after the patient wore applianceA and appliance B.Conclusion Anterior mandibular positioning appliances -either Jasper-Jumper or one-piece, are successfulconservative treatment appliances, for prevention of sleepapnea, improving the respiratory disturbances thatoccurred during sleep and enhancing the anatomicalrelationship of the upper airway space. Egypt J OralMaxillofac Surg 3:7–15
Automatic gender identification (2001)

In this paper, a new automatic gender identification method is proposed as a part of an Automatic Speaker Recognition (ASR) system. The short time raw speech signal (180–450 ms) was filtered by the nine-order Butterworth low pass filter and decomposed to different frequency bands by the wavelet filter bank analyzer. The energy of the 120 sub-bands was used as a feature vector and applied to a standard classifier. This classifier was trained by the gradient descent method with 1594 utterances spoken by various males and females. The system was tested with different 2542 utterances giving 99.2% correct classification rate. The high performance and simplicity of implementation are the characteristics of this system in comparison to the other methods. [Work supported by DARPA.]
Investigation of Surface Pits Originating in Dislocations in AlGaN/GaN Epitaxial Layer Grown on Si Substrate with Buffer Layer (2006)

An AlGaN/GaN heterostructural layer with a crack-free smooth surface was grown on multiple buffer layers formed on a Si(111) substrate. On the AlGaN surface, pit arrays forming a network structure were observed by atomic force microscopy (AFM). In order to clarify the origin of these pit arrays, the AlGaN/GaN layer was investigated using transmission electron microscopy (TEM). As a result, similar network structures of threading edge dislocations in the AlGaN/GaN layer were observed by plan-view TEM. It was thus confirmed that the surface pit arrays observed by AFM represent the surface termination of edge dislocations formed at the small-angle boundaries of slightly misoriented crystal domains.
The Unique Electronic Structure of Mg2Si: Shaping the Conduction Bands of Semiconductors with Multicenter Bonding (2017)

The electronic structures of the antifluorite-type compound Mg<sub>2</sub> Si is described in which a sublattice of short cation-cation contacts creates a very low conduction band minimum. Since Mg<sub>2</sub> Si shows n-type conductivity without intentional carrier doping, the present result indicates that the cage defined by the cations plays critical roles in carrier transport similar to those of inorganic electrides, such as 12 CaO⋅7 Al<sub>2</sub> O<sub>3</sub> :e<sup>-</sup> and Ca<sub>2</sub> N. A distinct difference in the location of conduction band minimum between Mg<sub>2</sub> Si and the isostructural phase Na<sub>2</sub> S is explained in terms of factors such as the differing interaction strengths of the Si/S 3s orbitals with the cation levels, with the more core-like character of the S 3s leading to a relatively low conduction band energy at the Γ point. Based on these results and previous research on electrides, approaches can be devised to control the energy levels of cation sublattices in semiconductors.