gebhart/patrepeval huggingface dataset:
Practical 4′-Phosphopantetheine Active Site Discovery from Proteomic Samples (2010)

Polyketide and nonribosomal peptides constitute important classes of small molecule natural products. Due to the proven biological activities of these compounds, novel methods for discovery and study of the polyketide synthase (PKS) and nonribosomal peptide synthetase (NRPS) enzymes responsible for their production remains an area of intense interest, and proteomic approaches represent a relatively unexplored avenue. While these enzymes may be distinguished from the proteomic milieu by their use of the 4'-phosphopantetheine (PPant) post-translational modification, proteomic detection of PPant peptides is hindered by their low abundance and labile nature which leaves them unassigned using traditional database searching. Here we address key experimental and computational challenges to facilitate practical discovery of this important post-translational modification during shotgun proteomics analysis using low-resolution ion-trap mass spectrometers. Activity-based enrichment maximizes MS input of PKS/NRPS peptides, while targeted fragmentation detects putative PPant active sites. An improved data analysis pipeline allows experimental identification and validation of these PPant peptides directly from MS² data. Finally, a machine learning approach is developed to directly detect PPant peptides from only MS² fragmentation data. By providing new methods for analysis of an often cryptic post-translational modification, these methods represent a first step toward the study of natural product biosynthesis in proteomic settings.
Linkage Specificity and Role of Properdin in Activation of the Alternative Complement Pathway by Fungal Glycans (2011)

Invasive fungal infections have increased in incidence with the widespread use of immunosuppressive therapy and invasive procedures. Activation of the complement system contributes to innate immunity against fungi by generating chemoattractants that recruit white blood cells and by coating the pathogen with complement fragments that "mark" them for phagocytosis. The fungal cell wall activates complement in an antibody-independent manner through the alternative pathway (AP). Properdin is a positive regulator of the AP. This study elucidates how the specificity of cell wall glycan linkages affects AP activation and the role properdin plays in this process. Particulate β1→3 glucans activated the AP even in the absence of properdin, while β1→6 glucans required properdin for AP activation. In contrast, the β1→4 glycans chitin and chitosan failed to activate the AP. These findings enhance our mechanistic understanding of how fungi activate complement and have implications for the use of glycans in biomedical applications.
SEISMIC PHASE UNWRAPPING: METHODS, RESULTS, PROBLEMS<sup>1</sup> (1992)

A bstract Six known methods of seismic phase unwrapping (or phase restoration) are compared. All the methods tested unwrap the phase satisfactorily if the initial function is a simple theoretical wavelet. None of the methods restore the phase of a synthetic trace exactly. An initial validity test of the phase‐unwrapping method is that the sum of the restored wavelet phase spectrum and the restored pulse‐trace phase spectrum (assuming the convolutional model for the seismic trace) must be equal to the restored phase spectrum of the synthetic trace. Results show that none of the tested methods satisfy this test. Quantitative estimation of the phase‐unwrapping accuracy by correlation analysis of the phase deconvolution results separated these methods, according to their efficiency, into three groups. The first group consists of methods using a priori wavelet information. These methods make the wavelet phase estimation more effective than the minimum‐phase approach, if the wavelet is non‐minimum‐phase. The second group consists of methods using the phase increment Δø(Δω) between two adjacent frequencies. These methods help to decrease the time shift of the initial synthetic trace relative to the model of the medium. At the same time they degrade the trace correlation with the medium model. The third group consists of methods using an integration of the phase derivative. These methods do not lead to any improvement of the initial seismic trace. The main problem in the phase unwrapping of a seismic trace is the random character of the pulse trace. For this reason methods based on an analysis of the value of Δø(Δω) only, or using an adaptive approach (i.e. as Δω decreases) are not effective. In addition, methods based on integration of the phase derivative are unreliable, due to errors in numerical integration and differentiation.
Fmoc Methodology: Cleavage from the Resin and Final Deprotection (2010)

This chapter contains sections titled: Introduction “Low” TFA-Labile Resins “High” TFA-Labile Resins Final Remarks References
Repeatability and Reproducibility of Measurements Using a NT-530P Noncontact Tono/Pachymeter and Correlation of Central Corneal Thickness with Intraocular Pressure (2013)

NT-530P offered repeatability and reproducibility in both IOP and CCT measurements. The corrected IOP calculated using the NT-530P was independent of the CCT, suggesting that this IOP may be less influenced by the central corneal thickness.
James M. Barrie's Concept Of Dramatic Action (1962)

IT WOULD DEMAND A THOROUGH EXPLORATION of modem British drama to determine, with any degree of authority, the precise reasons for the descent of J. M. Barrie's star in the dramatic firmament. Time will, of course, facilitate the final judgment, but for present purposes it should be sufficient to suggest that criticism finds his work, for the most part, unsuited to the contemporary palate. Critics remind us that his plays do not bespeak a sense of urgency and, above all, they do not preach. This we know was Barrie's intention. He deliberately avoided "idea" plays for many reasons, one of which was that he felt he could not write them. More important, in order that he might capitalize on the contemporary Victorian reaction to, and even fear of, the rise of scientific and skeptical thought, he wanted to avoid the type of social criticism that crept into the works of Pinero and Jones and made up the bulk of Galsworthy's plays. It would be wrong, though, to think of Barrie as purely Victorian. There is so much that is truly modem in his work along with all of that which is reminiscent of the theater of romance and spectacle that to be quite fair he must be placed on the bridge between the two periods or, more accurately, in his own special category. Barrie was not determined to revolutionize the drama, but the undeniable seriousness that pervades most of his work stands as evidence of his concern for modem man and his problems. It may come as a surprise to some that Shaw himself, perhaps in a rare moment of benevolence, in a letter to J. T. Grein gave Barrie credit for "the relegation of the nineteenth century London theatre to the dust bin."
Synthesis and chemistry of Cp2Zr(Ph)(THF)+. Selectivity of protolytic and oxidative Zr-R bond-cleavage reactions (1991)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTSynthesis and chemistry of Cp2Zr(Ph)(THF)+. Selectivity of protolytic and oxidative Zr-R bond-cleavage reactionsSamuel L. Borkowsky, Richard F. Jordan, and Garry D. HinchCite this: Organometallics 1991, 10, 5, 1268–1274Publication Date (Print):May 1, 1991Publication History Published online1 May 2002Published inissue 1 May 1991https://pubs.acs.org/doi/10.1021/om00051a012https://doi.org/10.1021/om00051a012research-articleACS PublicationsRequest reuse permissionsArticle Views336Altmetric-Citations70LEARN 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-Alertsclose Get e-Alerts
IM waiting (2008)

Responsiveness, or the time until a person responds to communication, can affect the dynamics of a conversation as well as participants' perceptions of one another. In this paper, we present a careful examination of responsiveness to instant messaging communication, showing, for example, that work-fragmentation significantly correlates with faster responsiveness. We show also that the presentation of the incoming communication significantly affects responsiveness (even more so than indicators that the communication was ongoing), suggesting the potential for dynamically influencing responsiveness. This work contributes to a better understanding of computer-mediated communication and to the design of new tools for computer-mediated communication.
Capacity and Cross-Traffic Estimation of All Links in a Path Using ICMP Timestamps (2006)

The estimation of the link capacity and its available bandwidth in an end-to-end path is crucial for network management, admission control and flow control for adaptive applications. This paper introduces an estimation mechanism able to accurately estimate the available bandwidth of all links in an end-to-end path, through its capacity and cross-traffic estimation. The estimation procedures resort to the dispersions of packet pairs and trains using the concepts of ICMP Timestamp and Traceroute that, efficiently used together, enable the measurement of the dispersions in all links in the path. These mechanisms were evaluated through simulation experiments, where we analyzed the influence of the several network parameters on each estimation mechanism. The results show that these estimation methods are able to accurately estimate both the capacity and the cross-traffic of all links in a path with moderate length and with low overhead.
On Refactoring Support Based on Code Clone Dependency Relation (2005)

Generally, code clones are regarded as one of the factors that make software maintenance more difficult. A code clone is a set of source code fragments identical or similar to each other from the viewpoint of software maintainability, code clones should be removed. However, sometimes there are dependency relations among each of which belong to the different code clone, and it is advisable to refactor all of such code clones at once. In this paper, we focus on the case that such code fragment corresponds to a method body in Java programs. We defined "chained method" as a set of methods that have dependency relations. A set of "chained methods" whose elements are each other's code clone is called "chained clone", and an equivalence class of "chained clone" is called a "chained clone set". We propose a refactoring support method for "chained clone set" by providing an appropriate refactoring pattern to them. Finally, we present the "chained clone set" refactoring support tool that we have developed, together with some case studies to show the usefulness of the proposed method
DFT Study on the Stabilities of the Heterofullerenes Sc<sub>3</sub>N@C<sub>67</sub>B, Sc<sub>3</sub>N@C<sub>67</sub>N, and Sc<sub>3</sub>N@C<sub>66</sub>BN (2007)

On the basis of calculations using density functional theory, we investigated the relative stabilities of all isomers of Sc3N@C67B and Sc3N@C67N as well as those of stable isomers of Sc3N@C66BN. As a result, we predict that Sc3N@C68 can be doped substitutionally with a boron atom much better than C60. This effect can be ascribed to the favorable electrostatic attraction between the encased Sc3N cluster and the polar C-B bonds of the fullerene cage, which show the important role played by the encapsulated atoms in stabilizing the fullerene. A difference in the interaction also determines the regiospecificity of Sc3N@C67B. On the contrary, N-doping of the fullerenes forming Sc3N@C67N is much less favorable than that in C60 or C70. A judicious choice of stable isomers of Sc3N@C66BN among a vast number of possible isomers indicates that Sc3N@C68 can also be doped with a pair of B and N atoms better than C60 under the simultaneous existence of B and N sources. Relative stabilities of various isomers of the BN-substituted fullerenes can be understood in terms of the combined electrostatic effects in the B- and N-substitutions of Sc3N@C68 complemented by a specific local preference in the N-substitution and the formation of a B-N bond.
THE FINE STRUCTURE OF THE GALL BLADDER EPITHELIUM OF THE MOUSE (1955)

Sections of mouse gall bladder epithelium fixed by perfusion with buffered osmium tetroxide have been studied in the electron microscope as an example of simple columnar epithelium. The free surface presents many microvilli, each presenting a dense tip, the capitulum, and displaying a radiating corona of delicate filaments, the antennulae microvillares. Very small pit-like depressions, representing caveolae intracellulares, are encountered along the cell membrane of the microvilli. The free cell surface between microvilli shows larger cave-like depressions, likewise representing caveolae intracellulares, containing a dense material. The lateral cell borders are extensively folded into pleats, which do not interdigitate extensively with corresponding folds of the adjacent cell membrane. The terminal bars are shown to consist of thickened densities of the cell membrane itself in the region of insertion of the lateral cell wall with the free cell surface. This thickening is associated with an accumulation of dense cytoplasmic material in the immediate vicinity. The terminal bar is thus largely a cytoplasmic and cell membrane structure, rather than being primarily intercellular in nature. The basal cell membrane is relatively straight except for a conical eminence near the center of the cell, projecting slightly into the underlying tunica propria. The basal cell membrane itself is overlain by a delicate limiting membrane, which does not follow the lateral contours of the cell. Unmyelinated intercellular nerve terminals with synaptic vesicles have been encountered between the lateral walls of epithelial cells. A division of the gall bladder epithelial cell into five zones according to Ferner has been found to be convenient for this study. The following cytoplasmic components have been noted, and their distribution and appearance described: dense absorption granules, mitochondria, Golgi or agranular membranes, endoplasmic reticulum or ergastoplasm, ring figures, and irregular dense bodies, perhaps lipoid in nature. The nucleus of these cells is also described.
Stabilization and modulation of laser oscillators by internal time-varying perturbation (1966)

The paper reviews the application of internal time-varying perturbation to the problem of laser mode control and stabilization. The spectral characteristics and time domain behavior obtained by means of phase type and loss type perturbations are considered. Two techniques which allow the attainment of high single frequency output powers from normally multimode lasers are described. A method for the absolute frequency stabilization of an FM laser is considered, and a brief discussion of an efficient method of internal modulation, termed coupling modulation, is given.
<title>Variable stiffness mechanisms with SMA actuators</title> (1996)

Variable stiffness is a new branch of smart structures development with several applications related to aircraft. Previous research indicates that temporarily reducing the stiffness of an airplane wing can decrease control actuator sizing and improve aeroelastic roll performance. Some smart materials like shape memory alloys (SMA) can change their material stiffness properties, but they tend to gain stiffness in their `power on' state. An alternative is to integrate mechanisms into a structure and change stiffness by altering boundary conditions and structural load paths. An innovative concept for an axial strut mechanism was discovered as part of research into variable stiffness. It employs SMA springs (specifically Ni-Ti) in a way that reduces overall stiffness when the SMA springs gain stiffness. A simplified mathematical model for static analysis was developed, and a 70% reduction in stiffness was obtained for a particular selection of springs. The small force capacity of commercially available SMA springs limits the practicality of this concept for large load applications. However, smart material technology is still immature, and future advances may permit development of a heavy-duty, variable stiffness strut that is small and light enough for use in aircraft structures.
A simplified protocol for differentiation of electrophysiologically mature neuronal networks from human induced pluripotent stem cells (2017)

Progress in elucidating the molecular and cellular pathophysiology of neuropsychiatric disorders has been hindered by the limited availability of living human brain tissue. The emergence of induced pluripotent stem cells (iPSCs) has offered a unique alternative strategy using patient-derived functional neuronal networks. However, methods for reliably generating iPSC-derived neurons with mature electrophysiological characteristics have been difficult to develop. Here, we report a simplified differentiation protocol that yields electrophysiologically mature iPSC-derived cortical lineage neuronal networks without the need for astrocyte co-culture or specialized media. This protocol generates a consistent 60:40 ratio of neurons and astrocytes that arise from a common forebrain neural progenitor. Whole-cell patch-clamp recordings of 114 neurons derived from three independent iPSC lines confirmed their electrophysiological maturity, including resting membrane potential (-58.2±1.0 mV), capacitance (49.1±2.9 pF), action potential (AP) threshold (-50.9±0.5 mV) and AP amplitude (66.5±1.3 mV). Nearly 100% of neurons were capable of firing APs, of which 79% had sustained trains of mature APs with minimal accommodation (peak AP frequency: 11.9±0.5 Hz) and 74% exhibited spontaneous synaptic activity (amplitude, 16.03±0.82 pA; frequency, 1.09±0.17 Hz). We expect this protocol to be of broad applicability for implementing iPSC-based neuronal network models of neuropsychiatric disorders.
Hemoglobin Function and Physiological Adaptation to Hypoxia in High-Altitude Mammals (2007)

Understanding the biochemical mechanisms that enable high-altitude animals to survive and function under conditions of hypoxic stress can provide important insights into the nature of physiological adaptation. Evidence from a number of high-altitude vertebrates indicates that modifications of hemoglobin function typically play a key role in mediating an adaptive response to chronic hypoxia. Because much is known about structure–function relationships of mammalian hemoglobins and their physiological role in oxygen transport, the study of hemoglobin variation in high-altitude mammals holds much promise for understanding the nature of adaptation to hypoxia from the level of blood biochemistry to the level of whole-organism physiology. In this review I 1st discuss basic biochemical principles of hemoglobin function and the nature of physiological adaptation to high-altitude hypoxia in mammals. I then discuss a case study involving a complex hemoglobin polymorphism in North American deer mice (Peromyscus maniculatus) that illustrates how integrative studies of protein function and fitness-related physiological performance can be used to obtain evolutionary insights into genetic mechanisms of adaptation.
The Pupillary Response in Traumatic Brain Injury (2007)

Trarumatic brain injuries (TBIs) affect more than 1.4 million Americans annually. Trauma nurses caring for these patients routinely perform serial neurologic assessments, including pupillary examinations. While trauma nurses are likely familiar with basic components of the pupillary examination, some confusion about more specific aspects of the examination and the physiologic basis of the pupillary response may still remain, particularly as it pertains to patients with TBI. Therefore, the purpose of this article is to identify the key components of a pupillary examination and its associated physiologic response. A case study is provided to illustrate the application of this information among patients with TBI.
1,3,5-Tri-t-butylbenzene and Some Derivatives<sup>1</sup> (1954)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXT1,3,5-Tri-t-butylbenzene and Some Derivatives1Paul D. Bartlett, Max Roha, and R. Martin StilesCite this: J. Am. Chem. Soc. 1954, 76, 9, 2349–2353Publication Date (Print):May 1, 1954Publication History Published online1 May 2002Published inissue 1 May 1954https://pubs.acs.org/doi/10.1021/ja01638a019https://doi.org/10.1021/ja01638a019research-articleACS PublicationsRequest reuse permissionsArticle Views1470Altmetric-Citations70LEARN 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-Alertsclose Get e-Alerts
Practical Application of Pulsed High Pressure Sodium Lamp Technology (1992)

(1992). Practical Application of Pulsed High Pressure Sodium Lamp Technology. Journal of the Illuminating Engineering Society: Vol. 21, No. 1, pp. 60-68.
Intestinal neoplasia in the ApcMin mouse: independence from the microbial and natural killer (beige locus) status. (1997)

We have tested the hypothesis that enteric bacteria are necessary for formation of intestinal adenomas in C57BL/6-ApcMin/+ mouse. Germ-free mice developed 2-fold fewer adenomas than conventional controls in the medial small intestine (7.3 versus 14.9; P < 0.003), but there were no significant differences in the rest of the intestinal tract. We conclude that microbial status does not strongly alter the adenoma phenotype in this mouse model of familial adenomatous polyposis. In parallel, we have found that C57BL/6-ApcMin/+ mice mutated at the beige locus, which controls natural killer activity, are also unaltered in adenoma multiplicity.
"Ramie" (1904)

"Ramie" Get access I. B. B I. B. B Search for other works by this author on: Oxford Academic Google Scholar Notes and Queries, Volume s10-II, Issue 27, 2 July 1904, Page 13, https://doi.org/10.1093/nq/s10-II.27.13c Published: 02 July 1904