gebhart/patrepeval huggingface dataset:
The Human Toll Signaling Pathway: Divergence of Nuclear Factor κB and JNK/SAPK Activation Upstream of Tumor Necrosis Factor Receptor–associated Factor 6 (TRAF6) (1998)

The human homologue of Drosophila Toll (hToll) is a recently cloned receptor of the interleukin 1 receptor (IL-1R) superfamily, and has been implicated in the activation of adaptive immunity. Signaling by hToll is shown to occur through sequential recruitment of the adapter molecule MyD88 and the IL-1R-associated kinase. Tumor necrosis factor receptor-activated factor 6 (TRAF6) and the nuclear factor kappaB (NF-kappaB)-inducing kinase (NIK) are both involved in subsequent steps of NF-kappaB activation. Conversely, a dominant negative version of TRAF6 failed to block hToll-induced activation of stress-activated protein kinase/c-Jun NH2-terminal kinases, thus suggesting an early divergence of the two pathways.
In-line aligned and bottom-up Ag nanorods for surface-enhanced Raman spectroscopy (2006)

We have demonstrated surface-enhanced Raman spectroscopy on arrays of Ag nanorods aligned in line by a dynamic oblique deposition technique. For the light polarized along the major axis of the nanorods, the plasma resonance of the Ag nanorods has been tuned to a wavelength suitable for Raman spectroscopy. The average width and the length-to-width ratio of the resulting nanorods are 56nm and 3.5, respectively, and the nanorods align in line with small gaps of a few 10nm. The Raman scattering for the polarized light along the nanorods is enhanced significantly as compared with that perpendicular to the nanorods. This polarization dependent Raman enhancement is attributed to the local field concentration at the ends of the nanorods. Since the preparation process is physical and completely bottom up, it is robust in its selection of the materials and is useful in providing the surface-enhanced Raman scattering sensors at low cost.
Palmer Amaranth (Amaranthus palmeri) Control in Soybean with Glyphosate and Conventional Herbicide Systems (2010)

Glyphosate typically controls Palmer amaranth very well. However, glyphosate-resistant (GR) biotypes of this weed are present in several southern states, requiring the development of effective alternatives to glyphosate-only management strategies. Field experiments were conducted in seven North Carolina environments to evaluate control of glyphosate-susceptible (GS) and GR Palmer amaranth in narrow-row soybean by glyphosate and conventional herbicide systems. Conventional systems included either pendimethalin or S -metolachlor applied PRE alone or mixed with flumioxazin, fomesafen, or metribuzin plus chlorimuron followed by fomesafen or no herbicide POST. S -metolachlor was more effective at controlling GR and GS Palmer amaranth than pendimethalin; flumioxazin and fomesafen were generally more effective than metribuzin plus chlorimuron. Fomesafen applied POST following PRE herbicides increased Palmer amaranth control and soybean yield compared with PRE-only herbicide systems. Glyphosate alone applied once POST controlled GS Palmer amaranth 97% late in the season. Glyphosate was more effective than fomesafen plus clethodim applied POST. Control of GS Palmer amaranth when treated with pendimethalin or S -metolachlor plus flumioxazin, fomesafen, or metribuzin plus chlorimuron applied PRE followed by fomesafen POST was equivalent to control achieved by glyphosate applied once POST. In fields with GR Palmer amaranth, greater than 80% late-season control was obtained only with systems of pendimethalin or S -metolachlor plus flumioxazin, fomesafen, or metribuzin plus chlorimuron applied PRE followed by fomesafen POST. Systems of pendimethalin or S -metolachlor plus flumioxazin, fomesafen, or metribuzin plus chlorimuron applied PRE without fomesafen POST controlled GR Palmer amaranth less than 30% late in the season. Systems of pendimethalin or S -metolachlor PRE followed by fomesafen POST controlled GR Palmer amaranth less than 60% late in the season.
High aldehyde dehydrogenase and expression of cancer stem cell markers selects for breast cancer cells with enhanced malignant and metastatic ability (2008)

Cancer stem cells (CSCs) have recently been identified in leukaemia and solid tumours; however, the role of CSCs in metastasis remains poorly understood. This dearth of knowledge about CSCs and metastasis is due largely to technical challenges associated with the use of primary human cancer cells in pre-clinical models of metastasis. Therefore, the objective of this study was to develop suitable pre-clinical model systems for studying stem-like cells in breast cancer metastasis, and to test the hypothesis that stem-like cells play a key role in metastatic behaviour. We assessed four different human breast cancer cell lines (MDA-MB-435, MDA-MB-231, MDA-MB-468, MCF-7) for expression of prospective CSC markers CD44/CD24 and CD133, and for functional activity of aldehyde dehydrogenase (ALDH), an enzyme involved in stem cell self-protection. We then used fluorescence-activated cell sorting and functional assays to characterize differences in malignant/metastatic behaviour in vitro (proliferation, colony-forming ability, adhesion, migration, invasion) and in vivo (tumorigenicity and metastasis). Sub-populations of cells demonstrating stem-cell-like characteristics (high expression of CSC markers and/or high ALDH) were identified in all cell lines except MCF-7. When isolated and compared to ALDH(low)CD44(low/-) cells, ALDH(hi)CD44(+)CD24(-) (MDA-MB-231) and ALDH(hi)CD44(+)CD133(+) (MDA-MB-468) cells demonstrated increased growth (P < 0.05), colony formation (P < 0.05), adhesion (P < 0.001), migration (P < 0.001) and invasion (P < 0.001). Furthermore, following tail vein or mammary fat pad injection of NOD/SCID/IL2gamma receptor null mice, ALDH(hi)CD44(+)CD24(-) and ALDH(hi)CD44(+)CD133(+) cells showed enhanced tumorigenicity and metastasis relative to ALDH(low)CD44(low/-) cells (P < 0.05). These novel results suggest that stem-like ALDH(hi)CD44(+)CD24(-) and ALDH(hi)CD44(+)CD133(+) cells may be important mediators of breast cancer metastasis.
Interleukin 3-dependent survival by the Akt protein kinase (1997)

Interleukin 3 (IL-3)-dependent survival of hematopoietic cells is known to rely on the activity of multiple signaling pathways, including a pathway leading to activation of phosphoinositide 3-kinase (PI 3-kinase), and protein kinase Akt is a direct target of PI 3-kinase. We find that Akt kinase activity is rapidly induced by the cytokine IL-3, suggesting a role for Akt in PI 3-kinase-dependent signaling in hematopoetic cells. Dominant-negative mutants of Akt specifically block Akt activation by IL-3 and interfere with IL-3-dependent proliferation. Overexpression of Akt or oncogenic v-akt protects 32D cells from apoptosis induced by IL-3 withdrawal. Apoptosis after IL-3 withdrawal is accelerated by expression of dominant-negative mutants of Akt, indicating that a functional Akt signaling pathway is necessary for cell survival mediated by the cytokine IL-3. Thus Akt appears to be an important mediator of anti-apoptotic signaling in this system.
A decrease of the butyrate-producing species Roseburia hominis and Faecalibacterium prausnitzii defines dysbiosis in patients with ulcerative colitis (2013)

The composition of the fecal microbiota of UC patients differs from that of healthy individuals: we found a reduction in R hominis and F prausnitzii, both well-known butyrate-producing bacteria of the Firmicutes phylum. These results underscore the importance of dysbiosis in IBD but suggest that different bacterial species contribute to the pathogenesis of UC and CD.
Removal of a Protruded Thoracic Disc Using Microsurgical Endoscopy (1994)

The microsurgical endoscopic technique allows spinal cord decompression with a substantial reduction in surgical trauma. It may shorten bed confinement and allow early return to active life. Application of this technique in other areas is being studied.
Are platelets activated after a rapid, one-step density gradient centrifugation? Evidence from flow cytometric analysis (2005)

This procedure describes the preparation of platelets from whole blood of healthy donors and pregnancy-induced hypertensive (PIH) patients by a rapid, one-step density gradient centrifugation, and the direct immunofluorescence staining of obtained platelets (CD63). Platelets are relatively fragile structures. Consequently, for the investigation of their biochemical properties it is recommended to isolate them by a simple method that does not damage their functional parameters and induce their activation. During platelet activation, several changes occur at the platelet surface. CD63 is the receptor for a lysosomal glycoprotein expressed in activated platelets. Currently, flow cytometry (fluorescence-activated cell sorting) is the most sensitive method to detect increased surface exposure of activation antigens on the platelet surface. The present technical note describes that compared with other whole blood flow cytometric techniques, our one-step density-gradient centrifugation method using OptiPrep can also prevent artificial, sample manipulation-related platelet activation.
Virtuoso: Narrowing the Semantic Gap in Virtual Machine Introspection (2011)

Introspection has featured prominently in many recent security solutions, such as virtual machine-based intrusion detection, forensic memory analysis, and low-artifact malware analysis. Widespread adoption of these approaches, however, has been hampered by the semantic gap: in order to extract meaningful information about the current state of a virtual machine, detailed knowledge of the guest operating system's inner workings is required. In this paper, we present a novel approach for automatically creating introspection tools for security applications with minimal human effort. By analyzing dynamic traces of small, in-guest programs that compute the desired introspection information, we can produce new programs that retrieve the same information from outside the guest virtual machine. We demonstrate the efficacy of our techniques by automatically generating 17 programs that retrieve security information across 3 different operating systems, and show that their functionality is unaffected by the compromise of the guest system. Our technique allows introspection tools to be effortlessly generated for multiple platforms, and enables the development of rich introspection-based security applications.
Catalytic H/D Exchange of Unactivated Aliphatic C–H Bonds (2013)

Complex Cp(iPr3P)RuH3 (1) catalyzes H/D exchange between a variety of organic substrates and C6D6 or D2O, including aliphatic groups. Experimental data show the preference in activation of methyl groups versus benzylic positions. Methylene positions react only if the substrate contains a functional group (arene, halogen, O- or N-based groups). DFT calculations were used for the model complex Cp(Me3P)RuH3 (2) to study the mechanism of C–H bond activation.
Global trends of whole-genome duplications revealed by the ciliate Paramecium tetraurelia (2006)

The duplication of entire genomes has long been recognized as having great potential for evolutionary novelties, but the mechanisms underlying their resolution through gene loss are poorly understood. Here we show that in the unicellular eukaryote Paramecium tetraurelia, a ciliate, most of the nearly 40,000 genes arose through at least three successive whole-genome duplications. Phylogenetic analysis indicates that the most recent duplication coincides with an explosion of speciation events that gave rise to the P. aurelia complex of 15 sibling species. We observed that gene loss occurs over a long timescale, not as an initial massive event. Genes from the same metabolic pathway or protein complex have common patterns of gene loss, and highly expressed genes are over-retained after all duplications. The conclusion of this analysis is that many genes are maintained after whole-genome duplication not because of functional innovation but because of gene dosage constraints.
The IGF‐II receptor system: A G protein‐linked mechanism (1993)

Based on the finding that stimulation of the IGF-II receptor (IGF-IIR) is capable of activating Gi2 and calcium channels in BALB/c 3T3 fibroblasts, it was found that purified IGF-IIR can couple directly to purified Gi2 in phospholipid vesicles. IGF-IIR-Gi2 coupling can be characterized as follows. IGF-IIR directly couples to Gi2 in response to IGF-II in a stoichiometrical manner, suggesting that IGF-IIR works as a transmembrane signaling molecule and that the seven-transmembrane structure is not essential for receptor-G protein coupling. The mode of IGF-IIR-G12 interaction is similar to that of conventional receptor-G protein coupling, suggesting that a common G protein recognition mechanism is shared by IGF-IIR and conventional G-coupled receptors. The action of IGF-IIR is specific on Gi2 among various G proteins. Finally, the activity of IGF-IIR on Gi2 is similarly potent across the species of the proteins. These characteristics led to the discovery of a 14-amino-acid region in IGF-IIR that can directly interact with and activate Gi2, and is located at residues 2410-2423 of the human receptor. Subsequent work has indicated that this region is responsible for Gi-coupling function of intact IGF-IIR. The most important extensions of this discovery are the following: (1) The structure-function relationship for the Gi-activating function of this 14-amino-acid sequence, (2) the prediction of G protein-coupled functions of receptors based on the results obtained from 1), and (3) clarification of the detailed mechanism whereby ligand-receptor complex recognizes G proteins. This paper reviews what we have learned from IGF-IIR in terms of receptor-G protein interfaces and discusses future prospects.
802.11 WLANs and IP Networking: Security, QoS, and Mobility (2005)

Preface. Acknowledgement. Introduction. Market and Business Case. IEEE 802.11 Current Status. Security. QoS. Mobility. WLAN Deployment and Integration with GPRS and UMTS. Future: Beyond 3G/4G. Abbreviations, Glossary and Index.
Substituent Effects in Photochromic Nitrobenzylpyridines (1966)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTSubstituent Effects in Photochromic NitrobenzylpyridinesJulius Weinstein, Aaron L. Bluhm, and John A. SousaCite this: J. Org. Chem. 1966, 31, 6, 1983–1985Publication Date (Print):June 1, 1966Publication History Published online1 May 2002Published inissue 1 June 1966https://pubs.acs.org/doi/10.1021/jo01344a514https://doi.org/10.1021/jo01344a514research-articleACS PublicationsRequest reuse permissionsArticle Views82Altmetric-Citations12LEARN 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
Design Exposition with Literate Visualization (2018)

We propose a new approach to the visualization design and communication process, literate visualization, based upon and extending, Donald Knuth's idea of literate programming. It integrates the process of writing data visualization code with description of the design choices that led to the implementation (design exposition). We develop a model of design exposition characterised by four visualization designer architypes: the evaluator, the autonomist, the didacticist and the rationalist. The model is used to justify the key characteristics of literate visualization: 'notebook' documents that integrate live coding input, rendered output and textual narrative; low cost of authoring textual narrative; guidelines to encourage structured visualization design and its documentation. We propose narrative schemas for structuring and validating a wide range of visualization design approaches and models, and branching narratives for capturing alternative designs and design views. We describe a new open source literate visualization environment, litvis, based on a declarative interface to Vega and Vega-Lite through the functional programming language Elm combined with markdown for formatted narrative. We informally assess the approach, its implementation and potential by considering three examples spanning a range of design abstractions: new visualization idioms; validation though visualization algebra; and feminist data visualization. We argue that the rich documentation of the design process provided by literate visualization offers the potential to improve the validity of visualization design and so benefit both academic visualization and visualization practice.
Musicality and the intrinsic motive pulse: evidence from human psychobiology and infant communication (1999)

Musicality in human motives, the psycho-biological source of music, is described as a talent inherent in the unique way human beings move, and hence experience their world, their bodies and one another. It originates in the brain images of moving and feeling that generate and guide behaviour in time, with goal-defining purposefulness and creativity. Intelligent perception, cognition and learning, and the potentiality for immediate sympathy between humans for expressions of intrinsic motives in narrative form (linguistic and non-linguistic), depend on this spontaneous, self-regulating brain activity. It is proposed that evolution of human bipedal locomotion and the pressure of social intelligence set free a new polyrhythmia of motive processes, and that these generate fugal complexes of the Intrinsic Motive Pulse (IMP), with radical consequences for human imagination, thinking, remembering and communicating. Gestural mimesis and rhythmic narrative expression of purposes and images of awareness, regulated by, and regulating, dynamic emotional processes, form the foundations of human intersubjectivity, and of musicality. Acquired musical skill and the conventions of musical culture are animated from this core process in the human mind. Research on the dynamics of protoconversations and musical games with infants elucidates the rhythmic and prosodic foundations of sympathetic engagement in expressive exchanges. Developments in the first year prove the importance of the impulses of natural musicality in the emergence of cooperative awareness, and show how shared participation in the expressive phrases and emotional transformations of vocal games can facilitate not only imitation of speech, but interest in all shared meanings, or conventional uses, of objects and actions. Disturbances of early communication attributable to emotional unavailability of a depressed mother, or those due to sensory, motor or emotional handicap that causes a child to fail to react in an expected normal way, both confirm the crucial function in the development of intelligence and personality of sympathetic motives shared between adult and child in a secure and affectionate relationship, and offer a way of promoting development by supporting these motives. These facts establish that the parameters of musicality are intrinsically determined in the brain, or innate, and necessary for human development. Through their effects in emotional integration and the collaborative learning that leads to mastery of cultural knowledge, cultural skills, and language, they express the essential generator of human cognitive development.
Human Kallikrein 14 (Klk14) Expression in Salivary Gland Tumors (2010)

The differences in the levels of KLK14 suggest that KLKs may aid in the differential diagnosis of salivary gland tumors. The coexpression of KLKs suggests their possible involvement in an enzymatic pathway activated in salivary gland. KLK14 may be a promising new biomarker in salivary gland tumors.
Phenols from Lignin (2008)

Abstract Lignin accounts for approximately 25–35 % of the organic matrix of wood and lignocellulosic biomass in itself is the most abundant renewable material on the planet. It has long been recognized as a potential feedstock for producing chemicals, fuels, and materials. Despite this excellent availabilty of lignin it is a low value compound and has so far mainly been used as energy source in combustion applications. Less than 5 % are being processed for other purposes. This article discusses the potential for an increased use of lignin as a renewable raw material, possible conversion routes towards monomeric phenolic compounds, and applications for these products. A brief overview about present state‐of‐the‐art is given and a high‐yielding, one‐step approach of producing alkylated phenolic compounds from lignin is presented.
The flavonoid naringenin stimulates the intercellular colonization of wheat roots by Azorhizobium caulinodans (1998)

We have studied intercellular colonization of wheat roots by Azorhizobium caulinodans and other diazotrophic bacteria, using strains marked with the lacZ reporter gene to facilitate their detection and identification. A. caulinodans was observed by light and electron microscopy to enter the roots of wheat at high frequency at the points of emergence of lateral roots (lateral root cracks). After lateral root crack colonization, bacteria moved into intercellular spaces within the cortical cell layer of roots. The flavonoid naringenin at 10 and 100 mmol m –3 significantly stimulated root colonization. The roles of the structural nodABC genes and the regulatory nodD gene were also studied; lateral root crack colonization of wheat was shown to be Nod factor‐ and NodD‐independent. Similar frequencies of lateral root crack colonization were observed following inoculation of wheat with Azospirillum brasilense. Colonization by A. brasilense was stimulated by naringenin and also by other flavonoid molecules.
A Novel Virtual Metrology Scheme for Predicting CVD Thickness in Semiconductor Manufacturing (2007)

In an advanced semiconductor fab, online quality monitoring of wafers is required for maintaining high stability and yield of production equipment. The current practice of only measuring monitor wafers may not be able to timely detect the equipment-performance drift happening in-between the scheduled measurements. This may cause defects of production wafers and, thereby, raise the production cost. In this paper, a novel virtual metrology scheme (VMS) is proposed for overcoming this problem. The proposed VMS is capable of predicting the quality of each production wafer using parameters data from production equipment. Consequently, equipment-performance drift can be detected promptly. A radial basis function neural network is adopted to construct the virtual metrology model. Also, a model parameter coordinator is developed to effectively increase the prediction accuracy of the VMS. The chemical vapor deposition (CVD) process in semiconductor manufacturing is used to test and verify the effectiveness of the proposed VMS. Test results show that the proposed VMS demonstrates several advantages over the one based on back-propagation neural network and can achieve high prediction accuracy with mean absolute percentage error being 0.34% and maximum error being 1.15%. The proposed VMS is simple yet effective, and can be practically applied to construct the prediction models of semiconductor CVD processes.