gebhart/patrepeval huggingface dataset:
Sequence Analysis Reveals Homology between Two Proteins of the Flagellar Radial Spoke (1992)

Flagellar radial spokes contribute to the regulation of dynein arm activity and thus the pattern of flagellar bending. We have sequenced the genes for radial spoke protein 4 (RSP4) and RSP6, two of the five proteins that make up the radial spoke head in Chlamydomonas reinhardtii. The two genes, which are tightly linked genetically (B. Huang, G. Piperno, Z. Ramanis, and D.J.L. Luck, J. Cell Biol. 88:80-88, 1981), are separated by only 435 bp. They encode proline-rich polypeptides of 49.8 kDa (RSP4) and 48.8 kDa (RSP6), which are 48% identical to each other but do not resemble any previously sequenced proteins. The transcription start sites of these genes and an additional radial spoke protein gene, that for RSP3, were determined, and patterns of mRNA accumulation during flagellar regeneration were examined for the three radial spoke protein genes. These studies provide the molecular tools for a detailed analysis of radial spoke head function and assembly and for a determination of the mechanism by which the genes required to build a complex organelle are regulated.
Activation of the Axl receptor tyrosine kinase induces mitogenesis and transformation in 32D cells. (1994)

axl is a transforming receptor tyrosine kinase isolated from DNA of patients with chronic myelogenous leukemia. Association of axl expression with myelogenous leukemias and its expression in primitive hematopoietic cells suggests a role for axl in myeloid biology. To study the cellular function of axl, we constructed a chimeric receptor tyrosine kinase composed of the extracellular and transmembrane domains of the EGF receptor and the cytoplasmic domain of axl; this chimera was named EAK for EGFR-Axl-Kinase. The EAK chimeric receptor was expressed in the mouse myeloid progenitor cell line 32D, which is dependent on interleukin 3 (IL-3) for proliferation and survival. Treatment of the 32D-EAK cells with EGF stimulated the tyrosine phosphorylation of the axl kinase domain and enabled proliferation through EGF rather than IL-3. Thus, axl can effectively couple with mitogenic signaling pathways intrinsic to 32D myeloid cells. Assay of proteins phosphorylated in response to different cytokine treatments showed that IL-3 and EGF exposure produced unique profiles in the 32D-EAK cells. Furthermore, Jak-2 is phosphorylated only in response to IL-3 treatment in these cells. This suggests that IL-3 receptor and axl transduce mitogenic signals through separate pathways. In addition, exposure of cells expressing the chimeric receptor to EGF for 19 days converted the cells to factor-independent growth, a phenomenon not seen with other receptor tyrosine kinases. Generation of this transformed phenotype is absolutely dependent on axl activation by foster ligand. The tyrosine phosphorylation level of the axl kinase domain in the factor-independent subclones is 40-fold greater than the factor-dependent cells. The association of a unique axl phosphorylation level with the factor-independent phenotype suggests that there is a threshold phosphorylation level of the axl kinase for transformation. The fact that activation of the axl receptor leads to transformation of 32D cells suggests that axl can play a role in leukemic conversion of myeloid cells, either through inappropriate expression or improper activation.
OMNICONF - Make OS Upgrade and Disk Crash Recovery Easier (1994)

OS upgrades are a headache because after installing a new OS, many files and directories need to be modified or created by hand, to restore the host's previous (pre-upgrade) configuration.

On the other hand, saving entire / and /usr file systems for crash recovery is redundant because most files are unchanged, and copies exist on distribution media. In addition, restoring from backups after a disk crash is not as easy as an OS installation from distribution media because OS installation software does not necessarily include utilities to aid in doing so.

Difficulties in performing OS upgrades and disk crash recoveries are dramatically reduced if a complete set of (a set of changes is called a in this paper) which have occurred throughout / and /usr can be observed and saved. Change means: 1) addition and deletion of files and directories; 2) modification of the content and status of files and directories. Dealing with changes is non- trivial because conventional commands such as tar, cpio, and dump cannot handle deletion and cannot alter the permissions of a file without restoring its contents.

If can be stored under a single directory, OS upgrades become easier because the configuration can be restored by a simple operation after the upgrade. Instead of saving all files in / and /usr, one only needs to save changes to those file systems. One can easily perceive what the entire configuration is and modify merely a part of it.

In this paper, the author introduces a tool called OMNICONF, which stores and restores configurations to and from a specified directory. OMNICONF is implemented in 2400 lines of Perl[1] code, under the concept shown above.
Toxicity and Feeding Deterrency of a Dihaloalkyl Arylsulfone Biocide, A-9248, Against the Formosan Subterranean Termite (Isoptera: Rhinotermitidae) (1988)

Journal Article Toxicity and Feeding Deterrency of a Dihaloalkyl Arylsulfone Biocide, A-9248, Against the Formosan Subterranean Termite (Isoptera: Rhinotermitidae) Get access Nan-Yao Su, Nan-Yao Su Ft. Lauderdale Research and Education Center, University of Florida, Institute of Food and Agricultural Sciences, Ft. Lauderdale, Florida 33314 Search for other works by this author on: Oxford Academic PubMed Google Scholar Rudolf H. Scheffrahn Rudolf H. Scheffrahn Ft. Lauderdale Research and Education Center, University of Florida, Institute of Food and Agricultural Sciences, Ft. Lauderdale, Florida 33314 Search for other works by this author on: Oxford Academic PubMed Google Scholar Journal of Economic Entomology, Volume 81, Issue 3, 1 June 1988, Pages 850–854, https://doi.org/10.1093/jee/81.3.850 Published: 01 June 1988 Article history Received: 16 January 1987 Accepted: 25 November 1987 Published: 01 June 1988
A Tissue Engineering Approach to Progenitor Cell Delivery Results in Significant Cell Engraftment and Improved Myocardial Remodeling (2007)

Cell replacement therapy has become an attractive solution for myocardial repair. Typical cell delivery techniques, however, suffer from poor cell engraftment and inhomogeneous cell distributions. Therefore, we assessed the hypothesis that an epicardially applied, tissue-engineered cardiac patch containing progenitor cells would result in enhanced exogenous cell engraftment. Human mesenchymal stem cells (hMSCs) were embedded into a rat tail type I collagen matrix to form the cardiac patch. Myocardial infarction was induced by left anterior descending coronary artery ligation in immunocompetent male cesarean-derived fischer rats, and patches with or without cells were secured to hearts with fibrin sealant. After patch formation, hMSCs retained a viability of >90% over 5 days in culture. In addition, >75% of hMSCs maintained a high degree of potency prior to patch implantation. After 4 days in culture, patches were applied to the epicardial surface of the infarct area and resulted in 23% +/- 4% engraftment of hMSCs at 1 week (n = 6). Patch application resulted in a reduction in left ventricle interior diameter at systole, increased anterior wall thickness, and a 30% increase in fractional shortening. Despite this improvement in myocardial remodeling, hMSCs were not detectable at 4 weeks after patch application, implying that improvement did not require long-term cell engraftment. Patches devoid of progenitor cells showed no improvement in remodeling. In conclusion, pluripotent hMSCs can be efficiently delivered to a site of myocardial injury using an epicardial cardiac patch, and such delivery results in improved myocardial remodeling after infarction. Disclosure of potential conflicts of interest is found at the end of this article.
Experimental assessment of the efficacy of sensitised emission in water from a europium ion, following intramolecular excitation by a phenanthridinyl group (2000)

The overall quantum yields for phenanthridinium sensitised emission from a europium ion have been measured in H2O and D2O for a series of five structurally related, octadentate ligands in which the distance from the phenanthridinium chromophore to the Eu ion varies from 2.5 to ca. 8.2 Å. Overall quantum yields (pD⩽2) range from 0.25 to 0.012 suggesting that the experimental distance for 50% efficiency of intramolecular energy transfer lies close to 5.5 Å for this system.
Mode of Action, Localization of Production, Chemical Nature, and Activity of Sorgoleone: A Potent PSII Inhibitor in Sorghum spp. Root Exudates1 (2001)

The root exudates produced by sorghums contain a biologically active constituent known as sorgoleone. Seven sorghum accessions were evaluated for their exudate components. Except for johnsongrass, which yielded 14.8 mg root exudate/g fresh root wt, sorghum accessions consistently yielded approximately 2 mg root exudate/g fresh root wt. Exudates contained four to six major components, with sorgoleone being the major component (> 85%). Three-dimensional structure analysis was performed to further characterize sorgoleone's mode of action. These studies indicated that sorgoleone required about half the amount of free energy (493.8 kcal/mol) compared to plastoquinone (895.3 kcal/mol) to dock into the QB-binding site of the photosystem II complex of higher plants. Light, cryo-scanning, and transmission electron microscopy were utilized in an attempt to identify the cellular location of root exudate production. From the ultrastructure analysis, it is clear that exudate is being produced in the root hairs and being deposited between the plasmalemma and cell wall. The exact manufacturing and transport mechanism of the root exudate is still unclear. Studies were also conducted on sorgoleone's soil persistence and soil activity. Soil impregnated with sorgoleone had activity against a number of plant species. Recovery rates of sorgoleone-impregnated soil ranged from 85% after 1 h to 45% after 24 h. Growth reduction of 9 14-d-old weed species was observed with foliar applications of sorgoleone.Nomenclature: Sorgoleone (2-hydroxy-5-methoxy-3-[(8′Z,11′Z)-8′,11′,14′-pentadecatriene]-p-hydroquinone); common purslane, Portulaca oleracea L. POROL; common ragweed, Ambrosia artemisiifolia L. AMBEL; cress, Lepidium sativum L. ;ns3 LEPSA; giant foxtail, Setaria faberi Herrm. SETFA; johnsongrass, Sorghum halepense (L.) Pers. SORHA; lambsquarters, Chenopodium album L. CHEAL; large crabgrass, Digitaria sanguinalis (L.) Scop. DIGSA; lettuce, Lactuca sativa L.; nightshade, Solanum spp.; purple photosynthetic bacterium, Rhodopseudomonas viridis; redroot pigweed, Amaranthus retroflexus L. AMARE; sicklepod, Cassia obtusifolia L. CASOB; spinach, Spinacea oleracea; shattercane, Sorghum bicolor (L.) Moensch SORVU; sorghum, S. bicolor (L.) Moensch SORVU; sudex, S. bicolor × Sorghum sudanense; sweet sorghum, S. bicolor ‘Della’; SX-15 and SX-17, S. bicolor × S. sudanense; 8446 and 855-F, S. bicolor (L.) Moensch SORVU; tomato, Lycopersicon esculentum L.; velvetleaf, Abutilon theophrasti Medicus ABUTH.Additional index words: Sorgoleone, root hairs, SORVU, SORHA.Abbreviations: ER, endoplasmic reticulum; HPLC, high-pressure liquid chromatography; PSII, photosystem II; QB, quinone binding; SEM, scanning electron microscopy; TEM, transmission electron microscopy; TLC, thin-layer chromatography; 3D, three dimensional; UV, ultraviolet.
Effect of Framework Charge Density on Catalytic Activity of Copper Loaded Molecular Sieves of Chabazite Structure in Nitrogen(II) Oxide Decomposition (2000)

NO decomposition over Cu-loaded molecular sieves of chabazite structure with different framework negative charge density was investigated. Cu-ZnAlPO-34 with framework charge density (Al + P)/Zn = 15 exhibited high and stable catalytic activity in NO decomposition while Cu-chabazite with Si/Al = 2.7 was inactive. This evidences that the number of aluminum atoms balancing Cu ions in cationic sites controls the catalytic activity of Cu ion. Ions balanced by single framework aluminum atoms exhibit high activity in NO decomposition while ions balanced by two framework aluminum atoms are inactive. Topology of cationic sites is not the limiting parameter for NO decomposition over Cu ions located in molecular sieves.
The effects of febuxostat on the pharmacokinetic parameters of rosiglitazone, a CYP2C8 substrate (2012)

Co-administration of febuxostat had no effect on rosiglitazone or N-desmethylrosiglitazone PK parameters, suggesting that febuxostat can be given safely with drugs metabolized through CYP2C8.
A Rapid Method for Inoculating Soybean Seedlings withHeterodera glycines (1991)

A mouth-pipetting method and a newly described method of inoculation of soybean (Glycine max) seedlings with resistance to the soybean cyst nematode (SCN) Heterodera glycines race 3 were evaluated. Neither method resulted in a change for the index of parasitism in soybean genotypes Peking, Pickett-71, PI 90763, or PI 88788. The auto-dispenser method resulted in a narrow range of cysts (160-184 per plant) produced on the susceptible cultivar Essex and gave a lower standard of deviation than the mouth-pipetting method. The new method is approximately 18 times faster than the mouth-pipetting method and requires only a single individual to conduct the inoculation (...)
Cell-Specific Integration of Artificial Organelles Based on Functionalized Polymer Vesicles (2008)

Cell organelles are subcellular structures characterized by specific functionalities. They often consist of membrane-delineated microcompartments with a unique set of enzymes. Here we report the design of synthetic organelles based on nanometer-sized polymer vesicles, show their introduction into cells in a target-specific fashion, document their intact biochemical functionality in the cellular environment, and study their intracellular trafficking. This novel paradigm of introducing polymer-based artificial organelles to specific target cells for expansion of their biochemical capabilities appears suited for biomedical applications such as enzyme replacement in genetic diseases or, more generically, to add a desired biochemical function to a cell.
CMOS APS imager employing 3.3 V 12 bit 6.3 MS/s pipelined ADC (2004)

A novel 256/spl times/256 CMOS active pixel sensor (APS) system with 12 bit, 6.3 Msample/s (MS/s) CMOS pipelined analog to digital converter (ADC) integrated on chip is presented. The test chip has been implemented in 0.35 /spl mu/m 2P4M process, operated by a 3.3 V supply and is expected to dissipate 55 mW. The total area of the prototype is 12 mm/sup 2/, and the core area of ADC is 18% from the total area. System architecture and operation are discussed and simulation results are presented.
Refined Synthesis of 5-Substituted Dipyrromethanes (1999)

ADVERTISEMENT RETURN TO ISSUEPREVNoteNEXTRefined Synthesis of 5-Substituted DipyrromethanesBenjamin J. Littler, Mark A. Miller, Chen-Hsiung Hung, Richard W. Wagner, Donal F. O'Shea, Paul D. Boyle, and Jonathan S. LindseyView Author Information Department of Chemistry, North Carolina State University, Raleigh, North Carolina 27695-8204 Cite this: J. Org. Chem. 1999, 64, 4, 1391–1396Publication Date (Web):January 27, 1999Publication History Received6 October 1998Published online27 January 1999Published inissue 1 February 1999https://doi.org/10.1021/jo982015+Copyright © 1999 American Chemical SocietyRIGHTS & PERMISSIONSArticle Views14111Altmetric-Citations364LEARN 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 Read OnlinePDF (85 KB) Get e-AlertsSupporting Info (1)»Supporting Information Supporting Information SUBJECTS:Chromatography,Condensation,Distillation,Purification,Pyrroles Get e-Alerts
Coating Optimization of Superparamagnetic Iron Oxide Nanoparticles for High T2 Relaxivity (2010)

We describe a new method for coating superparamagnetic iron oxide nanoparticles (SPIOs) and demonstrate that, by fine-tuning the core size and PEG coating of SPIOs, the T2 relaxivity per particle can be increased by >200-fold. With 14 nm core and PEG1000 coating, SPIOs can have T2 relaxivity of 385 s-1 mM-1, which is among the highest per-Fe atom relaxivities. In vivo tumor imaging results demonstrated the potential of the SPIOs for clinical applications.
Three-dimensional Optical-resolution Photoacoustic Microscopy (2011)

Optical microscopy, providing valuable insights at the cellular and organelle levels, has been widely recognized as an enabling biomedical technology. As the mainstays of in vivo three-dimensional (3-D) optical microscopy, single-/multi-photon fluorescence microscopy and optical coherence tomography (OCT) have demonstrated their extraordinary sensitivities to fluorescence and optical scattering contrasts, respectively. However, the optical absorption contrast of biological tissues, which encodes essential physiological/pathological information, has not yet been assessable. The emergence of biomedical photoacoustics has led to a new branch of optical microscopy optical-resolution photoacoustic microscopy (OR-PAM), where the optical irradiation is focused to the diffraction limit to achieve cellular or even subcellular level lateral resolution. As a valuable complement to existing optical microscopy technologies, OR-PAM brings in at least two novelties. First and most importantly, OR-PAM detects optical absorption contrasts with extraordinary sensitivity (i.e., 100%). Combining OR-PAM with fluorescence microscopy or with optical-scattering-based OCT (or with both) provides comprehensive optical properties of biological tissues. Second, OR-PAM encodes optical absorption into acoustic waves, in contrast to the pure optical processes in fluorescence microscopy and OCT, and provides background-free detection. The acoustic detection in OR-PAM mitigates the impacts of optical scattering on signal degradation and naturally eliminates possible interferences (i.e., crosstalks) between excitation and detection, which is a common problem in fluorescence microscopy due to the overlap between the excitation and fluorescence spectra. Unique for optical absorption imaging, OR-PAM has demonstrated broad biomedical applications since its invention, including, but not limited to, neurology, ophthalmology, vascular biology, and dermatology. In this video, we teach the system configuration and alignment of OR-PAM as well as the experimental procedures for in vivo functional microvascular imaging.
Quantitative Raman characterization of cross-linked collagen thin films as a model system for diagnosing early osteoarthritis (2016)

The onset of osteoarthritis (OA)in articular cartilage is characterized by degradation of extracellular matrix (ECM). Specifically, breakage of cross-links between collagen fibrils in the articular cartilage leads to loss of structural integrity of the bulk tissue. Since there are no broadly accepted, non-invasive, label-free tools for diagnosing OA at its early stage, Raman spectroscopyis therefore proposed in this work as a novel, non-destructive diagnostic tool. In this study, collagen thin films were employed to act as a simplified model system of the cartilage collagen extracellular matrix. Cross-link formation was controlled via exposure to glutaraldehyde (GA), by varying exposure time and concentration levels, and Raman spectral information was collected to quantitatively characterize the cross-link assignments imparted to the collagen thin films during treatment. A novel, quantitative method was developed to analyze the Raman signal obtained from collagen thin films. Segments of Raman signal were decomposed and modeled as the sum of individual bands, providing an optimization function for subsequent curve fitting against experimental findings. Relative changes in the concentration of the GA-induced pyridinium cross-links were extracted from the model, as a function of the exposure to GA. Spatially resolved characterization enabled construction of spectral maps of the collagen thin films, which provided detailed information about the variation of cross-link formation at various locations on the specimen. Results showed that Raman spectral data correlate with glutaraldehyde treatment and therefore may be used as a proxy by which to measure loss of collagen cross-links in vivo. This study proposes a promising system of identifying onset of OA and may enable early intervention treatments that may serve to slow or prevent osteoarthritis progression.
Object Instance Detection and Dynamics Modeling in a Long-Term Mobile Robot Context (2017)

In the last years, simple service robots such as autonomous vacuum cleaners and lawn mowers have become commercially available and increasingly common. The next generation of service robots should perform more advanced tasks, such as to clean up objects. Robots then need to learn to robustly navigate, and manipulate, cluttered environments, such as an untidy living room. In this thesis, we focus on representations for tasks such as general cleaning and fetching of objects. We discuss requirements for these specific tasks, and argue that solving them would be generally useful, because of their object-centric nature. We rely on two fundamental insights in our approach to understand environments on a fine-grained level. First, many of today's robot map representations are limited to the spatial domain, and ignore that there is a time axis that constrains how much an environment may change during a given period. We argue that it is of critical importance to also consider the temporal domain. By studying the motion of individual objects, we can enable tasks such as general cleaning and object fetching. The second insight comes from that mobile robots are becoming more robust. They can therefore collect large amounts of data from those environments. With more data, unsupervised learning of models becomes feasible, allowing the robot to adapt to changes in the environment, and to scenarios that the designer could not foresee. We view these capabilities as vital for robots to become truly autonomous. The combination of unsupervised learning and dynamics modelling creates an interesting symbiosis: the dynamics vary between different environments and between the objects in one environment, and learning can capture these variations. A major difficulty when modeling environment dynamics is that the whole environment can not be observed at one time, since the robot is moving between different places. We demonstrate how this can be dealt with in a principled manner, by modeling several modes of object movement. We also demonstrate methods for detection and learning of objects and structures in the static parts of the maps. Using the complete system, we can represent and learn many aspects of the full environment. In real-world experiments, we demonstrate that our system can keep track of varied objects in large and highly dynamic environments.​