gebhart/patrepeval huggingface dataset:
The F-box subunit of the SCF E3 complex is encoded by a diverse superfamily of genes in <i>Arabidopsis</i> (2002)

The covalent attachment of ubiquitin is an important determinant for selective protein degradation by the 26S proteasome in plants and animals. The specificity of ubiquitination is often controlled by ubiquitin-protein ligases (or E3s), which facilitate the transfer of ubiquitin to appropriate targets. One ligase type, the SCF E3s are composed of four proteins, cullin1/Cdc53, Rbx1/Roc1/Hrt1, Skp1, and an F-box protein. The F-box protein, which identifies the targets, binds to the Skp1 component of the complex through a degenerate N-terminal approximately 60-aa motif called the F-box. Using published F-boxes as queries, we have identified 694 potential F-box genes in Arabidopsis, making this gene superfamily one of the largest currently known in plants. Most of the encoded proteins contain interaction domains C-terminal to the F-box that presumably participate in substrate recognition. The F-box proteins can be classified via a phylogenetic approach into five major families, which can be further organized into multiple subfamilies. Sequence diversity within the subfamilies suggests that many F-box proteins have distinct functions and/or substrates. Representatives of all of the major families interact in yeast two-hybrid experiments with members of the Arabidopsis Skp family supporting their classification as F-box proteins. For some, a limited preference for Skps was observed, suggesting that a hierarchical organization of SCF complexes exists defined by distinct Skp/F-box protein pairs. Collectively, the data shows that Arabidopsis has exploited the SCF complex and the ubiquitin/26S proteasome pathway as a major route for cellular regulation and that a diverse array of SCF targets is likely present in plants.
Sensitivity of time‐lapse seismic to reservoir stress path (2006)

ABSTRACT The change in reservoir pore pressure due to the production of hydrocarbons leads to anisotropic changes in the stress field acting on the reservoir. Reservoir stress path is defined as the ratio of the change in effective horizontal stress to the change in effective vertical stress from the initial reservoir conditions, and strongly influences the depletion‐induced compaction behaviour of the reservoir. Seismic velocities in sandstones vary with stress due to the presence of stress‐sensitive regions within the rock, such as grain boundaries, microcracks, fractures, etc. Since the response of any microcracks and grain boundaries to a change in stress depends on their orientation relative to the principal stress axes, elastic‐wave velocities are sensitive to reservoir stress path. The vertical P‐ and S‐wave velocities, the small‐offset P‐ and SV‐wave normal‐moveout (NMO) velocities, and the P‐wave amplitude‐versus‐offset (AVO) are sensitive to different combinations of vertical and horizontal stress. The relationships between these quantities and the change in stress can be calibrated using a repeat seismic, sonic log, checkshot or vertical seismic profile (VSP) at the location of a well at which the change in reservoir pressure has been measured. Alternatively, the variation of velocity with azimuth and distance from the borehole, obtained by dipole radial profiling, can be used. Having calibrated these relationships, the theory allows the reservoir stress path to be monitored using time‐lapse seismic by combining changes in the vertical P‐wave impedance, changes in the P‐wave NMO and AVO behaviour, and changes in the S‐wave impedance.
Hedgehog Signaling in Development and Homeostasis of the Gastrointestinal Tract (2007)

The Hedgehog family of secreted morphogenetic proteins acts through a complex evolutionary conserved signaling pathway to regulate patterning events during development and in the adult organism. In this review I discuss the role of Hedgehog signaling in the development, postnatal maintenance, and carcinogenesis of the gastrointestinal tract. Three mammalian hedgehog genes, sonic hedgehog (Shh), indian hedgehog (Ihh), and desert hedgehog (Dhh) have been identified. Shh and Ihh are important endodermal signals in the endodermal-mesodermal cross-talk that patterns the developing gut tube along different axes. Mutations in Shh, Ihh, and downstream signaling molecules lead to a variety of gross malformations of the murine gastrointestinal tract including esophageal atresia, tracheoesophageal fistula, annular pancreas, midgut malrotation, and duodenal and anal atresia. These congenital malformations are also found in varying constellations in humans, suggesting a possible role for defective Hedgehog signaling in these patients. In the adult, Hedgehog signaling regulates homeostasis in several endoderm-derived epithelia, for example, the stomach, intestine, and pancreas. Finally, growth of carcinomas of the proximal gastrointestinal tract such as esophageal, gastric, biliary duct, and pancreatic cancers may depend on Hedgehog signaling offering a potential avenue for novel therapy for these aggressive cancers.
Optimization of Face Cone Element for Spiral Bevel and Hypoid Gears (2011)

In the blank design of spiral bevel and hypoid gears, the face cone is defined as an imaginary cone tangent to the tops of the teeth. Traditionally, the face cone element or generatrix is a straight line. On the other hand, the tooth root lines which are traced by the blade tips are normally not straight lines. As a result, the tooth top geometry generally does not fit the mating member’s real root shape, providing an uneven tooth root-tip clearance; additionally, in some cases root-tip interference between the tooth tip and the root tooth surfaces of the mating gear members may be observed. To address this issue, this paper describes a method of determining an optimized face cone element for spiral bevel and hypoid gears. The method is based on the incorporation of calculation of tooth surface and root geometries, the conjugate relationship of the mating gear members, the ease-off topography, and the tooth contact analysis. The resulting face cone element may not be a straight line but generally an optimized curve that, in addition to avoidance of the interference, offers maximized contact ratio and even tooth root-tip clearance. Manufacturing of bevel gear blanks with a curved face cone element can be implemented by using computer numerically controlled (CNC) machines.
Immunosuppressive Effects of Multiple Myeloma Are Overcome by PD-L1 Blockade (2011)

Multiple myeloma is an incurable plasma cell malignancy. Patients who fail conventional therapy are frequently treated with hematopoietic stem cell transplantation (HSCT), which results in reduced tumor burden, but the patients subsequently relapse from sites of chemotherapy-resistant disease. Using the 5T33 murine model of myeloma and a previously successful immunotherapy regimen consisting of autologous (syngeneic) HSCT and cell-based vaccine administration, we were unable to improve survival of myeloma-bearing mice. The 5T33 tumor line, similar to malignant plasma cells from myeloma patients, expresses high levels of programmed death receptor ligand-1 (PD-L1), which binds to the inhibitory receptor, PD-1. We observed that T cells from myeloma-bearing mice express high levels of PD-1, which has also been observed in patients with multiple myeloma. These PD-1(+) T cells were exhausted and produced IL-10. Based on these observations, we combined HSCT with whole-cell vaccination and PD-L1 blockade. Inhibition of the PD-1/PD-L1 pathway with HSCT and whole-cell vaccination increased the survival of myeloma-bearing mice from 0% to 40%. These data demonstrate a role for PD-L1 in suppressing immune responses to myeloma and suggest that blockade of this pathway may enhance immunotherapy for this disease.
Radiation Protection by the Ocimum Flavonoids Orientin and Vicenin: Mechanisms of Action (2000)

In previous studies, flavonoids, orientin and vicenin, that were isolated from the leaf extract of Ocimum sanctum, were found to protect mice against radiation injury. Several flavonoids are known to be good antioxidants. Therefore, the effect of orientin and vicenin on radiation-induced lipid peroxidation in vivo and their antioxidant activity in vitro were studied. Adult mice were injected intraperitoneally with 50 microgram/kg of orientin or vicenin and exposed whole-body to 3 Gy of gamma radiation. Lipid peroxidation was measured in the liver 15 min to 8 h postirradiation. The antioxidant activity of orientin/vicenin (10-500 microM) was studied by measuring inhibition of hydroxyl radicals generated by the Fenton reaction (Fe(3+)-EDTA-ascorbic acid-H(2)O(2)) in vitro. The compounds were also tested for possible pro-oxidant and iron chelation activities at the above concentrations in the in vitro system. Orientin and vicenin provided almost equal protection against radiation-induced lipid peroxidation in mouse liver. Both compounds showed a significantly greater free radical-inhibiting activity in vitro than DMSO. Neither orientin nor vicenin showed any pro-oxidant activity at the concentrations tested. Both compounds inhibited free radical formation in the absence of EDTA. Free radical scavenging appears to be a likely mechanism of radiation protection by these flavonoids.
Direct Measurement of the Microscale Conductivity of Conjugated Polymer Monolayers (2000)

The in-plane conductivity of conjugated polymer monolayers is mapped here for the first time on the microscale using a novel scanning micro four-point probe (see Figure). The probe allows the source, drain, and voltage electrodes to be positioned within the same domain and the mapping results demonstrate how microscopic ordering in the polymer domains controls the conductivity.
Thinning Rate of the Precorneal and Prelens Tear Films (2005)

Tear film thinning can be analyzed in terms of flow in three spatial directions: (1) outward (evaporation), (2) inward (into the epithelium or contact lens), and (3) parallel to the tear film surface. The results indicate that the second mechanism may be unimportant. Studies have shown a range of tear film evaporation rates from 0.24 to 1.45 microm/min, whereas, when the lipid layer is washed away from the tear film, the thinning rate, due to evaporation, would be approximately 7 microm/min. Thus, slow thinning rates may be due to tear film evaporation, whereas rapid rates (which are often greater than 7 microm/min) presumably include other mechanisms such as dewetting, Marangoni flow (i.e., surface tension gradients), and pressure-gradient flow.
Overexpression of β3/γ2 chains of laminin-5 and MMP7 in biliary cancer (2009)

Our results suggest that LNgamma2 and LNbeta3, in conjunction with MMP7, play a key role in the progression of biliary tract cancer.
<b>Functional diversity of synaptic AMPA/KA receptors from rat as revealed by subtype‐specific antagonists</b> (1998)

Subtype-specific pharmacological compounds represent important tools to identify the molecular components of synaptically activated glutamate receptors in central neurones. Here, we utilized a collection of subtype-specific antagonists and modulators to investigate the functional profile of glutamate receptors in identified synapses in thin slices of the cerebellum, hippocampus and brain stem. During whole-cell patch-clamp recordings alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionate/kainate (AMPA/KA) receptor-mediated synaptic currents (EPSCs) in cerebellar Purkinje cells were (i) prolonged by 100 microM cyclothiazide, (ii) not significantly changed after preincubation in 10 microM concanavalin A, (iii) not affected by 1 microM Evans Blue or polyamine toxin analogue N-(4-hydroxyphenylpropanolyl)-spermine (NHPPS), but (iv) significantly reduced by high (> or = 100 microM) concentrations of Evans Blue. These pharmacological properties were distinct from those observed in hippocampal granule cells and brain stem interneurones and markedly different from those of recombinant glutamate receptor channels GluR1-GluR6 previously investigated in heterologous expression systems.
Energy Transfer between Inorganic Perovskite Nanocrystals (2016)

Cesium lead halide nanocrystals are a new attractive material for optoelectronic applications since they combine the advantageous properties of perovskites and quantum dots. For future applications in optoelectronics and photovoltaics, an efficient energy and/or carrier exchange is a necessary condition. Here, we explicitly demonstrate nonradiative energy transfer for colloidal CsPbBr<SUB>3</SUB> nanocrystals. Using time-resolved optical characterization of purposefully prepared batches of nanocrystals with different sizes, we identify the energy transfer which can be driven by the concentration gradient of excited nanocrystals as well as by the bandgap energy difference. The latter process moves the energy from smaller to larger nanocrystals and opens a possibility of directional streaming of the excitation energy in these materials. The observed energy transfer is enabled in the colloids by proximity of individual nanocrystals due to clustering.
Anion Scavengers for Low-Level Radioactive Waste Repository Backfills (1998)

Minimization of 129/− and 99 TcO4 − transport to the biosphere is critical to the success of low level radioactive waste (LLRW) storage facilities. Here we experimentally identify and classify potential sorbent materials for inclusion in LLRW backfills. For low pH conditions (pH 4-5), Cu-sulfides and possibly imogolite-rich soils provide Kd's (distribution coefficients) of roughly 103 mL g−1 for /−, and 102 mL g−1 for TcO4 −. At near neutral pH, hydrotalcites, Cu-oxides, Cu-sulfides, and lignite coal possess Kd's on the order of 102 mL g−1 for both /− and TcO4 −. At high pH (pH>10), such as might occur in a cementitious LLRW facility, calcium monosulfate aluminate Kd's are calculated to be roughly 102 mL g−1 for both both /− and TcO4 −.
The Action of Diazomethane on Schiff's Bases (1961)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTThe Action of Diazomethane on Schiff's BasesPANKAJA K. KADABA and JOHN O. EDWARDSCite this: J. Org. Chem. 1961, 26, 7, 2331–2335Publication Date (Print):July 1, 1961Publication History Published online1 May 2002Published inissue 1 July 1961https://pubs.acs.org/doi/10.1021/jo01351a044https://doi.org/10.1021/jo01351a044research-articleACS PublicationsRequest reuse permissionsArticle Views179Altmetric-Citations42LEARN 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
Finite element analysis of the valgus knee joint of an obese child (2016)

The paired t test result shows that there is no significant difference between the two methods. The results of FE analysis method suggest that knee valgus malalignment could be the reason for abnormal knee load that may cause knee problems in obese children with valgus knee in the long-term. This study may help to understand biomechanical mechanism of valgus knees of obese children.
Notizen: Phosphazenylcyclophosphazene Syntheses Using Silylmonophosphazenes , (1977)

The reactions of the halogenocyclotriphosphazatrienes N 3 P 3 Fe 6 and N 3 P 3 Cl 6 with the reagentsMe 3 SiR [R = NP(NMe 2 )3, NPMe 3 , NPMe 2 Ph, NPMePh 2 , NPPh 3 , and NP(OEt) 3 ] are discussed, and conclusions are drawn about some of the factors controlling the course and rate of these reactions. Some novel phosphazenyl-derivatives, N 3 P 3 X 5 R [X = F or Cl, R = NP(NMe 2 ) 3 ; X = F, R = NP(OEt) 3 ] are reported.
An experimental investigation on spreading of droplets with evaporation and nucleation (2008)

Abstract An experimental investigation was conducted to visually observe the dynamic characteristics of water droplets with evaporation and nucleation on stainless steel and polished silicon surfaces. The water droplet diameter, contact area, and spreading speed were measured using a high‐speed CCD camera at surface temperatures ranging from 110 ° C to 190 ° C, and a model was proposed to describe the dynamic behavior of droplet spreading. The spreading of water droplets under evaporation and nucleate boiling is highly dependent on the dynamic bubble behavior in the droplets, particularly bubble volume, bubble interaction, as well as the surface properties and temperature. Water droplets were easiest to spread at the surface temperature of 130 ° C, and the spreading tendency increased with increasing surface coarseness. © 2008 Wiley Periodicals, Inc. Heat Trans Asian Res; Published online in Wiley InterScience ( www.interscience.wiley.com ). DOI 10.1002/htj.20231
Data mining application in credit card fraud detection system (2011)

Data mining is popularly used to combat frauds because of its effectiveness. It is a well-defined procedure that takes data as input and produces models or patterns as output. Neural network, a data mining technique was used in this study. The design of the neural network (NN) architecture for the credit card detection system was based on unsupervised method, which was applied to the transactions data to generate four clusters of low, high, risky and high-risk clusters. The self-organizing map neural network (SOMNN) technique was used for solving the problem of carrying out optimal classification of each transaction into its associated group, since a prior output is unknown. The receiver-operating curve (ROC) for credit card fraud (CCF) detection watch detected over 95 % of fraud cases without causing false alarms unlike other statistical models and the two-stage clusters. This shows that the performance of CCF detection watch is in agreement with other detection software, but performs better.
Studies on New Catechol Containing Cephalosporins. III. Synthesis and Structure-activity Relationships of Cephalosporins Having a Pyridone Moiety at the C-7 Position. (1997)

Recently, we reported the synthesis and antibacterial activity of cephalosporins containing a catechol moiety at C-3 and C-7 position, respectively1>2).
Restriction enzyme improves the efficiency of genetic transformations in Moniliophthora perniciosa, the causal agent of witches’ broom disease in Theobroma cacao (2008)

The presence of restriction enzymes in the transformation mixture improved the efficiency of transformation in Moniliophthora perniciosa. The influence of the vector shape (linear or circular), the patterns of plasmid integration in genomic sites and the influence of the promoter used to express the gene marker were also analyzed. The addition of BamHI or NotI increased the number of transformants by 3-10-fold and 3-fold, respectively, over the control without added enzyme. The use of pre-linearized plasmid did not increase the transformation efficiency in comparison with the circular plasmid. However, the frequency of multi-copy transformants increased significantly. The transformation procedure here reported resulted in better production of protoplasts and transformation efficiency. In addition, the time necessary for the detection of the first transformants and the number of insertions were reduced.
Reliable sampling method for analysis of the ecology of the human alimentary tract (1978)

An intubation method has been developed that allows removal of a sample of human intestinal fluid within a short period of time, that avoids contamination, and that minimizes exposure of the sample to air. Preliminary results obtained with this method have shown that the stomach and duodenum are essentially sterile and that the bacterial population present in the remainder of the small intestine is similar to that described by previous workers except that Veillonella species were encountered frequently and Haemophilus species were also detected in the lower jejunum and ileum of some individuals.
Cacti: biology and uses (2002)

List of Contributors Preface 1. Evolution and Systematics Robert S. Wallace and Arthur C. Gibson 2. Shoot Anatomy and Morphology Teresa Terrazas Salgado and James D. Mauseth 3. Root Structure and Function Joseph G. Dubrovsky and Gretchen B. North 4. Environmental Biology Park S. Nobel and Edward G. Bobich 5. Reproductive Biology Eulogio Pimienta-Barrios and Rafael F. del Castillo 6. Population and Community Ecology Alfonso Valiente Banuet and Hector Godinez-Alvarez 7. Consumption of Platyopuntias by Wild Vertebrates Eric Mellink and Monica E. Riojas-Lopez 8. Biodiversity and Conservation Thomas H. Boyle and Edward F. Anderson 9. Mesoamerican Domestication and Diffusion Alejandro Casas and Giuseppe Barbera 10.Cactus Pear Fruit Production Paolo Inglese, Filadelfio Basile, and Mario Schirra 11. Fruits of Vine and Columnar Cacti Avinoam Nerd, Noemi Tel-Zur, and Yosef Mizrahi 12. Forage, Fodder, and Animal Nutrition Ali Nefzaoui and Hichem Ben Salem 13. Nopalitos, Mucilage, Fiber, and Cochineal Carmen Saenz-Hernandez, Joel Corrales-Garcia, and Gildardo Aquino-Perez 14. Insect Pests and Diseases Helmuth G. Zimmermann and Giovanni Granata 15. Cactus Breeding and Biotechnology Brad Chapman, Candelario Mondragon Jacobo, Ronald A. Bunch, and Andrew H. Paterson Index
Non-parametric kernel ranking approach for social image retrieval (2010)

Social image retrieval has become an emerging research challenge in web rich media search. In this paper, we address the research problem of text-based social image retrieval, which aims to identify and return a set of relevant social images that are related to a text-based query from a corpus of social images. Regular approaches for social image retrieval simply adopt typical text-based image retrieval techniques to search for the relevant social images based on the associated tags, which may suffer from noisy tags. In this paper, we present a novel framework for social image re-ranking based on a non-parametric kernel learning technique, which explores both textual and visual contents of social images for improving the ranking performance in social image retrieval tasks. Unlike existing methods that often adopt some fixed parametric kernel function, our framework learns a non-parametric kernel matrix that can effectively encode the information from both visual and textual domains. Although the proposed learning scheme is transductive, we suggest some solution to handle unseen data by warping the non-parametric kernel space to some input kernel function. Encouraging experimental results on a real-world social image testbed exhibit the effectiveness of the proposed method.