gebhart/patrepeval huggingface dataset:
A Rice Autophagy Gene OsATG8b Is Involved in Nitrogen Remobilization and Control of Grain Quality (2020)

Enhancing nitrogen (N) use efficiency is a potential way to reduce excessive nitrogen application and increase yield. Autophagy is a conserved degradation system in the evolution of eukaryotic cells and plays an important role in plant development and stress response. Autophagic cores have two conjugation pathways that attach the product of autophagy-related gene 8 (ATG8) to phosphatidylethanolamine (PE) and ATG5 to ATG12, respectively, which then help with vesicle elongation and enclosure. Rice has six <i>ATG8</i> genes, which have not been functionally confirmed so far. We identified the rice gene <i>OsATG8b</i> and characterized its role in N remobilization to affect grain quality by generating transgenic plants with its over-expression and knockdown. Our study confirmed the autophagy activity of OsATG8b through the complementation of the yeast autophagy-defective mutant <i>scatg8</i> and by observation of autophagosome formation in rice. The autophagy activity is higher in <i>OsATG8b</i>-OE lines and lower in <i>OsATG8b</i>-RNAi than that in wild type (ZH11). <sup>15</sup>N pulse-chase analysis revealed that <i>OsATG8b</i>-OE plants conferred higher N recycling efficiency to grains, while <i>OsATG8b</i>-RNAi transgenic plants exhibited lower N recycling efficiency and poorer grain quality. The autophagic role of <i>OsATG8b</i> was experimentally confirmed, and it was concluded that OsATG8b-mediated autophagy is involved in N recycling to grains and contributes to the grain quality, indicating that OsATG8b may be a potential gene for molecular breeding and cultivation of rice.
Differential Regulation of c-Jun-dependent Transcription by SUMO-specific Proteases (2005)

c-Jun is a transcription factor that plays an important role in regulating cell growth, apoptosis, differentiation, and transformation. The transcriptional activity of c-Jun can be regulated by both phosphorylation and sumoylation. It has also been shown that c-Jun transcription can be regulated by SuPr-1, an alternatively spliced form of SUMO-specific protease 2 (SENP2). However, the ability of SuPr-1 to enhance c-Jun transcription is dependent on promyelocytic leukemia but is independent of the desumoylation activity of SuPr-1. Here, we show that SUMO-specific protease 1 (SENP1) also markedly enhances the transcription activity of c-Jun. The action of SENP1 on c-Jun transcription is independent of the sumoylation and phosphorylation status of c-Jun but is critically dependent on the desumoylation activity of SENP1. We further show that p300 is essential for SENP1 to enhance c-Jun-dependent transcription because SENP1 can desumoylate the CRD1 domain of p300, thereby releasing the cis-repression of CRD1 on p300. Thus, two SUMO-specific proteases regulate c-Jun-dependent transcription through entirely different mechanisms.
A 3D Model Retrieval Based on Combinations of Partial Shape Descriptors (2006)

Similarity retrieval techniques for 3D models have been intensively investigated the last few years. The purpose has been to improve precision of the similarity retrievals, and as a result various types of shape descriptors have been proposed. Several shape descriptors use the bounding box of a 3D model during a shape descriptor extraction process, and computation of the bounding box is important for accurately identifying shape descriptors. In our previous shape descriptor extraction approaches, only one bounding box was used for each 3D model. However, use of one bounding box is a very rough approximation of the shape for certain 3D models. When the bounding box becomes very sparse for certain targeted 3D models, the approach can not compute shape descriptors accurately. In this research, we have extended the shape descriptor computation technique by using a multiple number of bounding boxes. 3D models are decomposed into multiple parts, and multiple numbers of bounding boxes are used for each decomposed part. Shape descriptors are extracted from each decomposed 3D model part independently, and they are combined with weighted values based on the proportions of area size of each decomposed part. Our preliminary experiments showed that similarity retrievals results were improved for certain 3D models by using a combination of partial shape descriptors
Optimized 4,5-Diarylimidazoles as Potent/Selective Inhibitors of Protein Kinase CK1δ and Their Structural Relation to p38α MAPK (2017)

The involvement of protein kinase CK1δ in the pathogenesis of severe disorders such as Alzheimer's disease, amyotrophic lateral sclerosis, familial advanced sleep phase syndrome, and cancer has dramatically increased interest in the development of effective small molecule inhibitors for both therapeutic application and basic research. Unfortunately, the design of CK1 isoform-specific compounds has proved to be highly complicated due to the existence of six evolutionarily conserved human CK1 members that possess similar, different, or even opposite physiological and pathophysiological implications. Consequently, only few potent and selective CK1δ inhibitors have been reported so far and structurally divergent approaches are urgently needed in order to establish SAR that might enable complete discrimination of CK1 isoforms and related p38α MAPK. In this study we report on design and characterization of optimized 4,5-diarylimidazoles as highly effective ATP-competitive inhibitors of CK1δ with compounds 11b (IC<sub>50</sub> CK1δ = 4 nM, IC<sub>50</sub> CK1ε = 25 nM), 12a (IC<sub>50</sub> CK1δ = 19 nM, IC<sub>50</sub> CK1ε = 227 nM), and 16b (IC<sub>50</sub> CK1δ = 8 nM, IC<sub>50</sub> CK1ε = 81 nM) being among the most potent CK1δ-targeting agents published to date. Inhibitor compound <b>11b</b>, displaying potential as a pharmacological tool, has further been profiled over a panel of 321 protein kinases exhibiting high selectivity. Cellular efficacy has been evaluated in human pancreatic cancer cell lines Colo357 (EC<sub>50</sub> = 3.5 µM) and Panc89 (EC<sub>50</sub> = 1.5 µM). SAR is substantiated by X-ray crystallographic analysis of <b>16b</b> in CK1δ and <b>11b</b> in p38α.
Polyhedral Shapes of CeO<sub>2</sub> Nanoparticles (2003)

Ceria nanoparticles are a widely used nanomaterial for applications in catalysts, fuel cell, and microelectronics. An important factor that influences the performance of CeO2 is the particle shape. In this paper, a systematic study has been carried out to determine the shapes of CeO2 nanoparticles. For particles in the size range of 3−10 nm, the particle shape is dominated by truncated octahedral that is defined by the {100} and {111} facets. The fastest growth of the nanoparticles along 〈100〉 results in the disappearance of the {100} facets; thus, the large size CeO2 particles are dominated by the octahedral shape with flat surfaces. The nanoparticles agglomerate by minimizing the interface energy with the formation of a lattice matched “coherent interface”. The faceted shape also results in the textured distribution of nanoparticles deposited onto a substrate surface, with a preferred orientation of [110]. These structural characteristics are likely to affect their performance in technological applications.
Electrosurgery in laparoscopy. (1978)

The two factors that probably contributed most to the bowel burns that have occurred during monopolar laparoscopy were the use of higher-than-necessary voltages and the electrical isolation of the salpinx. Preferably, low-peak voltages should be used. If the two-burn technique is used, desiccation should be from distal to proximal to avoid electrical isolation of the salpinx. Bipolar laparoscopy is unquestionably safer than monopolar, but it is also harder to perform because the salpinx must be grasped repeatedly on both sides to desiccate the required 2 to 3 cm of tissue. Moreover, electrosurgical cutting with bipolar forceps is not very practical because the spark punches through to the opposite jaw and the cutting stops. Bipolar forceps that can make a mechanical cut after desiccation are available for those who desire this feature. Metal trocar sleeves are recommended for use with the monopolar, single-puncture technique only. They are not necessary for the bipolar or double-puncture monopolar techniques.
Infrared radiation generated by quasi-phase-matched difference-frequency mixing in a periodically poled lithium niobate waveguide (1991)

We report quasi-phase-matched difference-frequency generation of 2.1 μm radiation at room temperature using the d33 nonlinear coefficient in a periodically poled lithium niobate channel waveguide. A tunable Ti:Al2O3 laser (λ≊0.8 μm) and a Nd:YAG laser (λ=1.32 μm) were the pump and signal sources, respectively. With 160 mW of 0.81 μm and 1 mW of 1.32 μm radiation coupled into the waveguide, 1.8 μW of 2.1 μm radiation was generated, tunable over a 6 nm bandwidth. We also show that the annealed proton exchange process can change the shape of ferroelectric domains in lithium niobate.
Effects of ruminal or postruminal fish oil supplementation on intake and digestion in dairy cows (1997)

The effect of fish oil supplementation on intake, digestibility and the volatile fatty acid profile in dairy cows was investigated in two trials. In each of the two trials, six cows received a diet based on maize silage in a latin square design. In the first trial, the cows were fitted with ruminal and duodenal cannulae and their diet was either supplemented or not with 300 mL fish oil and infused either into the rumen or the duodenum. In the second trial, the cows were not cannulated and their diet was either supplemented or not with 200 or 400 mL fish oil given orally. In both trials, the fish oil reaching the rumen decreased (P < 0.01) feed intake, increased (P < 0.01) the organic matter and fibre digestibility, and the percentage of propionate in the volatile fatty acid profile. These increases were higher for the 400 mL supplement than for the 200 mL one. The long-chain fatty acid pattern in the duodenum showed a high degree of hydrogenation of 20- and 22-carbon fatty acids. All these results demonstrated the particular action of fish oil on ruminal digestion when compared to other lipid sources.
Quality Evaluation of Color Plus Depth Map-Based Stereoscopic Video (2009)

In the near future, many conventional video applications are likely to be replaced by immersive video to provide a sense of ldquobeing there.rdquo This transition is facilitated by the recent advancement of 3D capture, coding, transmission, and display technologies. Stereoscopic video is the simplest form of 3D video available in the literature. ldquoColor plus depth maprdquo based stereoscopic video has attracted significant attention, as it can reduce storage and bandwidth requirements for the transmission of stereoscopic content over communication channels. However, quality assessment of coded video sequences can currently only be performed reliably using expensive and inconvenient subjective tests. To enable researchers to optimize 3D video systems in a timely fashion, it is essential that reliable objective measures are found. This paper investigates the correlation between subjective and objective evaluation of color plus depth video. The investigation is conducted for different compression ratios, and different video sequences. Transmission over Internet protocol (IP) is also investigated. Subjective tests are performed to determine the image quality and depth perception of a range of differently coded video sequences, with packet loss rates ranging from 0% to 20%. The subjective results are used to determine more accurate objective quality assessment metrics for 3D color plus depth video.
Use of half-tetrad analysis to discriminate between two types of 2<i>n</i> egg formation in a potato haploid (1992)

The ratio of the first division restitution (FDR) to second division restitution (SDR) 2n eggs was estimated in 4182t, a haploid (2n = 2x = 24) of Solanum tuberosum L. that produces 2n eggs by the two modes. The segregation of three genes previously mapped relative to their centromeres, Pgm-2 (2.0 cM), Mdh-1 (33.5 cM), and 6-Pgdh-3 (30.1 cM) was analyzed in the tetraploid offspring of a 2x × 4x cross. Based on the segregation of the Pgm-2 locus, 39.7% of the progeny originated from FDR 2n eggs and 60.3% from SDR. Segregation patterns of the two distal loci within the FDR-derived 4x subpopulation indicated that the gene–centromere recombination rate during megasporogenesis was significantly reduced for Mdh-1 when compared with a previous estimate during microsporogenesis. In the SDR-derived 4x subpopulation, the gene–centromere recombination rates for Mdh-1 and 6-Pgdh-3 were not significantly different from previous estimates. Tetraploid progeny generated from one 2x × 4x cross where the 2x parent produces 2n gametes by two modes can be used to make an unbiased comparison of the potential breeding value of FDR and SDR gametes.Key words: potato, megasporogenesis, first division restitution, second division restitution, isozyme.
Biomechanics of hip dysplasia. (1999)

When walking, each hip alternately carries the body mass minus the supporting leg. This mass exerts a force K acting on the hip with a lever arm h'; it is counter-balanced by a force M exerted by the abductor muscles, which acts on the hip with a lever arm h. The hip joint transmits the resultant R of forces K and M. Force R evokes compressive stresses in the joint. In a normal hip, force R is exerted at the center of the force transmitting surface of the joint, and the stresses are evenly distributed over this surface. This is reflected by the narrow ribbon of subchondral sclerosis in the roof of the socket. The normal femoral neck is stressed in bending with shear. It has a medial bundle of cancellous trabeculae, stressed in compression, intersecting with a lateral bundle, stressed in tension. Dysplasia and an imbalance of the muscles may have similar mechanical consequences: a shortening of the lever arm h and a more vertical orientation of force M. Shortening of h results in an increase of the force M necessary to counterbalance the moment of force K; the change in direction of force M displaces the resultant R towards the edge of the socket. The result is an increased resultant force R which becomes unevenly distributed over a smaller surface. Subluxation of the femoral head due to a shallow socket will also result in an uneven distribution of force R on a smaller surface. The abnormal distribution of compressive stresses is reflected by the development of a triangular sclerosis at the edge of the socket. This is the beginning of subluxating osteoarthritis of the hip. In a coxa valga the femoral neck may be stressed in a pure compression. This appears in the structure of the cancellous bone of the neck. Coxa vara has opposite consequences: lengthening of the lever arm h of the abductor muscles and a more horizontal orientation of force M. This results in a decrease of the resultant force R, which is displaced medially over a larger surface, resulting into smaller compressive stresses in the joint. If the acetabular cartilage of the socket does not develop further medially, the distribution of compressive stresses may become uneven with a maximum medially, where a dense triangular sclerosis develops. This is the beginning of protrusive osteoarthritis of the hip. In coxa vara, the femoral neck is stressed in bending more than in a normal hip, which is reflected by more marked cancellous trabeculae which intersect at right angles in the femoral head. The medial bundle is stressed in compression, the lateral bundle in tension.
ACTIVATION OF THE LIME-FLYASH REACTION BY TRACE CHEMICALS (1959)

THE RESULTS OF AN INVESTIGATION OF THE EFFECT OF SMALL AMOUNTS OF FORTY-SEVEN DIFFERENT CHEMICALS ON THE STRENGTH OF OTTAWA SAND-LIME-FLYASH MIXTURES ARE PRESENTED. AN EXPLANATION IS OFFERED FOR THE MECHANISM OF STRENGTH IMPROVEMENT BY THE DIFFERENT GROUPS OF CHEMICALS STUDIES. /AUTHOR/
Simultaneous echo refocusing in EPI (2002)

A method to encode multiple two-dimensional Fourier transform (2D FT) images within a single echo train is presented. This new method, simultaneous echo refocusing (SER), is a departure from prior echo planar image (EPI) sequences which use repeated single-shot echo trains for multislice imaging. SER simultaneously acquires multiple slices in a single-shot echo train utilizing a shared refocusing process. The SER technique acquires data faster than conventional multislice EPI since it uses fewer gradient switchings and fewer preparation pulses such as diffusion gradients. SER introduces a new capability to simultaneously record multiple spatially separated sources of physiologic information in subsecond image acquisitions, which enables several applications that are dependent on temporal coherence in MRI data including velocity vector field mapping and brain activation mapping.
Towards a formal specification method for graphical user interfaces using modularized graph grammars (1996)

Well designed graphical user interfaces offer a high potential to increase the productivity of human users. The necessary condition for such a good performance is that the user interface represents the semantics of the underlying application in a clear and comprehensible way. This means, especially, that not only syntactical layout but also semantic consistency conditions between the various interaction objects have to be presented in a graphical user interface appropriately. This is usually termed semantic feedback. Many representation schemes have been proposed to express the properties of graphical man machine interfaces. However, many of them concentrate on control flow design and do not easily scale up to realistic problems. We propose a graph and graph grammar based approach which addresses the problem of semantic consistency of dialogs in graphical user interfaces. The main emphasis lies on an appropriate specification of the consistency conditions between the various graphical interaction objects of a man machine interface. We also propose a modularization technique in order to cope with large systems. We show the expressiveness and modularization features of our approach which is based on an analysis of the relationships between the various graphical interaction objects and conclude with remarks on future work.
Photoinitation of cationic polymerization. II. Laser flash photolysis of diphenyliodonium salts (1984)

Abstract Laser flash photolysis of diphenyliodonium salts produces phenyliodinium radical cation (PhI +· ), which was also generated independently by flash‐induced electron transfer from iodobenzene to a phenanthrolinium salt. Apparent second‐order rate constants were determined for reaction of the transient (PhI +· ) with nucleophiles, including iodobenzene and cyclohexene oxide. Quantum yields of formation of acid from stationary photolysis of diphenyliodonium hexafluoroarsenate were found to be significantly higher than yields of iodobenzene. These results may be explained by facile reaction of PhI +· with PhI to yield a new iodonium salt together with a proton. High reactivity of PhI +· with cyclohexene oxide suggests that the transient may directly initiate cationic polymerization of epoxides.
Indexing OODB instances based on access proximity (2002)

Queries in object-oriented databases (OODBs) may be asked with respect to different class scopes: a query may either request for object-instances which belong exclusively to a given class c, or those which belong to any class in the hierarchy rooted at c. To facilitate retrieval of objects both from a single class as well as from multiple classes in a class hierarchy, we propose a multi-dimensional class-hierarchy index called the /spl chi/-tree. The /spl chi/-tree dynamically partitions the data space using both the class and indexed attribute dimensions by taking into account the semantics of the class dimension as well as access patterns of queries. Experimental results show that it is an efficient index.
Real‐time endoscopic Raman spectroscopy for<i>in vivo</i>early lung cancer detection (2016)

Currently the most sensitive method for localizing lung cancers in central airways is autofluorescence bronchoscopy (AFB) in combination with white light bronchoscopy (WLB). The diagnostic accuracy of WLB + AFB for high grade dysplasia (HGD) and carcinoma in situ is variable depending on physician's experience. When WLB + AFB are operated at high diagnostic sensitivity, the associated diagnostic specificity is low. Raman spectroscopy probes molecular vibrations and gives highly specific, fingerprint-like spectral features and has high accuracy for tissue pathology classification. In this study we present the use of a real-time endoscopy Raman spectroscopy system to improve the specificity. A spectrum is acquired within 1 second and clinical data are obtained from 280 tissue sites (72 HGDs/malignant lesions, 208 benign lesions/normal sites) in 80 patients. Using multivariate analyses and waveband selection methods on the Raman spectra, we have demonstrated that HGD and malignant lung lesions can be detected with high sensitivity (90%) and good specificity (65%).
Evaluation of 7q31 region improves the accuracy of EGFR FISH assay in non small cell lung cancer (2009)

Our data strengthen the usefulness of 7q31 region evaluation to discriminate EGFR amplification from chromosome 7 polysomy in controversial EGFR FISH positive cases. Since it has been reported a possible different contribution of amplification and polysomy to TKIs susceptibility in NSCLC, the clear distinction between these two genetic events may be important to identify a subset of patients more responsive to the therapy.
MPEG-based personalized content delivery (2004)

In this paper, we present a personalized multimedia content delivery system dealing with both user preferences and terminal/network capabilities. In order to ease interoperability with third-party applications, content annotation, user preferences handling and terminal/network capabilities description are managed by MPEG-7 and MPEG-21 standards. Offline content adaptation and annotation tools are proposed for content preparation. Content delivery is handled by client-server architecture. This architecture is built around custom personalization and adaptation tools, and a commercial content streamer. The proposed system has been used to provide universal multimedia access within the EC-funded R&D project PERSEO.
Essentials of Spinal Microsurgery (1998)

Part 1 The microscope and other basic principles of microsurgery: a personal history of spinal microsurgery, R.W. Williams the microscope as a surgical aide instrumentation for spinal microsurgery, including ancillary equipment wound healing and mobilization (the foundation of microsurgery) bone grafting in the degenerative spine control of bleeding in microsurgery the teaching of spinal microsurgery. Part 2 Microsurgery for cervical disc disease: advantages and disadvantages of microsurgical approaches to the cervical spine pathophysiology and clinical syndromes in cervical disc degeneration surgical anatomy of the cervical spine, spinal cord and surrounding structures anterior microdiscectomy for soft disc anterior microsurgical approach to spondylosis cervical disc surgery - overall results posterior microlaminotomy/facetotomy for foraminal soft disc and spurs posterior cervical wide decompressive techniques perioperative care for cervical spine patients complications for cervical spine microsurgery. Part 3 Microsurgery for lumbar disc release. Part 4 Microsurgery for other special disorders.