gebhart/patrepeval huggingface dataset:
Detection of Novel (Swine Origin) H1N1 Influenza A Virus by Quantitative Real-Time Reverse Transcription-PCR (2009)

A novel H1N1 subtype influenza A virus, derived by reassortment between two known circulating swine influenza strains, has now been declared a human pandemic influenza A virus ([8][1]). The pandemic virus, centered initially in Mexico and the United States, has now spread to 74 countries with the
Are there sub-types of attentional deficits in patients with persisting post-concussive symptoms? A cluster analytical study (2003)

This study provides preliminary evidence suggesting that sub-types of attentional impairments exit in patients with post-concussive symptoms.
Development of an Efficient Agrobacterium-Mediated Gene Targeting System for Rice and Analysis of Rice Knockouts Lacking Granule-Bound Starch Synthase (Waxy) and β1,2-Xylosyltransferase (2012)

We have developed a high-frequency method for Agrobacterium-mediated gene targeting by combining an efficient transformation system using rice suspension-cultured calli and a positive/negative selection system. Compared with the conventional transformation system using calli on solid medium, transformation using suspension-cultured calli resulted in a 5- to 10-fold increase in the number of resistant calli per weight of starting material after positive/negative selection. Homologous recombination occurred in about 1.5% of the positive/negative selected calli. To evaluate the efficacy of our method, we show in this report that knockout rice plants containing either a disrupted Waxy (granule-bound starch synthase) or a disrupted Xyl (β1,2-xylosyltransferase) gene can be easily obtained by homologous recombination. Study of gene function using homologous recombination in higher plants can now be considered routine work as a direct result of this technical advance.
A multicenter, randomized, active‐controlled study to investigate the efficacy and safety of intravenous ferric carboxymaltose in patients with iron deficiency anemia (2013)

Two 750-mg FCM infusions are safe and superior to oral iron in increasing Hb levels in IDA patients with inadequate oral iron response.
Preparation of megabase‐size DNA from plant nuclei (1995)

A novel technique has been developed for the preparation of high molecular weight (HMW) DNA from plant nuclei. This technique involves physical homogenization of plant tissues, nuclei isolation, embedding of the nuclei in low‐melting‐point agarose microbeads or plugs, and DNA purification in situ . This technique is simple, rapid, and economical, and the majority of the DNA prepared is over 5.7 Mb in size. The genomic DNA content of the HMW DNA prepared by this technique is enriched by at least threefold and the chloroplast DNA content is reduced by over twofold relative to that prepared from plant protoplasts by existing methods. The DNA is readily digestible with different restriction enzymes and partial digestions of the DNA could be reproducibly performed. This method has been successfully used for the preparation of HMW DNA from a wide range of plant taxa, including grasses, legumes, vegetables, and trees. These results demonstrate that the DNA prepared by this technique is suitable for plant genome analysis by pulsed‐field gel electrophoresis and for the construction of yeast and bacterial artificial chromosomes.
Learning to Play Games Using a PSO-Based Competitive Learning Approach (2004)

A new competitive approach is developed for learning agents to play two-agent games. This approach uses particle swarm optimizers (PSO) to train neural networks to predict the desirability of states in the leaf nodes of a game tree. The new approach is applied to the TicTacToe game, and compared with the performance of an evolutionary approach. A performance criterion is defined to quantify performance against that of players making random moves. The results show that the new PSO-based approach performs well as compared with the evolutionary approach.
Mechanisms of drug resistance in chemotherapy for urogenital carcinoma (1999)

Cancer chemotherapy is the principal approach for urogenital cancers. However, the acquisition of resistance to anticancer agents is a critical factor that limits the successful treatment of malignancies. The multidrug resistant (MDR) phenotype has been widely recognized in cancer chemotherapy in urogenital tumors and the mechanisms underlying MDR have also been extensively studied. One of the principle mechanisms in MDR is caused by the overexpression of P-glycoprotein (P-gp), encoded by the multidrug resistance gene (MDR1). It functions as an ATP-dependent active efflux pump of chemotherapeutic agents in human cancer cells. Recently, other drug resistance proteins, including multidrug resistance-associated protein (MRP1) and cMOAT (or MRP2), were also identified from multidrug resistant cells. A functional analysis of MRP1 has shown that MRP1 may have the potential to act as a transporter of glutathione conjugates, which has been known as a central detoxification pathway in anticancer agents. Furthermore, several other resistance-related proteins (e.g. glutathione S-transferase, metallothionein, thioredoxin, topoisomerase I, II, O6-alkylguanine-DNA methyltransferase, etc.) have been found to be up- or down-regulated in resistant cells and these molecules are believed to contribute to the resistant phenotype as well. Based on the molecular characteristics identified in MDR, several experimental and clinical approaches have been studied to overcome MDR. One of these strategies is to reverse MDR by using such P-gp inhibitors as verapamil and cyclosporine A. In this review, we summarize the recent advances in MDR-related molecules and clinical trials to circumvent MDR in urogenital carcinomas.
Protein B61 as a new growth factor: expression of B61 and up-regulation of its receptor epithelial cell kinase during melanoma progression. (1995)

Epithelial cell kinase (ECK) is a receptor protein tyrosine kinase, the role of which in melanoma biology is unclear. Here we studied the role of ECK during melanoma progression. ECK mRNA was overexpressed in virtually all melanoma lines tested, and levels were significantly higher in cell lines from distant metastases than primary melanomas; melanocytes were negative. Gene amplification was not detected in melanomas. Levels of ECK protein corresponded well with mRNA levels. B61 or LERK-1, recently identified as an ECK ligand, stimulated the growth of ECK-expressing melanoma cell lines, its first identified biological activity. Melanoma chemotaxis and chemoinvasion were not affected by B61. Growth of normal melanocytes was not affected. mRNA for B61 was detected in both melanoma cell lines and normal melanocytes. B61 was also identified by Western blotting and ECK binding activity with the use of a BIAcore binding assay in melanoma cell-conditioned media. These results suggest that B61 is an autocrine growth factor for melanomas but not normal melanocytes.
Displaying Tactile Feeling Using Focused Ultrasound (2002)

皮膚に触感を呈示する方法として, 機械的なピンの運動や電気的刺激を用いる方法が試みられてきた。本研究では新しい提示法として超音波の利用を提案する。ゲル状固体や液体中の数MHz超音波は容易に1mm以下のスポットに集束することができ, 非線形音響効果によってそこに放射圧を発生することができる。その圧力は触覚より十分高い時間応答で容易に制御することができ, 触覚提示に有効と考えられる。もう一つの可能性が, 超音波を皮膚内部に透過させ, 直接触覚受容器を刺激する方法である。本論文ではこの2つの観点から超音波による触感呈示の可能性を検討する。
BUILDING EXTRACTION FROM HIGH RESOLUTION SATELLITE IMAGES USING HOUGH TRANSFORM (2010)

An approach was developed for the automatic extraction of the rectangular and circular shaped buildings from high resolution satellite imagery using Hough transform. First, the candidate building patches are detected from the imagery using the binary Support Vector Machines (SVM) classification technique. In addition to original image bands, the bands NDVI (Normalized Difference Vegetation Index), and nDSM (normalized Digital Surface Model) are also used in the classification. After detecting the building patches, their edges are detected using the Canny edge detection algorithm. The edge image is then converted into vector form using the Hough transform, which is a widely used technique for extracting the lines or curves of the objects. The vector lines and curves that represent the building edges are grouped based on perceptual groupings, and the building boundaries are constructed. The proposed approach was implemented using a program written in MATLAB (R) v. 7.1 programming environment. The experimental tests were carried out in the residential and industrial urban blocks selected in the Batikent district of Ankara, the capital city of Turkey using the pan-sharpened and panchromatic IKONOS images. The results obtained indicate that the proposed building extraction procedure based on SVM and Hough transform can be effectively used to extract the boundaries of the rectangular and circular shaped buildings. For the industrial buildings, we obtained quite satisfactory results with the average Building Detection Percentage (BDP) and the Quality Percentage (QP) values of 93.45% and 79.51%, respectively. For the residential rectangular buildings, the average BDP and QP values were computed to be 95.34% and 79.05%, respectively. For the residential circular buildings, the average BDP and QP values were found to be 78.74% and 66.81%, respectively.
Comprehensive analysis of the specificity of transcription activator-like effector nucleases (2014)

A key issue when designing and using DNA-targeting nucleases is specificity. Ideally, an optimal DNA-targeting tool has only one recognition site within a genomic sequence. In practice, however, almost all designer nucleases available today can accommodate one to several mutations within their target site. The ability to predict the specificity of targeting is thus highly desirable. Here, we describe the first comprehensive experimental study focused on the specificity of the four commonly used repeat variable diresidues (RVDs; NI:A, HD:C, NN:G and NG:T) incorporated in transcription activator-like effector nucleases (TALEN). The analysis of >15 500 unique TALEN/DNA cleavage profiles allowed us to monitor the specificity gradient of the RVDs along a TALEN/DNA binding array and to present a specificity scoring matrix for RVD/nucleotide association. Furthermore, we report that TALEN can only accommodate a relatively small number of position-dependent mismatches while maintaining a detectable activity at endogenous loci in vivo, demonstrating the high specificity of these molecular tools. We thus envision that the results we provide will allow for more deliberate choices of DNA binding arrays and/or DNA targets, extending our engineering capabilities.
TRPM8 Activation by Menthol, Icilin, and Cold Is Differentially Modulated by Intracellular pH (2004)

TRPM8 is a nonselective cation channel activated by cold and the cooling compounds menthol and icilin (Peier et al., 2002). Here, we have used electrophysiology and the calcium-sensitive dye Fura-2 to study the effect of pH and interactions between temperature, pH, and the two chemical agonists menthol and icilin on TRPM8 expressed in Chinese hamster ovary cells. Menthol, icilin, and cold all evoked stimulus-dependent [Ca2+]i responses in standard physiological solutions of pH 7.3. Increasing the extracellular [H+] from pH 7.3 to approximately pH 6 abolished responses to icilin and cold stimulation but did not affect responses to menthol. Icilin concentration-response curves were significantly shifted to the right when pH was lowered from 7.3 to 6.9, whereas those with menthol were unaltered in solutions of pH 6.1. When cells were exposed to solutions in the range of pH 8.1-6.5, the temperature threshold for activation was elevated at higher pH and depressed at lower pH. Superfusing cells with a low subactivating concentration of icilin or menthol elevated the threshold for cold activation at pH 7.4, but cooling failed to evoke [Ca2+]i responses at pH 6 in the presence of either agonist. In voltage-clamp experiments in which the intracellular pH was buffered to different levels, acidification reduced the current amplitude of icilin responses and shifted the threshold for cold activation to lower values with half-maximal inhibition at pH 7.2 and pH 7.6. The results demonstrate that the activation of TRPM8 by icilin and cold, but not menthol, is modulated by intracellular pH in the physiological range. Furthermore, our data suggest that activation by icilin and cold involve a different mechanism to activation by menthol.
Proinflammatory Role for let-7 MicroRNAS in Experimental Asthma (2010)

MicroRNAs (miRNAs) are short, non-coding RNAs that target and silence protein coding genes through 3'-UTR elements. Evidence increasingly assigns an immunosuppressive role for miRNAs in immunity, but relatively few miRNAs have been studied, and an overall understanding of the importance of these regulatory transcripts in complex in vivo systems is lacking. Here we have applied multiple technologies to globally analyze miRNA expression and function in allergic lung disease, an experimental model of asthma. Deep sequencing and microarray analyses of the mouse lung short RNAome revealed numerous extant and novel miRNAs and other transcript classes. Similar to mRNAs, lung miRNA expression changed dynamically during the transition from the naive to the allergic state, suggesting numerous functional relationships. A possible role for miRNA editing in altering the lung mRNA target repertoire was also identified. Multiple members of the highly conserved let-7 miRNA family were the most abundant lung miRNAs, and we confirmed in vitro that interleukin 13 (IL-13), a cytokine essential for expression for allergic lung disease, is regulated by mmu-let-7a. However, inhibition of let-7 miRNAs in vivo using a locked nucleic acid profoundly inhibited production of allergic cytokines and the disease phenotype. Our findings thus reveal unexpected complexity in the miRNAome underlying allergic lung disease and demonstrate a proinflammatory role for let-7 miRNAs.
Understanding eye deformation in non-contact tonometry (2006)

Non-contact tonometers are widely used to measure the internal eye pressure, i.e. the IntraOcular Pressure (IOP), which is an important parameter for the diagnosis and treatment of glaucoma. During the measurement, the eye is deformed by a short air pulse. Commonly the pressure dependent deformation is estimated from the time when the eye becomes flat, which is derived from the monitored reflection of an incident infrared light. We used a high speed camera to capture the complete motion of the eye directly and obtain more data during the pressure measurement. Assuming a simple eye model with non-linear material properties of the cornea, we extend our previous analysis of the motion of the eye, and obtain a similar principle shape of the eye deformation as observed in the experiments.
CoFeB/MgO based perpendicular magnetic tunnel junctions with stepped structure for symmetrizing different retention times of “0” and “1” information (2011)

We investigated perpendicular magnetic tunnel junctions (p-MTJs) with a stepped structure for spin-transfer torque random access memory (SPRAM). In conventional p-MTJs, the retention time for storing ℌ1ℍ is shorter than that for storing ℌ0,ℍ because of the mangetostatic energy difference between the two states caused by dipole interaction. To counter this, one had to develop materials with low magnetization. Here we show, by employing a stepped structure, that the retention time can be made equivalent regardless of the stored information (ℌ0ℍ or ℌ1ℍ), without resorting to the employed materials. This is because this structure reduces the dipole interlayer coupling between two ferromagnetic layers as the diameter difference of the free and reference layers of MTJ increases.
Identification of carbohydrates on the surface membrane of pathogenic and nonpathogenic piscine haemoflagellates, Cryptobia salmositica, C. bullocki and C. catostomi (Kinetoplastida) (1998)

Carbohydrates and protein glycoconjugates on the cell membranes of Cryptobia salmositica, C. bullocki and C. catostomi were analyzed using 13 highly purified lectins (unlabelled or digoxigenin/biotin labelled). No agglutinations were observed with C. salmositica, C. bullocki and C. catostomi using lectin TPA (Tetragonolobus purpureas agglutinin, for alpha-L-fucose). C. salmositica was agglutinated by 3 of 12 lectins [Con A, for alpha-man and alpha-D-glc; PSA, for alpha-man; PWM, for (glcNAc)3], while C. bullocki was agglutinated by 8 lectins and C. catostomi was agglutinated by 10 lectins. Glycoconjugate analysis with digoxigenin or biotin labelled lectins showed a species-specific staining pattern in pathogenic and nonpathogenic Cryptobia spp. The nonpathogenic C. catostomi had the strongest reaction. These results indicate that the surface carbohydrate residues and glycoconjugate compositions on Cryptobia spp. are different between species they may be related to the virulence of the parasite.
88 th Annual Meeting of the American Thyroid Association (2018)

Thyroid ultrasound screening has been involved in routine physical examination at hospitals. However, due to the uneven development of medical resources, the diagnostic accuracy for thyroid nodules varies greatly. The aim of this study was to explore a novel artificial intelligence-assisted ultrasound diagnostic system to improve the diagnosis efficiency and accuracy for thyroid nodules. The artificial intelligence-assisted ultrasound diagnostic system was developed based on computer deep learning, training and multi-frame dynamic image recognition techniques. In order to validate the accuracy of the system, 500 pathologically confirmed thyroid nodules were selected, including 208 benign and 292 malignant. The images of all nodules, acquired from 10 different types of ultrasound equipment, were dynamically stored in the form of the consecutively longitudinal and transverse sections. Then the AI-assisted diagnostic system automatically recognized and analyzed the features of the images, and gave recommendations for diagnosis. The diagnostic accuracy of the system was compared with that of junior and senior physicians. The results showed that the sensitivity of the AI-assisted diagnostic system, junior physicians, senior physicians, combo of junior physicians and the AI-assisted system was 82.9%, 52.6%, 87.4% and 98.6%, respectively; and the specificity was 70.2%, 95.7%, 83.2% and 83.7%, respectively. The diagnostic accuracy of the AI-assisted system alone was higher than that of junior physicians (77.6% vs. 70.5%), however, the accuracy can reach 92.4% when the junior physicians was assisted by the AI-assisted system, which was higher than that of the senior physicians (85.6%). At the same time, the diagnostic tests on thyroid nodules of different sizes (<1cm, 1-2cm, and >2cm) were performed using the system. The results showed that there was no significant difference in the diagnostic accuracy among the three groups (P < 0.05). The AI-assisted ultrasound diagnostic system can effectively assist ultrasound physicians in the diagnosis of benign and malignant thyroid nodules, reduce unnecessary puncture and over-treatment, and help the junior physicians to improve the diagnosis efficiency and accuracy.
Main drug-metabolizing enzyme systems in human breast tumors and peritumoral tissues. (1993)

In an attempt to better understand breast tumors sensitivity or resistance to anticancer drugs, the main drug-metabolizing enzyme systems were evaluated in both breast tumors and their corresponding peritumoral tissues in 12 patients. The following enzymes were assayed by Western blot: cytochromes P-450 (1A1/A2, 2B1/B2, 2C8-10, 2E1, 3A4); glutathione S-transferases (GST-alpha, -mu, and -pi); and epoxide hydrolase. The activity of the following enzymes or cofactor were determined by spectrophotometric or fluorometric assays: GST; total glutathione; UDP-glucuronosyltransferase; beta-glucuronidase; sulfotransferase; and sulfatase. Results showed the absence of all probed cytochromes P-450 in both tumoral and peritumoral tissues. GST activity was significantly (P < 0.05) higher in tumors (mean +/- SD, 399 +/- 362 nmol/min/mg) than in corresponding peritumoral tissues (86 +/- 67). The GST isoenzymes GST-mu and GST-pi (determined by immunoblotting) were also higher in tumors than in corresponding peritumoral tissues (3- and 5-fold, respectively). Both GST-mu and GST-pi levels were significantly correlated with GST activity. GST-alpha was not detected in either tumoral or peritumoral tissues. Glutathione levels in tumors (22 +/- 23 nmol/mg protein) were not statistically different from peritumoral tissues (11 +/- 12). Epoxide hydrolase was expressed at similar levels in tumors and peritumoral tissues. The glucuronide-forming enzyme UDP-glucuronosyltransferase was 5-fold lower in tumors (0.1 +/- 0.2 nmol/h/mg) than in peritumoral tissues (0.5 +/- 1), whereas the opposite was observed for the hydrolytic enzyme beta-glucuronidase, which was 6-fold higher in tumors (736 +/- 1392 nmol/h/mg) compared to peritumoral tissues (125 +/- 75). No difference was noted between tumoral and peritumoral tissues for sulfotransferase (1 +/- 2 nmol/h/mg), but the corresponding hydrolytic enzyme (sulfatase) was 2-fold higher in tumoral tissues (14 +/- 15 nmol/h/mg) than in peritumoral tissues (6 +/- 2). In conclusion, several differences were observed between human breast tumors and peritumoral tissues for many conjugating enzymes (GST-mu, GST-pi, and UDP-glucuronosyltransferase) and hydrolytic enzymes (sulfatase and beta-glucuronidase). These noteworthy differences between tumoral and peritumoral tissues with regard to their main drug-metabolizing enzymes could play a role in the relative drug sensitivity or insensitivity of human breast cancer tissues to chemotherapeutic agents and could be potential targets for chemotherapeutic interventions.
A Potent GAL4 Derivative Activates Transcription at a Distance in Vitro (1990)

Transcription of a typical eukaryotic gene by RNA polymerase II is activated by proteins bound to sites found near the beginning of the gene as well as to sites, called enhancers, located a great distance from the gene. According to one view, the primary difference between an activator that can work at a large distance and one that cannot is that the former bears a particularly strong activating region; the stronger the activating region, the more readily the activator interacts with its target bound near the transcriptional start site, with the intervening DNA looping out to accommodate the reaction. One alternative view is that the effect of proteins bound to enhancers might require some special aspect of cellular or chromosome structure. Consistent with the first view, an activator bearing an unusually potent activating region can stimulate transcription of a mammalian gene in a HeLa nuclear extract when bound as far as 1.3 kilobase pairs upstream or 320 base pairs downstream of the transcriptional start site.