gebhart/patrepeval huggingface dataset:
cDNA cloning and tissue distribution of five human EPH-like receptor protein-tyrosine kinases. (1995)

We have isolated cDNA clones from a human fetal brain library that encode five members of the EPH sub-family of receptor protein tyrosine kinases (PTKs). Comparison of the DNA sequences of these receptors to the Genbank database reveals that two of our clones correspond to the previously identified HEK and ERK receptors, two are apparently human homologues of the mouse receptors Sek and Bsk and one is novel. With these additions, the number of known human EPH sub-family members is nine and the total in all vertebrate species is 13 making it the largest known sub-family of PTKs. Analysis of the expression pattern of EPH sub-family mRNAs reveals that some are expressed in a wide variety of adult tissues while others are quite restricted. Consistent with the amplification of these sequences from a fetal brain cDNA library, all five members which we have isolated are expressed in the brain. We have named these receptors HEK4, HEK5, HEK7, HEK8 and HEK11, following the nomenclature of Wicks et al. (1992) and the numbering convention set forth by Sajjadi et al. (1991). Analysis of these new EPH sub-family members will increase our understanding of the biology of this receptor family and their isolation will provide reagents for the identification of ligands for this large family of orphan receptors.
Solution structure and dynamics of a serpin reactive site loop using interleukin 1β as a presentation scaffold (1999)

Human interleukin-1beta (IL1beta) was used as a presentation scaffold for the characterization of the reactive site loop (RSL) of the serpin alpha1-antitrypsin (A1AT), the physiological inhibitor of leukocyte elastase. A chimeric protein was generated by replacement of residues 50-53 of IL1beta, corresponding to an exposed reverse turn in IL1beta, with the 10-residue P5-P5' sequence EAIPMSIPPE from A1AT. The chimera (antitrypsin-interleukin, AT-IL) inhibits elastase specifically and also binds the IL1beta receptor. Multinuclear NMR characterization of AT-IL established that, with the exception of the inserted sequence, the structure of the IL1beta scaffold is preserved in the chimera. The structure of the inserted RSL was analyzed relative to that of the isolated 10-residue RSL peptide, which was shown to be essentially disordered in solution. The chimeric RSL was also found to be solvent exposed and conformationally mobile in comparison with the IL1beta scaffold, and there was no evidence of persisting interactions with the scaffold outside of the N- and C-terminal linkages. However, AT-IL exhibits sigificant differences in chemical shift and NOE patterns relative to the isolated RSL that are consistent with local features of non-random structure. The proximity of these features to the P1-P1' residues suggests that they may be responsible for the inhibitory activity of the chimera.
Tuberöse Sklerose und organische bipolare Störung bei einer 15jährigen Jugendlichen (1999)

We present the case of a 15-year-old girl with tuberous sclerosis who developed rapid cycling bipolar disorder under treatment with the anticonsulvant oxcarbazepine. Because of first occurrence of grand mal-seizures combined treatment with Valproate became necessary, but failed to prevent relapses of bipolar disorder. Mood stabilization was noticed under additional treatment with lithium, which was complicated by an increase of serum potassium.
Proper maturation of the Japanese encephalitis virus envelope glycoprotein requires cosynthesis with the premembrane protein (1993)

The role of the Japanese encephalitis virus (JEV) premembrane (prM) protein in maturation of the envelope (E) glycoprotein was evaluated by using recombinant vaccinia viruses encoding E in the presence (vP829) or absence (vP658) of prM. Immunofluorescence analyses showed that E appeared to be localized in the endoplasmic reticulum of cells infected with JEV, vP829, or vP658. However, reactivity with monoclonal antibodies and behavior in Triton X-114 indicated that E produced in the absence of prM behaved abnormally. Furthermore, E produced in the presence of prM by recombinant vaccinia viruses could be incorporated into flavivirus pseudotypes, whereas E synthesized in the absence of prM could not. These results demonstrate that cosynthesis of prM is required for proper folding, membrane association, and assembly of the flavivirus E protein.
A Chemical View of Oligonucleotides for Exon Skipping and Related Drug Applications (2013)

protein kinase; EI, exon inclusion; ES, exon skipping; LDL, lowdensity lipoprotein; LNA, locked nucleic acid; MCE, 2¢-O-[2-(N
Medical Biomethods Handbook (2005)

The purpose of the Medical Biomethods Handbook it to introduce the reader to a wide-ranging selection of those molecular biology techniques that are most frequently used by research workers in the field of medical and clinical research.
The anthelmintic drug mebendazole induces mitotic arrest and apoptosis by depolymerizing tubulin in non-small cell lung cancer cells. (2002)

Microtubules have a critical role in cell division, and consequently various microtubule inhibitors have been developed as anticancer drugs. In this study, we assess mebendazole (MZ), a microtubule-disrupting anthelmintic that exhibits a potent antitumor property both in vitro and in vivo. Treatment of lung cancer cell lines with MZ caused mitotic arrest, followed by apoptotic cell death with the feature of caspase activation and cytochrome c release. MZ induces abnormal spindle formation in mitotic cancer cells and enhances the depolymerization of tubulin, but the efficacy of depolymerization by MZ is lower than that by nocodazole. Oral administration of MZ in mice elicited a strong antitumor effect in a s.c. model and reduced lung colonies in experimentally induced lung metastasis without any toxicity when compared with paclitaxel-treated mice. We speculate that tumor cells may be defective in one mitotic checkpoint function and sensitive to the spindle inhibitor MZ. Abnormal spindle formation may be the key factor determining whether a cell undergoes apoptosis, whereas strong microtubule inhibitors elicit toxicity even in normal cells.
Developmental Regulation of Genes for Microsome and Plastid -3 Fatty Acid Desaturases in Wheat (Triticum aestivum L.) (1998)

ω3 fatty acid desaturase is responsible for the production of α-linolenic acid, which is a major fatty acid constituent of membrane lipids in higher plants. In this study, the developmental regulation of the expression of two genes, TaFAD3 and TaFAD7, which respectively encode the microsome and plastid ω3 fatty acid desaturases in wheat, was analyzed by in situ hybridization. The transcript of TaFAD3 was abundant in the apical meristems of both shoot and root, the leaf primordium, the leaf basal intercalary meristem, and the root vascular tissues. The level of TaFAD3 mRNA was also high in embryos developing after flowering. In mature embryos, however, it was low, whereas in germinating embryos it was once again high. These results suggest that the TaFAD3 mRNA is accumulated at a high level in cells that have an ability to proliferate. In contrast, the TaFAD7 mRNA level was very low in the shoot apical meristem, leaf primordium and leaf basal intercalary meristem, but a large accumulation of TaFAD7 mRNA was found in green tissues, suggesting that the accu? mutation of this mRNA is associated with chloroplast development. Although the spatial distribution patterns of TaFAD3 and TaFAD7 mRNAs clearly differed, the enhanced accumulation of the TaFAD3 and TaFAD 7 mRNAs was linked with the active membrane biogenesis required for cell division and with the development of the thylakoid system in plastids, respectively.
Oncogenic mutations of the p53 tumor suppressor: the demons of the guardian of the genome. (2000)

The p53 guardian of the genome is inactivated in the majority of cancers, mostly through missense mutations that cause single residue changes in the DNA binding core domain of the protein. Not only do such mutations result in the abrogation of wild-type p53 activity, but the expressed p53 mutant proteins also tend to gain oncogenic functions, such as interference with wild-type p53-independent apoptosis. Because p53 mutants are highly expressed in cancer cells and not in normal cells, their reactivation to wild-type p53 function may eliminate the cancer by apoptosis or another p53-dependent mechanism. Several studies that embarked on this quest for reactivation have succeeded in restoring wildtype p53 activity to several p53 mutants. However, mutants with more extensive structural changes in the DNA binding core domain may be refractory to reactivation to the wild-type p53 phenotype. Therefore, understanding the structure and functions of oncogenic p53 mutants may lead to more potent reactivation modalities or to the ability to eliminate mutant p53 gain of function.
Biosynthesis, primary structure and molecular cloning of snowdrop (Galanthus nivalis L.) lectin (1991)

Poly(A)-rich RNA isolated from ripening ovaries of snowdrop (Galanthus nivalis L.) yielded a single 17-kDa lectin polypeptide upon translation in a wheat-germ cell-free system. This lectin was purified by affinity chromatography. Translation of the same RNA in Xenopus leavis oocytes revealed a lectin polypeptide which was about 2 kDa smaller than the in vitro synthesized precursor, suggesting that the oocyte system had removed a 2-kDa signal peptide. A second post-translational processing step was likely to be involved since both the in vivo precursor and the Xenopus translation products were about 2 kDa larger than the mature lectin polypeptide. This hypothesis was confirmed by the structural analysis of the amino acid sequence of the mature protein and the cloned mRNA. Edman degradation and carboxypeptidase Y digestion of the mature protein, and structural analysis of the peptides obtained after chemical cleavage and modification, allowed determination of the complete 105 amino acid sequence of the snowdrop lectin polypeptide. Comparison of this sequence with the deduced amino acid sequence of a lectin cDNA clone revealed that besides the mature lectin polypeptide, the lectin mRNA also encoded a 23 amino acid signal-sequence and a C-terminal extension of 29 amino acids, which confirms the results from in vitro translation experiments.
Patent Internal Carotid Artery with Collateral Circulation from Contralateral External Carotid Artery after Common Carotid Artery Occlusion (2011)

Received April 6, 2010 Revised July 26, 2010 Accepted July 26, 2010 *Eung-Gyu Kim, MD Department of Neurology, Inje University College of Medicine, Busan Paik Hospital, Gaegeum-dong, Busanjin-gu, Busan 614-110, Korea Tel: +82-51-890-6248 Fax: +82-51-895-6367 E-mail: kgstroke@korea.com 동맥 협착(stenosis)이나 폐색(occlusion) 후에 곁순환(collateral circulation)이 생기는 것은 이미 알려져있다. 특히, 온목동맥 폐색(common carotid artery occlusion, CCAO) 의 경우에 원위부(distal) 속목동맥(internal carotid artery, ICA)혈류가 동측 바깥목동맥(external carotid artery, ECA) 에 의해서 유지된다는 보고는 많고 반대쪽 동맥에 의해 혈류가 유지되는 증례 보고가 외국에는 있었지만 국내에서는 보고된 바가 없다. 그래서 본 저자들은 우측 ICA의 심한 협착과 좌측 CCAO에 도 불구하고, 우측 ECA 가지-좌측 ECA 가지 사이에 곁순환 형 성 및 좌측 ECA의 역흐름을 통해 좌측 원위부 ICA에 혈류가 유 지되었던 예를 소개하고자 한다. 증 례
Speculative execution for information gathering plans (2002)

Although information gathering plans have enabled data from remote heterogeneous sources to be easily combined and queried, their execution performance suffers because access to remote sources is often slow. To address this problem, we have developed a method of speculative execution that increases the degree of run-time parallelism during plan execution. Our approach allows any information gathering plan to be automatically modified to support speculation in a manner that can lead to significant speedups, while ensuring that both safety and fairness are preserved. We demonstrate how speculative execution can be applied to a typical Internet information gathering plan to provide significant performance benefits.
Trichostatin and Leptomycin: Inhibition of Histone Deacetylation and Signal‐Dependent Nuclear Export (1999)

Trichostatin A (TSA), an inhibitor of the eukaryotic cell cycle and an inducer of morphological reversion of transformed cells, inhibits histone deacetylase (HDAC) at nanomolar concentrations. Recently, trapoxin, oxamflatin, and FR901228, antitumor agents structurally unrelated to TSA, were found to be potent HDAC inhibitors. These inhibitors activate expression of p21Waf1 and 16INK4A in a p53-independent manner. Changes in the expression of these cell cycle regulators by an increase in histone acetylation may be responsible for cell cycle arrest and antitumor activity by HDAC inhibitors. The target molecule of leptomycin B (LMB), a potent antitumor agent, was genetically and biochemically identified as CRM1, a protein reported as being required for chromosome structure control. We showed that CRM1 was a receptor for the nuclear export signal (NES) and that LMB inhibited nuclear export of proteins. Using LMB, we identified a novel NES in fission yeast transcription factor Pap1, the function of which is abolished by oxidative stress in a manner conserved in eukaryotes.
Evaluation of androgen, estrogen (ER alpha and ER beta), and progesterone receptor expression in human prostate cancer by real-time quantitative reverse transcription-polymerase chain reaction assays. (2001)

Steroid hormones can have profound effects on prostate tumor development making it important to define steroid receptor expression in prostate tissues. For this purpose, androgen receptor (AR) and estrogen receptor (ER alpha and ER beta) expression was quantified in 12 clinically localized and 11 hormone-refractory sporadic prostate tumors, using real-time quantitative reverse transcription-PCR assays. To gain more insight into hormone-responsiveness, estrogen-regulated progesterone receptor (PGR) and androgen-regulated prostatic acid phosphatase (PAP) mRNA levels were also quantified. There is a decrease in expression of ER beta in both clinically localized and hormone-refractory tumors relative to normal prostate tissues. Moreover, hormone-refractory tumors display a decreased expression of ER alpha and an increased expression of AR. There is a positive association between ER alpha, ER beta, and PGR expression (P < 0.0001) and a negative association between AR and the androgen-regulated gene PAP expression in hormone-refractory tumors. Taken together, these data indicate that, although increased expression of the AR gene might play a key role in endocrine treatment failure, it cannot be considered as the sole actor of this unresolved dilemma, and abnormalities in ER alpha and/or ER beta expression may also modulate the growth response of prostate cancer to hormone withdrawal. Our results also suggest that ER alpha and ER beta expression status could be used to identify advanced prostate tumor patients who may respond to antiestrogen therapy.
Oral Administration of Both Tetrahydrobiopterin and L-Arginine Prevents Endothelial Dysfunction in Rats With Chronic Renal Failure (2007)

We examined the mechanism of endothelial dysfunction in chronic renal failure (CRF), with reference to NO synthase. CRF was induced by 5/6 nephrectomy in rats. Either L-arginine (1.25 g/L in drinking water), tetrahydrobiopterin (BH4, 10 mg/kg per day in food), or a combination of the 2 were orally administered to CRF rats for 9 weeks. CRF rats showed elevation of systolic blood pressure compared with sham-operated rats. Endothelium-dependent relaxation induced by acetylcholine or A23187 in the isolated aorta was significantly reduced, and in vitro treatment with L-arginine, BH4, or superoxide dismutase restored the relaxation. Aortic segments from CRF rats showed significantly higher superoxide production in response to A23187, which was inhibited by L-NAME. Plasma concentrations of asymmetric dimethylarginine and symmetric dimethylarginine were higher in CRF rats. These changes in CRF rats were totally or partially decreased by L-arginine or BH4 supplementation in vivo. Interestingly, the combined treatment showed additive effects in certain parameters. These results suggest that vascular disorders in CRF rats may be partly due to NOS uncoupling caused by a relative deficiency of BH4 and partially due to accumulation of endogenous inhibitors of NOS and L-arginine uptake, resulting in the decrease of NO production and the increase of reactive oxygen species.
Recent Developments in Primer Design for DNA Markers in Higher Plants (2006)

Primer design is a critical step in the application of PCR-based technologies in genetic diversity analysis of horticultural plants. As more plant genomes have been sequenced in recent years, the emphasis of primer design strategy has shifted to genome-wide and high-throughput direction. This poster summarizes recent advances in primer design for profiling of DNA polymorphism in higher plants, including new primers for the classical plant DNA marker system such as simple sequence repeat (SSR) and single-nucleotide polymorphism (SNPs), as well as newly developed DNA marker systems such as sequence-related amplified polymorphism (SRAP), sequence-specific amplification polymorphism (SSAP), target region amplification polymorphism (TRAP), and universal rice primer (URP). Although most of these primers were designed for agronomical crops, they could be applied to horticultural plants because plant genomes are evolutionarily related. Also, these new primer design strategies could help horticultural researchers develop better primers specifically for profiling of polymorphism in a variety of horticultural crops, invasive weeds, or medicinal plants. We will present examples of their utilization in these diverse systems.
Molecular Characterization and Developmental Expression ofNORPEG, a Novel Gene Induced by Retinoic Acid (2001)

We have characterized NORPEG, a novel gene from human retinal pigment epithelial cells (ARPE-19), in which its expression is induced by all-trans-retinoic acid. Two transcripts ( approximately 3 and approximately 5 kilobases in size) have been detected for this gene, which is localized to chromosome band 5p13.2-13.3. Placenta and testis showed the highest level of expression among various human tissues tested. Six ankyrin repeats and a long coiled-coil domain are present in the predicted sequence of the NORPEG protein, which contains 980 amino acid residues. This approximately 110-kDa protein was transiently expressed in COS-7 cells as a FLAG fusion protein and immunolocalized to the cytoplasm. Confocal microscopic analysis of the NORPEG protein in ARPE-19 cells showed threadlike projections in the cytoplasm reminiscent of the cytoskeleton. Consistent with this localization, the expressed NORPEG protein showed resistance to solubilization by Triton X-100 and KCl. An ortholog of NORPEG characterized from mouse encoded a protein that showed 91% sequence similarity to the human NORPEG protein. The expression of Norpeg mRNA was detected in mouse embryo at embryonic day 9.5 by in situ hybridization, and the expression appears to be developmentally regulated. In adult mouse, the highest level of expression was detected in the seminiferous tubules of testis.
A variable cell culture chamber for ‘open’ and ‘closed’ cultivation, perfusion and high microscopic resolution of living cells (1992)

A multipurpose chamber is described for growing and testing cultured cells. The chamber can be converted from a perfusion chamber to an 'open' or 'closed' culture system. The chamber provides optimum conditions for microscopy using all common objectives and condensers for different microscopic methods.
Adaptive endurance coding for NAND Flash (2010)

A fundamental constraint in the use of newer NAND Flash devices in the enterprise space is the low cycling endurance of such devices. As an example, the latest 2-bit MLC devices have a cycling endurance ranging from 3K to 10K program/erase cycles. Upcoming higher-density devices are expected to have even lower endurance. In this paper we propose a coding technique called Adaptive Endurance Coding (AEC) which increases the number of program/erase cycles that a Flash device can endure. The key insight leveraged by the proposed technique is the data-dependent nature of Flash cell-wear. Data-dependent wear implies that Flash chip/device lifetime can be significantly increased by converting data into bit-patterns, prior to programming, which cause minimal wear. AEC can be used to generate a capacity-wear trade-off; for compressible data, AEC can be adapted to data compressibility in order to maximize endurance gains with low system overhead costs. The technique can be implemented in the Flash device controller without requiring any hardware changes to the device itself. We present empirical results on SLC and MLC Flash chips demonstrating the improvements in retention and bit-error rate which can be obtained via this technique, and present device-level simulation results quantifying the gains achievable by the use of AEC.
Serologic response in human papillomavirus‐associated invasive cervical cancer (1993)

Human papillomavirus (HPV) transforming proteins E6 and E7 are uniformly expressed in HPV-associated cervical cancer. Our objective was to measure antibodies to HPV-16 E6 and E7 proteins in cervical cancer patients using an assay which would detect antibodies to conformational epitopes. Serum specimens obtained from two case-control studies of HPVs and cervical cancer were tested. The studies were performed in Cali, Colombia, South America and in 9 provinces of Spain. Cases consisted of women with invasive cervical cancer associated with HPV-16 or other HPV types and women with HPV-16-associated high-grade cervical intra-epithelial neoplasia (CIN-3). Controls for invasive cases and CIN-3 cases were women who had no cytologic abnormalities and who were matched for age and country of residence. Serum antibodies to HPV-16 E6 and E7 proteins were detected by radio-immunoprecipitation of in vitro translated proteins. Antibodies to the E6 and E7 protein were observed among 56% and 43%, respectively, of invasive cases and 1.7% and 4.1%, respectively, of controls. Antibodies to either protein were detected in 72% of sera from invasive cases and 5.8% of sera from controls. High antibody reactivity and antibodies to both proteins were found almost exclusively in invasive cases. The frequency of antibodies to the E6 protein and the E7 protein among CIN-3 cases did not differ significantly from the CIN-3 controls. Five women with HPV-18-associated invasive cervical cancer were negative for serum antibody to HPV-16 E6 and E7 proteins. Antibodies to HPV-16 E6 and E7 proteins appear to be partially virus-specific and disease state-specific markers of HPV-associated cervical cancer.