gebhart/patrepeval huggingface dataset:
Identification of a recurrent transforming UBR5–ZNF423 fusion gene in EBV‐associated nasopharyngeal carcinoma (2013)

Nasopharyngeal carcinoma (NPC) is a distinct type of head and neck cancer which is prevalent in southern China, south-east Asia and northern Africa. The development and stepwise progression of NPC involves accumulation of multiple gross genetic changes during the clonal expansion of Epstein-Barr virus (EBV)-infected nasopharyngeal epithelial cell population. Here, using paired-end whole-transcriptome sequencing, we discovered a number of chimeric fusion transcripts in a panel of EBV-positive tumour lines. Among these transcripts, a novel fusion of ubiquitin protein ligase E3 component n-recognin 5 (UBR5) on 8q22.3 and zinc finger protein 423 (ZNF423) on 16q12.1, identified from the NPC cell line C666-1, was recurrently detected in 12/144 (8.3%) of primary tumours. The fusion gene contains exon 1 of UBR5 and exons 7-9 of ZNF423 and produces a 94 amino acid chimeric protein including the original C-terminal EBF binding domain (ZF29-30) of ZNF423. Notably, the growth of NPC cells with UBR5-ZNF423 rearrangement is dependent on expression of this fusion protein. Knock-down of UBR5-ZNF423 by fusion-specific siRNA significantly inhibited the cell proliferation and colony-forming ability of C666-1 cells. The transforming ability of UBR5-ZNF423 fusion was also confirmed in NIH3T3 fibroblasts. Constitutive expression of UBR5-ZNF423 in NIH3T3 fibroblasts significantly enhanced its anchorage-independent growth in soft agar and induced tumour formation in a nude mouse model. These findings suggest that expression of UBR5-ZNF423 protein might contribute to the transformation of a subset of NPCs, possibly by altering the activity of EBFs (early B cell factors). Identification of the oncogenic UBR5-ZNF423 provides new potential opportunities for therapeutic intervention in NPC.
Novel retroviral vectors to facilitate expression screens in mammalian cells (2002)

As tools for functional genomics, expression profiling and proteomics provide correlative data, while expression cloning screens can link genes directly to biological function. However, technical limitations of gene transfer, expression, and recovery of candidate genes have limited wider application of genome-wide expression screens. Here we describe the pEYK retroviral vectors, which maintain high titers and robust gene expression while addressing the major bottleneck of expression cloning--efficient candidate gene recovery. By exploiting schemes for enhanced PCR rescue or strategies for direct isolation of proviral DNA as plasmids in bacterial hosts, the pEYK vectors facilitate cDNA isolation from selected cells and enable rapid iteration of screens and genetic reversion analyses to validate gene candidates. These vectors have proven useful to identify genes linked to cell proliferation, senescence and apoptosis.
Secure internet access to SAP’s R–3: keeping dragons out (1998)

The security of the networking environment is critical for today’s corporations. Issues such as reliably identifying remote-access users, checking authorizations, data-transfer security and database security are of paramount importance. This article discusses a resolution of these problems for the Rs3 environment using CYBERSHIELD†. © 1998 John Wiley & Sons, Ltd.
尼日利亚的职业技术教育与培训：21世纪的问题、焦点以及新趋势 (2009)

本文的主题是通过职业技术教育和培训（TVET）实现人力资源开发与工作世界的紧密结合。成功的人力资源开发与制定谨慎和有效的教育战略计划密不可分。本文以尼日利亚为个案,所提出的框架,力求将教育产出与社会经济发展的需求相匹配,以实现更有效的人力资源开发。
High Expression of Inhibitory Receptor SHPS-1 and Its Association with Protein-tyrosine Phosphatase SHP-1 in Macrophages (1998)

SHPS-1 (or SIRP) is a member of the immunoglobulin (Ig) superfamily abundantly expressed in neurons and other cell types. Within its cytoplasmic domain, it possesses at least two immunoreceptor tyrosine-based inhibitory motifs, which are targets for tyrosine phosphorylation and mediate the recruitment of SHP-2, an Src homology 2 (SH2) domain-containing protein-tyrosine phosphatase. Since other immunoreceptor tyrosine-based inhibitory motifs-containing receptors have critical roles in the negative regulation of hemopoietic cell functions, we wanted to examine the expression of SHPS-1 in cells of hematological lineages. By analyzing a panel of hemopoietic cell lines, evidence was provided that SHPS-1 is abundantly expressed in macrophages and, to a lesser extent, in myeloid cells. No expression was detected in T-cell or B-cell lines. Expression of SHPS-1 could also be documented in normal ex vivo peritoneal macrophages. Further studies showed that SHPS-1 was an efficient tyrosine phosphorylation substrate in macrophages. However, unlike in non-hemopoietic cells, tyrosine-phosphorylated SHPS-1 in macrophages associated primarily with SHP-1 and not SHP-2. Finally, our analyses allowed us to identify several isoforms of SHPS-1 in mouse cells. In part, this heterogeneity was due to differential glycosylation of SHPS-1. Additionally, it was caused by the production of at least two distinct shps-1 transcripts, coding for SHPS-1 polypeptides having different numbers of Ig-like domains in the extracellular region. Taken together, these findings indicate that SHPS-1 is likely to play a significant role in macrophages, at least partially as a consequence of its capacity to recruit SHP-1.
Disk-Shaped Stacked Capacitor Cell for 256 Mb Dynamic Random-Access Memory (1994)

A new cell structure using the disk-shaped stacked capacitor is proposed for 256 Mb dynamic random-access memory (DRAM). This capacitor structure is formed on the sidewall of a cylindrical storage node by means of a self-alignment method. The lithographic process of the disk-shaped storage node is the same as that of the cylindrical one. The distance between adjacent storage node patterns of 0.1 µ m can be realized beyond the limits set by lithographic resolution. It is estimated that the capacitance of 25 fF/cell can be obtained in the 0.4 µ m storage node height in a 0.72 µ m 2 cell area. The disk-shaped stacked capacitor, to which ON dielectric film ( t eq =4 or 5 nm) is applied, is investigated with regard to electrical characteristics.
Montelukast, a Once-Daily Leukotriene Receptor Antagonist, in the Treatment of Chronic Asthma<subtitle>A Multicenter, Randomized, Double-blind Trial</subtitle> (1998)

Montelukast, compared with placebo, significantly improved asthma control during a 12-week treatment period. Montelukast was generally well tolerated, with an adverse event profile comparable with that of placebo.
Basic Biology of Fungi (1996)

Macroscopic fungi such as morels, mushrooms, puffballs, and the cultivated agarics available in grocery stores represent only a small fraction of the diversity in the kingdom Fungi. The molds, for example, are a large group of microscopic fungi that include many of the economically important plant parasites, allergenic species, and opportunistic pathogens of humans and other animals. They are characterized by filamentous, vegetative cells called hyphae. A mass of hyphae forms the thallus (vegetative body) of the fungus, composed of mycelium. The more phylogenetically primitive molds (e.g., water molds, bread molds, and other sporangial—saclike—forms) produce cenocytic filaments (multinucleate cells without cross-walls), while the more advanced forms produce hyphae with cross-walls (septa) that subdivide the filament into uninucleate and multinucleate compartments. The septum, however, still provides for cytoplasmic communication, including intercellular migration of nuclei. Many fungi occur not as hyphae but as unicellular forms called yeasts, which reproduce vegetatively by budding. Some of the opportunistic fungal pathogens of humans are dimorphic, growing as a mycelium in nature and as a vegetatively reproducing yeast in the body. Candida is an example of such a dimorphic fungus (Fig. 73-1). It can undergo rapid transformation from the yeast to the hyphal phase in vivo, which partly contributes to its success in invading host tissue.The true fungi obtain their carbon compounds from nonliving organic substrates (saprophytes) or living organic material (parasites) by absorption of nutrients through their cell wall. Small molecules (e.g., simple sugars and amino acids) accumulate in a watery film surrounding the hyphae or yeast and simply diffuse through the cell wall. Macromolecules and insoluble polymers (e.g., proteins, glycogen, starch, and cellulose), on the other hand, must undergo preliminary digestion before they can be absorbed by the fungal cell. This process involves release of specific proteolytic, glycolytic, or lipolytic enzymes from the hypha or yeast, extracellular breakdown of the substrate(s), and diffusion of the products of digestion through the fungal cell envelope (Fig. 73-2). Fungal pathogens rely on these digestive enzymes to penetrate natural host barriers.
Expression of hepatitis B surface antigen with a recombinant adenovirus. (1985)

Early region 1 of the adenovirus type 5 genome was replaced with a DNA sequence containing the gene coding for the hepatitis B surface antigen (HBsAg) flanked by the major late promoter from adenovirus 2 and processing and polyadenylylation signals from simian virus 40. In one type of hybrid virus only the adenovirus 2 major late promoter, including just 33 base pairs of the adenovirus type 2 tripartite leader, preceded the coding region of the HBsAg gene. In another, this region was preceded by both the adenovirus major late promoter and almost the entire tripartite leader. The structure of the substituted sequence in each of the recombinant viral DNAs was identical to that in the plasmids used to construct the viruses. Approximately equivalent amounts of HBsAg-specific mRNA were produced late in infection with each recombinant virus. Although HBsAg production was detected late in infection of the hybrid virus not containing the full tripartite leader sequence, its level was 1/70th of that obtained with the hybrid virus containing this sequence. One likely interpretation is that the presence of the tripartite leader at the 5' end of this mRNA is critical for the synthesis of HBsAg polypeptide in the late stage of infection. HBsAg produced upon infection with the hybrid adenoviruses was glycosylated and secreted into the culture medium as particles that were essentially indistinguishable from the 22-nm particles found in human serum.
Sharp versus smooth synchronization transition of locally coupled oscillators (2008)

We provide a general condition for the occurrence of a sudden transition to synchronization in an array of oscillators mutually coupled via the nearest neighbors. At the onset of synchronization a specific constraint must be fulfilled: precisely, the response time of a single system to signals from the adjacent sites must be smaller than the refractory period. We verify this criterion in some models for neuronal dynamics, namely, in excitable systems driven by noise as well as in chaotic oscillators.
New Strategic Reactions for Organic Synthesis:  Catalytic Asymmetric C−H Activation α to Nitrogen as a Surrogate for the Mannich Reaction (2003)

The asymmetric C-H activation reactions of methyl aryldiazoacetates are readily induced by the rhodium prolinate catalyst Rh(2)(S-DOSP)(4) (1) or the bridged prolinate catalysts Rh(2)(S-biDOSP)(2) (2a) and Rh(2)(S-biTISP)(2) (2b). The C-H activation of N-Boc-protected cyclic amines demonstrates that the donor/acceptor-substituted carbenoids display remarkable chemoselectivity, which allows for highly regioselective, diastereoselective, and enantioselective reactions to be achieved. Furthermore, the reactions can display high levels of double stereodifferentiation and kinetic resolution. The C-H activation is caused by a rhodium carbenoid induced C-H insertion. The potential of this chemistry is demonstrated by a very direct synthesis of threo-methylphenidate.
Declining Morbidity and Mortality among Patients with Advanced Human Immunodeficiency Virus Infection (1998)

The recent declines in morbidity and mortality due to AIDS are attributable to the use of more intensive antiretroviral therapies.
Linear 2' O-Methyl RNA probes for the visualization of RNA in living cells (2001)

U1snRNA, U3snRNA, 28 S ribosomal RNA, poly(A) RNA and a specific messenger RNA were visualized in living cells with microinjected fluorochrome-labeled 2' O-Methyl oligoribonucleotides (2' OMe RNA). Antisense 2' OMe RNA probes showed fast hybridization kinetics, whereas conventional oligodeoxyribonucleotide (DNA) probes did not. The nuclear distributions of the signals in living cells were similar to those found in fixed cells, indicating specific hybridization. Cytoplasmic ribosomal RNA, poly(A) RNA and mRNA could hardly be visualized, mainly due to a rapid entrapment of the injected probes in the nucleus. The performance of linear probes was compared with that of molecular beacons, which due to their structure should theoretically fluoresce only upon hybridization. No improvements were achieved however with the molecular beacons used in this study, suggesting opening of the beacons by mechanisms other than hybridization. The results show that linear 2' OMe RNA probes are well suited for RNA detection in living cells, and that these probes can be applied for dynamic studies of highly abundant nuclear RNA. Furthermore, it proved feasible to combine RNA detection with that of green fluorescent protein-labeled proteins in living cells. This was applied to show co-localization of RNA with proteins and should enable RNA-protein interaction studies.
Miniature optical coherence tomography-ultrasound probe for automatically coregistered three-dimensional intracoronary imaging with real-time display (2013)

We have developed a novel miniature integrated optical coherence tomography (OCT)-intravascular ultrasound (IVUS) probe, with a 1.5-mm-long rigid part and 0.9-mm outer diameter, for real-time intracoronary imaging of atherosclerotic plaques and guiding of interventional procedures. By placing the OCT ball lens and IVUS transducer back-to-back at the same axial position, this probe can provide automatically coregistered, coaxial OCT-IVUS imaging. To demonstrate its real-time capability, three-dimensional OCT-IVUS imaging of a pig's coronary artery displaying in polar coordinates, as well as images of three major types of atherosclerotic plaques in human cadaver coronary segments, were obtained using this probe and our upgraded system. Histology validation is also presented.
The Shp-2 Tyrosine Phosphatase Has Opposite Effects in Mediating the Activation of Extracellular Signal-regulated and c-Jun NH2-terminal Mitogen-activated Protein Kinases (1998)

Shp-2 is a widely expressed cytoplasmic tyrosine phosphatase with two SH2 domains. A targeted mutant allele of the Shp-2 gene with a deletion of 65 amino acids in the NH2-terminal SH2 domain was created that leads to embryonic lethality at mid-gestation in homozygous mutant mice. To define the Shp-2 function in cell signaling, we have established mutant fibroblast cell lines, and have examined the effect of the Shp-2 mutation on extracellular signal-regulated kinase (ERK) and c-Jun NH2-terminal kinase (JNK) mitogen-activated protein (MAP) kinase pathways. Insulin-like growth factor (IGF)-I-induced ERK activation was completely abolished, while ERK activity upon platelet-derived growth factor and epidermal growth factor stimulation was significantly reduced and shortened in mutant cells. Stimulation of ERK by phorbol 12-myristate 13-acetate was not affected in mutant cells, but the phorbol 12-myristate 13-acetate-induced ERK activity decayed much faster compared with that in wild-type cells. In contrast, JNK activation upon heat shock was significantly enhanced in Shp-2 mutant cells. Based on these results, we conclude that Shp-2 plays differential positive regulatory roles in various mitogenic signaling pathways leading to ERK activation, and that Shp-2 is a negative effector in JNK activation by cellular stress. This is the first evidence that a tyrosine phosphatase has opposite effects in mediating the activation of ERK and JNK MAP kinases.
sFLT01: A Novel Fusion Protein with Antiangiogenic Activity (2011)

sFLT01 is a novel fusion protein that consists of the VEGF/PlGF (placental growth factor) binding domain of human VEGFR1/Flt-1 (hVEGFR1) fused to the Fc portion of human IgG(1) through a polyglycine linker. It binds to both human VEGF (hVEGF) and human PlGF (hPlGF) and to mouse VEGF (mVEGF) and mouse PlGF (mPlGF). In vitro, sFLT01 inhibited the proliferation of human umbilical vein endothelial cells and pericytes stimulated by either hVEGF or hPlGF. In vivo, sFLT01 had robust and significant antitumor activity in numerous preclinical subcutaneous tumor models including H460 non-small cell lung carcinoma, HT29 colon carcinoma, Karpas 299 lymphoma, MOLM-13 AML (acute myeloid leukemia), 786-O, and RENCA renal cell carcinoma (RCC). sFLT01 also increased median survival in the orthotopic RENCA RCC model. sFLT01 had strong antiangiogenic activity and altered intratumoral microvessel density, blood vessel lumen size and perimeter, and vascular and vessel areas in RCC models. sFLT01 treatment resulted in fewer endothelial cells and pericytes within the tumor microenvironment. sFLT01 in combination with cyclophosphamide resulted in greater inhibition of tumor growth than either agent used alone as a monotherapy in the A673 Ewing's sarcoma model. Gene expression profiling indicated that the molecular changes in the A673 sarcoma tumors are similar to changes observed under hypoxic conditions. sFLT01 is an innovative fusion protein that possessed robust antitumor and antiangiogenic activities in preclinical cancer models. It is a dual targeting agent that neutralizes both VEGF and PlGF and, therefore, has potential as a next generation antiangiogenic therapeutic for oncology.
The Emerging Role of Epigenetics in Stroke (2011)

The transplantation of exogenous stem cells and the activation of endogenous neural stem and progenitor cells (NSPCs) are promising treatments for stroke. These cells can modulate intrinsic responses to ischemic injury and may even integrate directly into damaged neural networks. However, the neuroprotective and neural regenerative effects that can be mediated by these cells are limited and may even be deleterious. Epigenetic reprogramming represents a novel strategy for enhancing the intrinsic potential of the brain to protect and repair itself by modulating pathologic neural gene expression and promoting the recapitulation of seminal neural developmental processes. In fact, recent evidence suggests that emerging epigenetic mechanisms are critical for orchestrating nearly every aspect of neural development and homeostasis, including brain patterning, neural stem cell maintenance, neurogenesis and gliogenesis, neural subtype specification, and synaptic and neural network connectivity and plasticity. In this review, we survey the therapeutic potential of exogenous stem cells and endogenous NSPCs and highlight innovative technological approaches for designing, developing, and delivering epigenetic therapies for targeted reprogramming of endogenous pools of NSPCs, neural cells at risk, and dysfunctional neural networks to rescue and restore neurologic function in the ischemic brain.
Selective amplification of the cytoplasmic domain of the epidermal growth factor receptor gene in glioblastoma multiforme. (1988)

Primary brain tumors of glial origin often overexpress epidermal growth factor receptors (EGF-Rs). This may be associated with amplification of the EGF-R gene. We have examined tissue from 23 glioblastoma multiforme tumors and found amplification and rearrangement of the EGF-R gene in four of these. The cytoplasmic domain of the EGF-R gene was invariably amplified in these four tumors, while the epidermal growth factor binding domain was not uniformly amplified in three of these tumors. Western blot analysis of the EGF-R protein revealed high levels of a truncated EGF-R protein in two of the four tumors with EGF-R gene amplification.
ERK8, a New Member of the Mitogen-activated Protein Kinase Family (2002)

The ERKs are a subfamily of the MAPKs that have been implicated in cell growth and differentiation. By using the rat ERK7 cDNA to screen a human multiple tissue cDNA library, we identified a new member of the ERK family, ERK8, that shares 69% amino acid sequence identity with ERK7. Northern analysis demonstrates that ERK8 is present in a number of tissues with maximal expression in the lung and kidney. Fluorescence in situ hybridization localized the ERK8 gene to chromosome 8, band q24.3. Expression of ERK8 in COS cells and bacteria indicates that, in contrast to constitutively active ERK7, ERK8 has minimal basal kinase activity and a unique substrate profile. ERK8, which contains two SH3-binding motifs in its C-terminal region, associates with the c-Src SH3 domain in vitro and co-immunoprecipitates with c-Src in vivo. Co-transfection with either v-Src or a constitutively active c-Src increases ERK8 activation indicating that ERK8 can be activated downstream of c-Src. ERK8 is also activated following serum stimulation, and the extent of this activation is reduced by pretreatment with the specific Src family inhibitor PP2. The ERK8 activation by serum or Src was not affected by the MEK inhibitor U0126 indicating that activation of ERK8 does not require MEK1, MEK2, or MEK5. Although most closely related to ERK7, the relatively low sequence identity, minimal basal activity, and different substrate profile identify ERK8 as a distinct member of the MAPK family that is activated by an Src-dependent signaling pathway.
Marine Toxins as Sources of Drug Leads (2003)

Conotoxins, a class of marine peptides rich in disulfide bonds, contain many of the structural elements present in larger proteins, such as α-helices and β-turns. In addition, these natural products are remarkably stable and exhibit exceptional receptor selectivity. These properties make them ideal candidates for drug development.
High-Throughput Proteomics Using High-Efficiency Multiple-Capillary Liquid Chromatography with On-Line High-Performance ESI FTICR Mass Spectrometry (2001)

We report on the design and application of a high-efficiency multiple-capillary liquid chromatography (LC) system for high-throughput proteome analysis. The multiple-capillary LC system using commercial LC pumps was operated at a pressure of 10,000 psi to deliver mobile phases through a novel passive feedback valve arrangement that permitted mobile-phase flow path switching and efficient sample introduction. The multiple-capillary LC system uses several serially connected dual-capillary column devices. The dual-capillary column approach eliminates the time delays for column regeneration (or equilibration) since one capillary column was used for a separation while the other was being washed. Several serially connected dual-capillary columns and electrospray ionization (ESI) sources were operated independently and can be used either for "backup" operation or for parallel operation with other mass spectrometers. This high-efficiency multiple-capillary LC system utilizes switching valves for all operations, enabling automated operation. The separation efficiency of the dual-capillary column arrangement, optimal capillary dimensions (column length and packed particle size), capillary regeneration conditions, and mobile-phase compositions and their compatibility with electrospray ionization were investigated. A high magnetic field (11.4 T) Fourier transform ion cyclotron resonance (FTICR) mass spectrometer was coupled on-line with this high-efficiency multiple-capillary LC system using an ESI interface. The capillary LC provided a peak capacity of approximately 650, and the 2-D capillary LC-FTICR analysis provided a combined resolving power of > 6 x 10(7) components. For yeast cytosolic tryptic digests > 100,000 polypeptides were detected, and approximately 1,000 proteins could be characterized from a single capillary LC-FTICR analysis using the high mass measurement accuracy (approximately 1 ppm) of FTICR, and likely more if LC retention time information were also exploited for peptide identification.