gebhart/patrepeval huggingface dataset:
14-3-3 fusion oncogenes in high-grade endometrial stromal sarcoma (2012)

14-3-3 proteins are ubiquitously expressed regulators of various cellular functions, including proliferation, metabolism, and differentiation, and altered 14-3-3 expression is associated with development and progression of cancer. We report a transforming 14-3-3 oncoprotein, which we identified through conventional cytogenetics and whole-transcriptome sequencing analysis as a highly recurrent genetic mechanism in a clinically aggressive form of uterine sarcoma: high-grade endometrial stromal sarcoma (ESS). The 14-3-3 oncoprotein results from a t(10;17) genomic rearrangement, leading to fusion between 14-3-3ε (YWHAE) and either of two nearly identical FAM22 family members (FAM22A or FAM22B). Expression of YWHAE-FAM22 fusion oncoproteins was demonstrated by immunoblot in t(10;17)-bearing frozen tumor and cell line samples. YWHAE-FAM22 fusion gene knockdowns were performed with shRNAs and siRNAs targeting various FAM22A exons in an t(10;17)-bearing ESS cell line (ESS1): Fusion protein expression was inhibited, with corresponding reduction in cell growth and migration. YWHAE-FAM22 maintains a structurally and functionally intact 14-3-3ε (YWHAE) protein-binding domain, which is directed to the nucleus by a FAM22 nuclear localization sequence. In contrast to classic ESS, harboring JAZF1 genetic fusions, YWHAE-FAM22 ESS display high-grade histologic features, a distinct gene-expression profile, and a more aggressive clinical course. Fluorescence in situ hybridization analysis demonstrated absolute specificity of YWHAE-FAM22A/B genetic rearrangement for high-grade ESS, with no fusions detected in other uterine and nonuterine mesenchymal tumors (55 tumor types, n = 827). These discoveries reveal diagnostically and therapeutically relevant models for characterizing aberrant 14-3-3 oncogenic functions.
Emerging Approaches for Regulation and Control of CAR T Cells: A Mini Review (2020)

Chimeric antigen receptor (CAR) T cells have emerged as a promising treatment for patients with advanced B-cell cancers. However, widespread application of the therapy is currently limited by potentially life-threatening toxicities due to a lack of control of the highly potent transfused cells. Researchers have therefore developed several regulatory mechanisms in order to control CAR T cells <i>in vivo</i>. Clinical adoption of these control systems will depend on several factors, including the need for temporal and spatial control, the immunogenicity of the requisite components as well as whether the system allows reversible control or induces permanent elimination. Here we describe currently available and emerging control methods and review their function, advantages, and limitations.
Extracting structural paraphrases from aligned monolingual corpora (2003)

We present an approach for automatically learning paraphrases from aligned monolingual corpora. Our algorithm works by generalizing the syntactic paths between corresponding anchors in aligned sentence pairs. Compared to previous work, structural paraphrases generated by our algorithm tend to be much longer on average, and are capable of capturing long-distance dependencies. In addition to a standalone evaluation of our paraphrases, we also describe a question answering application currently under development that could immensely benefit from automatically-learned structural paraphrases.
First Report of Leaf Spot of Smooth Bromegrass Caused by <i>Pithomyces chartarum</i> in Nebraska (2006)

Smooth bromegrass (Bromus inermis Leyss.) is the most common perennial grass species cultivated for forage in North America. During late fall of 2004, smooth bromegrass plants in Lincoln, NE were observed to have brown lesions on leaf midveins that were several centimeters long. Symptomatic leaves were surface disinfested for 1 min in 2% NaOCl and incubated at 25°C on potato dextrose agar (PDA) and water agar. The fungus, Pithomyces chartarum (Berk. & Curt) Ellis, was isolated consistently and identified on the basis of morphological characteristics (1). Colonies were effused and black on PDA. Conidiophores measured 3.5 to 8 × 1.9 to 3.9 μm and were smooth and single. Conidia (7 to 25 × 9.5 to 14 μm) were broadly ellipsoidal, pale brown to dark brown, verrucose with mainly three transverse septa and one to two longitudinal septa. Pathogenicity tests were conducted on 50-day-old plants by spraying with a conidial suspension (2.5 × 10<sup>5</sup> spores per ml). Control plants were sprayed with sterile water. All plants were kept in a moist chamber (100% relative humidity) for 3 days and then transferred to a greenhouse (25°C, >70% relative humidity, and a 12-h photoperiod). One week after spraying, elongated lesions developed on leaf midveins of inoculated plants from which P. chartarum was consistently reisolated. No symptoms were observed on control plants. While P. chartarum has been described as a saprotroph or a parasite on a wide range of plants primarily in the tropics and subtropics, including the southern United States (2), it was reported previously on B. inermis only in Canada (3). This report expands the distribution and host range of P. chartarum as a pathogen in the United States. References: (1) M. B. Ellis. Dematiaceous Hyphomycetes. Commonwealth Mycological Institute, Kew, Surrey, England, 1971. (2) D. F. Farr et al. Fungal Databases, Systematic Botany and Mycology Laboratory, On-line publication. ARS, USDA, 2005. (3) J. H. Ginns. Compendium of Plant Disease and Decay Fungi in Canada 1960-1980. Res. Br. Can. Agric. Publ. 1813, 1986.
Robo-line storage: Low latency, high capacity storage systems over geographically distributed networks (1991)

Rapid advances in high performance computing are making possible more complete and accurate computer-based modeling of complex physical phenomena, such as weather front interactions, dynamics of chemical reactions, numerical aerodynamic analysis of airframes, and ocean-land-atmosphere interactions. Many of these "grand challenge" applications are as demanding of the underlying storage system, in terms of their capacity and bandwidth requirements, as they are on the computational power of the processor. A global view of the Earth's ocean chlorophyll and land vegetation requires over 2 terabytes of raw satellite image data! <p>In this paper, we describe our planned research program in high capacity, high bandwidth storage systems. The project has four overall goals. First, we will examine new methods for high capacity storage systems, made possible by low cost, small formfactor magnetic and optical tape systems. Second, access to the storage system will be low latency and high bandwidth. To achieve this, we must interleave data transfer at all levels of the storage system, including devices, controllers, servers, and communications links. Latency will be reduced by extensive caching throughout the storage hierarchy. Third, we will provide effective management of a storage hierarchy, extending the techniques already developed by Ousterhout for his Log Structured File System. Finally, we will construct a prototype high capacity file server, suitable for use on the National Research and Education Network (NREN). Such research must be a cornerstone of any coherent program in high performance computing and communications
Harnessing SIP for autonomous mobile peer-to-peer networking (2005)

There are several non-interoperable peer-to-peer (P2P) protocols available today with different functionalities. In order to exploit this functional diversity on mobile devices, we have developed a plug-and-play application platform (PnPAP). PnPAP provides autonomous, dynamic selection between multiple P2P protocols while ensuring the best available network connectivity. In this paper, we introduce methods for utilizing session initiation protocol (SIP) in inter-PnPAP communications. This communication may include downloads of distributed P2P resources such as polymorphic protocol libraries or dynamic state-machine control modules. These components are then used to optimize connectivity management between heterogeneous wireless access networks. In addition, context information may be exchanged between mobile nodes in order to facilitate extended service availability, operability and quality. We analyze the feasibility of merged P2P and All-IP (including SIP) architecture through the novel use of a specialized SIP server and the leveraging of the emerging instant messaging capabilities of SIP. Preliminary measurement results from the prototype implementation on a Symbian platform and test-bed, with overhead and latency analysis, illustrate the feasibility of this approach.
Introduction to Sterilization, Disinfection and Infection Control (1991)

An introduction to the principles and practice of methods used to prevent the spread of infections in health care and related settings. It considers the microbiology and mathematics of sterilization and the methods used to achieve this objective.
Attomolar Protein Detection Using in-Hole Surface Plasmon Resonance (2008)

An in-hole nanohole surface plasmon resonance sensing scheme is demonstrated. Arrays of periodic nanoholes milled through thin layers of SiO(x) and gold were used to detect the binding of organic and biological molecules inside the nanoholes, while blocking the gold surfaces outside the holes. This new approach is more efficient than the previous nanohole array method, where the response was related to binding events taking place inside of the holes and on the top gold surface. The improved sensitivity to binding events and lower detection limit are related to resonant surface plasmon enhanced transmission through the arrays of nanoholes. The sensitivity was found to be 650 nm/RIU and the detection of three attomoles of proteins was estimated from this scheme.
Vectorization of the KENO-IV Code (1986)

The multigroup criticality safety code KENO-IV has been vectorized and tested on the FACOM VP-100 vector processor. At first, the vectorized KENO-IV on a scalar processor was slower than the original one by a factor of 1.4 because of the overhead introduced by vectorization. Making modifications of algorithms and techniques for vectorization, the vectorized version has become faster than the original one by a factor of 1.4 on the vector processor. For further speedup of the code, some improvements on compiler and hardware, especially on addition of Monte Carlo pipelines to the vector processor, are discussed.
Auger Electron Emission from Slow Multicharged Ions Near a Metal Surface (1987)

Electron energy spectra from multicharged ion (N5+, N6+, Ar9+) impact on clean tungsten (impact energies ⩾ 500 eV) revealed Auger electron emission from the projectile particles. The impact energy dependence of emission yield and kinetic-energy shift for these Auger electrons lead to a fairly detailed explanation of slow multicharged ion neutralization near metal surfaces.
Risk and Protective Factors for Drug Use Among Polydrug-Using Urban Youth and Young Adults (2007)

The purpose of the study was to examine the influence of traditional risk and protective factors for drug use on six different popular drugs on a population that is primarily Black and Latino between the ages of 16 and 24. Multiple regression analysis was used to test the relative importance of risk and protective indexes, and their interaction, in predicting drug use. Findings suggested: (a) traditional risk and protective factors, as well as situationally specific factors such as gang involvement, predicted drug use; and(b) the relative contribution of risk and protective factors toward explained variances differs substantially among the drug outcomes. Thus, risk and protective factors may be operating differently for different drugs, indicating that more research is needed into the meanings associated with the use of particular drugs and the factors that may make youth vulnerable to some drugs but not others.
Physiology, biochemistry, and specific inhibitors of CH4, NH4+, and CO oxidation by methanotrophs and nitrifiers (1989)

Ammonia oxidizers (family Nitrobacteraceae) and methanotrophs (family Methylococcaceae) oxidize CO and CH4 to CO2 and NH4+ to NO2-. However, the relative contributions of the two groups of organisms to the metabolism of CO, CH4, and NH4+ in various environments are not known. In the ammonia oxidizers, ammonia monooxygenase, the enzyme responsible for the conversion of NH4+ to NH2OH, also catalyzes the oxidation of CH4 to CH3OH. Ammonia monooxygenase also mediates the transformation of CH3OH to CO2 and cell carbon, but the pathway by which this is done is not known. At least one species of ammonia oxidizer, Nitrosococcus oceanus, exhibits a Km for CH4 oxidation similar to that of methanotrophs. However, the highest rate of CH4 oxidation recorded in an ammonia oxidizer is still five times lower than rates in methanotrophs, and ammonia oxidizers are apparently unable to grow on CH4. Methanotrophs oxidize NH4+ to NH2OH via methane monooxygenase and NH4+ to NH2OH via methane monooxygenase and NH2OH to NO2- via an NH2OH oxidase which may resemble the enzyme found in ammonia oxidizers. Maximum rates of NH4+ oxidation are considerably lower than in ammonia oxidizers, and the affinity for NH4+ is generally lower than in ammonia oxidizers. NH4+ does not apparently support growth in methanotrophs. Both ammonia monooxygenase and methane monooxygenase oxidize CO to CO2, but CO cannot support growth in either ammonia oxidizers or methanotrophs. These organisms have affinities for CO which are comparable to those for their growth substrates and often higher than those in carboxydobacteria. The methane monooxygenases of methanotrophs exist in two forms: a soluble form and a particulate form. The soluble form is well characterized and appears unrelated to the particulate. Ammonia monooxygenase and the particulate methane monooxygenase share a number of similarities. Both enzymes contain copper and are membrane bound. They oxidize a variety of inorganic and organic compounds, and their inhibitor profiles are similar. Inhibitors thought to be specific to ammonia oxidizers have been used in environmental studies of nitrification. However, almost all of the numerous compounds found to inhibit ammonia oxidizers also inhibit methanotrophs, and most of the inhibitors act upon the monooxygenases. Many probably exert their effect by chelating copper, which is essential to the proper functioning of some monooxygenases. The lack of inhibitors specific for one or the other of the two groups of bacteria hampers the determination of their relative roles in nature.
Cellular resolution volumetric in vivo retinal imaging with adaptive optics–optical coherence tomography (2009)

Ultrahigh-resolution adaptive optics-optical coherence tomography (UHR-AO-OCT) instrumentation allowing monochromatic and chromatic aberration correction was used for volumetric in vivo retinal imaging of various retinal structures including the macula and optic nerve head (ONH). Novel visualization methods that simplify AO-OCT data viewing are presented, and include co-registration of AO-OCT volumes with fundus photography and stitching of multiple AO-OCT sub-volumes to create a large field of view (FOV) high-resolution volume. Additionally, we explored the utility of Interactive Science Publishing by linking all presented AO-OCT datasets with the OSA ISP software.
Molecular Pathways of Steroid Receptor Action (1992)

Over the past two decades, a great deal of evidence has accumulated in favor of the hypothesis that steroid hormones act at the level of nuclear DNA to regulate gene expression (Jensen EV, Suzuki T, Kawashima T, Stumpf WE, Jungblut PW, DeSombre ER, Proc Natl Acad Sci USA 1968; 59:632-638; Gorski J, Toft D, Shyamala G, Smith D, Notides A, Rec Prog Horm Res 1968; 24:45-80; O'Malley BW, Means AR, Science 1974; 183:610-620; O'Malley BW, Roop DR, Lai EC, Nordstrom JL, Catterall JF, Swaneck GE, Colbert DA, Tsai M-J, Dugaiczyk A, Woo SLC, Rec Prog Horm Res 1979; 35:1-46). The earliest studies were qualitative and involved experiments showing that steroid hormones (1) cause accumulation of new species of hybridizable RNAs that did not exist prior to stimulation; (2) cause stimulation of synthesis of new specific proteins; (3) cause a corresponding increase in the cellular levels of specific mRNAs; and (4) stimulate the rate of transcription of certain nuclear genes (O'Malley BW, McGuire WL, Kohler PO, Korenman SG, Rec Prog Horm Res 1969; 25:105-000). At that time, the early 1970s, the primary pathway for steroid hormone action was defined as follows: steroid----(steroid-receptor)----(steroid-receptor-DNA)----mRNA----fu nct ional response (O'Malley BW, Roop DR, Lai EC, Nordstrom JL, Catterall JF, Swaneck GE, Colbert DA, Tsai M-J, Dugaiczyk A, Woo SLC, Rec Prog Horm Res 1979; 35:1-46. Steroid enters cells by passive diffusion and allosterically activates receptors in either the cytoplasm or nucleus. The activated receptor binds usually at the 5'-flanking region of target genes and stimulates transcription and protein synthesis.(ABSTRACT TRUNCATED AT 250 WORDS)
Cataract surgery : technique, complications & management (1995)

Evaluation Preparation Extracapsular Techniques Technique of Phacoemulsification Special Techniqies for Cataract Extraction Intraocular Lenses Management of Complications Innovations and Future Trends for Cataract Extraction.
Hexagonally Poled Lithium Niobate: A Two-Dimensional Nonlinear Photonic Crystal (2000)

We report on the fabrication of what we believe is the first example of a two-dimensional (2D) nonlinear photonic crystal [Berger, Phys. Rev. Lett. 81, 4136 (1998)], where the refractive index is constant but where the 2nd order nonlinear susceptibility is spatially periodic. Such crystals allow for efficient quasi-phase-matched 2nd harmonic generation using multiple reciprocal lattice vectors. External 2nd harmonic conversion efficiencies >60% were measured with picosecond pulses. The fabrication technique is extremely versatile and should allow for the fabrication of a broad range of 2D crystals including quasicrystals.
The dopamine transporter gene and Parkinson's disease in a Chinese population (1997)

We studied a variable number tandem repeat polymorphism within the dopamine transporter gene (DAT) for an association with Parkinson's disease in a Chinese population. Five alleles were detected, consisting of 6, 8, 9, 10, and 11 copies of the 40 base pair repeat sequence. The 10-copy allele was most common, accounting for 90% of alleles. There were no significant differences between the patients and the control subjects in the distribution frequencies of the alleles or genotypes. Therefore, this polymorphism is not associated with Parkinson's disease in Chinese populations.
Analysis of<i>CFH</i>,<i>TLR4</i>, and<i>APOE</i>Polymorphism in India Suggests the Tyr402His Variant of<i>CFH</i>to be a Global Marker for Age-Related Macular Degeneration (2006)

The CFH polymorphism Tyr402His appears indicative of AMD pathogenesis. Diabetes, age, and gender in the presence of the homozygous "CC" genotype in CFH carry an increased risk of AMD. Hence this polymorphism could be used as a potential marker for predictive testing across continents.
Difluorostatine and difluorostatone containing peptides as potent and specific renin inhibitors (1985)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTDifluorostatine and difluorostatone containing peptides as potent and specific renin inhibitorsSuvit Thaisrivongs, Donald T. Pals, Warren M. Kati, Steve R. Turner, and Lisa M. ThomascoCite this: J. Med. Chem. 1985, 28, 11, 1553–1555Publication Date (Print):November 1, 1985Publication History Published online1 May 2002Published inissue 1 November 1985https://pubs.acs.org/doi/10.1021/jm00149a001https://doi.org/10.1021/jm00149a001research-articleACS PublicationsRequest reuse permissionsArticle Views166Altmetric-Citations62LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-Alertsclose Get e-Alerts
Cancer‐germline gene expression in pediatric solid tumors using quantitative real‐time PCR (2006)

Cancer-germline genes (CGGs) code for immunogenic antigens that are present on various human tumors but not on normal tissues. The importance of CGGs in cancer immunotherapy has led to detailed studies of their expression in a range of human tumors. We measured the levels of expression of 12 CGGs in various pediatric solid tumors to identify targets for therapeutic cancer vaccines. Quantitative real-time PCR (qPCR) was used to measure the expression of 8 MAGE genes and of genes LAGE-2/NY-ESO-1 and GAGE-1, 2, 8 in 9 osteosarcomas, 10 neuroblastomas, 12 rhabdomyosarcomas and 18 Ewing's sarcomas. Nine tumors were also examined by immunohistochemistry with monoclonal antibodies specific for the MAGE-A1, MAGE-A4 and NY-ESO-1 proteins. All osteosarcoma and 80% of neuroblastoma samples expressed several CGGs at high levels. Six of 12 rhabdomyosarcomas and 11 of 18 Ewing's sarcomas expressed at least one CGG. Immunohistochemistry data correlated well with qPCR results and showed a homogeneous protein distribution pattern in most positive tumors. No correlation was found between the levels of CGG expression in the tumors and clinicopathological parameters of the patients. Pediatric solid tumors express several CGGs, which encode antigens that could be targeted in therapeutic vaccination trials. Several CGGs of the MAGE, GAGE and LAGE families are coexpressed in a large proportion of osteosarcoma and neuroblastoma samples. Some rhabdomyosarcomas express several of these genes at high levels. Ewing's sarcomas have an overall low CGG expression.
Transcriptional Analysis of the hmw Gene Cluster of Mycoplasma pneumoniae (1999)

Mycoplasma pneumoniae adherence to host cells is a multifactorial process that requires the cytadhesin P1 and additional accessory proteins. The hmw gene cluster consists of the genes p30, hmw3, and hmw1, the products of which are known to be essential for cytadherence, the rpsD gene, and six open reading frames of unknown function. Putative transcriptional terminators flank this locus, raising the possibility that these genes are expressed as a single transcriptional unit. However, S1 nuclease protection and primer extension experiments identified probable transcriptional start sites upstream of the p32, p21, p50, and rpsD genes. Each was preceded at the appropriate spacing by the -10-like sequence TTAAAATT, but the -35 regions were not conserved. Analysis of the M. pneumoniae genome sequence indicated that this promoter-like sequence is found upstream of only a limited number of open reading frames, including the genes for P65 and P200, which are structurally related to HMW1 and HMW3. Promoter deletion studies demonstrated that the promoter-like region upstream of p21 was necessary for the expression of p30 and an hmw3-cat fusion in M. pneumoniae, while deletion of the promoter-like region upstream of p32 had no apparent effect. Analysis by reverse transcription-PCR confirmed transcriptional linkage of all the open reading frames in the hmw gene cluster. Taken together, these findings suggest that the genes of this locus constitute an operon expressed from overlapping transcripts.