gebhart/patrepeval huggingface dataset:
Critical tumor‐suppressor gene regions on chromosome 3P in major human epithelial malignancies: Allelotyping and quantitative real‐time PCR (2002)

To ascertain the involvement of human chromosome 3p and its established critical TSG regions in various epithelial malignancies, 21 polymorphic and 2 nonpolymorphic 3p markers were allelotyped in nonpapillary RCC, NSCLC, CC and BC from a total of 184 patients. LOH was observed with high frequency in all types of cancer studied: RCC (52/57, 91%), BC (41/51, 80%), NSCLC (30/40, 75%) and CC (27/36, 75%). Interstitial deletions, believed to signal TSG inactivation, were verified using the "L-allele rule" and real-time quantitative PCR. Significant correlation was observed between DNA copy numbers for 2 nonpolymorphic STS markers and LOH data for adjacent polymorphic loci. Interstitial deletions in 3p were demonstrated for all cancer types studied. However, the distribution of different types of deletion was characteristic for tumors from various locations. Large terminal deletions were predominantly seen in RCC and NSCLC (51% and 40%, respectively), correlating with clear cell RCC and squamous cell carcinomas of the lung. In addition to the LUCA region at 3p21.3 (centromeric), we found that the AP20 region (3p21.3, telomeric) was frequently affected in all 4 cancers, suggesting that this newly defined critical region contains multiple TSGs. Moreover, at least 3 candidate cancer-specific loci were identified. The telomeric 3p26.1-p25.3 region was predominantly deleted in RCC and NSCLC. The D3S1286 and D3S3047 markers (3p25.2-p24.3) were deleted nonrandomly in NSCLC. High-frequency LOH was detected in a segment mapped closely distal to the LUCA site (3p21.3), around the D3S2409 and D3S2456 markers.
Disturbed Vitamin A Metabolism in Non-Alcoholic Fatty Liver Disease (NAFLD) (2017)

Vitamin A is required for important physiological processes, including embryogenesis, vision, cell proliferation and differentiation, immune regulation, and glucose and lipid metabolism. Many of vitamin A's functions are executed through retinoic acids that activate transcriptional networks controlled by retinoic acid receptors (RARs) and retinoid X receptors (RXRs).The liver plays a central role in vitamin A metabolism: (1) it produces bile supporting efficient intestinal absorption of fat-soluble nutrients like vitamin A; (2) it produces retinol binding protein 4 (RBP4) that distributes vitamin A, as retinol, to peripheral tissues; and (3) it harbors the largest body supply of vitamin A, mostly as retinyl esters, in hepatic stellate cells (HSCs). In times of inadequate dietary intake, the liver maintains stable circulating retinol levels of approximately 2 μmol/L, sufficient to provide the body with this vitamin for months. Liver diseases, in particular those leading to fibrosis and cirrhosis, are associated with impaired vitamin A homeostasis and may lead to vitamin A deficiency. Liver injury triggers HSCs to transdifferentiate to myofibroblasts that produce excessive amounts of extracellular matrix, leading to fibrosis. HSCs lose the retinyl ester stores in this process, ultimately leading to vitamin A deficiency. Non-alcoholic fatty liver disease (NAFLD) is the hepatic manifestation of metabolic syndrome and is a spectrum of conditions ranging from benign hepatic steatosis to non-alcoholic steatohepatitis (NASH); it may progress to cirrhosis and liver cancer. NASH is projected to be the main cause of liver failure in the near future. Retinoic acids are key regulators of glucose and lipid metabolism in the liver and adipose tissue, but it is unknown whether impaired vitamin A homeostasis contributes to or suppresses the development of NAFLD. A genetic variant of patatin-like phospholipase domain-containing 3 (PNPLA3-I148M) is the most prominent heritable factor associated with NAFLD. Interestingly, PNPLA3 harbors retinyl ester hydrolase activity and PNPLA3-I148M is associated with low serum retinol level, but enhanced retinyl esters in the liver of NAFLD patients. Low circulating retinol in NAFLD may therefore not reflect true "vitamin A deficiency", but rather disturbed vitamin A metabolism. Here, we summarize current knowledge about vitamin A metabolism in NAFLD and its putative role in the progression of liver disease, as well as the therapeutic potential of vitamin A metabolites.
Selective Passage Through the Uterotubal Junction of Sperm from a Mixed Population Produced by Chimeras of Calmegin-Knockout and Wild-Type Male Mice1 (2004)

Loss of calmegin, a testis-specific putative chaperone protein of the endoplasmic reticulum, leads to male sterility because the sperm show defects in migration into the oviduct and do not bind to the zona pellucida. To clarify the mechanism of defective migration, XY <--> XY chimeras were produced by aggregating wild-type embryos with embryos of transgenic mice lacking functional calmegin genes and expressing enhanced green fluorescent protein (EGFP) in their acrosomes. Chimeric ejaculates contained wild-type, nonfluorescent sperm as well as sperm with EGFP-tagged acrosomes and the defective calmegin gene. Transgenic, wild-type, and chimeric males were mated to wild-type females; however, only wild-type sperm were ever found within the oviducts. Calmegin-knockout sperm, even when they were combined in chimeric ejaculates with wild-type sperm, remained outside of the uterotubal junction. These findings indicate that the presence of wild-type sperm cannot compensate for the inability of calmegin-knockout sperm to enter the oviduct and that successful ascent into the oviduct depends on the capabilities of individual sperm.
Cloning of theDrosophilaribosomal protein S3: another multifunctional ribosomal protein with AP endonuclease DNA repair activity (1993)

Journal Article Cloning of the Drosophila ribosomal protein S3: another multifunctional ribosomal protein with AP endonuclease DNA repair activity Get access David M. Wilson, III, David M. Wilson, III 1Program in Molecular Biology , Loyola University Medical School2160 S. First Ave, Maywood, IL 60153 Search for other works by this author on: Oxford Academic PubMed Google Scholar Walter A. Deutsch, Walter A. Deutsch 3Department of Biochemistry, Louisiana State UniversityBaton Rouge, LA, USA Search for other works by this author on: Oxford Academic PubMed Google Scholar Mark R. Kelley Mark R. Kelley * 1Program in Molecular Biology , Loyola University Medical School2160 S. First Ave, Maywood, IL 601532Department of Medicine, Loyola University Medical School2160 S. First Ave, Maywood, IL 60153 * To whom correspondence should be addressed at: Department of Biochemistry, Loyola University Medical School, 2160 S. First Ave., Maywood, IL 60153, USA Search for other works by this author on: Oxford Academic PubMed Google Scholar Nucleic Acids Research, Volume 21, Issue 10, 25 May 1993, Page 2516, https://doi.org/10.1093/nar/21.10.2516 Published: 25 May 1993 Article history Received: 02 April 1993 Accepted: 12 April 1993 Published: 25 May 1993
Traveling-wave parametric amplifier based on three-wave mixing in a Josephson metamaterial (2017)

We have developed a recently proposed Josephson traveling-wave parametric amplifier with three-wave mixing [A. B. Zorin, Phys. Rev. Applied 6, 034006, 2016]. The amplifier consists of a microwave transmission line formed by a serial array of nonhysteretic one-junction SQUIDs. These SQUIDs are flux-biased in a way that the phase drops across the Josephson junctions are equal to 90 degrees and the persistent currents in the SQUID loops are equal to the Josephson critical current values. Such a one-dimensional metamaterial possesses a maximal quadratic nonlinearity and zero cubic (Kerr) nonlinearity. This property allows phase matching and exponential power gain of traveling microwaves to take place over a wide frequency range. We report the proof-of-principle experiment performed at a temperature of T = 4.2 K on Nb trilayer samples, which has demonstrated that our concept of a practical broadband Josephson parametric amplifier is valid and very promising for achieving quantum-limited operation.
Applying the harmonic plus noise model in concatenative speech synthesis (2001)

This paper describes the application of the harmonic plus noise model (HNM) for concatenative text-to-speech (TTS) synthesis. In the context of HNM, speech signals are represented as a time-varying harmonic component plus a modulated noise component. The decomposition of a speech signal into these two components allows for more natural-sounding modifications of the signal (e.g., by using different and better adapted schemes to modify each component). The parametric representation of speech using HNM provides a straightforward way of smoothing discontinuities of acoustic units around concatenation points. Formal listening tests have shown that HNM provides high-quality speech synthesis while outperforming other models for synthesis (e.g., TD-PSOLA) in intelligibility, naturalness, and pleasantness.
Nucleotide sequence of a 25S rRNA gene from tomato (1989)

Journal Article Nucleotide sequence of a 25S rRNA gene from tomato Get access Tamás Kiss, Tamás Kiss Institute of Plant Physiology, Biological Research Center, Hungarian Academy of SciencesH-6701 Szeged, Hungary Search for other works by this author on: Oxford Academic PubMed Google Scholar Mihály Kis, Mihály Kis Institute of Plant Physiology, Biological Research Center, Hungarian Academy of SciencesH-6701 Szeged, Hungary Search for other works by this author on: Oxford Academic PubMed Google Scholar Ferenc Solymosy Ferenc Solymosy Institute of Plant Physiology, Biological Research Center, Hungarian Academy of SciencesH-6701 Szeged, Hungary Search for other works by this author on: Oxford Academic PubMed Google Scholar Nucleic Acids Research, Volume 17, Issue 2, 25 January 1989, Page 796, https://doi.org/10.1093/nar/17.2.796 Published: 25 January 1989
The Energetics of Hydrogen Bonds in Model Systems: Implications for Enzymatic Catalysis (1996)

Low-barrier or short, strong hydrogen bonds have been proposed to contribute 10 to 20 kilocalories per mole to transition-state stabilization in enzymatic catalysis. The proposal invokes a large increase in hydrogen bond energy when the pKa values of the donor and acceptor (where Ka is the acid constant) become matched in the transition state (delta pKa=0). This hypothesis was tested by investigating the energetics of hydrogen bonds as a function of delta pKa for homologous series of compounds under nonaqueous conditions that are conducive to the formation of low-barrier hydrogen bonds. In all cases, there was a linear correlation between the increase in hydrogen-bond energy and the decrease in delta pKa, as expected from simple electrostatic effects. However, no additional energetic contribution to the hydrogen bond was observed at delta pKa=0. These results and those of other model studies suggest alternative mechanisms by which hydrogen bonds can contribute to enzymatic catalysis, in accord with conventional electrostatic considerations.
Transfer of defective avian tumor virus genomes by a Rous sarcoma virus RNA packaging mutant (1981)

SE21Q1b, a Rous sarcoma virus mutant which packages cellular rather than viral RNA, is competent for infection of quail cells and can transmit defective transforming retrovirus genes. Stably transformed recipient clones have been obtained by using this mutant.
Boosting the efficiency of III-V/Si tandem solar cells (2016)

We have developed Si-based tandem solar cells with a certified 1-sun efficiency of 29.8% (AM1.5g). The four-terminal tandem devices consist of 1.8 eV rear-heterojunction GaInP top cells and silicon heterojunction bottom cells. The two subcells were fabricated independently in two different labs and merged using an optically transparent, electrically insulating epoxy. Work is ongoing to further improve the performance of each subcell and to push the tandem cell efficiency to > 30%.
Vaccination of a Melanoma Patient with Mature Dendritic Cells Pulsed with MAGE-3 Peptides Triggers the Activity of Nonvaccine Anti-Tumor Cells (2008)

We previously characterized the CTL response of a melanoma patient who experienced tumor regression following vaccination with an ALVAC virus coding for a MAGE-A3 Ag. Whereas anti-vaccine CTL were rare in the blood and inside metastases of this patient, anti-tumor CTL recognizing other tumor Ags, mainly MAGE-C2, were 100 times more frequent in the blood and considerably enriched in metastases following vaccination. In this study we report the analysis of the CTL response of a second melanoma patient who showed a mixed tumor response after vaccination with dendritic cells pulsed with two MAGE-A3 antigenic peptides presented, respectively, by HLA-A1 and HLA-DP4. Anti-MAGE-3.A1 CD8 and anti-MAGE-3.DP4 CD4 T cells became detectable in the blood after vaccination at a frequency of approximately 10(-5) among the CD8 or CD4 T cells, respectively, and they were slightly enriched in slowly progressing metastases. Additional anti-tumor CTL were present in the blood at a frequency of 2x10(-4) among the CD8 T cells and, among these, an anti-MAGE-C2 CTL clone was detected only following vaccination and was enriched by >1,000-fold in metastases relative to the blood. The striking similarity of these results with our previous observations further supports the hypothesis that the induction of a few anti-vaccine T cells may prime or restimulate additional anti-tumor T cell clones that are mainly responsible for the tumor regression.
Metabolic engineering of novel lignin in biomass crops (2012)

Lignin, a phenolic polymer in the secondary wall, is the major cause of lignocellulosic biomass recalcitrance to efficient industrial processing. From an applications perspective, it is desirable that second-generation bioenergy crops have lignin that is readily degraded by chemical pretreatments but still fulfill its biological role in plants. Because plants can tolerate large variations in lignin composition, often without apparent adverse effects, substitution of some fraction of the traditional monolignols by alternative monomers through genetic engineering is a promising strategy to tailor lignin in bioenergy crops. However, successful engineering of lignin incorporating alternative monomers requires knowledge about phenolic metabolism in plants and about the coupling properties of these alternative monomers. Here, we review the current knowledge about lignin biosynthesis and the pathways towards the main phenolic classes. In addition, the minimal requirements are defined for molecules that, upon incorporation into the lignin polymer, make the latter more susceptible to biomass pretreatment. Numerous metabolites made by plants meet these requirements, and several have already been tested as monolignol substitutes in biomimetic systems. Finally, the status of detection and identification of compounds by phenolic profiling is discussed, as phenolic profiling serves in pathway elucidation and for the detection of incorporation of alternative lignin monomers.
Low temperature activation of ion implanted dopants: a review (2002)

Ion implanted dopants can be electrically activated through low temperature annealing in the 450/spl deg/C to 800/spl deg/C as reported in literature over the past 25 years. However, researchers in the last few years have applied this technique to realize ultra shallow junctions (USJ) for source drain extensions to satisfy the device junction roadmap requirements for the 65 nm node and beyond. Therefore this paper will review the current status of low temperature annealing for USJ formation.
Postglacial Vegetation and Fire History in the Chirripó Páramo of Costa Rica (1993)

Abstract Pollen and charcoal analysis of a 5.6-m sediment core from Lago de las Morrenas (9°29′N, 83°29′W; 3480 m) provides evidence of postglacial vegetation and fire history in the highlands of the Cordillera de Talamanca, Costa Rica. The site is presently surrounded by treeless páramo vegetation and apparently has been so since deglaciation about 10,000 yr B.P. Pollen spectra suggest no pronounced changes in vegetation since ice retreat. Fires set by people or lightning have burned the páramo repeatedly, with fire activity probably highest during the late Holocene, but these fires have not carved páramo from forest. Pollen percentages for Gramineae and other páramo taxa decline upward, whereas percentages for certain subalpine, lower montane, and lowland forest taxa increase slightly; these changes may reflect the impact of prehistoric human activity or slight upslope migrations of forest taxa owing to climatic warming. There is no clear evidence of higher timberlines during the mid-Holocene.
An Introduction to Splines for Use in Computer Graphics and Geometric Modeling (1987)

Discusses the use of splines from the point of view of the computer scientist concentrating on parametric spline curves and parametric,tensor-product spline surfaces
Agrobacterium‐Mediated Genetic Transformation of Switchgrass (2002)

ABSTRACT Although Agrobacterium tumefaciens has been successfully used to transfer genes to a wide range of plant species, it has received little attention for transformation of forage grasses. Therefore, the objective of the present study was to demonstrate Agrobacterium ‐mediated transformation of switchgrass ( Panicum virgatum L.). The A. tumefaciens strain AGL 1 carrying the binary vector pDM805, coding for the phosphinothricin acetyltransferase ( bar ) and β‐glucuronidase ( gus ) genes, was utilized in these experiments. Somatic embryos, embryogenic calluses, mature caryopses, and plantlet segments served as target tissues for infection. Treated cultures were selected in the presence of 10 mg L −1 bialaphos and the resultant plantlets were treated with the herbicide Basta [monoammonium 2‐amino‐4(hydroxymethylphosphinyl)butanoate]. T‐DNA delivery efficiency was affected by genotype, explant used and the presence or absence of acetosyringone (3′,5′‐dimethoxy‐4′‐hydroxyacetophenone) during inoculation and cocultivation. Approximately 600 transgenic plants were produced, and transformation efficiencies ranged from 0 to nearly 100%. Stable integration, expression, and inheritance of both transgenes were confirmed by molecular and genetic analyses. Approximately 90% of the tested plants appeared to have only one or two copies of the T‐DNA inserts. Controlled crosses between T 0 and nontransgenic ‘Alamo’ plants indicated the expected ratio of 1:1 (transgenic:nontransgenic) in T 1 plants for both transgenes according to a χ 2 test at P = 0.05. These results indicate that the Agrobacterium method is effective for transferring foreign genes into switchgrass.
Culture of dispersed hair follicle cells from plucked out hairs without a feeder layer. (1989)

Dispersed hair follicle cells from plucked out hairs have been successfully grown on collagen type IV without a biological feeder layer. The optimal calcium concentration for the culture of these cells was also studied and decided to be 0.3-0.5 mM. In this calcium range and on collagen type IV, colony formation and colony growth were best and big colonies with a paving stone-like cell arrangement were formed. The availability of such cultured cells for the treatment of missing skin is proposed instead of cultured epidermal keratinocytes which have been commonly used for wound dressing.
Audio Coding based on Integer Transforms (2001)

Die Audiocodierung hat sich in den letzten Jahren zu einem sehr&#13;\npopulären Forschungs- und Anwendungsgebiet entwickelt. Insbesondere&#13;\ngehörangepasste Verfahren zur Audiocodierung, wie etwa MPEG-1 Layer-3&#13;\n(MP3) oder MPEG-2 Advanced Audio Coding (AAC), werden häufig zur&#13;\neffizienten Speicherung und Übertragung von Audiosignalen verwendet. Für&#13;\nprofessionelle Anwendungen, wie etwa die Archivierung und Übertragung im&#13;\nStudiobereich, ist hingegen eher eine verlustlose Audiocodierung angebracht.&#13;\n&#13;\nDie bisherigen Ansätze für gehörangepasste und verlustlose&#13;\nAudiocodierung sind technisch völlig verschieden. Moderne&#13;\ngehörangepasste Audiocoder basieren meist auf Filterbänken, wie etwa der&#13;\nüberlappenden orthogonalen Transformation "Modifizierte Diskrete&#13;\nCosinus-Transformation" (MDCT). Verlustlose Audiocoder hingegen&#13;\nverwenden meist prädiktive Codierung zur Redundanzreduktion. Nur wenige&#13;\nAnsätze zur transformationsbasierten verlustlosen Audiocodierung wurden&#13;\nbisher versucht.&#13;\n&#13;\nDiese Arbeit präsentiert einen neuen Ansatz hierzu, der das&#13;\nLifting-Schema auf die in der gehörangepassten Audiocodierung&#13;\nverwendeten überlappenden Transformationen anwendet. Dies ermöglicht&#13;\neine invertierbare Integer-Approximation der ursprünglichen&#13;\nTransformation, z.B. die IntMDCT als Integer-Approximation der MDCT. Die &#13;\nselbe Technik kann auch für Filterbänke mit niedriger Systemverzögerung&#13;\nangewandt werden. Weiterhin ermöglichen ein neuer, mehrdimensionaler&#13;\nLifting-Ansatz und eine Technik zur Spektralformung von&#13;\nQuantisierungsfehlern eine Verbesserung der Approximation der&#13;\nursprünglichen Transformation.&#13;\n&#13;\nBasierend auf diesen neuen Integer-Transformationen werden in dieser&#13;\nArbeit neue Verfahren zur Audiocodierung vorgestellt. Die Verfahren&#13;\numfassen verlustlose Audiocodierung, eine skalierbare verlustlose&#13;\nErweiterung eines gehörangepassten Audiocoders und einen integrierten&#13;\nAnsatz zur fein skalierbaren gehörangepassten und verlustlosen&#13;\nAudiocodierung. Schließlich wird mit Hilfe der Integer-Transformationen&#13;\nein neuer Ansatz zur unhörbaren Einbettung von Daten mit hohen&#13;\nDatenraten in unkomprimierte Audiosignale vorgestellt.
Retroviral integration: structure of the initial covalent product and its precursor, and a role for the viral IN protein. (1989)

An essential step in the life cycle of a retrovirus is the integration of a DNA copy of the viral genome into a host cell chromosome. We have analyzed the structure of the initial covalent product of an in vitro retroviral integration reaction and determined the structure of the ends of the unintegrated linear viral DNA molecules present in vivo in cells infected with murine leukemia virus (MLV). Our results lead to the following conclusions: (i) Circularization of viral DNA plays no role in integration. The direct precursor to the integrated MLV provirus is a linear molecule. (ii) The initial step in the integration reaction is probably a cleavage that removes the terminal 2 bases from each 3' end of the viral DNA. This cleavage depends on a virally encoded protein, IN, that has previously been shown genetically to be required for integration. (iii) The resulting viral 3' ends are joined to target DNA to form the initial recombination intermediate.