gebhart/patrepeval huggingface dataset:
Involvement of the Ku autoantigen in the cellular response to DNA double-strand breaks. (1994)

The Ku autoantigen is a well-characterized heterodimer of 70 and 86 kDa that binds to DNA ends, but its cellular function has been obscure. An electrophoretic mobility-shift assay and Ku antisera were used to show that Ku or a closely related protein was deficient in three mutant hamster cell lines from x-ray-sensitive complementation group 5, which is characterized by defects in DNA double-strand break repair and V(D)J recombination. Furthermore, Ku protein expression was restored when the cells reverted to x-ray resistance. The Ku p86 gene maps to human chromosome 2q33-35, and group 5 cells are rescued by almost precisely the same region, 2q34-36. Thus, biochemical and genetic evidence suggests that Ku is involved in pathways for DNA recombination and repair. By its association with a DNA-dependent protein kinase activated by DNA ends, Ku may also initiate a signaling pathway induced by DNA damage, perhaps for cell cycle arrest.
Review: Nomenclature and Biologic Significance of Cytokines Involved in Inflammation and the Host Immune Response (1995)

This is a brief review of 42 cytokines and interleukins that are involved inflammatory and immune responses. The cytokines are listed in tables organized as hematopoietic growth factors, interferons, lymphokines, monokines, chemokines, and other cytokines. Information on each cytokine includes the most commonly used abbreviations, the former or alternative names and abbreviations of the cytokines, the cells that form the major sources of production of the cytokines, the major biologic actions of the cytokines, and references to recent reviews or primary literature. Minor biologic actions and minor cellular sources of the cytokines may not be listed. This review should be useful as a quick reference guide to the cytokines and interleukins.
Direct Synthesis of Partially Substituted Cellulose Esters (2009)

We describe herein a new method for direct esterification of cellulose to partially substituted cellulose esters, using insoluble sulfonated polystyrene resin beads as the catalyst. The process has been extended to the esters of cellulose with long chain acids, which are materials of significant interest that are difficult to synthesize by other means. We offer some mechanistic observations about this interesting reaction. In addition, we present here for the first time a detailed description of the complementary synthetic method, titanium-catalyzed partial esterification in amide or urea solvents, which also provides direct access to partially substituted cellulose esters, including long chain esters. Both methods are practical, efficient and broad in scope. These novel methods address a long standing problem of efficiency in cellulose ester synthesis.
Infrared spectroscopy of human tissue. V. Infrared spectroscopic studies of myeloid leukemia (ML-1) cells at different phases of the cell cycle (1999)

Infrared spectra of myeloid leukemia (ML-1) cells are reported for cells derived from an asynchronous, exponentially growing culture, as well as for cells that were fractionated according to their stage within the cell division cycle. The observed results suggest that the cells' DNA is detectable by infrared spectroscopy mainly when the cell is in the S phase, during the replication of DNA. In the G1 and G2 phases, the DNA is so tightly packed in the nucleus that it appears opaque to infrared radiation. Consequently, the nucleic acid spectral contributions in the G1 and G2 phases would be mostly that of cytoplasmic RNA. These results suggest that infrared spectral changes observed earlier between normal and abnormal cells may have been due to different distributions of cells within the stages of the cell division cycle.
The ClpXP ATP-Dependent Protease Regulates Flagellum Synthesis inSalmonella entericaSerovar Typhimurium (2002)

The ClpXP protease is a member of the ATP-dependent protease family and plays a dynamic role in the control of availability of regulatory proteins and the breakdown of abnormal and misfolded proteins. The proteolytic activity is rendered by the ClpP component, while the substrate specificity is determined by the ClpX component that has ATPase activity. We describe here a new role of the ClpXP protease in Salmonella enterica serovar Typhimurium in which ClpXP is involved in the regulation of flagellum synthesis. Cells deleted for ClpXP show "hyperflagellate phenotype," exhibit overproduction of the flagellar protein, and show a fourfold increase in the rate of transcription of the fliC encoding flagellar filament. The assay for promoter activity of the genes responsible for expression of the fliC showed that the depletion of ClpXP results in dramatic enhancement of the expression of the fliA encoding sigma factor final sigma(28), leaving the expression level of the flhD master operon lying at the top of the transcription hierarchy of flagellar regulon almost normal. These results suggest that the ClpXP may be responsible for repressing the expression of flagellar regulon through the control of the FlhD/FlhC master regulators at the posttranscriptional and/or posttranslational levels. Proteome analysis of proteins secreted from the mutant cells deficient for flhDC and clpXP genes demonstrated that the DeltaflhD mutation abolished the enhanced effect by DeltaclpXP mutation on the production of flagellar proteins, suggesting that the ClpXP possibly defines a regulatory pathway affecting the expression of flagellar regulon that is dependent on FlhD/FlhC master regulators.
De Sign and Synthesis of 1,2,4‐Oxadiazole Derivatives as Non‐Steroidal 5α‐Reductase Inhibitors (2002)

Abstract The purpose of this study was to synthesize compounds in which the 1,2,4‐oxadiazole moiety replaced the amide bond of ONO3805 and to evaluate its 5α‐reductase inhibitory activity as a potential benign prostatic hyperplasia therapeutic target. Four 1,2,4‐oxadiazole derivatives, 1,2,8, and 20, were evaluated in vitro against 5α‐reductase of rat liver microsome. The prepared 1 and 2 possessed similar binding affinity (Ki) to that of ONO3805. Therefore, the use of 1,2,4‐oxadiazole ring as surrogate of the amide bond in ONO3805 has a successful result in this study. It leads not only to enhance chemical stability but also to maintain meaningful inhibitory activity. The butyric acid moiety of these inhibitors is considered to play an important role in mimicing the phosphoric acid portion of coenzyme‐NADPH in interacting with the active site of 5α‐reductase.
Prevention of Adhesion to Prosthetic Mesh (2003)

Sepramesh significantly reduced mesh surface covered by adhesions and prevented bowel adhesion to the mesh. Parietex composite mesh prevented bowel adhesions as well but increased infection rates in the current model.
Disc Chondrocyte Transplantation in a Canine Model: A Treatment for Degenerated or Damaged Intervertebral Disc (2003)

Autologous chondrocyte transplantation is technically feasible and biologically relevant to repairing disc damage and retarding disc degeneration.
Analysis of viewing parameters for two display methods based on integral photography (2001)

We describe and compare two methods of displaying autostereoscopic three-dimensional images by integral photography. One method is to display the image in front of the lens array, and the other method is to display the image behind the lens array. We compare and discuss these two methods from the viewpoints of lateral resolution, depth resolution, and viewing angle. We also discuss the effect of the optical parameter difference in the pickup and display.
Data management for mobile computing (1993)

Mobile Computing is a new emerging computing paradigm of the future. Data Management in this paradigm poses many challenging problems to the database community. In this paper we identify these new challenges and plan to investigate their technical significance. New research problems include management of location dependent data, wireless data broadcasting, disconnection management and energy efficient data access.
Zen of Graphics Programming, with CD-ROM, 2nd Ed. (1996)

From the Publisher:
Explains the PC graphics hardware to a very deep level, and how it impacts code performance. Treats both 2-D and 3-D graphics and animation in great detail. Shows that graphics optimization is largely a right-brain process, not simplyone of counting cycles and analyzing CPU execution speed. Provides tools and rationales for measuring performance of animated graphics. Provides examples of optimized graphics in both fundamental figures like lines, circles, and ellipses, as well as elaborate 3-D objects composed of multiple polygons. Presents the industry's best and most-detailed coverage of BSP trees, the cutting-edge algorithm that makes breathtaking real-time animated 3-D graphics possible!
PRAS40 Regulates Protein Synthesis and Cell Cycle in C2C12 Myoblasts (2010)

PRAS40 is an mTOR binding protein that has complex effects on cell metabolism. Our study tests the hypothesis that PRAS40 knockdown (KD) in C2C12 myocytes will increase protein synthesis via upregulation of the mTOR-S6K1 pathway. PRAS40 KD was achieved using lentiviruses to deliver short hairpin (sh)-RNA targeting PRAS40 or a scrambled control. C2C12 cells were used as either myoblasts or differentiated to myotubes. Knockdown reduced PRAS40 mRNA and protein content by >80% of time-matched control values but did not alter the phosphorylation of mTOR substrates, 4E-BP1 or S6K1, in neither myoblasts nor myotubes. No change in protein synthesis in myotubes was detected, as measured by the incorporation of (35)S-methionine. In contrast, protein synthesis was reduced 25% in myoblasts. PRAS40 KD in myoblasts also decreased proliferation rate with an increased percent of cells retained in the G1 phase. PRAS40 KD myoblasts were larger in diameter and had a decreased rate of myotube formation as assessed by myosin heavy chain content. Immunoblotting revealed a 25-30% decrease in total p21 and S807/811 phosphorylated Rb protein considered critical for G1 to S phase progression. Reduction in protein synthesis was not due to increased apoptosis, since cleaved caspase-3 and DNA laddering did not differ between groups. In contrast, the protein content of LC3B-II was decreased by 30% in the PRAS40 KD myoblasts, suggesting a decreased rate of autophagy. Our results suggest that a reduction in PRAS40 specifically impairs myoblast protein synthesis, cell cycle, proliferation and differentiation to myotubes.
Recording Notch Signaling in Real Time (2006)

Notch signaling is a highly conserved signaling pathway, which is critical for many cell fate decisions. Ligand activation of Notch leads to cleavage of the Notch receptor and liberation of the Notch intracellular domain (ICD) from the membrane-tethered receptor. After translocation to the nucleus, the Notch ICD interacts with the DNA-binding protein CSL to activate gene transcription. To better understand the temporal and spatial aspects of Notch signaling, we here describe a fluorescent protein-based reporter assay that allows Notch activation to be followed in real time in individual cells. We have generated a reporter construct composed of 12 CSL-binding motifs linked to fluorescent proteins with different half-lives: a stabler red fluorescent protein (DsRedExpressDR) and a destabilized form of green fluorescent protein (d1EGFP). The fluorescent reporters reflect the activation status of Notch signaling with single-cell resolution. The reporters rapidly respond to various forms of Notch activation, including ligand activation of full-length Notch receptors. Finally, we use this assay to gain insights into the level of Notch signaling in CNS progenitor cells in culture and in vivo.
Probabilistic Lane Estimation using Basis Curves (2010)

Lane estimation for autonomous driving can be formulated as a curve estimation problem, where local sensor data provides partial and noisy observations of spatial curves. The number of curves to estimate may be initially unknown and many of the observations may be outliers or false detections (due e.g. to to tree shadows or lens flare). The challenges lie in detecting lanes when and where they exist, and updating lane estimates as new observations are made.
Linear unbiased data estimation in mobile radio systems applying CDMA (1993)

Data estimation in the uplink of a synchronous mobile radio system applying code-division multiple access (CDMA) is considered. In mobile radio systems applying CDMA, multipath propagation leads to intersymbol interference (ISI) and together with time variance, to cross interference between the signals of different users regardless of whether the user codes are chosen orthogonal or not. A linear unbiased data estimation algorithm is presented that eliminates both ISI and cross interference perfectly by jointly detecting the different user signals, leading to unbiased estimates of the transmitted data symbols. By theoretical analysis and simulation, the performance of the linear unbiased data estimation algorithm is examined under the assumption that the radio channel impulse responses are known at the receiver. The price to be paid for the interference elimination are SNR degradations, which are calculated for typical mobile radio situations in urban areas. The resulting average uncoded bit error probabilities lead to the conclusion that systems applying the linear unbiased data estimation algorithm are well suited for mobile radio applications.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Antiproliferative Activity of G-Quartet-Forming Oligonucleotides with Backbone and Sugar Modifications (2002)

Oligonucleotide-based therapies have considerable potential in cancer, viral, and cardiovascular disease therapies. However, it is becoming clear that the biological effects of oligonucleotides are not solely due to the intended sequence-specific interactions with nucleic acids. Oligonucleotides are also capable of interacting with numerous cellular proteins owing to their polyanionic character or specific secondary structure. We have examined the antiproliferative activity, protein binding, and G-quartet formation of a series of guanosine-rich oligonucleotides, which are analogues of GRO29A, a G-quartet forming, growth-inhibitory oligonucleotide, whose effects we have previously described [Bates P. J., Kahlon, J. B., Thomas, S. D., Trent, J. O., and Miller, D. M. (1999) J. Biol. Chem. 274, 26369-26377]. The GRO29A analogues include phosphorothioate (PS29A), 2'-O-methyl RNA (MR29A), and mixed DNA/2'-O-methyl RNA (MRdG29A) oligonucleotides. We demonstrate by UV spectroscopy that all of the modified analogues form stable structures, which are consistent with G-quartet formation. We find that the phosphorothioate and mixed DNA/2'-O-methyl analogues are able to significantly inhibit proliferation in a number of tumor cell lines, while the 2'-O-methyl RNA has no significant effects. Similar to the original oligonucleotide, GRO29A, the growth inhibitory oligonucleotides were able to compete with the human telomere sequence oligonucleotide for binding to a specific cellular protein. The less active MR29A does not compete significantly for this protein. On the basis of molecular modeling of the oligonucleotide structures, it is likely that the inactivity of MR29A is due to the differences in the groove structure of the quadruplex formed by this oligonucleotide. Interestingly, all GRO29A analogues, including an unmodified DNA phosphodiester oligonucleotide, are remarkably resistant to nuclease degradation in the presence of serum-containing medium, indicating that secondary structure plays an important role in biological stability. The remarkable stability and strong antiproliferative activity of these oligonucleotides confirm their potential as therapeutic agents.
Isolation of streptococcal hyaluronate synthase (1986)

Hyaluronate synthase was isolated from protoblast membranes of streptococci by Triton X-114 extraction and cetylpyridinium chloride precipitation. It was identified as a 52,000-Mr protein, which bound to nascent hyaluronate and was affinity-labelled by periodate-oxidized UDP-glucuronic acid and UDP-N-acetylglucosamine. Antibodies directed against the 52,000-Mr protein inhibited hyaluronate synthesis. Mutants defective in hyaluronate synthase activity lacked the 52,000-Mr protein in membrane extracts. Synthase activity was solubilized from membranes by cholate in active form and purified by ion-exchange chromatography.
Seismic low-frequency effects in monitoring fluid-saturated reservoirs (2004)

Abstract There is a complex relationship between seismic attributes, including the frequency dependence of reflections and fluid saturation in a reservoir. Observations in both laboratory and field data indicate that reflections from a fluid-saturated layer have an increased amplitude and delayed traveltime at low frequencies, when compared with reflections from a gas-saturated layer. Comparison of laboratory-modeling results with a diffusive-viscous-theory model show that low (&amp;lt; 5) values of the quality factor Q can explain the observations of frequency dependence. At the field scale, conventional processing of time-lapse VSP data found minimal changes in seismic response of a gas-storage reservoir when the reservoir fluid changed from gas to water. Low-frequency analysis found significant seismic-reflection-attribute variation in the range of 15–50 Hz. The field observations agree with effects seen in laboratory data and predicted by the diffusive-viscous theory. One explanation is that very low values of Q are the result of internal diffusive losses caused by fluid flow. This explanation needs further theoretical investigation. The frequency-dependent amplitude and phase-reflection properties presented in this paper can be used for detecting and monitoring fluid-saturated layers.
Deracemization of unnatural amino acid: homoalanine using d-amino acid oxidase and ω-transaminase (2012)

A deracemization method was developed to generate optically pure L-homoalanine from racemic homoalanine using D-amino acid oxidase and ω-transaminase. A whole cell reaction using a biphasic system converted 500 mM racemic homoalanine to 485 mM L-homoalanine (>99% ee).
Complete nucleotide sequence of a hepatitis B virus, subtype adw2, and identification of three types of C open reading frame (1993)

Journal Article Complete nucleotide sequence of a hepatitis B virus, subtype adw2, and identification of three types of C open reading frame Get access S. Preisler-Adams, S. Preisler-Adams Department of Medicine, University of FreiburgFreiburg, Germany Search for other works by this author on: Oxford Academic PubMed Google Scholar H.-J. Schlayer, H.-J. Schlayer Department of Medicine, University of FreiburgFreiburg, Germany Search for other works by this author on: Oxford Academic PubMed Google Scholar T. Peters, T. Peters Department of Medicine, University of FreiburgFreiburg, Germany Search for other works by this author on: Oxford Academic PubMed Google Scholar R. Korp, R. Korp Department of Medicine, University of FreiburgFreiburg, Germany Search for other works by this author on: Oxford Academic PubMed Google Scholar J. Rasenack J. Rasenack * Department of Medicine, University of FreiburgFreiburg, Germany * To whom correspondence should be addressed Search for other works by this author on: Oxford Academic PubMed Google Scholar Nucleic Acids Research, Volume 21, Issue 9, 11 May 1993, Page 2258, https://doi.org/10.1093/nar/21.9.2258 Published: 11 May 1993 Article history Received: 08 February 1993 Revision received: 31 March 1993 Accepted: 31 March 1993 Published: 11 May 1993
Cox Regression with Incomplete Covariate Measurements (1993)

Abstract This article provides a general solution to the problem of missing covariate data under the Cox regression model. The estimating function for the vector of regression parameters is an approximation to the partial likelihood score function with full covariate measurements and reduces to the pseudolikelihood score function of Self and Prentice in the special setting of case-cohort designs. The resulting parameter estimator is consistent and asymptotically normal with a covariance matrix for which a simple and consistent estimator is provided. Extensive simulation studies show that the large-sample approximations are adequate for practical use. The proposed approach tends to be more efficient than the complete-case analysis, especially for large cohorts with infrequent failures. For case-cohort designs, the new methodology offers a variance-covariance estimator that is much easier to calculate than the existing ones and allows multiple subcohort augmentations to improve efficiency. Real data taken from clinical and epidemiologic studies are analyzed.
The Smethwick Engine (1985)

The Smethwick Engine is now displayed in the Birmingham Museum of Science and Industry. Initially preserved in 1897, this canal pumping engine by Boulton and Watt is the oldest working steam engine in the world. Recent research on the engine has involved documents, field work and finally the excavation of the original engine house in Smethwick. A number of safety problems arose during the excavation and these were discussed and appropriate action taken. In addition to compiling a history of the engine, a great deal has been discovered about early Watt engines and their engine houses. Plans exist to protect the excavated engine house and open it to the public.
Peak-to-average power ratio reduction of an OFDM signal using partial transmit sequences (2003)

Orthogonal frequency division multiplexing (OFDM) is an attractive technique for achieving high-bit-rate wireless data transmission. However, the potentially large peak-to-average power ratio (PAP) of a multicarrier signal has limited its application. Two promising techniques for improving the statistics of the PAP of an OFDM signal have previously been proposed: the selective mapping and partial transmit sequence approaches. Here, we summarize these techniques and present suboptimal strategies for combining partial transmit sequences that achieve similar performance but with reduced complexity.
CXC‐chemokines stimulate invasion and chemotaxis in prostate carcinoma cells through the CXCR2 receptor (1999)

BACKGROUND Metastasis of prostate carcinoma requires invasion through the basement membrane, a thin extracellular matrix that underlies the epithelial cells, which must be breached by tumor cells invading into surrounding tissue. The CXC-chemokines, which have been shown to promote the migration of neutrophils and carcinoma cells, are candidates to influence prostate carcinoma-cell invasion. METHODS CXC-chemokines were examined for the ability to stimulate prostate cell line PC3 invasion in vitro through a reconstituted basement membrane and long-term migration and short-term adhesion to laminin, a major component of the basement membrane. RESULTS PC3 cells responded to IL-8 and GROα with a 1.6–2-fold increase in invasion through reconstituted basement membrane. A corresponding 2–3-fold increase in chemotaxis toward IL-8 and GROa was seen on laminin. Anti-CXCR2 antibody inhibited IL-8-stimulated migration. Expression levels of the β1 integrins were not changed by IL-8, and α6β1 integrin was used for both stimulated and baseline migration. In addition to the increases in migration and invasion, 2–6-fold transient increases in adhesion on laminin were seen with both IL-8 and GROα. CONCLUSIONS These results suggest that the CXC-chemokines stimulate migration and invasion in part by altering the activation state of the β1 integrins. The CXC-chemokines act on prostate carcinoma cells through the CXCR2 receptor to promote behavior important for metastasis, and as such may be important in prostate carcinoma progression and metastasis. Prostate 41:78–88, 1999. © 1999 Wiley-Liss, Inc.