gebhart/patrepeval huggingface dataset:
Apo2L/TRAIL induction and nuclear translocation of inositol hexakisphosphate kinase 2 during IFN-β-induced apoptosis in ovarian carcinoma (2005)

Previously, we have reported that overexpression of IHPK2 (inositol hexakisphosphate kinase 2) sensitized NIH-OVCAR-3 ovarian carcinoma cell lines to the growth-suppressive and apoptotic effects of IFN-beta (interferon-beta) treatment and gamma-irradiation. In the present study, we demonstrate that Apo2L/TRAIL (Apo2L/tumour-necrosis-factor-related apoptosis-inducing ligand) is a critical mediator of IFN-induced apoptosis in these cells. Compared with IFN-alpha2, IFN-beta is a more potent inducer of Apo2L/TRAIL and IHPK2 activity. Overexpression of IHPK2 converts IFN-alpha2-resistant cells into cells that readily undergo apoptosis in response to IFN-alpha2. In untreated cells transfected with IHPK2-eGFP (where eGFP stands for enhanced green fluorescent protein), the fusion protein is localized to the cytoplasm and perinuclear region. After treatment with IFN-beta, IHPK2-eGFP translocated to the nucleus. In cells transfected with mutant IHPK2-NLS-eGFP (where NLS stands for nuclear localization sequence), containing point mutations in the NLS, the fusion protein remained trapped in the cytoplasm, even after IFN-beta treatment. Cells expressing mutant NLS mutation were more resistant to IFN-beta. The IC50 value of IHPK2-expressing cells was 2-3-fold lower than vector control. The IC50 value of NLS-mutant-expressing cells was 3-fold higher than vector control. Blocking antibodies to Apo2L/TRAIL or transfection with a dominant negative Apo2L/TRAIL receptor (DR5Delta) inhibited the antiproliferative effects of IFN-beta. Thus overexpression of IHPK2 enhanced apoptotic effects of IFN-beta, and expression of the NLS mutant conferred resistance to IFN-beta. Apo2L/TRAIL expression and nuclear localization of IHPK2 are both required for the induction of apoptosis by IFN-beta in ovarian carcinoma.
InGaAs/AlGaAs Quantum Wire DFB Buried HeteroStructure Laser Diode by One-Time Selective MOCVD on Ridge Substrate (2005)

A quasi-buried heterostructure (BH) quantum wire (QWR)-distributed feedback (DFB) laser was realized by one-time selective metalorganic chemical vapor deposition (MOCVD) on a ridge substrate with a submicron grating. One-time selective MOCVD led to the formation of a ridge waveguide with a BH structure and a QWR array for gain-guided DFB laser diode (LD) without additional etching or regrowth process. The threshold current is 15 mA, and the threshold current density is 850 A/cm 2 . A stable single longitudinal mode was preserved until 3 I th , after which another mode emerged at a high drive current at 813.6 nm. This suggests a complex-coupled DFB-mode operation. The elimination of the regrowth step enlarges the range of material for extended wavelengths and operational temperatures.
On the accuracy of admission control tests (2002)

In guaranteed performance networks, a connection admission control (CAC) algorithm determines whether or not a new connection can be admitted to the network such that all connections will obtain their required quality of service (QoS) guarantees. However, inaccuracies in a CAC algorithm lead to either under utilization of resources or violations of the promised QoS guarantees. We evaluate the accuracy of a broad range of CAC algorithms that have been proposed in the literature. Our approach is to perform experiments with long traces of MPEG compressed video, considering both heterogeneous traffic streams and priority schedulers. We compare the admissible regions and QoS parameters predicted by our implementations of the CAC algorithms with those obtained from trace driven simulations. We then identify the key aspects of a CAC test for achieving a high degree of accuracy and hence a high statistical multiplexing gain.
Detection of Corneal Fibrosis by Imaging Second Harmonic–Generated Signals in Rabbit Corneas Treated with Mitomycin C after Excimer Laser Surface Ablation (2008)

Imaging of SHG signals provides a sensitive means for detection of corneal fibrosis after surface ablation and can be used to assess the effects of antifibrotic therapy on corneal healing after refractive surgery.
SODIUM BOROHYDRIDE IN CARBOXYLIC ACID MEDIA. A REVIEW OF THE SYNTHETIC UTILITY OF ACYLOXYBOROHYDRIDES (1985)

(1985). SODIUM BOROHYDRIDE IN CARBOXYLIC ACID MEDIA. A REVIEW OF THE SYNTHETIC UTILITY OF ACYLOXYBOROHYDRIDES. Organic Preparations and Procedures International: Vol. 17, No. 4-5, pp. 317-384.
Security issues in a CDPD wireless network (1995)

The authors first discuss the basic cellular digital packet data (CDPD) architecture and its authentication protocols. They then present threats to the network. Next, they investigate the basic requirements of the security architecture and goals in light of attacks. Then they present the improved authentication protocol in operation, and how it deals with faults. Next, they add authenticated key exchange for confidentiality, followed by anonymity provisions. Then, they summarize the design and present the complete protocol, and identify which protocol transmissions goes on which CDPD message. Finally, they present further issues and concerns that are beyond the scope of this protocol.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Effect of Fasting on Hyperoxic Lung Injury in Mice: The Role of Glutathione (1990)

Fasted mice exposed to 100% oxygen have more lung damage and die sooner than do fed mice. The mechanism responsible for this phenomenon has not been identified. We performed the following experiments to test the hypothesis that reduced glutathione content in lung tissue of fasted mice contributes to the increased susceptibility to hyperoxic lung damage. First, air-exposed mice were fasted for as long as 3 days. They had little change in lung levels of superoxide dismutase (SOD) or catalase, but they had a 41% decrease in glutathione by Day 3 (p less than 0.001). Second, fed mice and fasted mice were exposed to 100% oxygen for as long as 4 days. Both groups had nearly identical values of lung SOD and catalase, but the fasted mice had lower levels of glutathione (p less than 0.001). Third, fed mice received the glutathione synthesis inhibitor buthionine sulfoximine (BSO; 20 mM) in their drinking water for 2 wk and were then exposed to either air or 100% oxygen. Air-exposed mice receiving BSO for 14 days had no change in lung SOD content, a 43% increase in catalase (p less than 0.001), and a 41% decrease in glutathione (p less than 0.01). Oxygen-exposed, BSO-treated mice had no change in SOD and an increase in catalase, but lower glutathione levels, more deaths, and increased lung damage on Day 3 (BAL protein: 1.72 +/- 0.21 versus 0.94 +/- 0.08 mg/ml; p less than 0.01) than did diluent-treated mice. Fourth, fasted mice were given liposomes containing glutathione intratracheally.(ABSTRACT TRUNCATED AT 250 WORDS)
Assessment of the Myogenic Stem Cell Compartment Following Transplantation of Pax3/Pax7-Induced Embryonic Stem Cell-Derived Progenitors (2011)

An effective long-term cell therapy for skeletal muscle regeneration requires donor contribution to both muscle fibers and the muscle stem cell pool. Although satellite cells have these abilities, their therapeutic potential so far has been limited due to their scarcity in adult muscle. Myogenic progenitors obtained from Pax3-engineered mouse embryonic stem (ES) cells have the ability to generate myofibers and to improve the contractility of transplanted muscles in vivo, however, whether these cells contribute to the muscle stem cell pool and are able to self-renew in vivo are still unknown. Here, we addressed this question by investigating the ability of Pax3, which plays a critical role in embryonic muscle formation, and Pax7, which is important for maintenance of the muscle satellite cell pool, to promote the derivation of self-renewing functional myogenic progenitors from ES cells. We show that Pax7, like Pax3, can drive the expansion of an ES-derived myogenic progenitor with significant muscle regenerative potential. We further demonstrate that a fraction of transplanted cells remains mononuclear, and displays key features of skeletal muscle stem cells, including satellite cell localization, response to reinjury, and contribution to muscle regeneration in secondary transplantation assays. The ability to engraft, self-renew, and respond to injury provide foundation for the future therapeutic application of ES-derived myogenic progenitors in muscle disorders.
Covalent Modification of N3 of Guanine by (+)-CC-1065 Results in Protonation of the Cross-Strand Cytosine (1997)

ADVERTISEMENT RETURN TO ISSUEPREVCommunicationNEXTCovalent Modification of N3 of Guanine by (+)-CC-1065 Results in Protonation of the Cross-Strand CytosineHyun-Ju Park and Laurence H. HurleyView Author Information Drug Dynamics Institute, College of Pharmacy The University of Texas at Austin Austin, Texas 78712-1074 Cite this: J. Am. Chem. Soc. 1997, 119, 3, 629–630Publication Date (Web):January 22, 1997Publication History Received13 September 1996Published online22 January 1997Published inissue 1 January 1997https://pubs.acs.org/doi/10.1021/ja9632264https://doi.org/10.1021/ja9632264rapid-communicationACS PublicationsCopyright © 1997 American Chemical SocietyRequest reuse permissionsArticle Views180Altmetric-Citations6LEARN 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-AlertscloseSupporting Info (1)»Supporting Information Supporting Information SUBJECTS:Adducts,Cytosine,Genetics,Guanine,Reaction mechanisms Get e-Alerts
Gut instincts: thoughts on intestinal epithelial stem cells (2000)

On stem cell biology
A 622-Mb/s bit/frame synchronizer for high-speed backplane data communication (1996)

A compact 622-Mb/s/port bit/frame synchronizer is presented. Sampling equally-phased clocks from a phase-locked loop (PLL) at the data transition edges, the bit synchronizer selects the optimum one as the extracted clock. An elastic serial-to-parallel converter is used for the frame synchronization. The circuit is designed for a 32-port ATM switch chip, achieving 622-Mb/s port capacity by four parallel 156-Mb/s bits. Using 0.5-/spl mu/m CMOS technology, the circuit was verified by simulations. The bit synchronizer consumes only 15 mW under typical conditions.
Genes for biosynthesis and assembly of CS3 pili of CFA/II enterotoxigenic Escherichia coli: novel regulation of pilus production by bypassing an amber codon (1989)

The complete nucleotide sequence of the 4746bp HindIII fragment encoding the genes for the biosynthesis and assembly of CS3 pili has been determined. By site-directed mutagenesis in conjunction with analysis of the plasmid-encoded proteins in minicells, the actual reading frames for the various products have been determined. This demonstrated that the genes for four of the proteins (63 kD, 48 kD, 33 kD, and 20 kD in size) are encoded entirely within the same open reading frame as a fifth protein (104 kD). However, for synthesis of this latter protein, suppression or readthrough of an internal amber codon is required. Termination at this codon is also necessary for synthesis of the former proteins. Two further proteins are also encoded within the HindIII fragment: a 27 kD precursor of a periplasmic protein and the 17.5kD precursor of the major CS3 fimbrial subunit.
Assessment in humans of a synthetic peptide-based vaccine against the sporozoite stage of the human malaria parasite, Plasmodium falciparum . (1988)

Eleven volunteers were injected with an anti-malaria (Plasmodium falciparum) sporozoite vaccine candidate consisting of a synthetic peptide, Ac-Cys-(NANP)3, coupled to tetanus toxoid (TT) and adsorbed to aluminum hydroxide. Two of the volunteers had no previously known exposure to TT. Eight volunteers made detectable antipeptide, anticircumsporozoite protein or antisporozoite antibodies, whose titers increased after multiple injections in four individuals. The maximum antisporozoite titer obtained in an immunofluorescence assay was 1280. In those individuals who produced antipeptide antibody, the overall correlation between IgG anti-Ac-Cys-(NANP)3 antibody in enzyme-linked immunosorbent assay and IgG antisporozoite reactivity in immunofluorescence was highly significant. However, the fine specificity of antibody varied among volunteers with two individuals producing mostly antipeptide antibody. Anti-TT antibody responses increased in all volunteers with the exception of that person who had the highest pretrial anti-TT titer; this individual was one of the two pre-TT-immunized volunteers who failed to produce anti-Ac-Cys-(NANP)3 or sporozoite antibody. For the two non-TT preimmunized volunteers, one produced an antisporozoite fluorescence titer of 320; the other made no detectable antibody against either Ac-Cys-(NANP)3 or sporozoites during a primary response. For the three volunteers monitored, after the first injection, significant T cell proliferative responses to (NANP)3 were observed, which increased up to 4 wk after immunization, when a second injection was given. Responsiveness then declined to background levels and did not reappear after further immunizations. In contrast, a marked TT-specific proliferation was observed for the duration of the study.
Effective amplification of long targets from cloned inserts and human genomic DNA. (1994)

We have used the polymerase chain reaction (PCR) to amplify up to 22 kb of the beta-globin gene cluster from human genomic DNA and up to 42 kb from phaga lambda DNA. We have also amplified 91 human genomic inserts of 9-23 kb directly from recombinant lambda plaques. To do this, we increased pH, added glycerol and dimethyl sulfoxide, decreased denaturation times, increased extension times, and used a secondary thermostable DNA polymerase that possesses a 3'-to 5'-exonuclease, or "proofreading," activity. Our "long PCR" protocols maintain the specificity required for targets in genomic DNA by using lower levels of polymerase and temperature and salt conditions for specific primer annealing. The ability to amplify DNA sequences of 10-40 kb will bring the speed and simplicity of PCR to genomic mapping and sequencing and facilitate studies in molecular genetics.
A Conduction-Cooled Module for High-Performance LSI Devices (1982)

The advent of LSI chip technology makes possible significantly increased performance and circuit densities by means of large-scale packaging of multiple devices on a single multi-layer ceramic (MLC) substrate. Integration at the chip and module levels has resulted in circuit densities as high as 2.5×10 <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">7</sup> circuits per cubic meter, with the necessity of removing heat fluxes on the order of 100 kW/m <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> . This paper describes the development and implementation of a novel packaging concept which meets the stringent and highly interactive demands on cooling, reliability, and reworkability of LSI technology. These requirements resulted in an innovative packaging approach, referred to as the thermal conduction module (TCM). The TCM uses individually spring-loaded “pistons” that contact each chip with helium gas, the conducting medium for removing heat efficiently. A dismountable hermetic seal makes multiple access possible for device and substrate rework, while ensuring mechanical and environmental protection of critical components. A wide range of thermal, mechanical, and environmental experiments are described with analytical and computer models. The one-dimensional approach used in the previous paper by Chu et al. is extended to three-dimensional computer modeling. Simulations of expected chip temperature distributions in the IBM 3081 Processor Unit are discussed. Enhanced thermal performance of the advanced packaging concept for future applications is also indicated.
Statistical Inference for a Modulated Power Law Process (1996)

The modulated power law process (MPLP) is a three-parameter stochastic point process model that can be used to describe the failure times of a repairable system. While the power law process implies that a system is in exactly the same condition just after a repair as it was just before the failure, the MPLP allows for the system to be affected by the failure and repair. We describe an algorithm for obtaining the maximum likelihood estimates (MLEs) of the three model parameters. Asymptotic results are used to give approximate confidence intervals and hypothesis tests for the parameters. A simulation study indicates that the confidence intervals and hypothesis tests have approximately the nominal level.
Glucose conjugation for the specific targeting and treatment of cancer (2013)

Cancers of diverse origins exhibit marked glucose avidity and high rates of aerobic glycolysis. Increased understanding of this dysfunctional metabolism known as the Warburg effect has led to an interest in targeting it for cancer therapy. One promising strategy for such targeting is glycoconjugation, the linking of a drug to glucose or another sugar. This review summarizes the most salient examples of glycoconjugates, in which known cytotoxins or targeted anticancer therapeutics have been linked to glucose (or another glucose transporter substrate sugar) for improved cancer targeting and selectivity. Building on these examples, this review also provides a series of guidelines for the design and mechanistic evaluation of future glycoconjugates.
Alterations of the c‐kit gene in testicular germ cell tumors (2003)

Expression and gain-of-function mutation of the c-kit gene, that encodes a receptor tyrosine kinase (KIT), have been reported in mast cell tumors and gastrointestinal stromal tumors (GISTs). Among human testicular germ cell tumors (GCTs), seminomas and seminoma components of mixed GCTs have also been shown to express KIT, but only one study has found the c-kit gene mutation at exon 17 in seminoma. To elucidate the frequency and location of the c-kit gene mutation of testicular GCTs, we analyzed the whole coding region of the c-kit complementary DNA along with 4 mutational hot spots (exons 9, 11, 13 and 17) of the c-kit genomic DNA by polymerase chain reaction and direct sequencing. Somatic mutations were found in 4 pure seminomas of 34 testicular GCTs (11.8%). One mutation was found in exon 11 (W557R) and the others were observed in exon 17 (D816H and D816V). These types of mutations were reported in GISTs (W557R), seminoma (D816H) and mastocytosis (D816V) and were considered to be gain-of-function mutations, although there were no differences of any clinicopathological factors or outcome between patients with and without mutations. Additionally, we also demonstrated coexpression of Gly-Asn-Asn-Lys510-513 (GNNK) + and GNNK - isoforms of the c-kit gene with dominance of the GNNK - transcript in all testicular GCTs. The mutations and/or preferential expression of GNNK - isoform of the c-kit gene might play an important role in the development of testicular GCTs, and these tumors may also be targets for STI571, which is a promising drug for advanced and metastatic GISTs.
The challenge of the microenvironment in B-cell lymphomas (2011)

B-cell non-Hodgkin lymphomas (B-NHL) represent the most common malignant lymphoid neoplasms, with the majority of these arising from germinal centre or post-germinal centre B cells, due to (at least) a disruption of the different phases of normal B-cell development. The most common B-cell lymphoma subtypes include follicular lymphoma, diffuse large B-cell lymphoma, marginal zone lymphoma and mantle cell lymphoma. As with other malignancies, it has been demonstrated that the development and progression of B-cell lymphomas involves complex interactions between the neoplastic B-cells and the surrounding microenvironment, including stromal cells, the intratumoral vasculature, the various types of macrophages, as well as T-cells, including regulatory T-cells (also termed T-regs). The complex communications between the cell populations involves interplay between chemokines, chemokine receptors and adhesion molecules, and the balance between these determines whether there is a tumour cell growth promotion or inhibition. The demonstration of the importance of the microenvironment in B-NHL has been shown recently using methodologies such as gene expression profiling, and has been validated in some B-NHL lymphoma subtypes using other techniques, such as immunohistochemistry. This is particularly in the case of follicular lymphomas, in which both T-regs and macrophages have been demonstrated to have prognostic value. As such, the microenvironment of B-cell lymphomas represents a challenge to the development of therapeutic agents, requiring re-direction and inclusion of these non-neoplastic supportive cells into future treatment strategies.
Incorporation of bioinformatics exercises into the undergraduate biochemistry curriculum (2002)

Abstract The field of bioinformatics is developing faster than most biochemistry textbooks can adapt. Supplementing the undergraduate biochemistry curriculum with data‐mining exercises is an ideal way to expose the students to the common databases and tools that take advantage of this vast repository of biochemical information. An integrated collection of exercises based on pet proteins has been assembled. The exercises described are applicable to either a lecture or laboratory format and require only basic desktop computers, an Internet connection, a current web browser, and the free Chime plug‐in module. In an open‐ended, inquiry‐based format, the assignments ask students to explore concepts such as the relative information content of the different biopolymers, the relationship between primary sequence and tertiary structure, and how sequence conservation can be used to find an enzyme active site.
Discovery and Evaluation of Clinical Candidate IDH305, a Brain Penetrant Mutant IDH1 Inhibitor (2017)

Inhibition of mutant IDH1 is being evaluated clinically as a promising treatment option for various cancers with hotspot mutation at Arg<sup>132</sup>. Having identified an allosteric, induced pocket of IDH1<sup>R132H</sup>, we have explored 3-pyrimidin-4-yl-oxazolidin-2-ones as mutant IDH1 inhibitors for <i>in vivo</i> modulation of 2-HG production and potential brain penetration. We report here optimization efforts toward the identification of clinical candidate <b>IDH305</b> (<b>13</b>), a potent and selective mutant IDH1 inhibitor that has demonstrated brain exposure in rodents. Preclinical characterization of this compound exhibited <i>in vivo</i> correlation of 2-HG reduction and efficacy in a patient-derived IDH1 mutant xenograft tumor model. <b>IDH305</b> (<b>13</b>) has progressed into human clinical trials for the treatment of cancers with IDH1 mutation.