gebhart/patrepeval huggingface dataset:
Personal Name Matching: New Test Collections and a Social Network based Approach. (2006)

This paper gives an overview of Personal Name Matching. Personal name matching is of great importance for all applications that deal with personal names. The problem with personal names is that they are not unique and sometimes even for one name many variations exist. This leads to the fact that databases on the one hand may have several entries for one and the same person and on the other hand have one entry for many different persons. For the evaluation of Personal Name Matching algorithms test collections are of great importance. Therefore existing test collections are outlined and three new test collections, based on real world bibliographic data, presented. Additionally state-of-the art techniques as well as a new approach based on semantics are described. 1
CCLXXX.—The condensation of aromatic aldehydes with malonanilic acid and its derivatives (1931)

G. S. Ahluwalia, M. A. Haq and J. N. Rây, J. Chem. Soc., 1931, 2059 DOI: 10.1039/JR9310002059
The cup of tea effect (2014)

Emma Vincent reveals how working in the community has opened her eyes to the complexity of patients’ lives
Transconductance enhancement in deep submicron strained Si n-MOSFETs (2002)

We report the first measurements on deep submicron strained-Si n-MOSFETs. In spite of the high channel doping and vertical effective fields, electron mobility is enhanced by /spl sim/75% compared to typical MOSFET mobilities. The extrinsic transconductance is increased by /spl sim/45% for channel lengths of 0.1 /spl mu/m, when AC measurements are used to reduce self-heating effects. The improved transconductance demonstrates the use of strain-induced enhancements in both mobility and high-field transport to increase the average electron velocity, while maintaining the channel doping required to suppress short channel effects.
INQIRE: a software approach to monitoring QoS in ATM networks (1998)

Unlike traditional best-effort packet networks, ATM networks support a wide range of services by providing a specified QoS on each ATM connection. Currently, QoS can be measured with specialized high-speed testing equipment but their complexity and cost prevent them from wide field use. This article describes the INQIRE project approach based on software for enabling common personal computers (with an ATM network interface card) to function as QoS monitoring stations at the edges of an ATM network. The main objective is to develop a low-cost, off-the-shelf alternative to broadband testing equipment. An INQIRE station, consisting of a PC running the INQIRE application, can actively probe any selected connection and collect sample measurements of the QoS. The monitoring approach is intended to be non-intrusive and work with any ATM network without requiring any modifications to existing ATM switch equipment or interruptions to active services.
Survey of the extrachromosomal gene pool of Streptococcus mutans (1977)

Fifty strains of Streptococcus mutans independently isolated from human dental plaque were examined for the presence of covalently closed circular plasmid deoxyribonucleic acid (DNA). Cesium chloride-ethidium bromide centrifugation of [3H]thymidine-labeled, Sarkosyl-lysed cells revealed that 2 of the 50 strains contained plasmid DNA. The plasmid DNA from these strains was characterized by velocity and equilibrium centrifugation and by electron microscopy. The plasmids in these strains were virtually identical in size, with molecular weights of 3.6 X 10(6) and 3.7 X 10(6), Both were present to the extent of approximately 20 molecules per genome equivalent. Interlocked catenated dimeric molecules of each plasmid were readily detected by velocity sedimentation and electron microscopy. These plasmid-containing strains were compared with representative plasmid-free S. mutans strains by using such criteria as bacteriocin production, antibiotic susceptibility, and hemolysis of mammalian erythrocytes. Although no correlation of phenotype to plasmid content could be made, production of bacteriocin-like activity differed significantly between the two plasmid-containing S. mutans isolates. Thus, although the plasmids in these two isolates appeared identical by the criteria of molecular weight, presence of dimers, and copy number, they appeared to be harbored by two distinct S. mutans strains.
Reduction of 14-3-3 Proteins Correlates with Increased Sensitivity to Killing of Human Lung Cancer Cells by Ionizing Radiation (2003)

The 14-3-3 proteins have a wide range of ligands and are involved in a variety of biological pathways. Importantly, 14-3-3 proteins are known to be overexpressed in some human lung cancers, suggesting that they may play a role in tumorigenesis. Here we examined 14-3-3 expression in several lung cancer-derived cell lines and found that four of the seven 14-3-3 isoforms, beta, epsilon, theta and zeta, were highly expressed in both lung cancer cell lines and normal lung fibroblasts. Two isoforms, sigma and gamma, were present only at very low levels. Immunoprecipitation data showed 14-3-3zeta could bind to CDC25C in irradiated A549 cells, and suppression of 14-3-3zeta in A549 cells with antisense resulted in a decrease in CDC25C localization in cytoplasm and CDC2 phosphorylation on Tyr15. As a consequence, CDC2 activity remained elevated which resulted in release from radiation-induced G(2)/M-phase arrest. Moreover, 16% 14-3-3zeta antisense-transfected cells underwent apoptosis when exposed to 10 Gy ionizing radiation. These data indicate that 14-3-3zeta is involved in G(2) checkpoint activation and that inhibition of 14-3-3 may be a useful approach to sensitize human lung cancers to ionizing radiation.
The Genetic Control of Apomixis: Asexual Seed Formation (2014)

Apomixis (asexual seed formation) is the result of a plant gaining the ability to bypass the most fundamental aspects of sexual reproduction: meiosis and fertilization. Without the need for male fertilization, the resulting seed germinates a plant that develops as a maternal clone. This dramatic shift in reproductive process has been documented in many flowering plant species, although no major seed crops have been shown to be capable of apomixis. The ability to generate maternal clones and therefore rapidly fix desirable genotypes in crop species could accelerate agricultural breeding strategies. The potential of apomixis as a next-generation breeding technology has contributed to increasing interest in the mechanisms controlling apomixis. In this review, we discuss the progress made toward understanding the genetic and molecular control of apomixis. Research is currently focused on two fronts. One aims to identify and characterize genes causing apomixis in apomictic species that have been developed as model species. The other aims to engineer or switch the sexual seed formation pathway in non-apomictic species, to one that mimics apomixis. Here we describe the major apomictic mechanisms and update knowledge concerning the loci that control them, in addition to presenting candidate genes that may be used as tools for switching the sexual pathway to an apomictic mode of reproduction in crops.
New World tetraploid cottons contain Old World cytoplasm (1989)

New World tetraploid cottons (Gossypium spp.) originated through hybridization of ancestral diploid species that presently have allopatric ranges in Asia-Africa (the A genome) and the New World tropics and subtropics (the D genome). Despite intensive study, the identity of the parental diploids and the antiquity of polyploidization remain unresolved. In this study, variation in the maternally inherited chloroplast genome was assessed among species representing both of the parental genomes and the tetraploids. Approximately 560 restriction sites were assayed in each accession, representing sequence information for about 3200 nucleotides. The resulting maternal phylogeny has no convergent restriction site mutations and demonstrates that the cytoplasm donor for all tetraploid species was an A genome diploid with a chloroplast genome that is similar to Gossypium arboreum and Gossypium herbaceum. No mutational differences were detected between these two species, and few mutations distinguish the chloroplast genomes of A genome diploids from those of tetraploid taxa. In contrast to expectations based on extensive taxonomic, geographic, and genetic diversity, a surprisingly low level of sequence divergence has accumulated subsequent to polyploidization. Chloroplast genomes of tetraploid species are distinguished from each other by between one and six apparent point mutations. The data suggest that tetraploid cotton originated relatively recently, perhaps within the last 1-2 million years, with subsequent rapid evolution and diversification throughout the New World tropics.
DNA Microarrays (2002)

Dramatic progress has been made in the technologies available to assess global alterations in mRNA levels in both clinical and research samples. Through commercial services and institutional core laboratories, these technologies are increasingly accessible to individual investigators. Although such transcript profiling can provide a powerful research tool, the broad range of options can be bewildering for the uninitiated and more often than not the limitations and pitfalls of this approach are not fully appreciated. Moreover, consensus standards for data collection, analysis, and validation have yet to emerge. It is important to recognize that the goals of transcript profiling experiments can be quite diverse. These goals range from hypothesis generation and identification of novel therapeutic targets to delineation of complex patterns of gene expression that provide a potentially pathognomonic molecular phenotype. We will first present a practical review of the commonly used approaches for data collection and analysis, and discuss possible standards for contextual validation. We will then examine the clinical and scientific applications of DNA microarray technology with an emphasis on important limitations and implications for cardiovascular medicine.
SCID Mouse Models of Human Stem Cell Engraftment (1998)

The discovery of the severe combined immunodeficiency (scid) mouse mutation has provided a tool for establishment of small animal models as hosts for the in vivo analysis of normal and malignant human pluripotent hemopoietic stem cells. Intravenous injection of irradiated scid mice with human bone marrow, cord blood, or G-CSF cytokine-mobilized peripheral blood mononuclear cells, all rich in human hemopoietic stem cell activity, results in the engraftment of a human hemopoietic system in the murine recipient. This model has been used to identify a pluripotent stem cell, termed "scid-repopulating cell" (SRC) that is more primitive than any of the hemopoietic stem cell populations identified using the currently available in vitro methodology. In this review, we describe the development and use of this model system, termed Hu-SRC-SCID, and summarize the discoveries that have resulted from the investigation of human stem cells in this model. Finally, we detail the recent extension of the original Hu-SRC-SCID model system based on the C.B-17-scid mouse as the murine host to the Hu-SRC-NOD-SCID model based on the NOD-scid mouse as the host. The engraftment of human stem cells in the Hu-SRC-NOD-SCID model is enhanced over that observed in the Hu-SRC-SCID model and results in exceptionally high levels of human hemopoietic cells in the murine recipient. Future directions to further improve the Hu-SRC-NOD-SCID model system and the potential utility of this model in the preclinical and diagnostic arenas of hematology and oncology are discussed.
ChemInform Abstract: The Knoevenagel Reaction of Aldehydes with Methylene Compounds Having Keto Enol Tautomerism. (1989)

Abstract The title reaction between the aldehydes (I) and the activated ketones (II), yielding the condensation products (III) and the rearranged compound (IV), is investigated by means of 1 H NMR.
Discovery of a Potent and Selective DDR1 Receptor Tyrosine Kinase Inhibitor (2013)

The DDR1 receptor tyrosine kinase is activated by matrix collagens and has been implicated in numerous cellular functions such as proliferation, differentiation, adhesion, migration, and invasion. Here we report the discovery of a potent and selective DDR1 inhibitor, DDR1-IN-1, and present the 2.2 Å DDR1 co-crystal structure. DDR1-IN-1 binds to DDR1 in the 'DFG-out' conformation and inhibits DDR1 autophosphorylation in cells at submicromolar concentrations with good selectivity as assessed against a panel of 451 kinases measured using the KinomeScan technology. We identified a mutation in the hinge region of DDR1, G707A, that confers >20-fold resistance to the ability of DDR1-IN-1 to inhibit DDR1 autophosphorylation and can be used to establish what pharmacology is DDR1-dependent. A combinatorial screen of DDR1-IN-1 with a library of annotated kinase inhibitors revealed that inhibitors of PI3K and mTOR such as GSK2126458 potentiate the antiproliferative activity of DDR1-IN-1 in colorectal cancer cell lines. DDR1-IN-1 provides a useful pharmacological probe for DDR1-dependent signal transduction.
CDKN2 (p16/MTS1) gene deletion or CDK4 amplification occurs in the majority of glioblastomas. (1994)

Forty-six glioblastomas, 16 anaplastic astrocytomas, and 8 astrocytomas were studied for the loss of the CDKN2 (p16/MTS1) gene on 9p. The CDKN2 locus was homozygously deleted in 19 of 46 glioblastomas (41%) and 1 allele was lost in an additional 13 cases (28%). The deleted regions were limited centromerically in some cases by the MTS2 locus and telomerically by the 1063.7 locus. CDKN2 was homozygously deleted in 3 of 16 anaplastic astrocytomas (19%) and 2 further cases showed loss of 1 allele. Amplification of the CDK4 gene was present in 7 of 14 (50%) glioblastomas and 3 of 11 (27%) anaplastic astrocytomas with no losses at the CDKN2 locus as well as in 2 of 32 (6%) glioblastomas with CDKN2 losses. Thus one or more of these two genes were shown to be aberrant in 85% of glioblastomas and 50% of anaplastic astrocytomas. None of the 8 astrocytomas showed abnormalities of these genes.
Development of a Genetic Modific ation System in Clostridium scatologenes ATCC 25775 for Generation of Mutants (2010)

Commons, and the Molecular Biology Commons This Thesis is brought to you for free and open access by TopSCHOLAR®. It has been accepted for inclusion in Masters Theses &amp;amp; Specialist Projects by an authorized administrator of TopSCHOLAR®. For more information, please contact connie.foster@wku.edu.
Rearrangement of a DNA sequence homologous to a cell-virus junction fragment in several Moloney murine leukemia virus-induced rat thymomas. (1984)

We have studied the integrated proviruses in Moloney murine leukemia virus-induced rat thymomas. By Southern blot analysis, we found several complete integrated proviruses in each tumor. In most tumors, we could not detect defective or recombinant proviruses. Several of these integrated proviruses (with their flanking cellular sequences) from a single tumor were cloned in Charon 4A. Their flanking cellular fragments were subcloned into pBR322 and used as a probe to screen other thymoma DNAs. With one clone (pMo-lC) used as a probe, we could detect novel fragments in 11 out of 20 thymoma DNAs analyzed. In three of these thymomas we could analyze in more detail, it appears that these novel fragments are generated by the insertion of a provirus. This specific integration of Moloney provirus in the host genome may represent an important genetic event leading to tumor formation.
Noise-contrastive estimation: A new estimation principle for unnormalized statistical models (2010)

We present a new estimation principle for parameterized statistical models. The idea is to perform nonlinear logistic regression to discriminate between the observed data and some artificially generated noise, using the model log-density function in the regression nonlinearity. We show that this leads to a consistent (convergent) estimator of the parameters, and analyze the asymptotic variance. In particular, the method is shown to directly work for unnormalized models, i.e. models where the density function does not integrate to one. The normalization constant can be estimated just like any other parameter. For a tractable ICA model, we compare the method with other estimation methods that can be used to learn unnormalized models, including score matching, contrastive divergence, and maximum-likelihood where the normalization constant is estimated with importance sampling. Simulations show that noise-contrastive estimation offers the best trade-off between computational and statistical efficiency. The method is then applied to the modeling of natural images: We show that the method can successfully estimate a large-scale two-layer model and a Markov random field. 1
Synthesis of Glycosyl Phosphates from 1,2-Orthoesters and Application to in Situ Glycosylation Reactions (2006)

[reaction: see text] A series of glycosyl phosphates were prepared in high yield by treatment of the corresponding 1,2-orthoesters with dibutyl phosphate. Glycosyl phosphates are efficient glycosylating agents even when used in crude form or when generated in situ. The immunodominant epitope trirhamnoside of group B Streptococcus was prepared to demonstrate the synthetic utility of the method.
Ac electrokinetics: a survey of sub-micrometre particle dynamics (2000)

Particles suspended in fluid exhibit motion when subjected to ac electric fields. The applied field results in forces on both the particles and the fluid, the study of which is referred to as ac electrokinetics. The ac electrokinetic techniques can be used for the controlled manipulation and characterization of particles, and the separation of mixtures. For sub-micrometre particles, Brownian motion is important and strong electric fields are required to overcome these effects. Planar micro-electrode arrays, fabricated using semiconductor manufacturing processes, can generate electric fields of the required strength from low potentials over a wide range of frequencies. This paper reviews and discusses sub-micrometre particle dynamics under the influence of dielectrophoretic and electrohydrodynamic forces. New experimental observations of the movement of sub-micrometre particles are also presented.
Slit-2/Robo-1 modulates the CXCL12/CXCR4-induced chemotaxis of T cells (2007)

Slit, which mediates its function by binding to the Roundabout (Robo) receptor, has been shown to regulate neuronal, dendritic, and leukocyte migration. However, the molecular mechanism by which the Slit/Robo complex inhibits the migration of cells is not well defined. Here, we showed that Slit-2 can inhibit the CXCL12-induced chemotaxis and transendothelial migration of T cells and monocytes. We observed that CXCR4 associates with Robo-1 and that Slit-2 treatment enhances this association with the Robo-1 receptor. Robo-1 is a single-pass transmembrane receptor whose intracellular region contains four conserved motifs designated as CC0, CC1, CC2, and CC3. Structural and functional analyses of Robo receptors revealed that interaction of the CC3 motif with the CXCR4 receptor may regulate the CXCL12-induced chemotaxis of T cells. We further characterized Slit-2-mediated inhibition of the CXCL12/CXCR4 chemotactic pathway and found that Slit-2 can block the CXCL12-induced activation of the Src and Lck kinases but not Lyn kinase. Although Slit-2 did not inhibit the CXCL12-induced activation of MAPKs, it did inhibit the Akt phosphorylation and Rac activation induced by this chemokine. Altogether, our studies indicate a novel mechanism by which the Slit/Robo complex may inhibit the CXCR4/CXCL12-mediated chemotaxis of T cells.
Molecular Mechanism and Evolution of Nuclear Pre-mRNA and Group II Intron Splicing: Insights from Cryo-Electron Microscopy Structures (2018)

Nuclear pre-mRNA splicing and group II intron self-splicing both proceed by two-step transesterification reactions via a lariat intron intermediate. Recently determined cryo-electron microscopy (cryo-EM) structures of catalytically active spliceosomes revealed the RNA-based catalytic core and showed how pre-mRNA substrates and reaction products are positioned in the active site. These findings highlight a strong structural similarity to the group II intron active site, strengthening the notion that group II introns and spliceosomes evolved from a common ancestor. Prp8, the largest and most conserved protein in the spliceosome, cradles the active site RNA. Prp8 and group II intron maturase have a similar domain architecture, suggesting that they also share a common evolutionary origin. The interactions between maturase and key group II intron RNA elements, such as the exon-binding loop and domains V and VI, are recapitulated in the interactions between Prp8 and key elements in the spliceosome's catalytic RNA core. Structural comparisons suggest that the extensive RNA scaffold of the group II intron was gradually replaced by proteins as the spliceosome evolved. A plausible model of spliceosome evolution is discussed.
Creep vs. Stretch: A Review of the Viscoelastic Properties of Skin (1998)

Possessing viscous and elastic rheological properties, skin is viscoelastic. Mechanical creep, defined as the elongation of skin with a constant load over time beyond intrinsic extensibility, has been described as the vehicle harnessed for wound closure with presuturing, intraoperative tissue expansion, skin-stretching devices, and skin retraction with undermining. Resulting from the generation of new tissue due to a chronic stretching force, biological creep plays a role in conventional tissue expansion.
The potential for NX-1207 in benign prostatic hyperplasia: an update for clinicians (2011)

Lower urinary tract symptoms associated with benign prostatic hyperplasia (BPH) affect many older men and can have a significant impact on health-related quality of life. BPH is a progressive condition that may lead to complications including acute urinary retention. There exists an unmet need for a safe and effective, office-based, catheter-free therapy for BPH patients. NX-1207 is a promising first-in-class drug currently in phase III trials for the treatment of BPH. This review provides an overview of the NX-1207 trial program and considers its potential application for patients with symptoms related to BPH. NX-1207 is administered as an office-based procedure by transrectal intraprostatic injection under ultrasound guidance. NX-1207 has selective pro-apoptotic properties, which induce focal cell loss in prostate tissue, leading to prostate volume reduction with both short- and long-term symptomatic improvement. In four US clinical trials to date, NX-1207 has shown evidence of symptomatic improvement substantially better than currently approved BPH medications with no significant safety issues. Larger phase III trials are ongoing to confirm further the efficacy, safety, and tolerability for this minimally invasive, anesthetic-free, clinic-based treatment for BPH.
Real-time foreground segmentation via range and color imaging (2008)

This paper describes a real-time method for foreground/background segmentation of a color video sequence based primarily on range data of a time-of-flight sensor. This method uses depth information of a TOF-sensor paired with a high resolution color video camera to efficiently segment foreground from background in a two-step process. First a trimap is produced using only range data: areas are located in each frame that have a high probability of being background or foreground, respectively. Pixels which cannot be definitively classified as foreground or background, typically about 1-2% of the frame, are assigned alpha-matte values using a cross bilateral filtering, applied directly to an estimate of the alpha-matte.