gebhart/patrepeval huggingface dataset:
The evolution of rapid prototyping in dentistry: a review (2009)

Purpose The goal of rapid mechanical prototyping is to be able to quickly fabricate complex‐shaped, 3D parts directly from computer‐aided design models. The key idea of this novel technology is based upon decomposition of 3D computer models data into thin cross‐sectional layers, followed by physically forming the layers and stacking them up; “layer by layer technique.” This new method of modeling has raised many attentions in dentistry especially in the field of surgery and implantology. The purpose of this review study is to represent the historical development and various methods currently used for building dental appliances. It is also aimed to show the many benefits which can be achieved by using this new technology in various branches of dentistry. Design/methodology/approach The major existing resources, including unpublished data on the internet, were considered. Findings Although, creating 3D objects in a layered fashion is an idea almost as old as human civilization but, this technology has only recently been employed to build 3D complex models in dentistry. It seems that in near future many other methods will develop which could change traditional dental practices. It is advisable to include more unit hours in dental curriculums to acquaint dental students with the many benefits of this novel technology. Originality/value It is hard to believe that the routine dental techniques were affected by revolutionary concepts originally theorized by engineering methods. It is a reality that in future, most of the restorative disciplines will be fully revised and the computer methods be evolved to an extent where dentistry can be performed by computer‐assisted methods with optimum safety, simplicity, and reliability.
Gene conversion in human immunoglobulin γ locus shown by unusual location of IgG allotypes (1986)

The constant region of the gamma 1, gamma 2 and gamma 3 heavy chains of the human IgG1, IgG2 and IgG3 immunoglobulins carries antigenic determinants or G1m, G2m and G3m allotypes, which are genetic markers of these subclasses. The exceptional presence on gamma 1 and gamma 2 chains of Gm allotypes usually located on the CH3 domain of gamma 3 shows an unexpected clustering of base changes and subsequent identity of short DNA sequences in the CH3 exon of the non-allelic gamma 1, gamma 2 and gamma 3 genes. Such clusters of substitutions are not easily explained on the classical basis of point mutations. A gene conversion, which substituted a segment of the gamma 1 or gamma 2 gene with the homologous region of the non-allelic gamma 3 gene, is more likely. Other examples of possible conversion involving the gamma genes are described. The conservation or the restoration of short sequences produced by the conversion events might be related to the biological properties of the constant region of the heavy chains.
Differential Effects of Intrauterine and Subcutaneous Administration of Recombinant Ovine Interferon Tau on the Endometrium of Cyclic Ewes1 (1999)

Interferon tau (IFNtau) is the antiluteolytic signal produced by the conceptus of ruminants. Intrauterine administration of recombinant ovine IFNtau suppresses expression of endometrial estrogen receptor (ER) and oxytocin receptor (OTR) in the luminal and superficial glandular epithelia to abrogate the production of luteolytic prostaglandin F(2alpha) (PGF(2alpha)) pulses. Subcutaneous (s.c.) injections of recombinant ovine (o) IFNtau appear to extend the interestrous interval by altering uterine PGF(2alpha) response to oxytocin. The present study tested the hypothesis that antiluteolytic effects of roIFNtau injected into the uterine lumen (paracrine) or s.c. (endocrine) are equivalent in suppressing expression of endometrial ER and OTR and inducing uterine expression of type I IFN-regulated Mx and ubiquitin cross-reactive proteins (UCRP). Sixteen cyclic ewes were fitted with uterine catheters on Day 5 (Day 0 = estrus), were assigned randomly to receive treatment with control proteins or roIFNtau (2 x 10(7) antiviral units/day) by either intrauterine or s.c. injections from Days 11 to 15, and were ovariohysterectomized on Day 16. Results indicated that expression of ER and OTR mRNAs in endometrial epithelium was suppressed by intrauterine but not by s.c. injections of roIFNtau. Intrauterine injections of roIFNtau increased expression of Mx and UCRP mRNA in the endometrium. Subcutaneous injections of roIFNtau increased endometrial Mx mRNA levels but not UCRP mRNA. Unexpectedly, intrauterine and s.c. injections of roIFNtau were equally effective in inducing expression of Mx and UCRP mRNA in the corpus luteum. Although s.c. injections of roIFNtau induced Mx mRNA in the endometrial epithelium, s.c. injections of roIFNtau did not abrogate activation of the uterine luteolytic mechanism by suppressing epithelial ER and OTR expression. Therefore, results of this study failed to support the assumption that endocrine roIFNtau mimics antiluteolytic effects of paracrine IFNtau to improve pregnancy rates in sheep.
Autocrine Production of IFN-γ by Macrophages Controls Their Recruitment to Kidney and the Development of Glomerulonephritis in MRL/lpr Mice (2002)

Anti-DNA autoantibody production is a key factor in lupus erythematosus development; nonetheless, the link between glomerular anti-DNA autoantibody deposition and glomerulonephritis development is not understood. To study the inflammatory and destructive processes in kidney, we used IFN-gamma(+/-) MRL/lpr mice which produce high anti-DNA Ab levels but are protected from kidney disease. The results showed that defective macrophage recruitment to IFN-gamma(+/-) mouse kidney was not caused by decreased levels of monocyte chemoattractant protein-1, a chemokine that controls macrophage migration to MRL/lpr mouse kidney. To determine which IFN-gamma-producing cell type orchestrates the inflammation pathway in kidney, we transferred IFN-gamma(+/+) monocyte/macrophages or T cells to IFN-gamma(-/-) mice, which do not develop anti-DNA autoantibodies. The data demonstrate that IFN-gamma production by infiltrating macrophages, and not by T cells, is responsible for adhesion molecule up-regulation, macrophage accumulation, and inflammation in kidney, even in the absence of autoantibody deposits. Therefore, in addition to monocyte chemoattractant protein-1, macrophage-produced IFN-gamma controls macrophage migration to kidney; the degree of IFN-gamma production by macrophages also regulates glomerulonephritis development. Our findings establish the level of IFN-gamma secretion by macrophages as a link between anti-DNA autoantibody deposition and glomerulonephritis development, outline the pathway of the inflammatory process, and suggest potential treatment for disease even after autoantibody development.
THE PHARMACOLOGY AND METABOLISM OF TESTOSTERONE UNDECANOATE (TU), A NEW ORALLY ACTIVE ANDROGEN (1975)

Testosterone undecanoate (TU), either dissolved in arachis oil or as micro-crystal suspension, displays androgenic activity on oral administration to rats in the Hershberger test. The solution in arachis oil is more active than the crystal suspension. When [3H]TU is administered orally to rats, most of it is metabolized in the intestinal wall. The majority of the metabolites probably lose their undecanoate group and are absorbed via the portal vein. The non-metabolized [3H]TU and at least two metabolites are absorbed exclusively via the lymphatic system. One of these metabolites has been identified as 5alpha-dihydrotestosterone undecanoate (5alpha-DHTU). TU has no harmful effects on the liver of the rabbits on oral administration.
Palladium-Catalyzed Cross-Coupling Reactions in a Homogeneous Aqueous Medium (1992)

A palladium(0) water-soluble catalyst prepared in situ from palladium(II) acetate-trisodium 3,3′,3″-phosphinetriyl-tribenzenesulfonate is an efficient catalyst for various cross-coupling reactions. Examples of the coupling in this aqueous media include: inter- and intramolecular Heck reactions (acyclic and cyclic alkenes); terminal alkynes [without any copper(I) promoter]; phenyl boronic acid with iodoaromatic compounds or vinyl halides; and allylic substitution with carbonucleophiles and nitrogen nucleophiles such as primary amines.
Murine pancreatic beta-cells express H-2K and H-2D but not Ia antigens. (1980)

Direct microcytotoxicity testing and absorption analyses were employed to determine whether H-2K, H-2D, and Ia antigens are present on murine islet of Langerhans cells. Products of the H-2K and H-2D loci were found on beta-cells from three different mouse strains, but I-region (Ia) antigens were not detected. The absence of Ia gene products from islet cells may be of importance in explaining the survival of islet allografts across major histocompatibility barriers.
Tuning of Metal Work Functions with Self‐Assembled Monolayers (2005)

Work functions of gold and silver are varied by over 1.4 and 1.7 eV, respectively, by using self-assembled monolayers. Using these modified electrodes, the hole current in a poly(2-methoxy-5-(2′-ethylhexyloxy)–1,4-phenylene vinylene) light-emitting diode is tuned by more than six orders of magnitude (see Figure). Suppression of the hole current enables measurement of the electron current in a polymer/polymer blend photovoltaic cell.
GTI-2040, an antisense agent targeting the small subunit component (R2) of human ribonucleotide reductase, shows potent antitumor activity against a variety of tumors. (2003)

GTI-2040 is a 20-mer oligonucleotide that is complementary to a coding region in the mRNA of the R2 small subunit component of human ribonucleotide reductase. In vitro studies using a number of human tumor cell lines have demonstrated that GTI-2040 decreases mRNA and protein levels of R2 in a sequence- and target-specific manner. In vivo studies have shown that GTI-2040 significantly inhibits growth of human colon tumors (adenocarcinoma), pancreatic tumors (adenocarcinoma), liver tumors, lung tumors, breast tumors (adenocarcinoma), renal tumors, ovarian tumors (adenocarcinoma), melanoma, brain glioblastoma-astrocytoma, prostatic tumors, and cervical tumors in nude and/or severe combined immunodeficient mice. Antitumor effects were not observed with an oligonucleotide containing four mismatches to the R2 sequence or with a scrambled sequence containing the same base content but not complementary to R2. This suggests that an antisense mechanism is responsible for the in vivo observations. In addition to tumor growth assays, GTI-2040 was tested in a murine model of human lymphoma. Treatment of severe combined immunodeficient mice bearing Burkitt's lymphoma with GTI-2040, but not control oligonucleotides, greatly extended the survival of mice, and survival extended well beyond the treatment period. Finally, GTI-2040 specifically inhibits metastasis of human melanoma cells to the lungs in nude mice. Taken together, the results of these studies indicate that GTI-2040 can act as a selective and specific anticancer agent against a broad range of human tumors.
Jasmonic Acid-Dependent and -Independent Signaling Pathways Control Wound-Induced Gene Activation in Arabidopsis thaliana (1997)

Plant response to mechanical injury includes gene activation both at the wound site and systemically in nondamaged tissues. The model developed for the wound-induced activation of the proteinase inhibitor II (Pin2) gene in potato (Solanum tuberosum) and tomato (Lycopersicon esculentum) establishes the involvement of the plant hormones abscisic acid and jasmonic acid (JA) as key components of the wound signal transduction pathway. To assess in Arabidopsis thaliana the role of these plant hormones in regulating wound-induced gene expression, we isolated wound- and JA-inducible genes by the differential mRNA display technique. Their patterns of expression upon mechanical wounding and hormonal treatments revealed differences in the spatial distribution of the transcripts and in the responsiveness of the analyzed genes to abscisic acid and JA. A correlation can be established between sensitivity to JA and the accumulation of the transcripts in systemic tissues upon wounding. A comparative study of the wound response in wild-type and JA-insensitive coi1 mutant plants indicated that in A. thaliana wound signals are transmitted via at least two different pathways. One of them does not involve JA as a mediator and is preferentially responsible for gene activation in the vicinity of the wound site, whereas the other requires JA perception and activates gene expression throughout the aerial part of the plant.
Affine-Invariant Image Retrieval Based on Wavelet Interest Points (2005)

This paper presents an affine-in variant image retrieval approach based on wavelet-based detector, which uses the space-tree property of the transform coefficients to estimate the interest points. Meanwhile, in order to retrieve images compressed by wavelet algorithm such as JPEG2000, the detector only uses the partial bit-planes of the wavelet coefficients to detect the interest points. To provide affine-invariant image matching, annular color histogram, annular texture histogram and spatial cohesion based on interest points are presented to describe image features. A series of experiments based on an image database consisting of 1000 images are performed to confirm the effectiveness of our method
Analyses of pig genomes provide insight into porcine demography and evolution (2012)

For 10,000 years pigs and humans have shared a close and complex relationship. From domestication to modern breeding practices, humans have shaped the genomes of domestic pigs. Here we present the assembly and analysis of the genome sequence of a female domestic Duroc pig (Sus scrofa) and a comparison with the genomes of wild and domestic pigs from Europe and Asia. Wild pigs emerged in South East Asia and subsequently spread across Eurasia. Our results reveal a deep phylogenetic split between European and Asian wild boars ∼1 million years ago, and a selective sweep analysis indicates selection on genes involved in RNA processing and regulation. Genes associated with immune response and olfaction exhibit fast evolution. Pigs have the largest repertoire of functional olfactory receptor genes, reflecting the importance of smell in this scavenging animal. The pig genome sequence provides an important resource for further improvements of this important livestock species, and our identification of many putative disease-causing variants extends the potential of the pig as a biomedical model.
The lcrB (yscN/U) gene cluster of Yersinia pseudotuberculosis is involved in Yop secretion and shows high homology to the spa gene clusters of Shigella flexneri and Salmonella typhimurium (1994)

Virulent bacteria of the genus Yersinia secrete a number of virulence determinants called Yops. These proteins lack typical signal sequences and are not posttranslationally processed. Two gene loci have been identified as being involved in the specific Yop secretion system (G. Cornelis, p. 231-265, In C. E. Hormache, C. W. Penn, and C. J. Smythe, ed., Molecular Biology of Bacterial Infection, 1992; S. C. Straley, G. V. Plano, E. Skrzypek, P. L. Haddix, and K. A. Fields, Mol. Microbiol. 8:1005-1010, 1993). Here, we have shown that the lcrB/virB locus (yscN to yscU) encodes gene products essential for Yop secretion. As in previously described secretion apparatus mutants, expression of the Yop proteins was decreased in the yscN/U mutants. An lcrH yscR double mutant expressed the Yops at an increased level but did not secrete Yops into the culture supernatant. The block in Yop expression of the ysc mutants was also circumvented by overexpression of the activator LcrF in trans. Although the Yops were expressed in elevated amounts, the Yops were still not exported. This analysis showed that the ysc mutants were unable to secrete Yops and that they were also affected in the negative Ca(2+)-regulated loop. The yscN/U genes showed remarkably high homology to the spa genes of Shigella flexneri and Salmonella typhimurium with respect to both individual genes and gene organization. These findings indicate that the genes originated from a common ancestor.
Adaptive Manifold Learning (2004)

Recently, there have been several advances in the machine learning and pattern recognition communities for developing manifold learning algo-rithms to construct nonlinear low-dimensional manifolds from sample data points embedded in high-dimensional spaces. In this paper, we de-velop algorithms that address two key issues in manifold learning: 1) the adaptive selection of the neighborhood sizes; and 2) better fitting the local geometric structure to account for the variations in the curvature of the manifold and its interplay with the sampling density of the data set. We also illustrate the effectiveness of our methods on some synthetic data sets. 1
Detection of Vascular Endothelial Growth Factor Messenger RNA and Vascular Endothelial Growth Factor-like Activity in Proliferative Diabetic Retinopathy (1994)

Vascular endothelial growth factor seems to be an appropriate candidate for mediating retinal diabetic neovascularization.
The MIT Dice project (1993)

A computer-based architecture program called the Distributed and Integrated Environment for Computer-Aided Engineering (Dice), which provides cooperation and coordination among multiple designers working in separate engineering disciplines, is described. Dice uses knowledge to estimate interface conditions between disciplines, records who used any piece of design data created by others and how such data were used, and checks for conflicts among disciplines, manufacturability, and manufacturing cost and schedule effects of design decisions.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
The phosphorylation of ephrin‐B2 ligand promotes glioma cell migration and invasion (2009)

To reveal molecular drivers of glioma invasion, two distinct glioblastoma (GBM) cell phenotypes (invading cells and tumor core cells) were collected from 19 GBM specimens using laser capture microdissection. Isolated RNA underwent whole human genome expression profiling to identify differentially expressed genes. Pathway enrichment analysis highlighted the bidirectional receptor/ligand tyrosine kinase system, EphB/ephrin-B, as the most tightly linked system to the invading cell phenotype. Clinical relevance of ephrin-B genes was confirmed in a clinically annotated expression data set of 195 brain biopsy specimens. Levels of ephrin-B1 and -B2 mRNA were significantly higher in GBM (n = 82) than in normal brain (n = 24). Kaplan-Meier analysis demonstrated ephrin-B2, but not ephrin-B1, expression levels were significantly associated with short term survival in malignant astrocytomas (n = 97, p = 0.016). In human brain tumor specimens, the production and phosphorylation of ephrin-B2 were high in GBM. Immunohistochemistry demonstrated ephrin-B2 localization primarily in GBM cells but not in normal brain. A highly invasive glioma cell line, U87, expressed high levels of ephrin-B2 compared with relatively less invasive cell lines. Treatment with EphB2/Fc chimera further enhanced migration and invasion of U87 cells, whereas treatment with an ephrin-B2 blocking antibody significantly slowed migration and invasion. Forced expression of ephrin-B2 in the U251 cell line stimulated migration and invasion in vitro and ex vivo, concomitant with tyrosine phosphorylation of ephrin-B2. These results demonstrate that high expression of ephrin-B2 is a strong predictor of short-term survival and that ephrin-B2 plays a critical role in glioma invasion rendering this signaling pathway as a potential therapeutic target.
Effect of colchicine analogs on the dissociation of .alpha..beta. tubulin into subunits: The locus of colchicine binding (1994)

A combination of ligand binding and sedimentation equilibrium studies was used to characterize the thermodynamic linkages between alpha beta tubulin association, nucleotide binding, and the interaction of colchicine analogues with dimeric and dissociated tubulins. The strength of binding of allocolchicine to the tubulin dimer was identical (8 x 10(5) M-1) whether the exchangeable nucleotide site (E site) was occupied by GTP or GDP. This drug bound to dimeric (alpha beta) tubulin and to one of the monomeric subunits, and the binding affinity for the dissociated state was linked to occupancy of the exchangeable nucleotide site. When the exchangeable site was occupied by GTP, the drug bound with very similar affinities to the dimeric and dissociated states of the protein. For tubulin-GDP, the binding of the drug to the dissociated state was significantly weaker (6.3 x 10(4) M-1) than to the dimeric state, suggesting the existence of an E-site-related conformational change in the dissociated state. Podophyllotoxin, which contains the A-ring portion of colchicine, bound with equal affinity to the dimeric and dissociated forms of both tubulin-GTP and tubulin-GDP, indicating that it is the C-ring portion of colchicine that is linked to the E-site-related conformational change.(ABSTRACT TRUNCATED AT 250 WORDS)
Prostate-specific antigen promoter/enhancer driven gene therapy for prostate cancer: construction and testing of a tissue-specific adenovirus vector. (2000)

A range of luciferase reporter vectors was constructed, incorporating 5'-flanking sequences from the prostate-specific antigen (PSA), human glandular kallikrein 2 (hKLK2), and cytomegalovirus (CMV) promoters for expression control. Tissue specificity was evaluated in the PSA-positive line LNCaP and PSA-negative cells from different tissues of origin (CoLo320, DG75, EJ, A2780, and Jurkat). The minimal 628-bp PSA and hKLK2 promoters showed only low-level expression in either PSA-positive or PSA-negative cells and showed no increase with the addition of androgen. Tandem duplication of the PSA promoter slightly increased expression in PSA-positive LNCaP cells. The addition of CMV enhancer sequences upstream of a single PSA or hKLK2 promoter substantially but nonspecifically increased luciferase expression in all cell lines tested. However, placing a 1455-bp PSA enhancer sequence upstream of either the PSA or hKLK2 promoters increased expression 20-fold in the PSA-positive cell line LNCaP but not in the PSA-negative lines. Tandem duplication of the PSA enhancer increased expression to approximately 50-fold higher than either promoter alone while retaining tissue-specific control. The level of expression was reduced by the addition of a third copy of the PSA enhancer. Expression from all enhancer constructs was increased 100-fold above basal levels when induced with the androgen dihydrotestosterone, with the PSA-based constructs consistently exhibiting roughly twice the level of expression of the hKLK2-based constructs at all androgen concentrations. Adenovirus vectors were produced in which either enhanced green fluorescent protein or nitroreductase could be expressed from the optimized PSA double enhancer-promoter construct and evaluated in LNCaP cells and the bladder-derived line EJ. Control vectors with the CMV promoter gave good levels of expression in both cell lines, whereas the PSA constructs only produced detectable levels of protein in the LNCaP cells as assessed by fluorescence of enhanced green fluorescent protein or by Western blotting of nitroreductase. LNCaP but not EJ cells were selectively sensitized to the prodrug CB1954 following infection with Ad-PSA(EEP)-NR. The PSA-based nitroreductase virus produced comparable amounts of nitroreductase and sensitization to CB1954 approaching that of the CMV-driven virus. Plasmid and adenovirus constructs combining PSA enhancer and promoter sequences demonstrate selective expression of linked genes in PSA-positive cells. The expression is induced by androgen and gives therapeutically relevant levels of effector proteins.