gebhart/patrepeval huggingface dataset:
Nonrandom utilization of codon pairs in Escherichia coli. (1989)

We have analyzed protein-coding sequences of Escherichia coli and find that codon-pair utilization is highly biased, reflecting overrepresentation or underrepresentation of many pairs compared with their random expectations. This effect is over and above that contributed by nonrandomness in the use of amino acid pairs, which itself is highly evident; it is much weaker when nonadjacent codon pairs are examined and virtually disappears when pairs separated by two or three intervening codons are evaluated. There appears to be a high degree of directionality in this bias: any codon that participates in many nonrandom pairs tends to make both over- and underrepresented pairs, but preferentially as a left- or right-hand member. We show a relationship between codon-pair utilization patterns and levels of gene expression: genes encoding proteins expressed at high levels tend to contain more abundant, but more highly underrepresented, codon pairs, relative to genes expressed at low levels. The nonrandom utilization of codon pairs may be a consequence of their effects on translational efficiency, which in turn may be related to the compatibility of adjacent aminoacyl-tRNA isoacceptors at the A and P sites of a translating ribosome.
DNA in Radical Prostatectomy Specimens: Prognostic Value of Tumor Ploidy (1991)

In a series of 94 patients with prostatic adenocarcinoma the prognostic significance of some factors was studied after radical prostatectomy. DNA ploidy was assessed by flow cytometry of cells from deparaffinized specimens. Gleason sum, seminal vesicle status and ploidy turned all out to be important predictors of disease progression. The ploidy status significantly enhanced the ability to prognostically evaluate patients with intermediate grade carcinoma compared to tumor grade alone. Patients with seminal vesicle invasion and aneuploidy had a very poor prognosis which prompts trials with alternatives of adjuvant therapy in this patient population.
Altered Expression of RET Proto-oncogene Product in Prostatic Intraepithelial Neoplasia and Prostate Cancer (1998)

Expression of the RET proto-oncogene in benign prostatic epithelium, high-grade PIN, and histopathologically advanced prostate cancer suggests that RET may play a role in the growth of both benign and neoplastic prostate epithelial cells.
3D Rigorous simulation of mask induced polarization (2005)

The polarization induced by the mask is studied by using a 3D rigorous model, wich solves Maxwell equations using the finite element method. Teh aerial image depends strongly on the change of polarization induced by the materials, thickness of the layer and pitch of the periodic masks.
Anterior cruciate ligament replacement. Knee stability and the effects of implants (1989)

The anteroposterior stability of cadaveric knees was investigated. There was a wide range of normal laxity; knees were more stable at 90 degrees than at 20 degrees flexion. Anterior cruciate ligament implants with different stiffnesses were inserted; normal stability could always be restored, and the stiffness or extensibility of implants did not affect knee behaviour significantly. The tightness of implants was critical--small tensioning errors caused subluxation, inhibited knee extension and allowed damagingly high implant tensions. It is concluded that the tension of ligament implants could not be adjusted simply with a pre-set instrument; the procedure will remain critically dependent on the judgment of the operating surgeon.
Disturbed Feto-Maternal Cell Traffic in Preeclampsia (1998)

These results suggest that the trafficking of fetal cells into the maternal periphery is disturbed in patients with preeclampsia. Because it is unlikely that such an altered flow of cells is restricted to the erythroblasts examined in this study, these findings also may lead to interesting new concepts regarding the development of preeclampsia and possibly the associated syndrome of hemolysis, elevated liver enzymes, and low platelets.
Gradient methods for minimizing composite objective function (2007)

In this paper we analyze several new methods for solving optimization problems with the objective function formed as a sum of two convex terms: one is smooth and given by a black-box oracle, and another is general but simple and its structure is known. Despite to the bad properties of the sum, such problems, both in convex and nonconvex cases, can be solved with efficiency typical for the good part of the objective. For convex problems of the above structure, we consider primal and dual variants of the gradient method (converge as O (1/k)), and an accelerated multistep version with convergence rate O (1/k2), where k is\nthe iteration counter. For all methods, we suggest some efficient "line search" procedures and show that the additional computational work necessary for estimating the unknown problem class parameters can only multiply the complexity of each iteration by a small constant factor. We present also the results of preliminary computational experiments, which confirm the superiority of the accelerated scheme.
In situ localized amplification and contact replication of many individual DNA molecules (1999)

We describe a method to clone and amplify DNA by performing the polymerase chain reaction (PCR) in a thin polyacrylamide film poured on a glass microscope slide. The polyacrylamide matrix retards the diffusion of the linear DNA molecules so that the amplification products remain localized near their respective templates. At the end of the reaction, a number of PCR colonies, or 'polonies', have formed, each one grown from a single template molecule. As many as 5 million clones can be amplified in parallel on a single slide. If an Acrydite modification is included at the 5' end of one of the primers, the amplified DNA will be covalently attached to the polyacrylamide matrix, allowing further enzymatic manipulations to be performed on all clones simultaneously. We describe techniques to make replicas of these polony slides, and high throughput sequencing protocols for this technology. Other applications are also discussed.
Estrogen Induces Lung Metastasis through a Host Compartment–Specific Response (2006)

Direct proliferative effects of estrogen (E(2)) on estrogen receptor-positive tumors are well documented; however, the potential for E(2) to mediate effects selective for the host (i.e., angiogenesis, vascular permeability, or stromal effects), which influence tumor growth and/or metastasis, has received less attention. In this study, we examine the capacity for E(2) to promote tumor growth and/or metastasis independent of direct effects on tumor cells. In these studies, we distinguish host versus tumor compartment components of E(2) action in tumor growth and metastasis by analysis of E(2)-nonresponsive tumor cells implanted in ovariectomized (OVX) mice that contain s.c. implants of placebo (OVX) or E(2)-containing slow-release pellets (OVX + E(2)). We show that the D121 lung carcinoma cell line is E(2)-nonresponsive, and following s.c. implantation in OVX versus OVX + E(2) mice, E(2) action on the host compartment leads to an increase in spontaneous metastasis but not primary tumor growth or neovascularization. Similarly, experimental lung metastasis of E(2)-nonresponsive 4T1 mammary carcinoma cells also leads to increased tumor burden in the lungs of OVX + E(2) mice. These results suggest that the E(2) status of the host compartment influences late steps in tumor cell metastasis that can provide important insights into the role of E(2) in the tumor versus host compartments.
Mechanisms of overlap formation in nonhomologous DNA end joining. (1994)

Rejoining of nonhomologous DNA termini plays a central role in processes of illegitimate recombination. In Xenopus egg extracts, DNA ends with noncomplementary 4-nucleotide antiparallel single-strand protrusions are assumed to be joined by formation of short mismatched overlap intermediates. The extents of these overlaps may be set by single fortuitously matching base pairs and determine the patterns of subsequent gap filling and nick ligation. Under conditions of alternative overlap settings, rules for the most probable joining pathway and the effects of mismatches on junction formation were analyzed. We show that in certain cases, fill-in and ligation converting overlap intermediates into covalently closed junctions may proceed in the presence of unrepaired mismatches, whereas in other cases, completion of junction formation is preceded by removal of mismatches. Results are discussed in relation with "alignment" proteins postulated to structurally support overlap heteroduplexes during junction formation.
Identification of a novel peptide derived from the melanocyte‐specific gp100 antigen as the dominant epitope recognized by an HLA‐A2.1‐restricted anti‐melanoma CTL line (1995)

Cytotoxic T lymphocytes (CTL) reactive with human melanoma tumor cells occasionally display cross-reactivity with normal melanocytes. Previously, we identified the melanocyte lineage-specific antigen gp 100 that is expressed by both melanoma cells and normal melanocytes, as a target antigen for tumor-infiltrating lymphocytes derived from a melanoma patient (TIL 1200). Here, we demonstrate that the oligoclonal HLA-A2.1-restricted TIL 1200 line is reactive with 2 distinct peptides derived from the gp 100 protein. Apart from the peptide corresponding to gp 100 amino acids 457-466, we identified the gp 100 peptide 154-162 as a second epitope recognized by TIL 1200. A 100-fold lower concentration of this novel gp 100 peptide was required for target-cell sensitization compared to peptide 457-466, indicating that the 154-162 peptide is the dominant gp 100 epitope for TIL 1200. Together with the recently described gp 100 280-288 epitope, 3 distinct CTL epitopes have now been identified in gp 100, all presented in the context of HLA-A2.1. Therefore, gp 100 is an attractive target antigen in the development of immuno-therapeutic protocols against melanoma.
Inhibition of vascular endothelial growth factor-induced endothelial cell migration by ETS1 antisense oligonucleotides. (1997)

Vascular endothelial growth factor (VEGF) increased the level of ETS1 mRNA in human umbilical vein endothelial cells (HUVEC) and human lung microvascular endothelial cells (HMVEC-L) over 5-fold. Protein levels were shown to increase concordantly. VEGF was also found to stimulate the invasiveness of endothelial cells as measured by migration through Matrigel- or gelatin-coated membranes. The VEGF-induced invasiveness was inhibited by ETS1 antisense oligonucleotides but not by a sense control. In addition, the ETS1 antisense oligonucleotides reduced the levels of ETS1 and urokinase-type plasminogen activator mRNAs. The antisense oligonucleotides directed against the ETS1 gene thus altered a cellular property of endothelial cells that is correlated with the ability of the cells to migrate through basement membranes. Together, these observations demonstrate a direct role for the ETS1 gene in angiogenesis.
Genetic definition of a protein-splicing domain: Functional mini-inteins support structure predictions and a model for intein evolution (1997)

Inteins are protein-splicing elements, most of which contain conserved sequence blocks that define a family of homing endonucleases. Like group I introns that encode such endonucleases, inteins are mobile genetic elements. Recent crystallography and computer modeling studies suggest that inteins consist of two structural domains that correspond to the endonuclease and the protein-splicing elements. To determine whether the bipartite structure of inteins is mirrored by the functional independence of the protein-splicing domain, the entire endonuclease component was deleted from the Mycobacterium tuberculosis recA intein. Guided by computer modeling studies, and taking advantage of genetic systems designed to monitor intein function, the 440-aa Mtu recA intein was reduced to a functional mini-intein of 137 aa. The accuracy of splicing of several mini-inteins was verified. This work not only substantiates structure predictions for intein function but also supports the hypothesis that, like group I introns, mobile inteins arose by an endonuclease gene invading a sequence encoding a small, functional splicing element.
BT1, a possible adenylate translocator, is developmentally expressed in maize endosperm but not detected in starchy tissues from several other species (1997)

Brittle 1 protein (BT1), the major protein in amyloplast envelope membranes of wild‐type maize endosperm, is required for normal levels of starch accumulation in maize kernels. To gain information about the Bt1 locus in control of starch synthesis in plants, we examined Bt1 expression in kernels from different ages and from different genotypes of maize as well as in starchy tissues from different species. Both BT1 protein and Bt1 transcripts were detected in kernels from about 10 days post‐pollination (DPP) and increased up to 14 DPP. BT1 protein level was similar in kernels after 14 DPP. Furthermore, membranes from amyloplasts containing larger starch granules contained more BT1 protein than those containing smaller starch granules from the same age of kernels. These results indicate that Bt1 gene expression was developmentally regulated and that BT1 protein level was correlated with starch accumulation in normal maize endosperm. Unexpectedly, except for a weak band at a higher molecular mass in microsomal proteins extracted from spring barley grain which reacted with maize BT1 antibody, no BT1 protein was observed in starchy tissues from several other species, including grains of sorghum, wheat, winter barley and oats, potato tubers, pea roots and cauliflower buds. Thus either the BT1 antibody raised against a fusion protein including the 56 amino acid residues in the carboxyl terminal sequence of maize endosperm BT1 protein does not recognize BT1 homologues in amyloplasts from other tissues or species or amyloplasts from different tissues or species have alternative membrane transporters.
Tertiary carbinamines by addition of organocerium reagents to nitriles and ketimines (1992)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTTertiary carbinamines by addition of organocerium reagents to nitriles and ketiminesEngelbert CiganekCite this: J. Org. Chem. 1992, 57, 16, 4521–4527Publication Date (Print):July 1, 1992Publication History Published online1 May 2002Published inissue 1 July 1992https://pubs.acs.org/doi/10.1021/jo00042a037https://doi.org/10.1021/jo00042a037research-articleACS PublicationsRequest reuse permissionsArticle Views2216Altmetric-Citations83LEARN 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 Get e-Alerts
Mechanisms of resistance to EGFR tyrosine kinase inhibitors (2015)

Since the discovery that non-small cell lung cancer (NSCLC) is driven by epidermal growth factor receptor (EGFR) mutations, the EGFR tyrosine kinase inhibitors (EGFR-TKIs, e.g., gefitinib and elrotinib) have been effectively used for clinical treatment. However, patients eventually develop drug resistance. Resistance to EGFR-TKIs is inevitable due to various mechanisms, such as the secondary mutation (T790M), activation of alternative pathways (c-Met, HGF, AXL), aberrance of the downstream pathways (K-RAS mutations, loss of PTEN), impairment of the EGFR-TKIs-mediated apoptosis pathway (BCL2-like 11/BIM deletion polymorphism), histologic transformation, ATP binding cassette (ABC) transporter effusion, etc. Here we review and summarize the known resistant mechanisms to EGFR-TKIs and provide potential targets for development of new therapeutic strategies.
An in Vitro and in Vivo Investigation of Bivalent Ligands That Display Preferential Binding and Functional Activity for Different Melanocortin Receptor Homodimers (2016)

Pharmacological probes for the melanocortin receptors have been utilized for studying various disease states including cancer, sexual function disorders, Alzheimer's disease, social disorders, cachexia, and obesity. This study focused on the design and synthesis of bivalent ligands to target melanocortin receptor homodimers. Lead ligands increased binding affinity by 14- to 25-fold and increased cAMP signaling potency by 3- to 5-fold compared to their monovalent counterparts. Unexpectedly, different bivalent ligands showed preferences for particular melanocortin receptor subtypes depending on the linker that connected the binding scaffolds, suggesting structural differences between the various dimer subtypes. Homobivalent compound 12 possessed a functional profile that was unique from its monovalent counterpart providing evidence of the discrete effects of bivalent ligands. Lead compound 7 significantly decreased feeding in mice after intracerebroventricular administration. To the best of our knowledge, this is the first report of a melanocortin bivalent ligand's in vivo physiological effects.
Group path formation (2006)

When people make choices within a group, they are frequently influenced by the choices made by others. We have experimentally explored the general phenomenon of group behavior where an early action facilitates subsequent actions. Our concrete instantiation of this problem is group path formation where people travel between destinations with the travel cost for moving onto a location inversely related to the frequency with which others have visited the location. We compare the resulting paths to optimal solutions [minimal Steiner trees (MSTs)] and the "Active Walker" model of pedestrian motion from biophysics. There were systematic deviations from beeline pathways in the direction of MST. These deviations showed asymmetries (people took different paths from A to B than they did from B to A) and varied as a function of the topology of the destinations, the duration of travel, and the absolute scale of the world. The Active Walker model accounted for many of these results, in addition to correctly predicting the approximate spatial distribution of steps.
Functional Characterization of Five eIF4E Isoforms inCaenorhabditis elegans (2000)

Recognition of the 5'-cap structure of mRNA by eIF4E is a critical step in the recruitment of most mRNAs to the ribosome. In Caenorhabditis elegans, approximately 70% of mRNAs contain an unusual 2,2,7-trimethylguanosine cap structure as a result of trans-splicing onto the 5' end of the pre-mRNA. The characterization of three eIF4E isoforms in C. elegans (IFE-1, IFE-2, and IFE-3) was reported previously. The present study describes two more eIF4E isoforms expressed in C. elegans, IFE-4 and IFE-5. We analyzed the requirement of each isoform for viability by RNA interference. IFE-3, the most closely related to mammalian eIF4E-1, binds only 7-methylguanosine caps and is essential for viability. In contrast, three closely related isoforms (IFE-1, IFE-2, and IFE-5) bind 2,2, 7-trimethylguanosine caps and are partially redundant, but at least one functional isoform is required for viability. IFE-4, which binds only 7-methylguanosine caps, is most closely related to an unusual eIF4E isoform found in plants (nCBP) and mammals (4E-HP) and is not essential for viability in any combination of IFE knockout. ife-2, ife-3, ife-4, and ife-5 mRNAs are themselves trans-spliced to SL1 spliced leaders. ife-1 mRNA is trans-spliced to an SL2 leader, indicating that its gene resides in a downstream position of an operon.
Transmembrane Domain-induced Oligomerization Is Crucial for the Functions of Syndecan-2 and Syndecan-4 (2005)

The syndecans are known to form homologous oligomers that may be important for their functions. We have therefore determined the role of oligomerization of syndecan-2 and syndecan-4. A series of glutathione S-transferase-syndecan-2 and syndecan-4 chimeric proteins showed that all syndecan constructs containing the transmembrane domain formed SDS-resistant dimers, but not those lacking it. SDS-resistant dimer formation was hardly seen in the syndecan chimeras where each transmembrane domain was substituted with that of platelet-derived growth factor receptor (PDGFR). Increased MAPK activity was detected in HEK293T cells transfected with syndecan/PDGFR chimeras in a syndecan transmembrane domain-dependent fashion. The chimera-induced MAPK activation was independent of both ligand and extracellular domain, implying that the transmembrane domain is sufficient to induce dimerization/oligomerization in vivo. Furthermore, the syndecan chimeras were defective in syndecan-4-mediated focal adhesion formation and protein kinase Calpha activation or in syndecan-2-mediated cell migration. Taken together, these data suggest that the transmembrane domains are sufficient for inducing dimerization and that transmembrane domain-induced oligomerization is crucial for syndecan-2 and syndecan-4 functions.
Solid‐state thermolysis of poly(p‐t‐butoxycarbonyloxystyrene) catalyzed by polymeric phenol: Effect of phase separation (1986)

Abstract Thermolysis of poly( p‐t ‐butoxycarbonyloxystyrene) (PBOCST) catalyzed by polymeric phenol in the solid state is very much dependent on the extent of phase separation. Poly( p ‐hydroxystyrene) (PHOST, a thermolysis product of PBOCST) is not miscible with PBOCST. Therefore, this phenolic resin can not effectively catalyze the solid‐state thermolysis reaction when simply blended with PBOCST. However, if the phenolic functionality is forced to be in the vicinity of the t ‐butoxycarbonyl ( t BOC) group, the thermolysis takes place facilely at 130°C. The effect of casting solvent on thermolysis in PBOCST/Varcum films is also discussed.
Chronic Recurrent Multifocal Osteomyelitis: Review (2011)

Chronic Recurrent Multifocal Osteomyelitis: ReviewRamesh S. Iyer1, Mahesh M. Thapa1 2 and Felix S. Chew1Audio Available | Share Claim CME