gebhart/patrepeval huggingface dataset:
Involvement of deregulated epiregulin expression in tumorigenesis in vivo through activated Ki-Ras signaling pathway in human colon cancer cells. (2000)

To identify the genes located downstream of the activated Ki-Ras signaling pathways in human colon cancer cells, a PCR-based cDNA subtraction library was constructed between HCT116 cells and HCT116-derived activated Ki-ras-disrupted cells (HKe3). One of the genes in HCT116 that was evidently up-regulated was epiregulin, a member of the epidermal growth factor family that is expressed in many kinds of human cancer cells. HKe3-stable transfectants expressing activated Ki-Ras regained over-expression of epiregulin. To further elucidate the biochemical structure and significance of epiregulin expression in tumorigenesis, HKe3-stable transfectants expressing epiregulin (e3-pSE cells) were established. Epiregulin existed as highly glycosylated membrane-bound forms, and TPA rapidly induced ectodomain shedding of epiregulin. Furthermore, the conditioned medium of e3-pSE cells showed more DNA synthesis for 32D cells expressing epidermal growth factor receptor (DER) cells than that of HKe3. Although anchorage-independent growth in soft agar was not observed for e3-pSE cells, tumorigenicity in nude mice was observed evidently, and their growth rate was correlated with each amount of exogenous epiregulin expression. These results suggested that activated Ki-Ras will be one of the factors contributing to the overexpression of epiregulin in human colon cancer cells, and that epiregulin will play a critical role in human tumorigenesis in vivo.
A chemical enucleation method for the transfer of mitochondrial DNA to cells (2003)

The study of pathogenic mitochondrial DNA mutations has, in most cases, relied on the production of transmitochondrial cybrids. Although the procedure to produce such cybrids is well established, it is laborious and cumbersome. Moreover, the mechanical enucleation procedure is inefficient and different techniques have to be used depending on the adherence properties of the cell. To circumvent these difficulties, we developed a chemical enucleation method that can have wide applicability for the production of transmitochondrial cybrids. The method is based on the use of actinomycin D to render the nuclear genome transcription/replication inactive and unable to recover after treatment. Such treated cells are fused to cells devoid of mitochondrial DNA and selected for the presence of a functional oxidative phosphorylation system. Our results showed that 95% of the clones recovered by this procedure are true transmitochondrial cybrids. This method greatly facilitates the production of transmitochondrial cybrids, thereby increasing the number of mtDNA mutations and the recipient cell types that can be studied by this system.
The propagation of active-passive interfaces in bacterial swarms (2018)

Propagating interfaces are ubiquitous in nature, underlying instabilities and pattern formation in biology and material science. Physical principles governing interface growth are well understood in passive settings; however, our understanding of interfaces in active systems is still in its infancy. Here, we study the evolution of an active-passive interface using a model active matter system, bacterial swarms. We use ultra-violet light exposure to create compact domains of passive bacteria within Serratia marcescens swarms, thereby creating interfaces separating motile and immotile cells. Post-exposure, the boundary re-shapes and erodes due to self-emergent collective flows. We demonstrate that the active-passive boundary acts as a diffuse interface with mechanical properties set by the flow. Intriguingly, interfacial velocity couples to local swarm speed and interface curvature, raising the possibility that an active analogue to classic Gibbs-Thomson-Stefan conditions may control this boundary propagation.
Principles of Multivariate Analysis, A User's Perspective. (1989)

Part I: Looking at multivariate data Part II: Samples, populations, and models Part III: Analysing ungrouped data Part IV: Analysing grouped data Part V: Analysing association among variables Appendix: some basic matrix theory A1 Definitions A2 Elementary arithmetic operations A3 Determinants and inverses A4 Quadratic forms A5 Latent roots and vectors A6 Matrix square root A7 Partitioned matrices A8 Vector differentiation References Index
Nanostructured Reduced Graphene Oxide/Fe2O3 Composite As a High-Performance Anode Material for Lithium Ion Batteries (2011)

Reduced graphene oxide/Fe(2)O(3) composite was prepared using a facile two-step synthesis by homogeneous precipitation and subsequent reduction of the G-O with hydrazine under microwave irradiation to yield reduced graphene oxide (RG-O) platelets decorated with Fe(2)O(3) nanoparticles. As an anode material for Li-ion batteries, the RG-O/Fe(2)O(3) composite exhibited discharge and charge capacities of 1693 and 1227 mAh/g, respectively, normalized to the mass of Fe(2)O(3) in the composite (and ∼1355 and 982 mAh/g, respectively, based on the total mass of the composite), with good cycling performance and rate capability. Characterization shows that the Fe(2)O(3) nanoparticles are uniformly distributed on the surface of the RG-O platelets in the composite. The total specific capacity of RG-O/Fe(2)O(3) is higher than the sum of pure RG-O and nanoparticle Fe(2)O(3), indicating a positive synergistic effect of RG-O and Fe(2)O(3) on the improvement of electrochemical performance. The synthesis approach presents a promising route for a large-scale production of RG-O platelet/metal oxide nanoparticle composites as electrode materials for Li-ion batteries.
One Fungus = One Name: DNA and fungal nomenclature twenty years after PCR (2011)

Some fungi with pleomorphic life-cycles still bear two names despite more than 20 years of molecular phylogenetics that have shown how to merge the two systems of classification, the asexual "Deuteromycota" and the sexual "Eumycota". Mycologists have begun to flout nomenclatorial regulations and use just one name for one fungus. The International Code of Botanical Nomenclature (ICBN) must change to accommodate current practice or become irrelevant. The fundamental difference in the size of fungi and plants had a role in the origin of dual nomenclature and continues to hinder the development of an ICBN that fully accommodates microscopic fungi. A nomenclatorial crisis also looms due to environmental sequencing, which suggests that most fungi will have to be named without a physical specimen. Mycology may need to break from the ICBN and create a MycoCode to account for fungi known only from environmental nucleic acid sequence (i.e. ENAS fungi).
Efficient production of human FVIII in hemophilic mice using lentiviral vectors (2003)

Lentiviral vectors (LV) have the ability to integrate their proviral DNA containing a therapeutic gene into the host cell's genome. Therefore, these vectors have a great potential for gene therapy especially in the treatment of hereditary diseases like hemophilia A, which require lifelong expression of the transgene. We constructed an HIV-1-based LV containing human B-domain-deleted factor VIII (FVIII) cDNA under the control of a promoter consisting of the chicken beta-actin promoter, CMV enhancers, and a large synthetic intron (CAG), which is a robust transcription promoter. High levels of FVIII expression from this vector could be demonstrated in vitro in 293T cells, primary liver cells, and hematopoietic progenitor cells. To test whether this viral vector was able to correct the bleeding disorder of C57BL/6 FVIII knockout mice, we transduced these mice with the FVIII LV either by intraperitoneal injection or by transplantation with transduced syngeneic bone marrow. FVIII production was analyzed in the blood plasma for a period of 3 months; however, only low levels of FVIII (<50 mU), which were below 5% of normal FVIII levels of 1000 mU, could be detected. Further analysis revealed that the low levels of FVIII activity present in the blood plasma were due to the presence of neutralizing antibodies to FVIII and not due to lack of expression of FVIII from the viral vector. FVIII expression could be detected in the tissues of the transduced mice by Western blot analysis and in ex vivo cultures. These data demonstrate that LVs are able to produce therapeutic levels of FVIII in knockout mice when administered by ip infection or by transduced hematopoietic cells. The challenge is to overcome the immune barriers to the therapeutic gene product.
Surface Modifications with Adsorbed PEO-Based Block Copolymers: Physical Characteristics and Biological Use (1997)

Surface Modifications with Adsorbed PEO-Based Block Copolymers: Physical Characteristics and Biological Use
Tau‐66: evidence for a novel tau conformation in Alzheimer's disease (2001)

We have characterized a novel monoclonal antibody, Tau-66, raised against recombinant human tau. Immunohistochemistry using Tau-66 reveals a somatic-neuronal stain in the superior temporal gyrus (STG) that is more intense in Alzheimer's disease (AD) brain than in normal brain. In hippocampus, Tau-66 yields a pattern similar to STG, except that neurofibrillary lesions are preferentially stained if present. In mild AD cases, Tau-66 stains plaques lacking obvious dystrophic neurites (termed herein 'diffuse reticulated plaques') in STG and the hippocampus. Enzyme-linked immunosorbent assay (ELISA) analysis reveals that Tau-66 is specific for tau, as there is no cross-reactivity with MAP2, tubulin, Abeta(1-40), or Abeta(1-42), although Tau-66 fails to react with tau or any other polypeptide on western blots. The epitope of Tau-66, as assessed by ELISA testing of tau deletion mutants, appears discontinuous, requiring residues 155-244 and 305-314. Tau-66 reactivity exhibits buffer and temperature sensitivity in an ELISA format and is readily abolished by SDS treatment. Taken together these lines of evidence indicate that the Tau-66 epitope is conformation-dependent, perhaps involving a close interaction of the proline-rich and the third microtubule-binding regions. This is the first indication that tau can undergo this novel folding event and that this conformation of tau is involved in AD pathology.
Identification of a (CUG)n Triplet Repeat RNA-Binding Protein and Its Expression in Myotonic Dystrophy (1996)

Myotonic dystrophy (DM) is an autosomal dominant neuromuscular disease that is associated with a (CTG)n repeat expansion in the 3'-untranslated region of the myotonin protein kinase (Mt-PK) gene. This study reports the isolation and characterization of a (CUG)n triplet repeat pre-mRNA/mRNA binding protein that may play an important role in DM pathogenesis. Two HeLa cell proteins, CUG-BP1 and CUG-BP2, have been purified based upon their ability to bind specifically to (CUG)8 oligonucleotides in vitro. While CUG-BP1 is the major (CUG)8-binding activity in normal cells, nuclear CUG-BP2 binding activity increases in DM cells. Both CUG-BP1 and CUG-BP2 have been identified as isoforms of a novel heterogeneous nuclear ribonucleoprotein (hnRNP), hNab50. The CUG-BP/hNab50 protein is localized predominantly in the nucleus and is associated with polyadenylated RNAs in vivo. In vitro RNA-binding/photocrosslinking studies demonstrate that CUG-BP/hNab50 binds to RNAs containing the Mt-PK 3'-UTR. We propose that the (CUG)n repeat region in Mt-PK mRNA is a binding site for CUG-BP/hNab50 in vivo, and triplet repeat expansion leads to sequestration of this hnRNP on mutant Mt-PK transcripts.
MAGNETIC RESONANCE IMAGING OF THE PERIOSTEUM AND CORTICAL BONE WITH ULTRASHORT TE (UTE) PULSE SEQUENCES (2004)

Introduction: Normal adult periosteum and cortical and produces no signal with typical bone has a short T 2 Magnetic Resonance pulse sequence echo times available in clinical practice. We wished to assess the value of using pulse sequences with a very short echo time to detect signal from periosteum and cortical bone. Materials and Methods: Ultrashort echo time (UTE) pulse sequences (TE = 0.08 msec) were used with and without preceding fat suppression and/or long T 2 component suppression pulses. Later echo images and difference images produced by subtracting these from the first echo image were also obtained. Two volunteers and ten patients were examined, four of whom had contrast enhancement with intravenous Gadodiamide. Two sheep tibiae were also examined before and after stripping of the periosteum. The separated periosteum was also examined. Results: The periosteum was seen on the sheep tibiae before stripping but there was only a faint signal adjacent to cortical bone afterwards and the removed tissue produced a high signal when examined separately. High signal regions were observed adjacent to cortical bone in the femur, tibia, spine, calcaneus, radius, ulna and carpal bones. Fat suppression and long T 2 suppression generally increased the conspicuity of these regions. The high signal regions were more obvious with contrast enhancement. Periosteum could generally be distinguished from susceptibility artifacts on difference images by its high signal on the initial image and its failure to increase in extent with images with increased TE’s. Signal in cortical bone was detected with UTE sequences in normal adults and patients. This signal was usually made more obvious by subtracting a later echo image from the first provided that the SNR was sufficiently high. Normal mean adult T 1 ’s ranged from 140 msec to 260 msec, and mean T 2 ’s ranged from 0.42 to 0.50 msec. Increased signal was observed after contrast enhancement in a normal volunteer and in all three patients in whom it was administered. Changes in signal in short T 2 components were seen in acute fractures in cortical bone and after fracture malunion. In a case of osteoporosis, bone volume and signal were reduced. Furthermore, in fractures increased signal was seen in the periosteum and this showed marked enhancement. Three weeks after fracture, tissue with properties consistent with periosteum was seen displaced from the bone by callus. Discussion: The normal adult periosteum and cortex can be visualized with ultrashort TE sequences. Conspicuity is usually improved by fat suppression and the use of difference images. Use of subtraction images was useful for selectively demonstrating periosteal and cortical contrast enhancement and separating this from enhancement of surrounding blood. Obvious periosteal and cortical enhancement was seen after fractures. This novel MRI sequence images for the first time the soft tissue component of cortical bone and enables visualization of different haemodynamic situations.
MHC interaction and T cell recognition of carbohydrates and glycopeptides (1992)

The T cell independence of complex polysaccharide Ag has suggested the possibility that carbohydrates may be incapable of T cell recognition because of a failure to interact with MHC restriction elements and/or a failure of MHC/carbohydrate complexes to interact with and be recognized by Ag-specific TCR. We have used two approaches to obtain information about T cell recognition of carbohydrate. First, we have determined the capacity of a series of oligosaccharides and glycolipids to bind a murine class II MHC molecule, IAd. No significant binding was observed with the 26 compounds tested, but the limitation to these studies was that there was a relatively limited collection of synthetic carbohydrate and glycolipid structures of limited complexity available for analysis. The second approach involved the study of the effect of glycosylation of a known peptide T cell epitope (OVA 323-339) on MHC binding of the peptide and on T cell recognition. Three patterns of effects were observed: 1) no effect on either binding or T cell recognition. This pattern was observed when the carbohydrate was located at residues removed from the core MHC-binding region. When the carbohydrate was located within the core MHC-binding regions, either 2) glycosylation destroyed both MHC binding and T cell recognition; or 3) glycosylation did not ablate MHC binding or T cell recognition. In this latter instance, there was evidence to indicate that the carbohydrate moiety was an important part of the antigenic determinant recognized by T cells.
Automatic Room Detection and Room Labeling from Architectural Floor Plans (2012)

This paper presents an automatic system for analyzing and labeling architectural floor plans. In order to detect the locations of the rooms, the proposed systems extracts both, structural and semantic information from given floor plans. Furthermore, OCR is applied on the text layer to retrieve the meaningful room labeling. Finally, a novel post-processing is proposed to split rooms into several sub-regions if several semantic rooms share the same physical room. Our fully automatic system is evaluated on a publicly available dataset of architectural floor plans. In our experiments, we could clearly outperform other state-of-the-art approaches for room detection.
Germ-Line Genetic Variation in the Key Androgen-Regulating Genes Androgen Receptor, Cytochrome P450, and Steroid-5-α-Reductase Type 2 Is Important for Prostate Cancer Development (2006)

Prostate cancer risk may be influenced by single genetic variants in the hormone-regulating genes androgen receptor (AR), cytochrome P450 (CYP17), and steroid-5-alpha-reductase type 2 (SRD5A2). In this study, we comprehensively investigated polymorphisms in these three loci and their joint effect in a large population-based study. We selected 23 haplotype-tagging single-nucleotide polymorphisms (htSNP) that could uniquely describe >95% of the haplotypes (6 in AR, 6 in CYP17, and 11 in SRD5A2). These htSNPs were then genotyped in the Cancer Prostate in Sweden population (2,826 case subjects and 1,705 controls). We observed significant association for several SNPs in the AR gene (P = 0.004-0.02) and CYP17 (P = 0.009-0.05) and one SNP in SRD5A2 (P = 0.02). Carriers of the most common AR haplotype had a significant excess risk to develop prostate cancer [odds ratio (OR), 1.25; 95% confidence interval (95% CI), 1.1-1.5; P = 0.002], yielding an estimated population attributable risk of 16% (95% CI, 0.06-0.25). Combining risk alleles from these genes yielded a 12% risk increase for each additional high-risk allele carried (95% CI, 1.1-1.2; P for trend = 9.2 x 10(-5)), with an overall OR of 1.87 (95% CI, 1.0-3.4) for carriers of all five included risk alleles, an OR of 2.13 (P for trend = 8 x 10(-4)) for advanced disease, and an OR of 4.35 (P for trend = 7 x 10(-5)) for disease onset before age 65 years. Genetic variation in key genes in the androgen pathway is important for development of prostate cancer and may account for a considerable proportion of all prostate cancers. Carriers of five high-risk alleles in the AR, CYP17, and SRD5A2 genes are at approximately 2-fold excess risk to develop prostate cancer.
Sequence dependent binding of cis-dichlorodiammineplatinum(II) to DNA (1980)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTSequence dependent binding of cis-dichlorodiammineplatinum(II) to DNAGary L. Cohen, Jay A. Ledner, William R. Bauer, H. Michael Ushay, Carl Caravana, and Stephen J. LippardCite this: J. Am. Chem. Soc. 1980, 102, 7, 2487–2488Publication Date (Print):March 1, 1980Publication History Published online1 May 2002Published inissue 1 March 1980https://pubs.acs.org/doi/10.1021/ja00527a072https://doi.org/10.1021/ja00527a072research-articleACS PublicationsRequest reuse permissionsArticle Views170Altmetric-Citations90LEARN 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-Alertsclose Get e-Alerts
Antisense inhibition of oncogene expression. (1992)

To understand the role of individual genes in regulating biological processes, one must be able to interfere specifically with either their expression or function. While monoclonal antibodies have proven very useful in studying cell surface proteins, the specific inhibition of intracellular proteins in viable cells is a much more difficult problem. The goal of antisense technology is to develop small oligonucleotides, plasmids, or retroviral vectors which can be readily introduced into living cells in order to inhibit specific gene expression. In this review, we briefly describe the principles of antisense usage, including problems of cellular uptake and intracellular distribution, mechanism of antisense action, and the properties of various oligonucleotide derivatives. In addition we present several examples of the biological effects of antisense administration used to study the role of specific genes in the regulation of cell growth and differentiation.
Mathematical model of skin exposed to thermal radiation (1969)

Abstract : Prediction of dermal injury resulting from exposure to thermal energy of any given intensity and duration depends entirely upon the resultant skin temperature-time history. Means are now available for assessing heat transfer by low temperature radiation, convection and conduction to the bare skin and through thin protective coverings of known physical properties. However, thermal effects of nuclear detonations constitute a special problem because much of the radiation lies in the visible range where the optical properties of the skin and its coverings, if any, greatly influence the heating pattern. Blackening of the skin eliminates effects due to its optical properties but enhances the ever-present variations in the thermal 'constants' of the skin. The present report describes the utilization of a mathematical equation and computer techniques for extracting these variations from empirical data obtained at relatively low levels of radiation (<0.5 Cal/sq cm sec.), and applying extrapolations of these values in calculations of temperature-time histories at higher levels of irradiance where empirical data are lacking. This procedure is subject to validation by experimentation within a limited range of exposures. If validation is achieved in the blackened skin then the entire system may be utilized in the determination of optical properties of unblackened skin.