gebhart/patrepeval huggingface dataset:
Llama single‐domain antibodies directed against nonconventional epitopes of tumor‐associated carcinoembryonic antigen absent from nonspecific cross‐reacting antigen (2009)

Single-domain antibodies (sdAbs), which occur naturally in camelids, are endowed with many characteristics that make them attractive candidates as building blocks to create new antibody-related therapeutic molecules. In this study, we isolated from an immunized llama several high-affinity sdAbs directed against human carcinoembryonic antigen (CEA), a heavily glycosylated tumor-associated molecule expressed in a variety of cancers. These llama sdAbs bind a different epitope from those defined by current murine mAbs, as shown by binding competition experiments using immunofluorescence and surface plasmon resonance. Flow cytometry analysis shows that they bind strongly to CEA-positive tumor cells but show no cross-reaction toward nonspecific cross-reacting antigen, a highly CEA-related molecule expressed on human granulocytes. When injected into mice xenografted with a human CEA-positive tumor, up to 2% of the injected dose of one of these sdAbs was found in the tumor, despite rapid clearance of this 15 kDa protein, demonstrating its high potential as a targeting moiety. The single-domain nature of these new anti-CEA IgG fragments should facilitate the design of new molecules for immunotherapy or diagnosis of CEA-positive tumors.
Channel capacity of spatial division multiple access schemes (2002)

The radio frequency spectrum for wireless communications is a finite and scarce resource, there is a fundamental limit on the radio channels which can be made available to mobile communication. We study the capacity limit of a wireless system with multiple receivers using an information theoretic model. We showed that the capacity region expands and varies between two boundaries depending on the relative positions of the users.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
A case control study of selenium in cancer. (1993)

As selenium has been shown to be a risk modifier of cancer at several sites in a case-control approach, selenium nutriture was studied in oral and oesophageal cancer patients. The mean selenium level in oral cancer patients was 102.6 ng/ml and in oesophageal cancer 103.3 ng/ml, while in the matched controls it was 117.5 and 116.2 ng/ml respectively. Relative risk estimates were 3.16 (P < 0.02) and 16.0 (P < 0.01) in oral and oesophageal cancer patients respectively. The risk appears to increase with selenium levels lower than 115 ng/ml.
Interleukin-21 triggers effector cell responses in the gut (2010)

In the gut of patients with Crohn's disease and patients with ulcerative colitis, the major forms of inflammatory bowel diseases (IBD) in humans, the tissue-damaging immune response is mediated by an active cross-talk between immune and non-immune cells. Accumulating evidence indicates also that cytokines produced by these cells play a major role in initiating and shaping this pathologic process. One such cytokine seems to be interleukin (IL)-21, a member of the common gamma-chain-receptor family. IL-21 is produced in excess in the inflamed intestine of patients with IBD mostly by activated CD4+ T helper cells co-expressing interferon-gamma and follicular T helper cells. Moreover, both in vitro and in vivo studies indicate that excessive IL-21 production leads to the activation of multiple signaling pathways that expand and sustain the ongoing mucosal inflammation. In this article, we review the available data supporting the pathogenic role of IL-21 in IBD.
Switchable Electrode Controlled by Enzyme Logic Network System: Approaching Physiologically Regulated Bioelectronics (2008)

The logic network composed of three enzymes (alcohol dehydrogenase, glucose dehydrogenase, and glucose oxidase) operating in concert as four concatenated logic gates (AND/OR), was designed to process four different chemical input signals (NADH, acetaldehyde, glucose, and oxygen). The cascade of biochemical reactions culminated in pH changes controlled by the pattern of the applied biochemical input signals. The "successful" set of inputs produced gluconic acid as the final product and yielded an acidic medium, lowering the pH of a solution from its initial value of pH 6-7 to the final value of ca. 4. The whole set of the input signal combinations included 16 variants resulting in different output signals. Those that corresponded to the logic output 1, according to the Boolean logic encoded in the logic circuitry, resulted in the acidic medium. The pH changes produced in situ were coupled with a pH-sensitive polymer-brush-functionalized electrode, resulting in the interface switching from the OFF state, when the electrochemical reactions are inhibited, to the ON state, when the interface is electrochemically active. Soluble [Fe(CN)(6)](3-/4-) was used as an external redox probe to analyze the state of the interface and to follow the changes produced in situ by the enzyme logic network, depending on the pattern of the applied biochemical signals. The chemical signals processed by the enzyme logic system and transduced by the sensing interface were read out by electrochemical means (cyclic voltammetry and Faradaic impedance spectroscopy). This readout step features a "sigmoid" processing of the signals that provides "filtering" and significantly suppresses errors. Coupling between signal-processing enzyme logic networks and electronic transducers will allow future "smart" bioelectronic devices to respond to immediate physiological changes and provide autonomous signaling/actuation depending on the concentration patterns of the physiological markers.
Zinc in wound healing: Theoretical, experimental, and clinical aspects (2007)

Zinc is an essential trace element in the human body and its importance in health and disease is appreciated. It serves as a cofactor in numerous transcription factors and enzyme systems including zinc-dependent matrix metalloproteinases that augment autodebridement and keratinocyte migration during wound repair. Zinc confers resistance to epithelial apoptosis through cytoprotection against reactive oxygen species and bacterial toxins possibly through antioxidant activity of the cysteine-rich metallothioneins. Zinc deficiency of hereditary or dietary cause can lead to pathological changes and delayed wound healing. Oral zinc supplementation may be beneficial in treating zinc-deficient leg ulcer patients, but its therapeutic place in surgical patients needs further clarification. Topical administration of zinc appears to be superior to oral therapy due to its action in reducing superinfections and necrotic material via enhanced local defense systems and collagenolytic activity, and the sustained release of zinc ions that stimulates epithelialization of wounds in normozincemic individuals. Zinc oxide in paste bandages (Unna boot) protects and soothes inflamed peri-ulcer skin. Zinc is transported through the skin from these formulations, although the systemic effects seem insignificant. We present here the first comprehensive account of zinc in wound management in relation to current concepts of wound bed preparation and the wound-healing cascade. This review article suggests that topical zinc therapy is underappreciated even though clinical evidence emphasizes its importance in autodebridement, anti-infective action, and promotion of epithelialization.
The role of the catalytic particle in the growth of carbon nanotubes by plasma enhanced chemical vapor deposition (2004)

Vertically aligned carbon nanotubes were synthesized by plasma enhanced chemical vapor deposition using nickel as a metal catalyst. High resolution transmission electron microscopy analysis of the particle found at the tip of the tubes reveals the presence of a metastable carbide Ni3C. Since the carbide is found to decompose upon annealing at 600 °C, we suggest that Ni3C is formed after the growth is stopped due to the rapid cooling of the Ni-C interstitial solid solution. A detailed description of the tip growth mechanism is given, that accounts for the composite structure of the tube walls. The shape and size of the catalytic particle determine the concentration gradient that drives the diffusion of C atoms across and though the metal.
Presence of transforming growth factors in human breast cancer cells. (1984)

Conditioned medium (CM) from a human mammary carcinoma cell line, MCF-7, and ten individual clones derived from these cells was examined for the presence of transforming growth factors (TGFs). Concentrated CM from all of the MCF-7 cell lines was found to stimulate the anchorage-independent growth of normal rat kidney cells in soft agar and to inhibit the binding of epidermal growth factor (EGF) to mouse NIH/3T3 fibroblasts and to A431 human epidermoid carcinoma cell membranes. The soft agar stimulating activity was heat stable but sensitive to treatment with dithiothreitol. EGF receptors were measured on the MCF-7 cell lines to determine whether the amount of TGFs associated with the CM from the various cell lines was correlated with the level of EGF receptors being expressed on these cells. Moreover, the intrinsic cloning efficiency of these lines in soft agar was measured to ascertain if any correlation might exist between the level of TGFs associated with these cells and the ability of these cell lines to form colonies in soft agar. Although all the MCF-7 cell lines had approximately the same number of EGF receptors per cell, ranging from 3 to 6 X 10(3) sites/cell, CM from these lines varied in potency with respect to inducing the growth of normal rat kidney cells as colonies in soft agar and in inhibiting the binding of EGF to NIH/3T3 cells. Likewise, the level of TGFs associated with the CM from the various clones showed no correlation with the ability of these individual lines to grow as colonies in soft agar. TGF activity was also detected in acid-ethanol extracts prepared from MCF-7 cells propagated in nude mice as tumors and in the extracts from two transplantable human mammary adenocarcinomas, Clouser I and II. In addition, approximately 50% of the normal rat kidney colonies formed in response to the Clouser II tumor extracts exhibited a branching morphology in contrast to spherical colonies produced by Clouser I or MCF-7 extracts. These results demonstrate that human mammary carcinoma cells from both established cell lines and cells maintained in nude mice as tumors contain TGF-like activities. Furthermore, the variation in TGFs associated with the CM from the MCF-7 clones suggests that the parent MCF-7 cell line contains a heterogeneous population of cells.
Quantum Privacy Amplification and the Security of Quantum Cryptography over Noisy Channels (1996)

Existing quantum cryptographic schemes are not, as they stand, operable in the presence of noise on the quantum communication channel. Although they become operable if they are supplemented by classical privacy-amplification techniques, the resulting schemes are difficult to analyze and have not been proved secure. We introduce the concept of quantum privacy amplification and a cryptographic scheme incorporating it which is provably secure over a noisy channel. The scheme uses an ``entanglement purification'' procedure which, because it requires only a few quantum controlled-not and single-qubit operations, could be implemented using technology that is currently being developed.
Efficient Diastereoselective Syntheses of Chiral Macrocycles via Zirconocene Coupling. Synthetic Control of Size and Geometry (2001)

ADVERTISEMENT RETURN TO ISSUEPREVCommunicationNEXTEfficient Diastereoselective Syntheses of Chiral Macrocycles via Zirconocene Coupling. Synthetic Control of Size and GeometryLaurel L. Schafer and T. Don TilleyView Author Information Center for New Directions in Organic Synthesis Department of Chemistry, University of California, Berkeley and The Chemical Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720 Cite this: J. Am. Chem. Soc. 2001, 123, 11, 2683–2684Publication Date (Web):February 21, 2001Publication History Received4 January 2001Published online21 February 2001Published inissue 1 March 2001https://pubs.acs.org/doi/10.1021/ja015509ohttps://doi.org/10.1021/ja015509orapid-communicationACS PublicationsCopyright © 2001 American Chemical SocietyRequest reuse permissionsArticle Views1175Altmetric-Citations55LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-AlertscloseSupporting Info (1)»Supporting Information Supporting Information SUBJECTS:Macrocycles,Materials,Mathematical methods,Sandwich compounds,Stereoselectivity Get e-Alerts
The intelligent digital scanning in phased-array ultrasonic tomography (1988)

Traditional ultrasound image systems use analog converters to modulate the intensity of CRT according to the echo signal amplitude. Using a minicomputer and ICs the authors developed an intelligent digital scanning system for use in phased-array ultrasonic equipment. The digital scanning system has a 256*256-pixel grid image with 16 gray levels. Four different models can be displayed on a TV monitor. Interpolation is carried out to eliminate moire artifacts.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Comparison of conserved structural and regulatory domains within divergent 16S rRNA–23S rRNA spacer sequences of cyanobacteria The GenBank accession numbers for the sequences reported in this paper are AF180968 and AF180969 for ITS-L and ITS-S, respectively. (2000)

PCR amplification of the internal transcribed spacer (ITS) between the 16S rRNA and 23S rRNA genes of the cyanobacterium NOSTOC: PCC 7120 gave three products. Two represented true ITS regions of different sizes, while the third was a heteroduplex. The longer spacer (ITS-L) contained 512 nucleotides and carried tRNA(Ile) and tRNA(Ala) genes, separated by a large stem-loop structure (V2) composed of short tandemly repeated repetitive sequences. Both tRNA genes, and the 5' half of the intervening stem, were absent from the shorter spacer (ITS-S), of length 283 nucleotides, which was otherwise almost completely identical to ITS-L. The two spacer regions of NOSTOC: PCC 7120 were aligned to published ITS sequences of cyanobacteria, the cyanelle of Cyanophora paradoxa and Escherichia coli. Although the ITS regions of cyanobacteria vary in length from 283 to 545 nucleotides and contain either both tRNA(Ile) and tRNA(Ala) genes, only the tRNA(Ile) gene, or neither, there is no correlation between ITS size and coding capacity for tRNAs. Putative secondary structures were determined for the deduced transcripts of the rrn operons of several cyanobacteria and were compared to that of E. coli. Highly conserved motifs important for folding and for maturation of the rRNA transcripts were identified, and regions homologous to bacterial antiterminators (box B-box A) were located. The conserved and variable regions of the cyanobacterial ITS are potential targets of PCR primers and oligonucleotide probes for detection and identification of cyanobacteria at different taxonomic levels.
The pavA gene of Streptococcus pneumoniae encodes a fibronectin‐binding protein that is essential for virulence (2001)

Streptococcus pneumoniae colonizes the nasopharynx in up to 40% of healthy subjects, and is a leading cause of middle ear infections (otitis media), meningitis and pneumonia. Pneumococci adhere to glycosidic receptors on epithelial cells and to immobilized fibronectin, but the bacterial adhesins mediating these reactions are largely uncharacterized. In this report we describe a novel pneumococcal protein PavA, which binds fibronectin and is associated with pneumococcal adhesion and virulence. The pavA gene, present in 64 independent isolates of S. pneumoniae tested, encodes a 551 amino acid residue polypeptide with 67% identical amino acid sequence to Fbp54 protein in Streptococcus pyogenes. PavA localized to the pneumococcal cell outer surface, as demonstrated by immunoelectron microscopy, despite lack of conventional secretory or cell-surface anchorage signals within the primary sequence. Full-length recombinant PavA polypeptide bound to immobilized human fibronectin in preference to fluid-phase fibronectin, in a heparin-sensitive interaction, and blocked binding of wild-type pneumococcal cells to fibronectin. However, a C-terminally truncated PavA' polypeptide (362 aa residues) failed to bind fibronectin or block pneumococcal cell adhesion. Expression of pavA in Enterococcus faecalis JH2-2 conferred > sixfold increased cell adhesion levels to fibronectin over control JH2-2 cells. Isogenic mutants of S. pneumoniae, either abrogated in PavA expression or producing a 42 kDa C-terminally truncated protein, showed up to 50% reduced binding to immobilized fibronectin. Inactivation of pavA had no effects on growth rate, cell morphology, cell-surface physico-chemical properties, production of pneumolysin, autolysin, or surface proteins PspA and PsaA. Isogenic pavA mutants of encapsulated S. pneumoniae D39 were approximately 104-fold attenuated in virulence in the mouse sepsis model. These results provide evidence that PavA fibronectin-binding protein plays a direct role in the pathogenesis of pneumococcal infections.
Purification and structure of mutacin B‐Ny266: a new lantibiotic produced by Streptococcus mutans (1997)

Mutacins are bactericidal substances of proteinaceous nature produced by Streptococcus mutans. Lantibiotics are antibacterial substances containing post-translationally modified amino acids such as lanthionine. Mutacin B-Ny266 was purified from the cell pellet of S. mutans strain Ny266 by ethanol extraction at pH 2.0 followed by reversed-phase chromatography (Sep-Pak cartridge) and by HPLC on a C18 column. The mean purification factor was 3240 +/- 81 and the mean yield was 1.0 +/- 0.1%. Molecular mass of mutacin B-Ny266 as determined by mass spectroscopy is 2270.29 +/- 0.21 Da. The amino acid sequence of the purified active fraction was obtained by Edman degradation after treatment with alkaline ethanethiol. Twenty-one amino acids were detected in this analysis. Mutacin B-Ny266 belongs to the type A lantibiotics. The proposed sequence is: F-K-A-W-U-F-A-Abu-P-G-A-A-K-O-G-A-F-N-U-Y-A. The molecule differs from that of epidermin/staphylococcin 1580 and gallidermin at positions 1, 2, 4, 5 and 6.
Reduced Fertility in Female Mice Lacking Copper-Zinc Superoxide Dismutase (1998)

Copper-zinc superoxide dismutase (CuZn-SOD) is believed to play a major role in the first line of antioxidant defense by catalyzing the dismutation of superoxide anion radicals to form hydrogen peroxide and molecular oxygen. Recent studies have shown that missense mutations in this gene contribute, evidently through a gain-of-function mechanism, to about 20% of familial amyotrophic lateral sclerosis. To define further the physiologic role of this enzyme, a model of mice deficient in this enzyme was generated using gene targeting technology. Mice lacking this enzyme were apparently healthy and displayed no increased sensitivity to hyperoxia. However, they exhibited a pronounced susceptibility to paraquat toxicity. Most surprisingly, female homozygous knock-out mice showed a markedly reduced fertility compared with that of wild-type and heterozygous knock-out mice. Further studies revealed that although these mice ovulated and conceived normally, they exhibited a marked increase in embryonic lethality. These data, for the first time, suggest a role of oxygen free radicals in causing abnormality of female reproduction in mammals.
Transgenic mice with increased plasma levels of TGF-beta 1 develop progressive renal disease. (1996)

Several lines of evidence suggest that local production of transforming growth factor-beta (TGF-beta) contributes to renal disease, particularly to the accumulation of the extracellular matrix protein that characterizes glomerulosclerosis and interstitial fibrosis. We have examined whether elevated levels of circulating TGF-beta adversely affect the kidney. We have studied mice that are transgenic for an active form of TGF-beta 1 under the control of murine albumin promoter and enhancer DNA sequences. These mice express the transgene exclusively in the liver and have elevated plasma concentrations of TGF-beta 1. Renal disease was seen in two of three lines of Alb/TGF-beta 1 transgenic mice; these two lines had the highest levels of hepatic transgene expression and the highest plasma TGF-beta 1 levels. Histologic abnormalities, which included mesangial expansion and thickened capillary loops, were noted in the glomeruli by 3 weeks of age. Interstitial fibrosis and tubular atrophy appeared subsequently. Mice from Line 25, the line with highest levels of TGF-beta 1, developed proteinuria by 5 weeks of age. These mice subsequently manifested nephrotic syndrome with ascites and progressive azotemia; uremic death occurred in more than 25% of the mice by 15 weeks of age. The glomeruli contained immune deposits in subendothelial and mesangial locations, but complement deposition was infrequent. Ultrastructural examination revealed an increase in extracellular matrix material, including collagen fibrils, in subendothelial and mesangial locations. Increased levels of circulating TGF-beta 1 induced progressive renal disease that was characterized by mesangial expansion, accumulation of glomerular immune deposits and matrix proteins, and interstitial fibrosis in this transgenic mouse model. These data suggest that chronically elevated circulating levels of TGF-beta 1 induce progressive glomerulosclerosis.