gebhart/patrepeval huggingface dataset:
Shewanella secretes flavins that mediate extracellular electron transfer (2008)

Bacteria able to transfer electrons to metals are key agents in biogeochemical metal cycling, subsurface bioremediation, and corrosion processes. More recently, these bacteria have gained attention as the transfer of electrons from the cell surface to conductive materials can be used in multiple applications. In this work, we adapted electrochemical techniques to probe intact biofilms of Shewanella oneidensis MR-1 and Shewanella sp. MR-4 grown by using a poised electrode as an electron acceptor. This approach detected redox-active molecules within biofilms, which were involved in electron transfer to the electrode. A combination of methods identified a mixture of riboflavin and riboflavin-5'-phosphate in supernatants from biofilm reactors, with riboflavin representing the dominant component during sustained incubations (>72 h). Removal of riboflavin from biofilms reduced the rate of electron transfer to electrodes by >70%, consistent with a role as a soluble redox shuttle carrying electrons from the cell surface to external acceptors. Differential pulse voltammetry and cyclic voltammetry revealed a layer of flavins adsorbed to electrodes, even after soluble components were removed, especially in older biofilms. Riboflavin adsorbed quickly to other surfaces of geochemical interest, such as Fe(III) and Mn(IV) oxy(hydr)oxides. This in situ demonstration of flavin production, and sequestration at surfaces, requires the paradigm of soluble redox shuttles in geochemistry to be adjusted to include binding and modification of surfaces. Moreover, the known ability of isoalloxazine rings to act as metal chelators, along with their electron shuttling capacity, suggests that extracellular respiration of minerals by Shewanella is more complex than originally conceived.
Infrequent alterations of the RAR alpha gene in acute myelogenous leukemias, retinoic acid-resistant acute promyelocytic leukemias, myelodysplastic syndromes, and cell lines (1996)

Retinoids are important regulators of cell growth and differentiation in vitro and in vivo and they exert their biologic activities by binding to nuclear retinoic acid receptors (RARs; alpha, beta, and gamma) and retinoid X receptors (RXRs; alpha, beta, and gamma). All-trans retinoic acid (RA) induces complete remission in patients with acute promyelocytic leukemia (APL) presumably by binding directly to RAR alpha of APL cells. Leukemic blasts from APL patients initially responsive to RA can become resistant to the agent. HL-60 myeloblasts cultured with RA have developed mutations of the ligand-binding region of RAR alpha and have become resistant to RA. Furthermore, insertion of an RAR alpha with an alteration in the ligand-binding region into normal murine bone marrow cells can result in growth factor-dependent immortalization of the early hematopoietic cells. To determine if alterations of the ligand binding domain of RAR alpha might be involved in several malignant hematologic disorders, the mutational status of this region (exons 7, 8, and 9) was examined in 118 samples that included a variety of cell lines and fresh cells from patients with myelodysplastic syndromes (MDS) and acute myeloid leukemias (AML), including 20 APL patients, 5 of whom were resistant to RA and 1 who was refractory to RA at diagnosis, using polymerase chain reaction-single-strand conformational polymorphism (PCR-SSCP) analysis and DNA sequencing. In addition, 7 of the 20 APLs were studied for alterations of the other coding exons of the gene (exons 2 through 6). No mutations of RAR alpha were detected. Although the sensitivity of PCR-SSCP analysis is less than 100%, these findings suggest that alterations of RAR alpha gene are rare and therefore other mechanisms must be involved in the onset of resistance to retinoids and in the lack of differentiation in disorders of the myeloid lineage.
Somatic Mutations ofIDH1andIDH2in the Leukemic Transformation of Myeloproliferative Neoplasms (2010)

To the Editor: Somatic mutations affecting the R132 residue of isocitrate dehydrogenase 1 (IDH1) and the homologous IDH2 R172 occur in central nervous system tumors.1,2 Recently (in the Sept. 10 issue of the Journal 3), alterations of IDH1 R132 (in exon 2) were reported in 16 of 188 patients with de novo acute myeloid leukemia, with a strong association with a normal karyotype; however, mutations of IDH2 R172 (in exon 4) were not detected. We sequenced exon 2 of the IDH1 gene and exon 4 of the IDH2 gene in patients with leukemia that had evolved from . . .
A large scale characterization of RO-PUF (2010)

To validate the effectiveness of a Physical Unclonable Function (PUF), it needs to be characterized over a large population of chips. Though simulation methods can provide approximate results, an on-chip experiment produces more accurate result. In this paper, we characterize a PUF based on ring oscillator (RO) using a significantly large population of 125 FPGAs. We analyze the experimental data using a ring oscillator loop delay model, and quantify the quality factors of a PUF such as uniqueness and reliability. The RO-PUF shows an average inter-die Hamming distance of 47.31%, and an average intra-die Hamming distance of 0.86% at normal operating condition. Additionally, we intend to make this large RO frequency dataset available publicly for the research community.
Characterization of Human Complement Receptor Type 2 (CR2/CD21) as a Receptor for IFN-α: A Potential Role in Systemic Lupus Erythematosus (2006)

Human complement receptor type 2 (CR2/CD21) is a B lymphocyte membrane glycoprotein that plays a central role in the immune responses to foreign Ags as well as the development of autoimmunity to nuclear Ags in systemic lupus erythematosus. In addition to these three well-characterized ligands, C3d/iC3b, EBV-gp350, and CD23, a previous study has identified CR2 as a potential receptor for IFN-alpha. IFN-alpha, a multifunctional cytokine important in the innate immune system, has recently been proposed to play a major pathogenic role in the development of systemic lupus erythematosus in humans and mice. In this study, we have shown using surface plasmon resonance and ELISA approaches that CR2 will bind IFN-alpha in the same affinity range as the other three well-characterized ligands studied in parallel. In addition, we show that IFN-alpha interacts with short consensus repeat domains 1 and 2 in a region that serves as the ligand binding site for C3d/iC3b, EBV-gp350, and CD23. Finally, we show that treatment of purified human peripheral blood B cells with the inhibitory anti-CR2 mAb 171 diminishes the induction of IFN-alpha-responsive genes. Thus, IFN-alpha represents a fourth class of extracellular ligands for CR2 and interacts with the same domain as the other three ligands. Defining the role of CR2 as compared with the well-characterized type 1 IFN-alpha receptor 1 and 2 in mediating innate immune and autoimmune roles of this cytokine should provide additional insights into the biologic roles of this interaction.
Topical Imiquimod: Mechanism of Action and Clinical Applications (2006)

Imiquimod is a synthetic imidazoquinoline heterocyclic amine of 240.3 Da (C14H16N4). Imiquimod is a cytokine inducer and a modifier of the innate immune response, as well as acquired antiviral and antitumor immune responses. Imiquimod 5% cream has proven to be an effective treatment for external genital warts, superficial basal cell carcinoma, and actinic keratosis.
Comparative Analysis of Natural Antibody Specificities among Hybridomas Originating from Spleen and Peritoneal Cavity of Adult NZB and BALB/c Mice (1988)

A preliminary experiment showed that the supernatants of in vitro cultured peritoneal cells (rich in Ly-1 B cell subset shown to secrete most IgM autoantibodies against bromelain-treated mouse red blood cells (BrMRBC) and DNA) from different mouse strains did not contain any significant antibody activity against DNA and cytoskeleton proteins, although the presence of anti-BrMRBC antibodies was clearly evident. Therefore, we investigated comparative natural antibody (NAb) specificities against an antigen panel (DNA, cytoskeleton proteins, IgG, bovine serum albumin (BSA), BrMRBC, trinitrophenyl (TNP), and trimethylammonium (TMA) haptens) among Ig-secreting hybridoma collections from the splenic (158) and peritoneal (230) immune compartments of autoimmune New Zealand black (NZB) and lipopolysaccharide (LPS)-stimulated BALB/c mice. The data showed: (i) isotypic restriction (mu and gamma 3 only), predominance of TMA ion-reactive (including BrMRBC) but negligible anti-DNA-reactive antibody specificities, and lack of simultaneous polyspecific widespread reactivity (i.e. at least four or more antigens) against DNA and cytoskeleton proteins in the peritoneal cavity; (ii) predominance of simultaneous widespread polyspecific reactivity against DNA and cytoskeleton proteins but negligible or no TMA hapten-reactive antibody specificities in the spleen. These observations reflect certain differences in the B cell repertoire of peritoneal cavity (rich in Ly-1 B cells) compared with spleen. The NAb against BrMRBC and those reactive with DNA and cytoskeleton proteins, which have been suggested to be secreted by the Ly-1 B cell subset, are distinguishable on the basis of the presence of separate recurrent idiotypes and preferential localization of B lymphocytes directed against these autoantigens.
An electronic nose: a sensitive and discriminating substitute for a mammalian olfactory system (1990)

The dream of a direct electronic analogue for a biological nose may still be some way from realisation, but considerable progress can be reported towards prototype computerised instruments capable of equivalent, or even better, performance in certain applications. The achievements are partly attributable to success in new circuit and systems approaches, as well as in developing sensing devices, with the prospect of further rapid progress based on the exploitation of materials and integrated sensor technology. Other important advances are being created in information processing, particularly in relation to pattern recognition.
A critical comparison of the hemolytic and fungicidal activities of cationic antimicrobial peptides (1999)

The hemolytic and fungicidal activity of a number of cationic antimicrobial peptides was investigated. Histatins and magainins were inactive against human erythrocytes and Candida albicans cells in phosphate buffered saline, but displayed strong activity against both cell types when tested in 1 mM potassium phosphate buffer supplemented with 287 mM glucose. The HC50/IC50 ratio, indicative of the therapeutic index, was about 30 for all peptides tested. PGLa was most hemolytic (HC50 = 0.6 microM) and had the lowest therapeutic index (HC50/IC50 = 0.5). Susceptibility to hemolysis was shown to increase with storage duration of the erythrocytes and also significant differences were found between blood collected from different individuals. In this report, a sensitive assay is proposed for the testing of the hemolytic activities of cationic peptides. This assay detects subtle differences between peptides and allows the comparison between the hemolytic and fungicidal potency of cationic peptides.
The use of retinoic acid to probe the relation between hyperproliferation-associated keratins and cell proliferation in normal and malignant epidermal cells. (1989)

When cells from normal human epidermis and from the human squamous cell carcinoma line SCC-13 were seeded on floating rafts of collagen and fibroblasts, they stratified and underwent terminal differentiation. Although the program of differentiation in SCC-13 cells was morphologically abnormal, the cultures resembled normal epidermal raft cultures by expressing the terminal differentiation-specific keratins, K1/K10, and by restricting their proliferative capacity to the basal-like cells of the population. In addition, the differentiating cells of both normal and SCC-13 raft cultures expressed keratins K6 and K16, which are not normally expressed in epidermis, but are synthesized suprabasally during wound-healing and in various epidermal diseases associated with hyperproliferation. While the behavior of normal and SCC-13 rafts was quite similar when they were cultured over normal medium, significant biochemical differences began to emerge when the cultures were exposed to retinoic acid. Most notably, while the SCC-13 cultures still stratified extensively, they showed a marked inhibition of both abnormal (K6/K16) and normal (K1/K10) differentiation-associated keratins, concomitantly with an overall disappearance of differentiated phenotype. Surprisingly, the reduction in K6/K16 in retinoid-treated SCC-13 cultures was not accompanied by a decrease in cell proliferation. Using immunohistochemistry combined with [3H]thymidine labeling, we demonstrate that while the expression of K6 and K16 are often associated with hyperproliferation, these keratins are only produced in the nondividing, differentiating populations of proliferating cultures. Moreover, since their expression can be suppressed without a corresponding decrease in proliferation, the expression of these keratins cannot be essential to the nature of the hyperproliferative epidermal cell.
Learning network node representations from structural identity (2017)

Submitted by Christianne Fontes de Andrade (cfontes@ct.ufrj.br) on 2019-07-04T13:56:00Z No. of bitstreams: 1 880228.pdf: 950941 bytes, checksum: d9f9159f51b57cc01c842ac88388e684 (MD5)
Elevated serum APRIL levels in patients with systemic sclerosis: distinct profiles of systemic sclerosis categorized by APRIL and BAFF. (2007)

The results suggest that elevated serum APRIL and BAFF levels were differentially associated with disease severity in SSc.
Long term shear stress leads to increased phosphorylation of multiple MAPK species in cultured human aortic endothelial cells (2009)

Fluid dynamics strongly influences endothelial cell function, and participates in the localization of atherosclerotic plaques at blood vessel branches. We investigated the hypothesis that wild-type human aortic endothelial cells (HAEC) exposed to prolonged pulsatile flow stimulation have levels of phosphorylated mitogen-activated protein kinases (MAPK) that are significantly greater than those observed in statically grown cultures. HAEC were exposed to pulsatile laminar shear stress in a parallel-plate flow chamber and analyzed for levels of phosphorylated ERK, JNK and p38 at 1, 10 and 20 h. While some MAPK exhibited alternating patterns of phosphorylation, others were characterized by steady increases or unchanged profiles until the terminal (20 h) time point. However, at 20 h, each MAPK demonstrated an increase in phosphorylation versus statically cultivated cells. Further, 20 h cultures from 10 dyn/cm(2) pulsatile shear stress had higher levels of phosphorylation for each MAPK than those from 2 dyn/cm(2). The finding that MAPK species can be phosphorylated in response to a prolonged pulsatile shear stress in both a time and magnitude dependent manner is an interesting result that may help to explain how the differential behaviors observed between cells from different flow environments can be generated and maintained.
Synthetic bactericidal peptide based on CAP37: a 37-kDa human neutrophil granule-associated cationic antimicrobial protein chemotactic for monocytes. (1993)

CAP37 (cationic antimicrobial protein of molecular mass 37 kDa) is a multifunctional protein isolated from the granules of human neutrophils. It is antibiotic and chemotactic and binds lipopolysaccharide. A synthetic peptide, amino acid sequence NQGRHFCGGALIHARFVMTAASCFQ, based on residues 20-44 of CAP37 protein mimics its antibiotic and lipopolysaccharide binding action. Peptide 20-44, at the concentrations tested, has antibacterial activity against Salmonella typhimurium, Pseudomonas aeruginosa, Escherichia coli, Enterococcus faecalis, and Staphylococcus aureus. The bactericidal action of the peptide was pH dependent, with maximum activity at pH 5.0 and pH 5.5 and decreased activity at pH 7.0. Various truncations, substitutions, and other modifications in the sequence deteriorate its activity. Free sulfhydryl groups and/or disulfide bridge formation are required for optimum antibiotic activity, since substitution of serines for, or alkylation of, cysteine residues 26 and 42 eliminates bactericidal activity. Evidently amino acids 20-44 represent an important, perhaps principal, antibacterial domain of CAP37. This peptide should provide new insight into the mechanism of antimicrobial activity of CAP37 and may serve as a model for new, useful, synthetic antibiotics.
Lean Tissue Imaging (2014)

Body composition refers to the amount of fat and lean tissues in our body; it is a science that looks beyond a unit of body weight, accounting for the proportion of different tissues and its relationship to health. Although body weight and body mass index are well-known indexes of health status, most researchers agree that they are rather inaccurate measures, especially for elderly individuals and those patients with specific clinical conditions. The emerging use of imaging techniques such as dual energy x-ray absorptiometry, computerized tomography, magnetic resonance imaging, and ultrasound imaging in the clinical setting have highlighted the importance of lean soft tissue (LST) as an independent predictor of morbidity and mortality. It is clear from emerging studies that body composition health will be vital in treatment decisions, prognostic outcomes, and quality of life in several nonclinical and clinical states. This review explores the methodologies and the emerging value of imaging techniques in the assessment of body composition, focusing on the value of LST to predict nutrition status.
The human alpha-fetoprotein gene. Sequence organization and the 5' flanking region. (1985)

The human a-fetoprotein (AFP) gene was isolated into three overlapping clones in bacteriophage X vectors and its sequence organization analyzed by restriction endonuclease mapping and nucleotide sequencing.The human AFP gene is about 20 kilobase pairs long and contains 15 exons and 14 introns.The overall organization of the human AFP gene is similar to that of the mouse AFP gene, with all but two exons showing identical sizes.Nucleotide sequences at all exonlintron junctions display similarity to the consensus boundary sequence (Breathnach, R., and Chambon, P. ( 1981) Annu.Rev. Biochem.50,, with the GT-AG rule applied to the splicing point.The cap site maps 44 nucleotides upstream from the translation initiation site.The "TATA box" is located 27 nucleotides upstream from the putative cap site and is flanked by sequences with dyad symmetry.The TATA box can thus be placed in the loop portion of a possible stemloop structure formed by intrastrand base-pairing.Other characteristic nucleotide sequences in the 5' flanking region include a CCAAC pentamer, a 14-base pair (bp) enhancer-like sequence, and a 9-bp sequence homologous to the glucocorticoid responsive element.A long (90 bp) direct repeat and several alternating purinelpyrimidine sequences are also present in the 5' flanking region.A 736-bp sequence of the 5' flanking region adjacent to the cap site of the human AFP gene shows a 61% similarity with the corresponding region of the mouse AFP gene.There are two Alu family sequences and two poly(dT-dG) repeats in the human AFP gene that show different distribution patterns from those in the mouse AFP gene.a-Fetoprotein (AFP') is a major serum protein during fetal life (1-3).Interest in the AFP gene stems from the fact that it is developmentally regulated and often re-expressed at high levels in hepatocarcinoma and teratocarcinoma patients (4, 5).In addition, its similarities to albumin in certain physico-
Easy Synthesis and Imaging Applications of Cross-Linked Green Fluorescent Hollow Carbon Nanoparticles (2011)

We propose an ingenious method for synthesizing cross-linked hollow fluorescent carbon nanoparticles (HFCNs) with green emission by simply mixing acetic acid, water, and diphosphorus pentoxide. This is an automatic method without external heat treatment to rapidly produce large quantities of HFCNs, in contrast to other syntheses of fluorescent carbon nanoparticles that required high temperature, complicated operations, or long reaction times. Characterizations of HFCNs through high-resolution transmission electron microscopy, infrared/Raman spectroscopy, and X-ray diffraction indicate that abundant small oxygenous graphite domains existed and endowed the HFCNs with fluorescent properties. After simple post-treatments, the cross-linked HFCNs can be used for cell-imaging applications. Compared with traditional dyes and CdTe quantum dots, HFCNs are the superior fluorescent bioimaging agent according to their low toxicity, stability, and resistance to photobleaching. The HFCNs were also applied to watermark ink and fluorescent powder, showing their promising potentials for further wide usage.
Human mast cell carboxypeptidase. Purification and characterization. (1989)

A carboxypeptidase activity was recently identified in highly purified human lung mast cells and dispersed mast cells from skin. Using affinity chromatography with potato-tuber carboxypeptidase inhibitor as ligand, mast cell carboxypeptidase was purified to homogeneity from whole skin extracts. The purified enzyme yielded a single staining band of approximately 34,500 D on SDS-PAGE. Carboxypeptidase enzyme content estimated by determination of specific activity, was 0.5, 5, and 16 micrograms/10(6) mast cells from neonatal foreskin, adult facial skin, and adult foreskin, respectively. Human mast cell carboxypeptidase resembled bovine carboxypeptidase A with respect to hydrolysis of synthetic dipeptides and angiotensin I, but was distinguished from carboxypeptidase A in its inability to hydrolyze des-Arg9 bradykinin. The amino acid composition of human mast cell carboxypeptidase was similar to the composition of rat mast cell carboxypeptidase. The amino-terminal amino acid sequence of mast cell carboxypeptidase demonstrated 65% positional identity with human pancreatic carboxypeptidase B, but only 19% with human carboxypeptidase A. Thus, human mast cell carboxypeptidase is a novel member of the protein family of zinc-containing carboxypeptidases, in that it is functionally similar but not identical to bovine carboxypeptidase A, but has structural similarity to bovine and human pancreatic carboxypeptidase B.
Therapeutic silencing of mutant huntingtin with siRNA attenuates striatal and cortical neuropathology and behavioral deficits (2007)

Huntington's disease (HD) is a neurodegenerative disorder caused by expansion of a CAG repeat in the huntingtin (Htt) gene. HD is autosomal dominant and, in theory, amenable to therapeutic RNA silencing. We introduced cholesterol-conjugated small interfering RNA duplexes (cc-siRNA) targeting human Htt mRNA (siRNA-Htt) into mouse striata that also received adeno-associated virus containing either expanded (100 CAG) or wild-type (18 CAG) Htt cDNA encoding huntingtin (Htt) 1-400. Adeno-associated virus delivery to striatum and overlying cortex of the mutant Htt gene, but not the wild type, produced neuropathology and motor deficits. Treatment with cc-siRNA-Htt in mice with mutant Htt prolonged survival of striatal neurons, reduced neuropil aggregates, diminished inclusion size, and lowered the frequency of clasping and footslips on balance beam. cc-siRNA-Htt was designed to target human wild-type and mutant Htt and decreased levels of both in the striatum. Our findings indicate that a single administration into the adult striatum of an siRNA targeting Htt can silence mutant Htt, attenuate neuronal pathology, and delay the abnormal behavioral phenotype observed in a rapid-onset, viral transgenic mouse model of HD.