gebhart/patrepeval huggingface dataset:
Development of Miniature Manipulators for Applications in Biology and Nanotechnologies (2003)

In the precision engineering industry, research and development is undertaken towards the development of microfactories, miniaturized environments for fabrication and assembly of small components. Micro handling and micromanipulation, especially in biology, but also in other fields, often require dedicated devices and special environments (pressure, humidity and temperature controlled) as well. It would be a logical step to miniaturize micromanipulation and micro handling devices to a certain extent in a similar manner as tools and environments, with the same advantages as microfactories have for manufacturing: lower energy consumption, better control of the operation environment and smaller space required for an entire laboratory. This paper presents several miniature positioning and manipulation devices based on piezoelectric transducers, which can serve to build a âMicrofactoryâ for application in Microbiology for either telemanipulation or semi- and fully autonomous manipulation. The proposed devices employ an amplification of the piezoelectric motion with bimorph, monolithic flexure bridges or inertial principles.
Presence of Cyclophilin A in Synovial Fluids of Patients with Rheumatoid Arthritis (1997)

Cyclophilins have been suggested to act as leukocyte chemotactic factors produced in the course of inflammation. Therefore we looked for the presence of cyclophilins in the synovial fluids (SF) from patients with rheumatoid arthritis (RA). Peptidyl prolyl cis-trans isomerase activity (PPIase) was measured in SF from knee punctures of 26 patients with RA and five patients with knee osteoarthritis (OA). PPIase was detected in SF from RA patients, but not in samples from OA patients. Enzyme activity was sensitive to inhibition by cyclosporin A (IC50 = 28-50 nM). Estimated concentrations of the SF-derived cyclophilin based on the enzyme activity were in the range of 11 to 705 nM. The presence of cyclophilin in the SF showed disease correlation; its concentration correlated with the number of cells in the SF (r = 0.91, P < 0.0001) and with the percentage of neutrophils in the cellular infiltrate and was higher in more acute cases of joint swelling. In immunoblots of partially purified preparations of SF from RA patients, an approximately 18-kD protein band reacted with polyclonal antibodies that recognize cyclophilin A and B, but not with antibodies specific for cyclophilin B. Sequencing of this protein revealed identity of the NH2-terminal amino acids with those of human cyclophilin A. The finding is unexpected since cyclophilin B rather than A is generally regarded as the secreted isoform, the presence of cyclophilin A being confined to the cytoplasm. Our data support the hypothesis that cyclophilins may contribute to the pathogenesis of inflammatory diseases, possibly by acting as cytokines. This may offer a possible explanation of the effectiveness of cyclosporin A in RA, in addition to the known immunosuppressive effects of the drug.
Dose-response relationship between objective measures of histamine-induced weals and dose of terfenadine. (1991)

Terfenadine is a safe non-sedative H1-receptor antagonist. This study aimed to quantify the relative reduction in weal and flare area, thickness and erythema at 4, 8, 12 and 24 h following a single but variable oral dose of terfenadine compared with pre-treatment measurements, in order to compare the dose-effect relationship and time course of the different dosages. In a double-blind randomized cross-over study, 12 healthy volunteers were given 60, 120 or 240 mg of terfenadine or placebo. Twenty micrograms of histamine acid phosphate was then injected intradermally at 4, 8, 12 and 24 h. The weal and flare areas were measured by planimetry, the thickness of the weal by an A-scan pulsed ultrasound device and the redness of both the weal and flare by an erythema-meter. A definite dose-response relationship was demonstrated between the weal and flare areas and the three active treatments. For the weal area, there was a significant difference between 60 mg and 240 mg of terfenadine at 4 h (p less than 0.01), at 8 and 12 h (p less than 0.05). For the flare area there was a similar significant difference at 4 h (p less than 0.01) and at 8 h (p less than 0.05). A dose-response relationship was demonstrated between weal erythema and 120 mg or 240 mg and 60 mg of terfenadine (p less than 0.05). There was a correlation between the plasma levels of the major metabolite and the initial dose of terfenadine, demonstrating their expected proportionality. This metabolite was also demonstrated in tissue fluid.
The Kinetics of Electron Transfer Through Ferrocene-Terminated Alkanethiol Monolayers on Gold (1995)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTThe Kinetics of Electron Transfer Through Ferrocene-Terminated Alkanethiol Monolayers on GoldJohn F. Smalley, Stephen W. Feldberg, Christopher E. D. Chidsey, Matthew R. Linford, Marshall D. Newton, and Yi-Ping LiuCite this: J. Phys. Chem. 1995, 99, 35, 13141–13149Publication Date (Print):August 1, 1995Publication History Published online1 May 2002Published inissue 1 August 1995https://pubs.acs.org/doi/10.1021/j100035a016https://doi.org/10.1021/j100035a016research-articleACS PublicationsRequest reuse permissionsArticle Views3613Altmetric-Citations527LEARN 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 options Get e-Alerts
The effect of anti‐CD40 ligand antibody on B cells in human systemic lupus erythematosus (2002)

These are the first mechanistic studies of the effect of anti-CD40L therapy in human autoimmune disease. The results suggest that further studies of CD40L blockade are warranted.
12-O-tetradecanoylphorbol-13-acetate- and tumor necrosis factor alpha-mediated induction of intercellular adhesion molecule-1 is inhibited by dexamethasone. Functional analysis of the human intercellular adhesion molecular-1 promoter. (1994)

Transcription regulation of the human intercellular adhesion molecule-1 gene by the phorbol ester 12-O-tetradecanoylphorbol-13-acetate (TPA), tumor necrosis factor alpha (TNF alpha), and the glucocorticoid dexamethasone was studied using transient transfections in 293 cells with intercellular adhesion molecule-1 promoter-luciferase constructs (together with a glucocorticoid receptor expression vector). TPA and TNF alpha induced promoter activity, which was repressed by dexamethasone. Four TPA-responsive DNA regions were identified, each containing a potential TPA-responsive enhancer sequence: 1) -677/-340 an AP3-like sequence; 2) -290/278 a TPA-response element (TRE); 3) -227/-175 an NF kappa B-like sequence; 4) -105/-38 an AP2-like sequence. TNF alpha enhanced transcription only through region 3. The TRE in region 2 appeared to be functionally coupled to a distal TATA box at -313 and differed from the consensus TRE with respect to binding characteristics for members of the AP1 family. The newly identified NF kappa B enhancer (TGGAAATTCC) is bound by a TNF alpha-induced nuclear protein and appears to be the key element in rapid transcription induction by TNF alpha (and TPA), while transactivation of this element is repressed by the ligand-bound glucocorticoid receptor. We propose a negative cross-talk between the NF kappa B transcription factor and the glucocorticoid receptor.
Delivery of short interfering RNA using endosomolytic cell‐penetrating peptides (2007)

Cell-penetrating peptides (CPPs) are peptides able to promote uptake of various cargos, including proteins and plasmids. Advances in recent years imply the uptake to be endocytic, where the current hurdle for efficient intracellular delivery is material being retained in the endosomes. In this study we wanted to compare the ability of various established CPPs to deliver siRNA and induce gene silencing of luciferase, with a novel designed penetratin analog having endosomolytic properties, using a noncovalent strategy. In principal, the penetratin analog EB1 will, upon protonation in the early-late endosomes, be able to form an amphipathic alpha helix resulting in permeabilization of the endosomal membrane. We demonstrate that even though all CPPs evaluated in this study can form complexes with siRNA, there is not a direct relationship between the complex formation ability and delivery efficacy. More important, although all CPPs significantly promote siRNA uptake, in some cases no gene silencing effect can be observed unless endosomal escape is induced. We find the designed endosomolytic peptide EB1 to be far more effective both in forming complexes and transporting biologically active siRNA than its parent peptide penetratin. We believe that developing CPPs with increased endosomolytical properties is a necessary step toward achieving biological effects at low concentrations for future in vivo applications.
Fibronectin polymerization stimulates cell growth by RGD-dependent and-independent mechanisms (2000)

Many aspects of cell behavior are regulated by cell-extracellular matrix interactions, including cell migration and cell growth. We previously showed that the addition of soluble fibronectin to collagen-adherent fibronectin-null cells enhances cell growth. This growth-promoting effect of fibronectin depended upon the deposition of fibronectin into the extracellular matrix; occupancy and clustering of fibronectin-binding integrins was not sufficient to trigger enhanced cell growth. To determine whether the binding of integrins to fibronectin's RGD site is required for fibronectin-enhanced cell growth, the ability of fibronectin lacking the integrin-binding RGD site (FN(Delta)RGD) to promote cell growth was tested. FN(Delta)RGD promoted cell growth when used as an adhesive substrate or when added in solution to collagen-adherent fibronectin-null cells. Addition of FN(Delta)RGD to collagen-adherent fibronectin-null cells resulted in a 1.6-1.8x increase in cell growth in comparison with cells grown in the absence of fibronectin. The growth-promoting effects of FN(Delta)RGD and wild-type fibronectin were blocked by inhibitors of fibronectin polymerization, including the anti-fibronectin antibody, L8. In addition, FN(Delta)RGD-induced cell growth was completely inhibited by the addition of heparin, and was partially blocked by either heparitinase-treatment or by addition of recombinant fibronectin heparin-binding domain. Heparin and heparitinase-treatment also partially blocked the growth-promoting effects of wild-type fibronectin, as well as the deposition of wild-type fibronectin into the extracellular matrix. These data suggest that cell surface heparan-sulfate proteoglycans contribute to the growth-promoting effects of FN(Delta)RGD and wild-type fibronectin. Addition of heparin, treatment with heparitinase, or incubation with monoclonal antibody L8 all inhibited the formation of short linear FN(Delta)RGD fibrils on the cell surface. Inhibitory (beta)1 integrin antibodies had no effect on FN(Delta)RGD fibril formation, FN(Delta)RGD-induced cell growth, or cell adhesion on FN(Delta)RGD-coated substrates. These data suggest that fibronectin fibril formation can promote cell growth by a novel mechanism that is independent of RGD-integrin binding, and that involves cell surface proteoglycans.
Rapid right ventricular pacing is an alternative to adenosine in catheter interventional procedures for congenital heart disease (2004)

Rapid right ventricular pacing is a safe and effective method to provide balloon stability during balloon dilatation of the aortic valve. It may be applied in other fields of catheter intervention where it is desirable to maintain stable device positions during the critical phase of the procedure.
Insertional Mutagenesis in the n -Alkane-Assimilating Yeast Yarrowia lipolytica : Generation of Tagged Mutations in Genes Involved in Hydrophobic Substrate Utilization (2001)

Tagged mutants affected in the degradation of hydrophobic compounds (HC) were generated by insertion of a zeta-URA3 mutagenesis cassette (MTC) into the genome of a zeta-free and ura3 deletion-containing strain of Yarrowia lipolytica. MTC integration occurred predominantly at random by nonhomologous recombination. A total of 8,600 Ura(+) transformants were tested by replica plating for (i) growth on minimal media with alkanes of different chain lengths (decane, dodecane, and hexadecane), oleic acid, tributyrin, or ethanol as the C source and (ii) colonial defects on different glucose-containing media (YPD, YNBD, and YNBcas). A total of 257 mutants were obtained, of which about 70 were affected in HC degradation, representing different types of non-alkane-utilizing (Alk(-)) mutants (phenotypic classes alkA to alkE) and tributyrin degradation mutants. Among Alk(-) mutants, growth defects depending on the alkane chain length were observed (alkAa to alkAc). Furthermore, mutants defective in yeast-hypha transition and ethanol utilization and selected auxotrophic mutants were isolated. Flanking borders of the integrated MTC were sequenced to identify the disrupted genes. Sequence analysis indicated that the MTC was integrated in the LEU1 locus in N083, a leucine-auxotrophic mutant, in the isocitrate dehydrogenase gene of N156 (alkE leaky), in the thioredoxin reductase gene in N040 (alkAc), and in a peroxine gene (PEX14) in N078 (alkD). This indicates that MTC integration is a powerful tool for generating and analyzing tagged mutants in Y. lipolytica.
Growth characteristics of group A streptococci in a new chemically defined medium (1980)

A new chemically defined medium for the growth of group A streptococci has been formulated. The advantages of this new medium over previously described defined media are: (i) rates of growth (i.e., doubling times) of 20 strains were comparable to the rates of growth in complex media; (ii) each strain grew to a higher culture density in the new defined medium than in complex media; (iii) transfer from complex media with small inocula was possible without any prior adaptation regimen; and (iv) the production of virulence factors (i.e., M protein and hyaluronic acid) and extracellular enzymes during growth in this new medium was comparable to that in complex media.
Islet-Specific Glucose-6-Phosphatase Catalytic Subunit-Related Protein-Reactive CD4+ T Cells in Human Subjects (2006)

Islet-specific glucose-6-phosphatase catalytic subunit-related protein (IGRP) is recognized as a major autoantigen for autoimmune type 1 diabetes (T1D) in the NOD mouse model. This study was undertaken to examine CD4+ T cell responses toward IGRP in human subjects. The tetramer-guided epitope mapping approach was used to identify IGRP-specific CD4+ T cell epitopes. IGRP(23-35) and IGRP(247-259) were identified as DRA1*0101/DRB1*0401-restricted epitopes. IGRP(13-25) and IGRP(226-238) were identified as DRA1*0101/DRB1*0301-restricted epitopes. IGRP-specific tetramers were used to evaluate the prevalence of IGRP-reactive T cells in healthy and T1D subjects. More than 80% of subjects with either DRB1*0401 or DRB1*0301 haplotype have IGRP-specific CD4+ T cell responses for at least one IGRP epitope. IGRP-specific T cells from both healthy and T1D groups produce both gamma-IFN and IL-10. DRA1*0101/DRB1*0401 IGRP(247-259)-restricted T cells also show cross-reactivity to an epitope derived from liver/kidney glucose-6-phosphatase. The detection of IGRP-reactive T cells in both type 1 diabetic subjects and healthy subjects and recent reports of other autoreactive T cells detected in healthy subjects underscore the prevalence of potentially autoreactive T cells in the peripheral immune system of the general population.
Endothelial cell transplantation. (1999)

After more than 20 years of autologous endothelial cell transplantation, controversy is slowly giving way to consensus. The ongoing discussion regarding the optimal methods of creating an endothelial layer on synthetic vascular prostheses has been replaced by the realization that both in vitro endothelialization with cultured venous endothelial cells and mixed microvascular sodding result in equilibrated luminal tissue layers covered by a persistant endothelium. Clinical trials with almost 200 in vitro endothelialized prostheses are in their 10th year, and patency results are distinctly better than in nonendothelialized prostheses, particularly in below-the-knee grafts.
β‐Glucosidase, β‐galactosidase, family A cellulases, family F xylanases and two barley glycanases form a superfamily of enzymes wit 8‐fold β/α architecture and with two conserved glutamates near the carboxy‐terminal ends of β‐strands four and seven (1995)

Comparison of the recently determined crystal structures Pseudomonas fluorescens subsp. cellulosa family F xylanase, (1-3)-beta-glucanase and (1-3,1-4)-beta-glucanase and the catalytic domain of E. coli beta-galactosidase reveals that they belong to a superfamily of 8-fold beta/alpha-barrels with similar amino acid residues at their active sites. In the three families that these enzymes represent, the nucleophile is a glutamate, which is located close to the carboxy-terminus of beta-strand seven. In addition all three enzymes have the sequence asparagine-glutamate close to the carboxy-terminus of beta-strand four. This glutamate has been identified as the acid/base in the family F xylanases and is essential for catalysis in beta-galactosidase. We suggest that the equivalent residue in the barley glucanases is the acid/base. Analysis of the sequences of family 1 beta-glucosidases and family 5 cellulases shows that these enzymes also belong to this superfamily which we call the 4/7 superfamily.
Relationship of Pneumocystis jiroveci Humoral Immunity to Prevention of Colonization and Chronic Obstructive Pulmonary Disease in a Primate Model of HIV Infection (2010)

Pulmonary colonization by the opportunistic pathogen Pneumocystis jiroveci is common in HIV(+) subjects and has been associated with development of chronic obstructive pulmonary disease (COPD). Host and environmental factors associated with colonization susceptibility are undefined. Using a simian-human immunodeficiency virus (SHIV) model of HIV infection, the immunologic parameters associated with natural Pneumocystis jiroveci transmission were evaluated. SHIV-infected macaques were exposed to P. jiroveci by cohousing with immunosuppressed, P. jiroveci-colonized macaques in two independent experiments. Serial plasma and bronchoalveolar lavage (BAL) fluid samples were examined for changes in antibody titers to recombinant Pneumocystis-kexin protein (KEX1) and evidence of Pneumocystis colonization by nested PCR of BAL fluid. In experiment 1, 10 of 14 monkeys became Pneumocystis colonized (Pc(+)) by 8 weeks post-SHIV infection, while 4 animals remained Pneumocystis colonization negative (Pc(-)) throughout the study. In experiment 2, 11 of 17 animals became Pneumocystis colonized by 16 weeks post-SHIV infection, while 6 monkeys remained Pc(-). Baseline plasma KEX1-IgG titers were significantly higher in monkeys that remained Pc(-), compared to Pc(+) monkeys, in experiments 1 (P = 0.013) and 2 (P = 0.022). Pc(-) monkeys had greater percentages of Pneumocystis-specific memory B cells after SHIV infection compared to Pc(+) monkeys (P = 0.037). After SHIV infection, Pc(+) monkeys developed progressive obstructive pulmonary disease, whereas Pc(-) monkeys maintained normal lung function throughout the study. These results demonstrate a correlation between the KEX1 humoral response and the prevention of Pneumocystis colonization and obstructive lung disease in the SHIV model. In addition, these results indicate that an effective Pneumocystis-specific memory B-cell response is maintained despite progressive loss of CD4(+) T cells during SHIV infection.
Quantum phase noise and field correlation in single frequency semiconductor laser systems (1984)

The influence of quantum phase fluctuations which affect single frequency semiconductor lasers in various coherent detection systems is discussed in terms of photocurrent autocorrelation and spectral density functions. The general treatment given in this paper can be applied in diverse practical cases and points out the problems of phase correlation and phase matching between the two mixed optical beams. In the more general case the photocurrent spectrum is found to be composed of discrete and quasi-Lorentzian parts whose energies and spectral spreads are discussed as a function of the laser line width, the phase matching and the phase correlation between the two coherently combined fields.
Vertically standing Ge nanowires on GaAs(110) substrates (2008)

The growth of epitaxial Ge nanowires is investigated on (100), (111) B and (110) GaAs substrates in the growth temperature range from 300 to 380 °C. Unlike epitaxial Ge nanowires on Ge or Si substrates, Ge nanowires on GaAs substrates grow predominantly along the [Formula: see text] direction. Using this unique property, vertical [Formula: see text] Ge nanowires epitaxially grown on GaAs(110) surface are realized. In addition, these Ge nanowires exhibit minimal tapering and uniform diameters, regardless of growth temperatures, which is an advantageous property for device applications. Ge nanowires growing along the [Formula: see text] directions are particularly attractive candidates for forming nanobridge devices on conventional (100) surfaces.
Conformation/activity studies of rationally designed potent anti‐adhesive RGD peptides (1992)

The Arg-Gly-Asp (RGD) sequence is a universal cell-recognition site of various extracellular proteins that interact with integrin cell-surface receptors. In order to design low-molecular-mass RGD protein antagonists, the determination of the biologically active conformation is a prerequisite. We present a method that yields detailed insight into the steric factors which govern the binding of the ligands to their receptors by systematically scanning the conformational space accessible for the tripeptide sequence RGD. The investigation is based on the conformationally controlled design of homodetic cyclic oligopeptides and their structural determination, coupled with biological assays. For this purpose, a whole set of cyclic pentapeptides and hexapeptides has been synthesized and their three-dimensional structures in solution analyzed by modern two-dimensional NMR techniques in combination with restrained and free molecular dynamics simulations. Their biological activity was compared with that of linear GRGDS in inhibition assays of tumor cell adhesion to laminin P1 and vitronectin substrates. An up to 100-fold, and in part selective, increase in activity was observed for two cyclic pentapeptides. Most other peptides showed a decreased activity which, however, was useful to correlate activity with rather small variations in conformation. Detailed comparative studies of the systematically designed conformations and the corresponding anti-adhesive activities offer an access to lead structures for a rational indirect drug design of peptide and peptidomimetic pharmaceuticals with strong interfering activity for integrin-mediated cell-cell and cell-matrix interactions.