gebhart/patrepeval huggingface dataset:
Three-state denaturation of DnaK induced by guanidine hydrochloride. Evidence for an expandable intermediate (1993)

The denaturation of the heat shock protein DnaK induced by guanidine hydrochloride (Gdn-HCl) was investigated by circular dichroism, fluorescence, size-exclusion HPLC, and dynamic light scattering. DnaK unfolding takes place in two discrete steps. The midpoint (Cm) of the first transition (0.5 M) was shifted to higher denaturant concentrations (0.8 M) in the presence of Mg/ADP or Mg/ATP, whereas the second transition (Cm = 1.6 M) was unaffected by nucleotides. An intermediate state which continuously expands with increasing Gdn.HCl concentration was observed; its relation to molten globules is discussed. In addition, a direct correlation between molecular volume and ellipticity at 222 nm was found, regardless of the conformational state (native, intermediate, unfolded); the implications of these findings are discussed. The unfolding of DnaK is best explained by a hierarchical model of unfolding.
Enormous Hyper-Rayleigh Scattering from Nanocrystalline Gold Particle Suspensions (1998)

The recent emergence of advanced technological applications for colloidal gold suspensions and related particle assemblies and interfaces has created a demand for new chemical and physical techniques with which to characterize them. For macroscopic samples/interfaces, coherent second harmonic generation (SHG) has proven itself a useful characterization tool due, at least in part, to metal-based plasmon enhancement. In an effort to defeat or bypass the size restrictions inherent to SHG, we have utilized a related incoherent methodology, hyper-Rayleigh scattering (HRS), to interrogate aqueous colloidal suspensions of 13 nm diameter gold particles. The nanoscale particles have proven to be remarkably efficient scatterers; when evaluated in terms of the first hyperpolarizability (β), HRS signals from the gold particles substantially surpass those observable from the best available molecular chromophores. Moreover, the present experiments indicate that β is highly sensitive to colloid aggregation and imply that HRS is an effective tool for the characterization of symmetry-reducing perturbations of nanoscale interfaces.
Efficient and consistent vision-aided inertial navigation using line observations (2013)

This paper addresses the problem of estimating the state of a vehicle moving in 3D based on inertial measurements and visual observations of lines. In particular, we investigate the observability properties of the corresponding vision-aided inertial navigation system (VINS) and prove that it has five (four) unobservable degrees of freedom when one (two or more) line(s) is (are) detected. Additionally, we leverage this result to improve the consistency of the extended Kalman filter (EKF) estimator introduced for efficiently processing line observations over a sliding time-window at cost only linear in the number of line features. Finally, we validate the proposed algorithm experimentally using a miniature-size camera and a micro-electromechanical systems (MEMS)-quality inertial measurement unit (IMU).
Operation of an efficient site-specific recombination system ofZygosaccharomyces rouxiiin tobacco cells (1991)

Recombinase encoded by the R gene of pSR1 of Zygosaccharomyces rouxii mediates reciprocal recombination between two specific recombination sites (RSs) to induce excision or inversion of the DNA segment that is flanked by the RSs. We report here that site-specific recombination mediated by this system takes place effeciently in tobacco cells. To monitor the recombination events in tobacco cells, we have constructed two types of cryptic beta-glucuronidase reporter gene in such a way that recombination such as inversion of the construct or excision of the intervening sequence results in their expression. When these cryptic reporter constructs were transiently introduced together with the R gene by electroporation into protoplasts of tobacco cells, beta-glucuronidase activity was detected. The cryptic reporter genes, when stably resident in the chromosome of tobacco cells, were also activated by the R gene. Structural analyses of the genomic DNA isolated from these tobacco cells showed that the R protein did in fact catalyze precise recombination between two copies of RSs in tobacco cells, with resultant activation of the cryptic reporter genes. This observation provides the basis for development of a DNA technology whereby large regions of DNA can be manipulated in plant chromosomes. Potential uses of this recombination system are discussed.
MR Imaging–guided Focused Ultrasound Surgery of Uterine Leiomyomas: A Feasibility Study (2003)

The feasibility and safety of magnetic resonance (MR) imaging-guided focused ultrasound surgery for uterine leiomyomas is reported. Sequential sonications were delivered to nine targets. Temperature-sensitive phase-difference MR imaging monitored the location of the focus and measured tissue temperature elevations, ensuring therapeutic dose. MR images and hysterectomy specimens were evaluated. Six leiomyomas received full therapeutic doses, and 98.5% of the sonications were visualized. MR thermometry was successful in all sonications and cases. Focal necrotic lesions were seen in all cases at MR, and five were pathologically confirmed. MR imaging-guided focused ultrasound causes thermocoagulation and necrosis in uterine leiomyomas and is feasible and safe, without serious consequences.
Ablation of cytoskeletal filaments and mitochondria in live cells using a femtosecond laser nanoscissor. (2005)

Analysis of cell regulation requires methods for perturbing molecular processes within living cells with spatial discrimination on the nanometer-scale. We present a technique for ablating molecular structures in living cells using low-repetition rate, low-energy femtosecond laser pulses. By tightly focusing these pulses beneath the cell membrane, we ablate cellular material inside the cell through nonlinear processes. We selectively removed sub-micrometer regions of the cytoskeleton and individual mitochondria without altering neighboring structures or compromising cell viability. This nanoscissor technique enables non-invasive manipulation of the structural machinery of living cells with several-hundred-nanometer resolution. Using this approach, we unequivocally demonstrate that mitochondria are structurally independent functional units, and do not form a continuous network as suggested by some past studies.
A new non-Hodgkin's B-cell line (DoHH2) with a chromosomal translocation t(14;18)(q32;q21). (1991)

A spontaneously growing EBV-negative B-cell line (DoHH2) was established from the pleural fluid cells of a 60-year-old man with centroblastic/centrocytic non-Hodgkin's lymphoma, that had transformed into an immunoblastic lymphoma. The pleural fluid cells and the DoHH2 cells expressed IgG lambda, were reactive with CD10 and CD19 monoclonal antibodies, and showed by cytogenetic analysis 48,XY, +7, +del(12)(q24), t(14;18)(q32;q21). Southern blot analysis of mini-satellite DNA patterns, and of rearrangements of the immunoglobulin genes and bcl-2, confirmed that the cell line was derived from the patient's clonal lymphoma cells. Direct nucleotide sequence analysis on polymerase chain reaction (PCR) products of the t(14;18) junction revealed an identical sequence for the JH-bcl-2 junction at JH6 and in the major breakpoint region of bcl-2 in both the original tumor cells and the DoHH2 cell line. The cell line was valuable as a standard quantification control for PCR analysis of the t(14;18) breakpoint. Titration experiments demonstrated the detection of up to one tumor cell in 10(5) normal blood lymphocytes.
Low-k dielectric materials (2004)

Performance improvements in microelectronic integrated circuits (ICs) over the past few decades have, for the most part, been achieved by increasing transistor speed, reducing transistor size, and packing more transistors onto a single chip. Smaller transistors work faster, so ICs have become faster and more complex. An emerging factor that may disrupt this trend is the slowing speed of signal propagation within the chip. Signal delays, caused by the interconnection wiring, increase with each generation of scaling and may soon limit the overall performance of the integrated system.
Senescence and the Fluidity of Rose Petal Membranes (1982)

In previous work, senescence of rose petal cells has been shown to be accompanied by a gradual decrease of membrane fluidity, as measured by a fluorescence polarization technique. Concomitantly, an increase in the free sterol-to-phospholipid ratio was found. Both observations were verified in this study. Further, experiments carried out on whole tissue and isolated protoplasts during senescence revealed that there was no quantitative change in the level of free sterols. The content of phospholipids decreased without any significant change in their composition. Results from experiments measuring the incorporation of [(32)P]orthophosphate indicated a reduced capacity for phospholipid synthesis in senescent cells. Both young and old tissue showed phospholipase A and D activity, the former increasing with age. It was concluded that the fluidity of rose petal membranes decreases with age as a result of a decrease in phospholipid content, brought about by both reduced synthesis and enhanced degradation. Evidence supporting the view that the phenomena observed are related specifically to changes in the plasmalemma is discussed.
In Vitro Selection of Multiple Libraries Created by Genetic Code Reprogramming To Discover Macrocyclic Peptides That Antagonize VEGFR2 Activity in Living Cells (2013)

We report the in vitro selection of thioether-macrocyclized peptides against vascular endothelial growth factor receptor 2 (VEGFR2) from multiple, highly diverse peptide libraries constructed utilizing genetic code reprogramming. The macrocyclic peptide libraries consisted of combinations of four types of amino acid linkers for cyclization and two types of elongator amino acid compositions, including four backbone-modified non-proteinogenic amino acids. Affinity selection from these libraries, using our recently developed TRAP (Transcription-translation coupled with Association of Puromycin-linker) display, yielded multiple anti-VEGFR2 macrocyclic peptide leads. Further antagonizing activity-based screening of the chemically synthesized lead peptides identified a potent macrocyclic peptide that inhibited VEGF-induced VEGFR2 autophosphorylation, proliferation, and angiogenesis of living vascular endothelial cells. The TRAP display-based selection from multiple, highly diverse peptide libraries followed by activity-based screening of selected peptides is a powerful strategy for discovering biologically active peptides targeted to various biomolecules.
Chemical methods for the site-specific cleavage of genomic DNA (1990)

Pyrimidine oligodeoxyribonucleotides bind duplex DNA at homopurine sites to form a triple helix structure. The pyrimidine oligodeoxyribonucleotide is oriented in the major groove of DNA parallel to the Watson-Crick purine strand. Specificity is due to Hoogsteen hydrogen bonds wherein T recognizes A-T base pairs (T•AT triplet) and protonated C recognizes GC base pairs (C + GC triplet). Oligonucleotides 18 bases in length, equipped with a DNA cleaving function EDTA•Fe at the 5' end. cause sequence specific double strand breaks at one site in the 48.5 kbp bacteriophage λ genome. Due to the length of the recognition site, in a formal sense. this is 10^6 times more sequence-specific that restriction enzymes. The triple helix motif can be extended from homopurine target sequences to mixed sequences. Oligonucleotide directed triple helix formation could be useful for mapping genomic DNA.
The urinary proteome in Fanconi syndrome implies specificity in the reabsorption of proteins by renal proximal tubule cells (2004)

Polypeptides present in the glomerular filtrate are almost completely reabsorbed in the first segment of the proximal tubule by receptor-mediated endocytosis; in renal Fanconi syndrome (FS), there is failure to reabsorb many of these polypeptides. We have compared the urinary proteomes in patients with Dent's disease (due to a CLC5 mutation), a form of FS, with normal subjects using three different proteomic methods. No differences in the levels of several plasma proteins were detected when standardized to total protein amounts. In contrast, several vitamin and prosthetic group carrier proteins were found in higher amounts in Dent's urine (with respect to total protein). Similarly, complement components, apolipoproteins, and some cytokines represented a larger proportion of the Dent's urinary proteome, suggesting that such proteins are reabsorbed more efficiently than other classes of proteins. Conversely, proteins of renal origin were found in proportionately higher amounts in normal urine. Thus the uptake of filtered vitamins, which are normally bound to their respective carrier proteins to prevent urinary losses, seems a key function of the proximal tubule; in addition, this nephron segment may also play a critical role in reabsorbing potentially cytotoxic polypeptides of plasma origin, preventing them from acting at more distal nephron sites.
Construction, production, and characterization of humanized anti-Lewis Y monoclonal antibody 3S193 for targeted immunotherapy of solid tumors. (2000)

The Lewis Y (Ley) antigen is a blood group-related antigen that is expressed in a high proportion of epithelial cancers (including breast, colon, ovary, and lung cancer) and is an attractive target for monoclonal antibody-directed therapy. The murine monoclonal 3S193 (IgG3) was generated in BALB/c mice by immunization with Ley-expressing cells of the MCF-7 breast carcinoma cell-line. The murine 3S193 showed high specificity for Ley in ELISA tests with synthetic Ley and Ley-containing glycoproteins and glycolipids and also reacted strongly in rosetting assays and cytotoxic tests with Ley-expressing cells. We generated a humanized form of the murine 3S193 antibody by linking cDNA sequences encoding the variable region of murine 3S913 with frameworks of the human KOL heavy chain and REI K chain. The genes for the humanized 3S193 monoclonal antibody IgG1 were transfected into mouse myeloma NS0 cells and cloned for the establishment of high antibody-producing colonies. Humanized 3S193 antibody was subsequently produced through in vitro culture and under good manufacturing practice conditions using hollow-fiber bioreactors. The purified humanized 3S193 (hu3S193) was subsequently characterized and validated for use in preliminary immunotherapy investigations. hu3S193 reacted specifically with Ley antigen, with similar avidity to the murine form. hu3S193 demonstrated potent immune effector function, with higher antibody-dependent cell-mediated cytotoxicity than its murine counterpart and potent complement-dependent cytotoxicity (ED50, 1.0 microg/ml). The in vivo immunotherapeutic potential of hu3S193 was assessed in a human breast xenograft model using MCF-7, Ley-positive cells. Six i.v. doses of up to 1 mg of hu3S193 were administered to animals bearing established tumors (120-130 mm3) with no significant effect on tumor growth. In contrast, in an MCF-7 xenograft preventive model, a 1-mg hu3S193 dosage schedule was able to significantly slow tumor growth compared with placebo and isotype-matched control IgG1 antibody. hu3S193 has promise for immunotherapy of Ley-positive tumors and is currently entering Phase I clinical trials.
The outcome of renal denervation for managing loin pain haematuria syndrome (2004)

Renal denervation has only a 25% success rate for managing pain associated with LPHS and should be used cautiously for this indication. Men had more benefit from the treatment; a third of patients had less requirement for analgesic after non-curative denervation.
Teneurin-1, a vertebrate homologue of the Drosophila pair-rule gene Ten-m, is a neuronal protein with a novel type of heparin-binding domain (1999)

The Drosophila gene ten-m is the first pair-rule gene not encoding a transcription factor, but an extracellular protein. We have characterized a highly conserved chicken homologue that we call teneurin-1. The C-terminal part harbors 26 repetitive sequence motifs termed YD-repeats. The YD-repeats are most similar to the core of the rhs elements of Escherichia coli. Related repeats in toxin A of Clostridium difficile are known to bind specific carbohydrates. We show that recombinantly expressed proteins containing the YD-repeats of teneurin-1 bind to heparin. Furthermore, heparin lyase treatment of extracts of cells expressing recombinant YD-repeat protein releases this protein from high molecular mass aggregates. In situ hybridization and immunostaining reveals teneurin-1 expression in neurons of the developing visual system of chicken and Drosophila. This phylogenetic conservation of neuronal expression from flies to birds implies fundamental roles for teneurin-1 in neurogenesis. This is supported by the neurite outgrowth occurring on substrates made of recombinant YD-repeat proteins, which can be inhibited by heparin. Database searches resulted in the identification of ESTs encoding at least three further members of the teneurin family of proteins. Furthermore, the human teneurin-1 gene could be identified on chromosome Xq24/25, a region implied in an X-linked mental retardation syndrome.
Relative reactivities and graft distributions of polystyrene Macromers® in vinyl chloride copolymerization (1994)

Abstract Polystyrene macromonomers terminated with methacrylate, vinyl ether, or maleic half ester functionalities were evaluated in free radical initiated copolymerizations with vinyl chloride in aqueous suspension polymerization. Macromers® (M 1 ) terminated with methacrylate disappeared very rapidly in copolymerization with vinyl chloride (M 2 ). The relative reactivity ratio, r 2 , was determined to be 0.05 in good agreement with literature values of about 0.04. Vinyl ether‐terminated Macromers® had unexpectedly uniform reactivity with vinyl chloride in early conversion samples, but macromonomer conversion was incomplete. Macromers® having maleic half ester functionality were incorporated rapidly in vinyl chloride copolymerization at pH 2.5 ( r 2 = 0.13). However, at pH 10 these Macromers® had reduced reactivity ( r 2 = 0.34), which improved graft polymer uniformity. These Macromer® copolymerization relative reactivities are shown to be useful in predicting and controlling graft densities and graft polymer heterogeneity which influence morphology, processing, and mechanical properties.
Cell-Associated Pheromone Peptide (cCF10) Production and Pheromone Inhibition in Enterococcus faecalis (2000)

In Enterococcus faecalis, the peptide cCF10 acts as a pheromone, inducing transfer of the conjugative plasmid pCF10 from plasmid-containing donor cells to plasmid-free recipient cells. In these studies, it was found that a substantial amount of cCF10 associates with the envelope of the producing cell. Pheromone activity was detected in both wall and membrane fractions, with the highest activity associated with the wall. Experiments examining the effects of protease inhibitor treatments either prior to or following cell fractionation suggested the presence of a cell envelope-associated pro-cCF10 that can be processed to mature cCF10 by a maturase or protease. A pCF10-encoded membrane protein, PrgY, was shown to prevent self-induction of donor cells by reducing the level of pheromone activity in the cell wall fraction.
EB/RP gene family encodes tubulin binding proteins (1999)

Mutations in the adenomatous polyposis coli (APC) gene are linked to the dysplastic transformation of colorectal polyps and represent an early step in the development of colorectal tumors. Ninety-four percent of all mutations result in the expression of a truncated APC protein lacking the C-terminal region. The C-terminal region of the APC protein may have a tumor suppressor function as its absence appears to be linked to the development of dysplastic lesions. Recently, we discovered and characterized a protein called RP1 which binds specifically to the C-terminal region of the APC protein. We show now that RP1 and the other known members of the EB/RP family (EB1 and RP3) also bind directly to tubulin, both in vitro and in vivo. Immunohistochemical analyses reveal a distinct staining pattern during interphase as well as an association of RP1/EB1 with mitotic microtubule structures. The previously described puncta of the APC protein at the leading edge of membrane protrusions contact microtubule fibers that contain RP1 or EB1.
Periaxin expression in myelinating Schwann cells: modulation by axon-glial interactions and polarized localization during development (1995)

Periaxin is a newly described protein that is expressed exclusively by myelinating Schwann cells. In developing nerves, periaxin is first detected as Schwann cells ensheathe axons, prior to the appearance of the proteins that characterize the myelin sheath. Periaxin is initially concentrated in the adaxonal membrane (apposing the axon) but, during development, as myelin sheaths mature, periaxin becomes predominately localized at the abaxonal Schwann cell membrane (apposing the basal lamina). In permanently axotomized adult nerves, periaxin is lost from the abaxonal and adaxonal membranes, becomes associated with degenerating myelin sheaths and is phagocytosed by macrophages. In crushed nerves, in which axons regenerate and are remyelinated, periaxin is first detected in the adoxonal membrane as Schwann cells ensheathe regenerating axons, but again prior to the appearance of other myelin proteins. Periaxin mRNA and protein levels change in parallel with those of other myelin-related genes after permanent axotomy and crush. These data demonstrate that periaxin is expressed by myelinating Schwann cells in a dynamic, developmentally regulated manner. The shift in localization of periaxin in the Schwann cell after completion of the spiralization phase of myelination suggests that periaxin participates in membrane-protein interactions that are required to stabilize the mature myelin sheath.
Feature‐guided analysis for reduction of false positives in CAD of polyps for computed tomographic colonography (2003)

We evaluated the effect of our novel technique of feature-guided analysis of polyps on the reduction of false-positive (FP) findings generated by our computer-aided diagnosis (CAD) scheme for the detection of polyps from computed tomography colonographic data sets. The detection performance obtained by use of feature-guided analysis in the segmentation and feature analysis of polyp candidates was compared with that obtained by use of our previously employed fuzzy clustering technique. We also evaluated the effect of a feature called modified gradient concentration (MGC) on the detection performance. A total of 144 data sets, representing prone and supine views of 72 patients that included 14 patients with 21 colorectal polyps 5-25 mm in diameter, were used in the evaluation. At a 100% by-patient (95% by-polyp) detection sensitivity, the FP rate of our CAD scheme with feature-guided analysis based on round-robin evaluation was 1.3 (1.5) FP detections per patient. This corresponds to a 70-75% reduction in the number of FPs obtained by use of fuzzy clustering at the same sensitivity levels. Application of the MGC feature instead of our previously used gradient concentration feature did not improve the detection result. The results indicate that feature-guided analysis is useful for achieving high sensitivity and a low FP rate in our CAD scheme.
Fabrication of Superhydrophobic and Superoleophilic Polystyrene Surfaces by a Facile One‐Step Method (2007)

Abstract A facile one‐step method has been developed to prepare both superhydrophobic and superoleophilic surfaces of polystyrene (PS) without any chemical modification. A rough film consisting of micro‐bead and nano‐fiber mixed structures is formed by spraying a PS solution onto a large area and any type of substrate. The mixed structures with such unique wettability properties can be used in oil/water separation and as oil sorbents. magnified image