gebhart/patrepeval huggingface dataset:
Cyclins as markers of tumor proliferation: immunocytochemical studies in breast cancer. (1995)

We have developed methods to use anticyclin A, B, and E antibodies as reagents to specifically detect proliferating cells in specific phases of the cell cycle in formalin-fixed, paraffin-embedded sections of tissues and cells. Staining of 48 archival cases of breast cancer showed that these antibodies estimate the tumor proliferation fraction and therefore are potentially useful for the prediction of prognosis. A subset of cancers had a high frequency of tumor cells expressing cyclins A and E, out of proportion to other proliferation markers, suggesting that these tumors may have deregulated cyclin expression. In addition to recognizing authentic cyclin E in the nucleus of proliferating cells, anticyclin E antibody cross-reacted with a cytoplasmic protein in nonproliferating endothelial cells. This cross-reaction allows the simultaneous visualization and quantitation of microvessels in the tumors, measuring a second potential predictor of breast cancer prognosis, tumor angiogenesis.
Second harmonic generation in microcrystallite films of ultrasmall Si nanoparticles (2000)

We dispersed crystalline Si into a colloid of ultrasmall nano particles (∼1 nm), and reconstituted it into microcrystallites films on device-quality Si. The film is excited by near-infrared femtosecond two-photon process in the range 765–835 nm, with incident average power in the range 15–70 mW, focused to ∼1 μm. We have observed strong radiation at half the wavelength of the incident beam. The results are analyzed in terms of second-harmonic generation, a process that is not allowed in silicon due to the centrosymmetry. Ionic vibration of or/and excitonic self-trapping on novel radiative Si–Si dimer phase, found only in ultrasmall nanoparticles, are suggested as a basic mechanism for inducing anharmonicity that breaks the centrosymmetry.
The Conversion of Phenols to the Corresponding Aryl Halides Under Mild Conditions (2005)

Mild, novel procedures have been developed for the syntheses of aryl halides from the corresponding phenols in modest to good yields via boronate ester intermediates.
α-Enolase, a Multifunctional Protein: Its Role on Pathophysiological Situations (2012)

α-Enolase is a key glycolytic enzyme in the cytoplasm of prokaryotic and eukaryotic cells and is considered a multifunctional protein. α-enolase is expressed on the surface of several cell types, where it acts as a plasminogen receptor, concentrating proteolytic plasmin activity on the cell surface. In addition to glycolytic enzyme and plasminogen receptor functions, α-Enolase appears to have other cellular functions and subcellular localizations that are distinct from its well-established function in glycolysis. Furthermore, differential expression of α-enolase has been related to several pathologies, such as cancer, Alzheimer's disease, and rheumatoid arthritis, among others. We have identified α-enolase as a plasminogen receptor in several cell types. In particular, we have analyzed its role in myogenesis, as an example of extracellular remodelling process. We have shown that α-enolase is expressed on the cell surface of differentiating myocytes, and that inhibitors of α-enolase/plasminogen binding block myogenic fusion in vitro and skeletal muscle regeneration in mice. α-Enolase could be considered as a marker of pathological stress in a high number of diseases, performing several of its multiple functions, mainly as plasminogen receptor. This paper is focused on the multiple roles of the α-enolase/plasminogen axis, related to several pathologies.
p21 is necessary for the p53-mediated G1 arrest in human cancer cells. (1995)

DNA-damaging agents induce a p53-dependent G1 arrest that may be critical for p53-mediated tumor suppression. It has been suggested that p21WAF1/CIP1, a cdk inhibitory protein transcriptionally regulated by p53, is an effector of this arrest. To test this hypothesis, an isogenic set of human colon adenocarcinoma cell lines differing only in their p21 status was created. The parental cell line underwent the expected cell cycle changes upon induction of p53 expression by DNA damage, but the G1 arrest was completely abrogated in p21-deficient cells. These results unambiguously establish p21 as a critical mediator of one well-documented p53 function and have important implications for understanding cell cycle checkpoints and the mechanism(s) through which p53 inhibits human neoplasia.
YASARA View—molecular graphics for all devices—from smartphones to workstations (2014)

Supplementary data are available at Bioinformatics online.
Two-dimensional photoacoustic imaging by use of Fourier-transform image reconstruction and a detector with an anisotropic response (2003)

Theoretical and experimental aspects of two-dimensional (2D) biomedical photoacoustic imaging have been investigated. A 2D Fourier-transform-based reconstruction algorithm that is significantly faster and produces fewer artifacts than simple radial backprojection methods is described. The image-reconstruction time for a 208 x 482 pixel image is approximately 1 s. For the practical implementation of 2D photoacoustic imaging, a rectangular detector geometry was used to obtain an anisotropic detection sensitivity in order to reject out-of-plane signals, thereby permitting a tomographic image slice to be reconstructed. This approach was investigated by the numerical modeling of the broadband directional response of a rectangular detector and imaging of various spatially calibrated absorbing targets immersed in a turbid phantom. The experimental setup was based on a Q-switched Nd:YAG excitation laser source and a mechanically line-scanned Fabry-Perot polymer-film ultrasound sensor. For a 800 microm x 200 microm rectangular detector, the reconstructed image slice thickness was 0.8 mm up to a vertical distance of z = 3.5 mm from the detector, increasing thereafter to 2 mm at z = 10 mm. Horizontal and vertical spatial resolutions within the reconstructed slice were approximately 200 and 60 microm, respectively.
Isolation and cultivation of Lyme disease spirochetes. (1985)

The successful isolation and cultivation of Lyme disease spirochetes traces its lineage to early attempts at cultivating relapsing fever borreliae. Observations on the growth of Lyme disease spirochetes under different in vitro conditions may yield important clues to both the metabolic characteristics of these newly discovered organisms and the pathogenesis of Lyme disease.
Interaction of a recombinant form of apolipoprotein[a] with human fibroblasts and with the human hepatoma cell line HepG2 (1996)

We have studied the binding, uptake, and degradation of a recombinant form of apolipoprotein[a] (r-apo[a]) using a cultured cell model. In HepG2 cells and in human fibroblasts, r-apo[a] complexed with low density lipoprotein(LDL) is bound and internalized via high affinity (Kd = 10 nM) receptors; in both cell types, low affinity (Kd = 200-300 nM) sites also mediate free apo[a] uptake. Using competition studies, we found that the high affinity binding component corresponds to the LDL receptor. Involvement of the LDL receptor in r-apo[a] uptake by fibroblasts was confirmed using fibroblasts derived from an individual homozygous for familial hypercholesterolemia; in contrast to normal fibroblasts, these cells lacked the high affinity r-apo[a] binding component. Cell association of 125I-labeled r-apo[a] was increased and decreased concomitantly with the up- and down-regulation of the LDL receptor in response to a number of compounds. The addition of alpha 2-macroglobulin as well as treatment with heparinase, chondroitinase ABC, and sodium chlorate did not decrease total specific binding of r-apo[a], suggesting that neither the low density lipoprotein receptor-related protein nor cell surface proteoglycans are involved in r-apo[a] clearance. The low affinity binding component present in both fibroblasts and HepG2 cells likely corresponds to the plasminogen receptor, as binding of r-apo[a] to these sites was specifically decreased by the addition of plasminogen or the lysine analogue epsilon-aminocaproic acid, but not by the addition of tissue-type plasminogen activator. Heparin abolished uptake of r-apo[a] by the LDL receptor component only; this indicates that apo[a] must be associated with LDL to be cleared by this receptor. In contrast, free apo[a] can be effectively cleared by the plasminogen receptor which may represent a significant route of clearance for free apo[a] in vivo.
3D path planning and stereo-based obstacle avoidance for rotorcraft UAVs (2008)

We present a synthesis of techniques for rotorcraft UAV navigation through unknown environments which may contain obstacles. D* Lite and probabilistic roadmaps are combined for path planning, together with stereo vision for obstacle detection and dynamic path updating. A 3D occupancy map is used to represent the environment, and is updated online using stereo data. The target application is autonomous helicopter-based structure inspections, which require the UAV to fly safely close to the structures it is inspecting. Results are presented from simulation and with real flight hardware mounted onboard a cable array robot, demonstrating successful navigation through unknown environments containing obstacles.
Silicon and glass very large scale microfluidic droplet integration for terascale generation of polymer microparticles (2018)

Microfluidic chips can generate emulsions, which can be used to synthesize polymer microparticles that have superior pharmacological performance compared to particles prepared by conventional techniques. However, low production rates of microfluidics remains a challenge to successfully translate laboratory discoveries to commercial manufacturing. We present a silicon and glass device that incorporates an array of 10,260 (285 × 36) microfluidic droplet generators that uses only a single set of inlets and outlets, increasing throughput by >10,000× compared to microfluidics with a single generator. Our design breaks the tradeoff between the number of generators and the maximum throughput of individual generators by incorporating high aspect ratio flow resistors. We test these design strategies by generating hexadecane microdroplets at >1 trillion droplets per h with a coefficient of variation CV <3%. To demonstrate the synthesis of biocompatible microparticles, we generated 8-16 µm polycaprolactone particles with a CV <5% at a rate of 277 g h<sup>-1</sup>.
Localization of the N-Methyl-<i>D</i>-Aspartate R<sub>1</sub> Receptor Subunit in Specific Anterior Pituitary Hormone Cell Types of the Female Rat (1995)

N-methyl-D-aspartate (NMDA), a specific agonist of the NMDA-type glutamate receptor, has been shown to stimulate the release of several anterior pituitary hormones when administered in vivo. The primary site of action of NMDA has been suggested to be at the level of the hypothalamus via the control of hypothalamic releasing factors. However, recent studies have demonstrated that NMDA can exert stimulatory effects directly upon anterior pituitary cells perifused in vitro, suggesting that the anterior pituitary may also be a site of action for glutamate. Hence, the purpose of the present study was to determine whether the NMDA R1 receptor subunit is co-localized in specific hormone-secreting cells of the anterior pituitary. To achieve this aim, immunohistochemical studies were performed using an antibody specific for the NMDA R1 receptor subunit to stain sections from the pituitaries of steroid-treated ovariectomized immature rats. Double-immunohistochemistry was employed to demonstrate co-localization. The results of the studies revealed that moderate immunoreactive NMDA R1 receptor staining was observed in the anterior and intermediate lobe of the pituitary with little staining observed in the posterior lobe. Double-immunohistochemistry using antibodies for the NMDA R1 receptor subunit and specific anterior pituitary hormones revealed that the NMDA R1 receptor subunit is co-localized in many cell types of the anterior pituitary including LH (11.2%), FSH (9%), GH (4.6%), TSH (5.7%) and PRL cells (8%). Only one ACTH cell was found to co-localize the NMDA R1 receptor subunit.(ABSTRACT TRUNCATED AT 250 WORDS)
The Construct Validity of Measures of the Tripartite Conceptualization of Punishment Attitudes (1997)

ABSTRACT This study examined whether retribution, deterrence, and rehabilitation are three distinct components of global punishment attitudes. Three verbal measures of each component were independently constructed using the Likert method of eliminated ratings, Thurstonc's method of equal appearing intervals, and Guilford's self-rating procedure. Administration of these nine scales on 188 respondents yielded a 9 × 9 multitrait-multimethod matrix. The traditional Campbell and Fiske (1959) procedure as well as new structural equation models (e.g., Bagozzi, 1993) were applied to the matrix. Results indicated that convergent and discriminant validity was achieved for the measures of the three components of punishment attitudes when each was treated as a latent variable in a confirmatory factor analysis and correlated uniquenesses were permitted within each method.
A novel technique for high impedance fault identification (1998)

A novel technique using wavelet analysis filter banks (WAFB) to identify distribution high impedance faults (HIFs) is presented. A new model of HIF is used. HIFs and capacitor bank switching operations are simulated by the Electromagnetic Transients Program (EMTP) and their current signals are studied. High frequency components with the time localization information of both HIFs and capacitor bank switching operations are obtained using WAFB and their behavior is differentiated clearly. Results demonstrate that WAFB can be used as an element in a HIF detector for fast and accurate identification of distribution HIFs.
The plasminogen activator/plasmin system. (1991)

proteases and inhibitors has been shown to be under the control of hormones and growth factors. Plasminogen activators (PAs) and their inhibitors (PAIs) are thought to be key participants in the balance ofproteolytic and antiproteolytic activities that regulates matrix turnover. This article summarizes the evidence that supports this contention, discusses the role ofPAspecific cell surface binding sites, and also draws attention to a number of instances in which the presence ofPAs cannot be reconciled with an exclusive function in ECM degradation.
Inhibitor of Growth 4 Suppresses Cell Spreading and Cell Migration by Interacting with a Novel Binding Partner, Liprin α1 (2007)

Inhibitor of growth 4 (ING4) is a candidate tumor suppressor that plays a major role in gene regulation, cell cycle control, apoptosis, and angiogenesis. ING4 expression is down-regulated in glioblastoma cells and head and neck squamous cell carcinoma. Here, we identified liprin alpha1/PPFIA1, a cytoplasmic protein necessary for focal adhesion formation and axon guidance, as a novel interacting protein with ING4. ING4 and liprin alpha1 colocalized at lamellipodia in the vicinity of vinculin. Overexpressed ING4 suppressed cell spreading and cell migration. In contrast, overexpressed liprin alpha1 enhanced cell spreading and cell migration. Knockdown of endogenous ING4 with RNA interference induced cell motility, whereas knockdown of endogenous liprin alpha1 suppressed cell motility. ING4 also suppressed cell motility that was enhanced by liprin alpha1. However, ING4 did not further suppress cell motility when liprin alpha1 was suppressed with RNA interference, suggesting a functional and mechanistic interdependence between these proteins. In addition to its nuclear functions, cytoplasmic ING4 interacts with liprin alpha1 to regulate cell migration and, with its known antiangiogenic function, may prevent invasion and metastasis.
Breast Density and Parenchymal Patterns as Markers of Breast Cancer Risk: A Meta-analysis (2006)

Mammographic features are associated with breast cancer risk, but estimates of the strength of the association vary markedly between studies, and it is uncertain whether the association is modified by other risk factors. We conducted a systematic review and meta-analysis of publications on mammographic patterns in relation to breast cancer risk. Random effects models were used to combine study-specific relative risks. Aggregate data for > 14,000 cases and 226,000 noncases from 42 studies were included. Associations were consistent in studies conducted in the general population but were highly heterogeneous in symptomatic populations. They were much stronger for percentage density than for Wolfe grade or Breast Imaging Reporting and Data System classification and were 20% to 30% stronger in studies of incident than of prevalent cancer. No differences were observed by age/menopausal status at mammography or by ethnicity. For percentage density measured using prediagnostic mammograms, combined relative risks of incident breast cancer in the general population were 1.79 (95% confidence interval, 1.48-2.16), 2.11 (1.70-2.63), 2.92 (2.49-3.42), and 4.64 (3.64-5.91) for categories 5% to 24%, 25% to 49%, 50% to 74%, and > or = 75% relative to < 5%. This association remained strong after excluding cancers diagnosed in the first-year postmammography. This review explains some of the heterogeneity in associations of breast density with breast cancer risk and shows that, in well-conducted studies, this is one of the strongest risk factors for breast cancer. It also refutes the suggestion that the association is an artifact of masking bias or that it is only present in a restricted age range.
Formation, Stability, and Mechanical Properties of Bovine Serum Albumin Stabilized Air Bubbles Produced Using Coaxial Electrohydrodynamic Atomization (2014)

Bovine serum albumin (BSA) microbubbles were generated using coaxial electrohydrodynamic atomization (CEDHA) using various concentrations of BSA solutions. The bubble characteristics and the long-term stability of the microbubbles were studied through adjustment of processing parameters and the collection media. Bubbles in the range of 40-800 μm were obtained in a controlled fashion, and increasing the flow rate of the BSA solution reduced the polydispersity of the microbubbles. Use of distilled water-glutaraldehyde, glycerol, and glycerol-Tween 80 collection media allowed a remarkable improvement in bubble stability compared to BSA solution collection medium. Possible physical mechanisms were developed to explain the stability of the microbubbles. The collection distance showed a marked influence on stability of the microbubbles. Near-monodisperse particle-reinforced microbubbles were formed with various concentrations of 2,2'-azobis(isobutyramidine) dihydrochloride (AIBA)-polystyrene particle in BSA solution. The bubble size and the size distribution showed negligible change over a period of time irrespective of the concentration of particles at the bubble surface. The compression stiffness of the microbubbles was determined using nanoindentation at ambient temperature and showed that the stiffness of the microbubbles increased from 8 N/m to 20 N/m upon changing the concentration of BSA solution from 5 wt % to 15 wt %.
Delineation of the glycosaminoglycan-binding site in the human inflammatory response protein lactoferrin. (1994)

Lactoferrin is an iron-binding protein which is synthesized by mucosal epithelium and neutrophils and released by these cells in response to inflammatory stimuli. It promotes neutrophil aggregation and manifests iron-dependent and -independent antimicrobial properties in vitro. Since lactoferrin binds to glycosaminoglycans (GAGs) and sulfated polysaccharides can inhibit its clearance in vivo and in vitro, we sought to examine its interaction with the GAGs chondroitin sulfate and heparin. Amino-terminal sequencing of proteolytic fragments of human lactoferrin that were fractionated by GAG chromatography suggested that the amino-terminal 6 kDa of the secreted protein mediates its interaction with GAGs. Synthetic peptides were used to show that the first 33 residues of human lactoferrin can bind well to solid-phase or solution-phase GAGs. The first 33 residues bound fluoresceinamine-labeled heparin with an IC50 (611 nM) which approximated that of the intact protein (124 nM). In contrast, when the first six residues (GRRRRS) were removed from this peptide, it then bound poorly to heparin (IC50 = 49 microM). Our results suggest that the GRRRRS sequence at the amino terminus of human lactoferrin acts synergistically with an RKVR sequence at positions 28-31 to form the predominate functional GAG-binding site of human lactoferrin. Molecular modeling of the crystalline structure of lactoferrin supports a synergistic activity between these two sites since it shows that they juxtapose each other on the surface of the folded protein. Solid docking calculations indicate that they can form a cationic cradle as a binding site for chondroitin sulfate.
Smart interfaces for human-computer intelligent interaction (2004)

This paper describes smart interfaces for human-computer intelligent interaction (HCII) and their application to VCR remote control using handgestures. The VCR interface is capable of learning the user's operational habits and can help her, aka wizard mode of operation. The adaptive interface monitors the user's gestures in an attempt to assist her through feedback and recommendations using video display and/or loudspeaker. The availability of user's profiles is used to enhance human-computer interactions and to make them appear intelligent, i.e., causal. The smart interface is also suitable for handicapped users and security purposes.
Activation of target-tissue immune-recognition molecules by double-stranded polynucleotides (1999)

Abnormal expression of major histocompatibility complex (MHC) class I and class II in various tissues is associated with autoimmune disease. Autoimmune responses can be triggered by viral infections or tissue injuries. We show that the ability of a virus or a tissue injury to increase MHC gene expression is duplicated by any fragment of double-stranded (ds) DNA or dsRNA introduced into the cytoplasm of nonimmune cells. Activation is sequence-independent, is induced by ds polynucleotides as small as 25 bp in length, and is not duplicated by single-stranded polynucleotides. In addition to causing abnormal MHC expression, the ds nucleic acids increase the expression of genes necessary for antigen processing and presentation: proteasome proteins (e.g., LMP2), transporters of antigen peptides; invariant chain, HLA-DM, and the costimulatory molecule B7.1. The mechanism is different from and additive to that of gamma-interferon (gammaIFN), i.e., ds polynucleotides increase class I much more than class II, whereas gammaIFN increases class II more than class I. The ds nucleic acids also induce or activate Stat1, Stat3, mitogen-activated protein kinase, NF-kappaB, the class II transactivator, RFX5, and the IFN regulatory factor 1 differently from gammaIFN. CpG residues are not responsible for this effect, and the action of the ds polynucleotides could be shown in a variety of cell types in addition to thyrocytes. We suggest that this phenomenon is a plausible mechanism that might explain how viral infection of tissues or tissue injury triggers autoimmune disease; it is potentially relevant to host immune responses induced during gene therapy.