gebhart/patrepeval huggingface dataset:
Investigation of iterative image reconstruction in three-dimensional optoacoustic tomography (2012)

Iterative image reconstruction algorithms for optoacoustic tomography (OAT), also known as photoacoustic tomography, have the ability to improve image quality over analytic algorithms due to their ability to incorporate accurate models of the imaging physics, instrument response and measurement noise. However, to date, there have been few reported attempts to employ advanced iterative image reconstruction algorithms for improving image quality in three-dimensional (3D) OAT. In this work, we implement and investigate two iterative image reconstruction methods for use with a 3D OAT small animal imager: namely a penalized least-squares (PLS) method employing a quadratic smoothness penalty and a PLS method employing a total variation norm penalty. The reconstruction algorithms employ accurate models of the ultrasonic transducer impulse responses. Experimental data sets are employed to compare the performances of the iterative reconstruction algorithms to that of a 3D filtered backprojection (FBP) algorithm. By the use of quantitative measures of image quality, we demonstrate that the iterative reconstruction algorithms can mitigate image artifacts and preserve spatial resolution more effectively than FBP algorithms. These features suggest that the use of advanced image reconstruction algorithms can improve the effectiveness of 3D OAT while reducing the amount of data required for biomedical applications.
Monoclonal Antibodies in the Treatment of Malignancy: Basic Concepts and Recent Developments (2001)

Antibodies have long been considered to be potential anticancer agents because of their specificity for cell-membrane antigens. Applications of hybridoma and recombinant DNA technology have led to the production of unlimited quantities of clinical-grade murine, chimeric, and humanized monoclonal antibodies for clinical use. Whole antibodies may produce anticancer effects in conjunction with the immune system by interaction with complement proteins and/or effector cells via the Fc portion of the antibody molecule. Antibodies may also neutralize circulating ligands or block cell membrane receptors and thus interrupt ligand/receptor interactions and signal transduction that are associated with proliferative or anti-apoptotic effects. The anti-idiotype network cascade provides a rationale for antibodies as vaccine therapy. Antibodies may also serve as the guiding or targeting system for other cytotoxic pharmaceutical products such as (i) radiolabeled antibodies for radioimmunodetection and radioimmunotherapy; (ii) immunotoxins; (iii) chemotherapy/antibody conjugates; (iv) cytokine/antibody conjugates; and (v) immune cell/antibody conjugates. After years of anticipation, as of late 1999 there were four monoclonal antibodies that had been approved by the U.S. Food and Drug Administration based on activity against human malignancy, all of which are in widespread clinical use. Several other products are in various stages of clinical trial testing. Monoclonal antibodies have joined interferon-alpha, interleukin-2 (IL-2), and various hematopoietic growth factors as well-established components of biological therapy, the fourth modality of cancer treatment.
Two neutralizing domains in the V3 region in the envelope glycoprotein gp125 of HIV type 2. (1994)

The purposes of this study were to map the targets for neutralizing Abs in the HIV-2 glycoproteins with particular emphasis on the role of the V3 region. Sera obtained from guinea pig immunized with peptides representing five immunogenic regions of the envelope proteins were used in cross-neutralization experiments with nine HIV-2 isolates. Broad cross-neutralizing activity was elicited by immunization with two peptides representing the central and COOH-terminal portions of the HIV-2 V3 loop. Murine mAbs were established from animals immunized with two corresponding overlapping peptides. Six mAbs showed neutralizing activity against the homologous virus isolate SBL-6669. Peptide absorption experiments were performed to define the target regions for human neutralizing Abs in the HIV-2 envelope glycoproteins. A significant blocking of neutralizing activity of five HIV-2 Ab-positive sera was seen in the presence of two peptides corresponding to the V3 region. Two overlapping deletion sets of peptides, representing amino acids Ser311 and Arg337, were used to identify the role of individual HIV-2 V3 amino acids in the binding of polyclonal and mAbs. Two distinct antigenic sites were identified in this region, the first corresponding to a region including the conserved motif Phe-His-Ser (amino acid 315-317) and the second in proximity of the COOH-terminal cysteine Trp-Cys-Arg (amino acid 329-331). Potentially these two sites can interact to represent a single discontinuous antigenic site. Taken together, these results indicate that V3 is an important neutralizing domain of HIV-2.
Procedural sedation in the acute care setting. (2005)

Many patients require sedation during diagnostic or therapeutic procedures. Ideally, procedural sedation minimizes the patient's awareness and discomfort while maintaining the patient's safety. Appropriate monitoring by trained personnel is the key to successful procedural sedation. These techniques should be used only by health care professionals skilled in managing complications, including cardiorespiratory compromise. It is important to take a complete history and perform a thorough physical examination, paying special attention to the selection of pharmacologic agents. Common sedative agents include etomidate, ketamine, fentanyl, and midazolam. These have become the agents of choice for procedural sedation because of their ease of use, predictable action, and excellent safety profiles. All patients requiring procedural sedation should be monitored by qualified staff at the bedside until they have recovered to an age-appropriate baseline mental status and function.
Oral administration of a novel taxane, an antisense oligonucleotide targeting protein kinase A, and the epidermal growth factor receptor inhibitor Iressa causes cooperative antitumor and antiangiogenic activity. (2001)

This is the first demonstration of the cooperative antitumor and antiangiogenic activity of three novel agents that block multiple signaling pathways after oral administration. Because all agents are under clinical evaluation in cancer patients, our results provide a rationale to translate this feasible therapeutic strategy in a clinical setting.
Patient tumor EGFR and PDGFRA gene amplificationsretained in an invasive intracranial xenograft model of glioblastomamultiforme (2005)

We have previously described a panel of serially transplantable glioblastoma multiforme xenograft lines established by direct subcutaneous injection of patient tumor tissue in the flanks of nude mice. Here we report the characterization of four of these lines with respect to their histopathologic, genetic, and growth properties following heterotopic-to-orthotopic (flank-to-intracranial) transfer. Cells from short-term cultures, established from excised flank xenografts, were harvested and injected into the brains of nude mice (10(6) cells per injection). The intracranial tumors generated from these injections were all highly mitotic as well as highly invasive, but they lacked necrotic features in most instances and failed to show endothelial cell proliferation in all instances. For mice receiving injections from a common explant culture, tumor intracranial growth rate was consistent, as indicated by relatively narrow ranges in survival time. In contrast to the loss of epidermal growth factor receptor gene (EGFR) amplification in cell culture, high-level amplification and overexpression of EGFR were retained in intracranial tumors established from two EGFR-amplified flank tumors. A third intracranial tumor retained patient tumor amplification and high-level expression of platelet-derived growth factor receptor alpha gene. Because the heterotopic-to-orthotopic transfer and propagation of glioblastoma multiforme preserves the receptor tyrosine kinase (RTK) gene amplification of patient tumors, this approach should facilitate investigations for determining the extent to which RTK amplification status influences tumor response to RTK-directed therapies. The fact that such studies were carried out by using an invasive tumor model in an anatomically appropriate context should ensure a rigorous preclinical assessment of agent efficacy.
Recent Advances in Radiation Oncology (1995)

Radiotherapy remains an important component of the management of malignant disease. Especially when combined with cytotoxic chemotherapy, limited surgical excision, or both, irradiation has been shown to control disease in the primary site and regional nodes without the need for surgical extirpation as frequently as in past years. New developments in three-dimensional treatment planning and the precise delivery of high-dose radiation promise to increase the benefit of radiation treatment. Finally, molecular studies of the cell's response to radiation and the phenomena of DNA damage and repair are providing explanations for heretofore unexplained radiobiologic observations. Such research is laying the groundwork for targeted manipulation of the cell's response to radiation, which will be tested in the near future.
Hybrid approaches to physiologic modeling and prediction (2005)

This paper explores how the accuracy of a first-principles physiological model can be enhanced by integrating data-driven, "black-box" models with the original model to form a "hybrid" model system. Both linear (autoregressive) and nonlinear (neural network) data-driven techniques are separately combined with a first-principles model to predict human body core temperature. Rectal core temperature data from nine volunteers, subject to four 30/10-minute cycles of moderate exercise/rest regimen in both CONTROL and HUMID environmental conditions, are used to develop and test the approach. The results show significant improvements in prediction accuracy, with average improvements of up to 30% for prediction horizons of 20 minutes. The models developed from one subject's data are also used in the prediction of another subject's core temperature. Initial results for this approach for a 20-minute horizon show no significant improvement over the first-principles model by itself.
Molecular biomimetics: GEPI‐based biological routes to technology (2010)

In nature, the viability of biological systems is sustained via specific interactions among the tens of thousands of proteins, the major building blocks of organisms from the simplest single-celled to the most complex multicellular species. Biomolecule-material interaction is accomplished with molecular specificity and efficiency leading to the formation of controlled structures and functions at all scales of dimensional hierarchy. Through evolution, Mother Nature developed molecular recognition by successive cycles of mutation and selection. Molecular specificity of probe-target interactions, e.g., ligand-receptor, antigen-antibody, is always based on specific peptide molecular recognition. Using biology as a guide, we can now understand, engineer, and control peptide-material interactions and exploit them as a new design tool for novel materials and systems. We adapted the protocols of combinatorially designed peptide libraries, via both cell surface or phage display methods; using these we select short peptides with specificity to a variety of practical materials. These genetically engineered peptides for inorganics (GEPI) are then studied experimentally to establish their binding kinetics and surface stability. The bound peptide structure and conformations are interrogated both experimentally and via modeling, and self-assembly characteristics are tested via atomic force microscopy. We further engineer the peptide binding and assembly characteristics using a computational biomimetics approach where bioinformatics based peptide-sequence similarity analysis is developed to design higher generation function-specific peptides. The molecular biomimetic approach opens up new avenues for the design and utilization of multifunctional molecular systems in a wide-range of applications from tissue engineering, disease diagnostics, and therapeutics to various areas of nanotechnology where integration is required among inorganic, organic and biological materials. Here, we describe lessons from biology with examples of protein-mediated functional biological materials, explain how novel peptides can be designed with specific affinity to inorganic solids using evolutionary engineering approaches, give examples of their potential utilizations in technology and medicine, and, finally, provide a summary of challenges and future prospects.
Measurement of the Elastic Properties and Intrinsic Strength of Monolayer Graphene (2008)

We measured the elastic properties and intrinsic breaking strength of free-standing monolayer graphene membranes by nanoindentation in an atomic force microscope. The force-displacement behavior is interpreted within a framework of nonlinear elastic stress-strain response, and yields second- and third-order elastic stiffnesses of 340 newtons per meter (N m(-1)) and -690 Nm(-1), respectively. The breaking strength is 42 N m(-1) and represents the intrinsic strength of a defect-free sheet. These quantities correspond to a Young's modulus of E = 1.0 terapascals, third-order elastic stiffness of D = -2.0 terapascals, and intrinsic strength of sigma(int) = 130 gigapascals for bulk graphite. These experiments establish graphene as the strongest material ever measured, and show that atomically perfect nanoscale materials can be mechanically tested to deformations well beyond the linear regime.
Both amidated and nonamidated forms of glucagon-like peptide I are synthesized in the rat intestine and the pancreas. (1990)

Biologically active peptides are initially synthesized in the form of protein precursors, and the peptides are liberated by post-translational processing from the precursors in a tissue-specific manner. Mammalian proglucagon, which is synthesized in the neuroendocrine L-cells of the intestine and the alpha-cells of the pancreas, contains within its structure the sequences of glucagon and two glucagon-like peptides (GLP-I and GLP-II) flanked at their amino and carboxyl termini by dibasic residues. Tissue-specific processing liberates different peptides in the intestine compared with the pancreas. One of these intestinal peptides, glucagon-like peptide I(7-37) (GLP-I(7-37], is one of the most potent insulin secretagogues studied to date. It contains within its carboxyl-terminal domain an arginine residue that, because of an adjacent glycine residue, may alternatively be used during post-translational processing as a site for amidation. Using a chromatographic system and radioimmunoassays that discriminate among the closely related GLP-I peptides, we find that the processing of proglucagon in the rat intestine and to a lesser extent in the rat pancreas results in the formation of at least three GLP-I peptides, of 37, 31, and 30 residues. The 30-residue peptide is in the form of an alpha-carboxyl-terminal arginine amide, a modification that is not usually found in proteins. Remarkably, the relative potencies for the stimulation of insulin secretion from the perfused rat pancreas of the nonamidated (GLP-I(7-37] and the amidated (GLP-I(7-36) amide) peptides are the same (Weir, G. C., Mojsov, S., Hendrik, G. K., and Habener, J. F. (1989) Diabetes 38, 338-342; Suzuki, S., Kawai, K., Okashir, S., Mukal, H., and Yamashita, K. (1989) Endocrinology 125, 3109-3114).
Activating mutations of Tn3 resolvase marking interfaces important in recombination catalysis and its regulation (2003)

Catalysis of DNA recombination by Tn3 resolvase is conditional on prior formation of a synapse, comprising 12 resolvase subunits and two recombination sites (res). Each res binds a resolvase dimer at site I, where strand exchange takes place, and additional dimers at two adjacent 'accessory' binding sites II and III. 'Hyperactive' resolvase mutants, that catalyse strand exchange at site I without accessory sites, were selected in E. coli. Some single mutants can resolve a res x site I plasmid (that is, with one res and one site I), but two or more activating mutations are necessary for efficient resolution of a site I x site I plasmid. Site I x site I resolution by hyperactive mutants can be further stimulated by mutations at the crystallographic 2-3' interface that abolish activity of wild-type resolvase. Activating mutations may allow regulatory mechanisms of the wild-type system to be bypassed, by stabilizing or destabilizing interfaces within and between subunits in the synapse. The positions and characteristics of the mutations support a mechanism for strand exchange by serine recombinases in which the DNA is on the outside of a recombinase tetramer, and the tertiary/quaternary structure of the tetramer is reconfigured.
The Influence of Coping on Mental Health in University Students (Second Report)--The Relatoinship Among Stress, Coping and Coping Efficacy (2001)

We tried to study the direct effect and buffering effect of stress, coping efficacy on mental health. Usig 315 university students as subjects, we conducted a survey using a Japanese edition of the GHQ mental health questionnaire, stress event questionnaire, coping scale, and coping efficacy questionnaire. The results elucidated the following: 1) Although positive thinking helps improve health, blaming others and evasion tend to cause health to deteriorate. 2) Problem solving type coping and requesting assistance type coping resultin better health if exercised less when efficacy is low and exercised frequently when efficacy is high. Evasion type coping results in better health if exercised frequently when efficacy is low and exercised less when efficacy is high.
The purification and characterization of fetal liver hematopoietic stem cells. (1995)

Thy-1loSca-1+Lin-Mac-1+CD4- cells have been isolated from the livers of C57BL-Thy-1.1 fetuses. This population appears to be an essentially pure population of hematopoietic stem cells (HSC), in that injection of only six cells into lethally irradiated adult recipients yields a limit dilution frequency of donor cell-reconstituted mice. Sixty-seven to 77% of clones in this population exhibit long-term multilineage progenitor activity. This population appears to include all long-term multilineage reconstituting progenitors in the fetal liver. A high proportion of cells are in cycle, and the absolute number of cells in this population doubles daily in the fetal liver until 14.5 days postcoitum. At 15.5 days postcoitum, the frequency of this population falls dramatically. Long-term reconstituting HSC clones from the fetal liver give rise to higher levels of reconstitution in lethally irradiated mice than long-term reconstituting HSC from the bone marrow. The precise phenotypic and functional characteristics of HSC vary according to tissue and time during ontogeny.
The biosynthesis of tuberin from tyrosine and glycine; observations on the stereochemistry associated with the conversion of glycine through methylenetetrahydrofolate into methenyltetrahydrofolate (1987)

Tuberin (1) is shown to derive from glycine by way of tetrahydrofolate metabolism and from tyrosine. Glycine is incorporated into the N-formyl group of tuberin with (partial) stereospecific retention of the 2-pro-S proton; there is also some non-stereospecific loss of deuterium label from [2-13C, 2-2H2]glycine on incorporation into the C1 units present in tuberin. [2-14C]-threo-3-Hydroxytyrosine [as (7)] is only incorporated into tuberin after degradation; exclusive labelling of the two C1 units was observed. [2-3H]Octopamine [as (6)] is a poor precursor for tuberin.
RGD-dependent Binding of Procathepsin X to Integrin αvβ3 Mediates Cell-adhesive Properties (2006)

Secreted lysosomal cysteine proteases (cathepsins) are involved in degradation and remodeling of the extracellular matrix, thus contributing to cell adhesion and migration. Among the eleven human lysosomal cysteine proteases, only procathepsin X contains an RGD motif located in a highly exposed region of the propeptide, which may allow binding of the proenzyme to RGD-recognizing integrins. Here, we have tested procathepsin X for cell-adhesive properties and found that it supports integrin alpha(v)beta(3)-dependent attachment and spreading of human umbilical vein endothelial cells. Using site-directed mutants of procathepsin X, we proved that this effect is mediated by the RGD sequence within the proregion of the protease. Endogenous procathepsin X is transported to the plasma membrane, accumulates in vesicles at lamellipodia of the human umbilical vein endothelial cell, and is partly associated with the cell surface, as shown by immunofluorescence. In addition, procathepsin X is partly co-localized with integrin beta(3), as detected by immunogold electron microscopy. A direct interaction between endogenous procathepsin X and alpha(v)beta(3) was demonstrated by co-immunoprecipitation. Moreover, surface plasmon resonance analysis revealed significant and RGD-dependent binding of procathepsin X to integrin alpha(v)beta(3). Our results provide for the first time evidence that the extracellular function of cathepsin X may include binding to integrins thereby modulating the attachment of migrating cells to ECM components.
Microwave and mechanical considerations in the design of MEM switches for aerospace applications (1997)

Microelectromechanical Systems (MEMS) technology is expected to have tremendous impact on aerospace systems. Indeed, phased array antennas, frequency multiplexers, spacecraft GN&C, on-board communications, autonomous health monitoring and safety, space structures, thermal control, and on-board system reconfigurability will favorably and decisively impacted MEMS technology. One of the most fundamental and ubiquitous components in these functions, enabled by MEMS technology, will be the electrostatic microelectromechanical (MEM) switch. The MEM switch, due to its simplicity and high performance potential, is poised to become the pioneering MEMS component, particularly, for microwave signal processing-related applications in space-based communications systems. This paper will discuss the impact of microwave performance specifications of the MEM switch on its mechanical structure and design. In particular, quantitative discussion of switch parameters including actuation voltage, actuation frequency, loss, and isolation will be presented.