gebhart/patrepeval huggingface dataset:
Chemical structure of the hexapeptide chromophore of the Aequorea green-fluorescent protein (1993)

The green-fluorescent proteins (GFP) are a unique class of proteins involved in bioluminescence of many cnidaria. The GFPs serve as energy-transfer acceptors, receiving energy from either a luciferase-oxyluciferin complex or a Ca(2+)-activated photoprotein, depending on the organism. Upon mechanical stimulation of the organism, GFP emits green light spectrally identical to its fluorescence emission. These highly fluorescent proteins are unique due to the nature of the covalently attached chromophore, which is composed of modified amino acid residues within the polypeptide. This report describes the characterization of the Aequorea victoria GFP chromophore which is released as a hexapeptide upon digestion of the protein with papain. The chromophore is formed upon cyclization of the residues Ser-dehydroTyr-Gly within the polypeptide. The chromophore structure proposed here differs from that described by Shimomura [(1979) FEBS Lett. 104, 220] in a number of ways.
Synthesis of Short Polyoxyethylene-Based Heterobifunctional Cross-Linking Reagents. Application to the Coupling of Peptides to Liposomes (1996)

We describe the synthesis of [2-[2-[2-[(2-bromoacetyl)amino]ethoxy]ethoxy]ethoxy acetic acid (7), [2-[2-(2,5-dioxo-2,5-dihydropyrrol-1-yl)ethoxy]ethoxy] acetic acid (11), and [2-[2-(pyridin-2-yldisulfanyl)ethoxy]ethoxy] acetic acid (16), three new thiol-reactive heterobifunctional reagents, and the preparation of their corresponding dipalmitoylphosphatidylethanolamine derivatives (8, 12, and 17). Such phospholipid amide derivatives were aimed to be incorporated into the bilayers of liposomal constructs used for immunization with e.g. synthetic peptides. The spacer arms introduced by 8, 12, and 17 are hydrophilic polyoxyethylene chains of variable lengths that were expected to provide a good accessibility to their conjugates and have a lesser intrinsic immunogenicity than the spacer introduced by N-[4-(p-maleimidophenyl)butyryl]phosphatidylethanolamine (MPB-PE), a classical reagent used for conjugation of ligands to the surface of liposomes. Such an immunogenicity might be prejudicial (e.g. carrier-induced epitopic suppression) to the development of synthetic vaccination formulations. Moreover, the derivatives 8, 12, and 17 allowed the coupling of peptides, bearing a thiol function, to their liposomal carrier via two types of linkages, i.e. stable thio ether (8 and 12) and bioreducible disulfide (17) bonds; this might be of importance in the mechanism of antigen presentation by competent cells. Using CG-IRGERA as a model peptide, the rate of coupling to 8, 12, and 17 was assessed as a function of pH.
Using Stochastic Game Theory to Compute the Expected Behavior of Attackers (2006)

This paper presents ongoing work on using stochastic game theory as a mathematical tool for computing the expected behavior of attackers. The possible use of the Nash Equilibrium as a part of the transition probabilities in state transition models is defined and motivated. To demonstrate the approach, a simple example of an attack against a computer network is modelled and analyzed.
A Novel Class of Anti-HIV Agents with Multiple Copies of Enfuvirtide Enhances Inhibition of Viral Replication and Cellular Transmission In Vitro (2012)

We constructed novel HIV-1 fusion inhibitors that may overcome the current limitations of enfuvirtide, the first such therapeutic in this class. The three prototypes generated by the Dock-and-Lock (DNL) technology to comprise four copies of enfuvirtide tethered site-specifically to the Fc end of different humanized monoclonal antibodies potently neutralize primary isolates (both R5-tropic and X4-tropic), as well as T-cell-adapted strains of HIV-1 in vitro. All three prototypes show EC(50) values in the subnanomolar range, which are 10- to 100-fold lower than enfuvirtide and attainable whether or not the constitutive antibody targets HIV-1. The potential of such conjugates to purge latently infected cells was also demonstrated in a cell-to-cell viral inhibition assay by measuring their efficacy to inhibit the spread of HIV-1(LAI) from infected human peripheral blood mononuclear cells to Jurkat T cells over a period of 30 days following viral activation with 100 nM SAHA (suberoylanilide hydroxamic acid). The IgG-like half-life was not significantly different from that of the parental antibody, as shown by the mean serum concentration of one prototype in mice at 72 h. These encouraging results provide a rationale to develop further novel anti-HIV agents by coupling additional antibodies of interest with alternative HIV-inhibitors via recombinantly-produced, self-assembling, modules.
Recent Developments in Nanofabrication Using Focused Ion Beams (2005)

Focused ion beam (FIB) technology has become increasingly popular in the fabrication of nanoscale structures. In this paper, the recent developments of the FIB technology are examined with emphasis on its ability to fabricate a wide variety of nanostructures. FIB-based nanofabrication involves four major approaches: milling, implantation, ion-induced deposition, and ion-assisted etching of materials; all these approaches are reviewed separately. Following an introduction of the uniqueness and strength of the technology, the ion source and systems used for FIB are presented. The principle and specific techniques underlying each of the four approaches are subsequently studied with emphasis on their abilities of writing structures with nanoscale accuracy. The differences and uniqueness among these techniques are also discussed. Finally, concluding remarks are provided where the strength and weakness of the techniques studied are summarized and the scopes for technological improvement and future research are recommended.
FusionNet (1996)

FusionNet targets seamless integration of two information networks with different characteristics so that their complimentary functionalities can be synergistically combined to enhance their existing applications and to create new ones. Our prototype system demonstrates anew application made possible by FusionNet, a real-time multimedia informationon-demand system with guaranteed quality of service (QoS). The prototype system allows the users to browse mukimedia databases using the worldwide web (WWW) functionalities and to retrieve their selections over ISDN connections.
A.S.P.E.N. Clinical Guidelines (2013)

(1) What maternal risk factors predispose the neonate to metabolic bone disease? (2) What is the optimal type of feeding to promote neonatal bone health? (3) When and how should vitamin D supplements be administered? (4) Does parenteral nutrition (PN) predispose a neonate to metabolic bone disease, and if so, are there PN formulation recommendations to minimize this risk?
Susceptibility of the bedbug, Cimex lectularius, to selected insecticides and various treated surfaces (1993)

Adult bedbugs, Cimex lectularius, were exposed for 24 h (25 degrees C) to filter paper treated with various dilutions of the technical grade of nine insecticides dissolved in acetone to determine the concentration-response relationships. The order of toxicity, from most to least based on the LC50's was: dichlorvos, pirimiphos methyl, lambda-cyhalothrin, bendiocarb, permethrin, malathion, carbaryl, tetrachlorvinphos, and fenvalerate. The residual toxicities of commercial formulations of six of the chemicals diluted with water and applied to wood, cardboard, cloth and galvanized metal, were determined by exposing adult bedbugs at 3, 7 and 12 weeks after treatment. The formulation of bendiocarb (FICAM 76% W) had little residual activity on all surfaces at 12 weeks after treatment. The formulation of carbaryl (SEVIN 21.5% L) was toxic to bedbugs on all surfaces at 12 weeks after treatment, but required high concentrations on wood, cardboard, and cloth. The formulation of pirimiphos methyl (ACTELLIC 57% EC) had no residual activity on any of the surfaces at 12 weeks after treatment. The formulation of tetrachlorovinphos (RABON 50% W) had residual activity for 12 weeks on all surfaces except metal. The formulation of permethrin (ATROBAN 11% EC) had residual activity on only metal and wood while the formulation of lambda-cyhalothrin (KARATE 13.1% EC) had residual activity 12 weeks on all surfaces.
Targeting Macrophage-Recruiting Chemokines as a Novel Therapeutic Strategy to Prevent the Progression of Solid Tumors (2018)

Solid tumors are initiated by genetic mutations in non-hematopoietic cells and progress into invasive malignant tumors. This tumor progression often culminates in metastatic disease that is largely refractory to current therapeutic modalities and thus dramatically reduces survival of tumor patients. As solid tumors account for more than 80% of cancer-related deaths, it is necessary to develop novel therapeutic strategies to treat the diseases. An attractive strategy is to target macrophages in both primary tumors [known as tumor-associated macrophages (TAMs)] and metastatic tumors [called metastasis-associated macrophages (MAMs)]. TAMs and MAMs are abundant in most solid tumors and can promote tumor metastasis. Several studies in various models of solid tumors suggest that the accumulation of TAMs, MAMs, and their progenitor cells is regulated by chemokine ligands released by tumor and stromal cells. Consequently, these macrophage-recruiting chemokines could be potential therapeutic targets to prevent malignant tumor development through disruption of the accumulation of pro-metastatic macrophages. This review will discuss the role of chemokine ligands and their receptors in TAM and MAM accumulation in primary and secondary tumor sites, and finally discuss the therapeutic potential of inhibitors against these macrophage-recruiting chemokines.
Atlas of prenatal rat brain development (1994)

The result of 3 decades of original research and instruction by internationally referenced authors, Drs. Joseph Altman and Shirley A. Bayer, the Atlas of Prenatal Rat Brain Development provides a complete, state-of-the-art presentation of the developing prenatal rat brain. With the aid of advanced computer graphics, Altman and Bayer revolutionize the study of the highly vulnerable prenatal brain and bring us closer to understanding the dynamics of its development, its malfunctions, deficits, and abnormalities. Their contributions to the field of brain research, and hence to our knowledge of brain disorders, are unsurpassed. The Atlas contains more than 265 platesUeach plate accompanied by a computer-aided drawing, a 3-dimensional reconstruction of brain slices never before achieved with such accuracy and clarity, that assists in the visualization of the brain and of the relationships among various brain regions. A new, user-friendly alphanumeric coding system is used, allowing for easy identification of brain regions.
Opposite Effects of SDF-1 on Human Immunodeficiency Virus Type 1 Replication (1999)

The alpha-chemokine SDF-1 binds CXCR4, a coreceptor for human immunodeficiency virus type 1 (HIV-1), and inhibits viral entry mediated by this receptor. Since chemokines are potent chemoattractants and activators of leukocytes, we examined whether the stimulation of HIV target cells by SDF-1 affects the replication of virus with different tropisms. We observed that SDF-1 inhibited the entry of X4 strains and increased the infectivity of particles bearing either a CCR5-tropic HIV-1 envelope or a vesicular stomatitis virus G envelope. In contrast to the inhibitory effect of SDF-1 on X4 strains, which is at the level of entry, the stimulatory effect does not involve envelope-receptor interactions or proviral DNA synthesis. Rather, we observed an increased ability of Tat to transactivate the HIV-1 long terminal repeat in the presence of the chemokine. Therefore, the effects of SDF-1 on the HIV-1 life cycle can be multiple and opposite, including both an inhibition of viral entry and a stimulation of proviral gene expression.
2005 AHA Guidelines for CPR and Emergency Cardiac Care (2006)

The American Heart Association (AHA) recently released new guidelines for cardiopulmonary resuscitation (CPR) and emergency cardiac care.
<title>Laser spot size as a function of tissue depth and laser wavelength in human sclera</title> (1998)

We determined the wavelength dependence of the minimum spot size of a laser beam focused through human sclera to evaluate the potential for transcleral glaucoma surgical techniques using ultrashort-pulsed lasers. The spectrum of the forward scattered light was measured by collimating the incident and transmitted beam in a spectrophotometer. This spectrum shows that sclera is highly scattering until 1100 nm, after which, the transmission spectrum is similar to water. To measure the minimal spot size, a laser beam was focused on the back surface of sclera of differing thickness. The minimum spot at 800 nm, 1060 nm, 1301 nm, and 1557 nm was imaged. At 800 nm, the spot size was invariant upon focal lens position, being a thousand fold larger than the incident beam spot size. As the wavelength increased, the area of the spot decreased, so that at 1557 nm, the minimal spot size was on the order of the incident beam spot size.
Electrical and Optical Properties of Germanium-Doped Zinc Oxide Thin Films (2004)

Germanium-doped zinc oxide thin films with Ge content of 0∼8.1 at% were deposited by an RF magnetron sputtering. The electrical and optical properties of the films were investigated. The Ge doping caused the reduction of resistivity of the films, and at about 3% of the Ge content showed the minimum resistivity of about 2 × 10−3 Ωcm. With high content of Ge, however, the crystalline structure changed and the resistivity of the film increased.
Serum antibody responses of juvenile and infant rhesus monkeys injected with Haemophilus influenzae type b and pneumococcus type 6A capsular polysaccharide-protein conjugates (1984)

Juvenile and infant rhesus monkeys were injected subcutaneously with saline solutions of Haemophilus influenzae type b (Hib) and pneumococcus type 6A (Pn6A) capsular polysaccharides conjugated to either tetanus toxoid (TT), horseshoe crab hemocyanin, or cholera toxin (CT), and the antibody responses of the monkeys to both bacterial components were measured. All three Hib conjugates were immunogenic and elicited booster responses; their comparative immunogenicity was Hib-CT greater than Hib-TT greater than Hib-horseshoe crab hemocyanin. Hib alone did not elicit antibodies in the juveniles. Juveniles responded earlier and with higher levels of antibodies than did infants. TT, as well as diphtheria-tetanus toxoids-pertussis vaccine adsorbed injected concurrently at a separate site, increased both Hib and TT antibody responses in juveniles (P less than 0.05). Concurrent injection of 5 Lf of fluid TT with a nonimmunogenic 5-micrograms dose in infants elicited levels of Hib antibodies comparable to those elicited by 50 micrograms of Hib-TT. Hib antibodies elicited by the conjugates remained at protective levels in both juveniles and infants 2 months after the last injection, were bactericidal, and conferred passive immunity against bacteremia in infant rats. Passive immunization of juveniles with tetanus immune globulin before each injection of Hib-TT did not suppress Hib antibodies. Hib-TT and Hib-CT elicited increases of Hib antibodies of the immunoglobulin M and G isotypes in the infants. The Pn6A-TT conjugate was considerably less immunogenic than the Hib-TT conjugate; only a few of the juveniles or infants responded with protective levels of Pn6A antibodies. Pn6A antibodies from responders conferred protection in mice against intraperitoneal challenge with Pn6A organisms. TT antibodies were elicited in both juvenile and infant animals after one injection of 50 micrograms of Hib-TT and in the infants injected with 5 micrograms of Hib-TT plus 5 Lf of TT; 5 micrograms of Hib-TT and Pn6A-TT in combination alone did not elicit TT antibodies. Hib-CT elicited CT antibodies in both juveniles and infants.
Reduced viability of human vascular endothelial cells cultured on Matrigel™ (1998)

Optimal vascular homeostasis requires efficient control of both proliferation and elimination of vascular endothelial cells. Programmed cell death, or apoptosis, is the main mechanism controlling cell elimination, and it is an essential component of vascular formation. Human vascular endothelial cells die in vitro, if prevented from obligatory survival factors like growth factors or attachment and cell spreading, but very little is known about the mechanisms controlling endothelial cell elimination. Signaling from the extracellular matrix affects the behavior and functions of human umbilical vein endothelial cells (HUVECs), and we have recently demonstrated the beneficial effects of plating on the reconstituted extracellular matrix Matrigel, on the inducible nitric oxide production of freshly isolated HUVECs. In this work we observed that cultured HUVECs formed typical capillary-like structures on Matrigel, but unexpectedly, after 24-48 hours their viability was gradually lost. Viability was measured with an assay based on mitochondrial reduction of reagent XTT. No decrease in viability was seen in freshly isolated HUVECs or in cultured fibroblasts during this time. It is known that cells often turn into apoptosis if they receive conflicting information from their surroundings, and apparently signaling from Matrigel to HUVECs, while at their in vitro proliferating phenotype, resulted in launching of the apoptotic machinery. Thus, proliferating and differentiated phenotypes of endothelial cells seemed to have different sensitivity to signals that induce apoptosis.
Mapping the Cellular Response to Small Molecules Using Chemogenomic Fitness Signatures (2013)

Genome-wide characterization of the in vivo cellular response to perturbation is fundamental to understanding how cells survive stress. Identifying the proteins and pathways perturbed by small molecules affects biology and medicine by revealing the mechanisms of drug action. We used a yeast chemogenomics platform that quantifies the requirement for each gene for resistance to a compound in vivo to profile 3250 small molecules in a systematic and unbiased manner. We identified 317 compounds that specifically perturb the function of 121 genes and characterized the mechanism of specific compounds. Global analysis revealed that the cellular response to small molecules is limited and described by a network of 45 major chemogenomic signatures. Our results provide a resource for the discovery of functional interactions among genes, chemicals, and biological processes.
Patellofemoral and tibiofemoral articular cartilage and subchondral bone health following arthroscopic partial medial meniscectomy (2011)

III.
Topologically exact evaluation of polyhedra defined in CSG with loose primitives (1996)

Abstract Floating point round‐off causes erroneous and inconsistent decisions in geometric modelling algorithms. These errors lead to the generation of topologically invalid boundary models for CSG objects and significantly reduce the reliability of CAD applications. Previously known methods that guarantee topological consistency by relying on arbitrary precision rational arithmetic or on symbol‐manipulation techniques are too expensive for practical purposes. This paper presents a new solution which takes as input a “fixed precision” regularized Boolean combination of linear half‐spaces and produces a polyhedral boundary model that has the exact topology of the corresponding solid. Each half‐space is represented by four homogeneous coefficients infixed precision format (L a bits for the three direction cosines and L d bits for the constant term, i.e. the distance from the origin). Exact answers to all topological and ordering questions are computed using a fixed length, 3 L a + L d + 2 bits, integer format. This new guaranteed tight limit on the number of bits necessary for performing intermediate calculations is achieved by expressing all of the topological decisions based on geometric computations in terms of the signs of 4 by 4 determinants of the input coefficients. The coordinates of intersection vertices are not required for making the correct topological decisions and hence vertices and lines are represented implicitly in terms of planes.
Xenografts and Retroviruses (1999)

Pigs have been suggested as a source of tissues and organs for transplantation. However, as [Weiss][1] discusses in a Perspective, one of the main safety concerns has been that porcine retroviruses present in pig tissue might take up residence in the human host after transplantation, resulting in the emergence of a new infectious disease. Weiss argues that we should be encouraged by recent data (reported by [ Paradis et al. ][2] in this issue) demonstrating that none of 160 patients exposed to pig tissues over the last 12 years show evidence of pig retroviruses in their blood cells or serum. Weiss suggests that we proceed with xenotransplantation cautiously while vigilantly monitoring all transplant recipients and patients exposed to pig cells for any signs of infection with porcine retroviruses.

 [1]: http://www.sciencemag.org/cgi/content/full/285/5431/1221
 [2]: http://www.sciencemag.org/cgi/content/short/285/5431/1236
Design and Creation of Superwetting/Antiwetting Surfaces (2006)

Abstract Recent achievements in the construction of surfaces with special wettabilities, such as superhydrophobicity, superhydrophilicity, superoleophobicity, superoleophilicity, superamphiphilicity, superamphiphobicity, superhydrophobicity/superoleophilicity, and reversible switching between superhydrophobicity and superhydrophilicity, are presented. Particular attention is paid to superhydrophobic surfaces created via various methods and surfaces with reversible superhydrophobicity and superhydrophilicity that are driven by various kinds of external stimuli. The control of the surface micro‐/nanostructure and the chemical composition is critical for these special properties. These surfaces with controllable wettability are of great importance for both fundamental research and practical applications.
Nanodiscs for Immobilization of Lipid Bilayers and Membrane Receptors: Kinetic Analysis of Cholera Toxin Binding to a Glycolipid Receptor (2008)

Nanodiscs are self-assembled soluble discoidal phospholipids bilayers encirculated by an amphipathic protein that together provide a functional stabilized membrane disk for the incorporation of membrane-bound and membrane-associated molecules. The scope of the present work is to investigate how nanodiscs and their incorporated membrane receptors can be attached to surface plasmon resonance sensorchips and used to measure the kinetics of the interaction between soluble molecules and membrane receptors inserted in the bilayer of nanodiscs. Cholera toxin and its glycolipid receptor G(M1) constitute a system that can be considered a paradigm for interactions of soluble proteins with membrane receptors. In this work, we have investigated different technologies for capturing nanodiscs containing the glycolipid receptor G(M1) in lipid bilayers, enabling measurements of binding of its soluble interaction partner cholera toxin B subunit to the receptor with the sensorchip-based surface plasmon resonance (SPR) technology. The measured stoichiometric and kinetic values of the interaction are in agreement with those reported by previous studies, thus providing proof-of-principle that nanodiscs can be employed for kinetic SPR studies.
Modeling, Estimation and Control of Systems with Uncertainty (1991)

This volume contains the papers that have been presented at the Conference on Modeling and Control of Uncertain Systems held in Sopron, Hungary on September 3-7, 1990, organised within the framework o