gebhart/patrepeval huggingface dataset:
A new one-pot method for the synthesis of Cu nanoparticles for low temperature bonding (2012)

We developed a new one-pot method for the synthesis of Cu nanoparticles capped with fatty acids and amines from an insoluble salt, such as Cu carbonate and Cu hydroxide, in ethylene glycol. This method could be completed within a short period of time and provides a high collection rate from inexpensive raw materials without impurities. The mean diameter of the Cu nanoparticles was controlled from 93 to 13 nm as the alkyl carbon number increased from C10 to C22. The same fraction of fatty acids and amines used for capping agents was suitable to obtain the minimum size of Cu nanoparticles. The thermal decomposition temperature of the capping layer was lower than 300 °C even in an inert atmosphere. Higher strengths of the Cu plates bonded by the Cu nanoparticles were achieved owing to the more densely packed sintered structures by the smaller Cu nanoparticles. The shear strength of the Cu plates bonded by the Cu nanoparticles was higher than 30 MPa which was the same level as for ordinary solders even though the process temperature of 300 °C was much lower than high-temperature solders. The minimum electrical resistivity of the sintered Cu nanoparticle film was 13 μΩ cm which was obtained after annealing at 300 °C.
New Paradigms and Future Challenges in Radiation Oncology: An Update of Biological Targets and Technology (2013)

Radiation oncology exploits the biological interaction of radiation within tissue to promote tumor death while minimizing damage to surrounding normal tissue. The clinical delivery of radiation relies on principles of radiation physics that define how radiation energy is deposited in the body, as well as technology that facilitates accurate tumor targeting. This review will summarize the current landscape of recent biological and technological advances in radiation oncology, describe the challenges that exist, and offer potential avenues for improvement.
Comparison of Cost Functions for Electrically Driven Running Robots (2012)

In this work we apply optimal control to create running gaits for the model of an electrically driven one legged hopper, and compare the results obtained for five different objective functions. By using high compliant series elastic actuators, the motions of joint and motor are decoupled, which allows the exploitation of natural dynamics. Depending on the cost function, this exploitation varies. Energy is injected at different points of time, the amplitude of actuator action changes significantly, and the optimal gear ratios differ by a factor of two. Variations are, however, comparable over a wide range of hopping heights and running velocities. Purely force-based cost functions prove to be ill-suited for such non-conservative systems, and it is shown that thermal electrical losses, in contrast to common belief, do not dominate energy expenditure. The numerical results are corroborated by detailed analytical considerations which give general insights into optimal excitation with electric actuators.
Towards Semantic Web Information Extraction (2003)

Abstract. The approach towards Semantic Web Information Extraction (IE) presented here is implemented in KIM – a platform for semantic indexing, annotation, and retrieval. It combines IE based on the mature text engineering platform (GATE1) with Semantic Web-compliant knowledge representation and management. The cornerstone is automatic generation of named-entity (NE) annotations with class and instance references to a semantic repository. Simplistic upper-level ontology, providing detailed coverage of the most popular entity types (Person, Organization, Location, etc.; more than 250 classes) is designed and used. A knowledge base (KB) with de-facto exhaustive coverage of real-world entities of general importance is maintained, used, and constantly enriched. Extensions of the ontology and KB take care of handling all the lexical resources used for IE, most notable, instead of gazetteer lists, aliases of specific entities are kept together with them in the KB. A Semantic Gazetteer uses the KB to generate lookup annotations. Ontologyaware pattern-matching grammars allow precise class information to be handled via rules at the optimal level of generality. The grammars are used to recognize NE, with class and instance information referring to the KIM ontology and KB. Recognition of identity relations between the entities is used to unify their references to the KB. Based on the recognized NE, template relation construction is performed via grammar rules. As a result of the latter, the KB is being enriched with the recognized relations between entities. At the final phase of the IE process, previously unknown aliases and entities are being added to the KB with their specific types. 1
Structure of the Mg-Chelatase Cofactor GUN4 Reveals a Novel Hand-Shaped Fold for Porphyrin Binding (2005)

In plants, the accumulation of the chlorophyll precursor Mg-protoporphyrin IX (Mg-Proto) in the plastid regulates the expression of a number of nuclear genes with functions related to photosynthesis. Analysis of the plastid-to-nucleus signaling activity of Mg-Proto in Arabidopsis thaliana led to the discovery of GUN4, a novel porphyrin-binding protein that also dramatically enhances the activity of Mg-chelatase, the enzyme that synthesizes Mg-Proto. GUN4 may also play a role in both photoprotection and the cellular shuttling of tetrapyrroles. Here we report a 1.78-A resolution crystal structure of Synechocystis GUN4, in which the porphyrin-binding domain adopts a unique three dimensional fold with a "cupped hand" shape. Biophysical and biochemical analyses revealed the specific site of interaction between GUN4 and Mg-Proto and the energetic determinants for the GUN4.Mg-Proto interaction. Our data support a novel protective function for GUN4 in tetrapyrrole trafficking. The combined structural and energetic analyses presented herein form the physical-chemical basis for understanding GUN4 biological activity, including its role in the stimulation of Mg-chelatase activity, as well as in Mg-Proto retrograde signaling.
In vivo Therapeutic Synergism of Anti–Epidermal Growth Factor Receptor and Anti-HER2 Monoclonal Antibodies against Pancreatic Carcinomas (2007)

Anti-HER2 mAb has a synergistic therapeutic effect when combined with an anti-EGFR mAb on pancreatic carcinomas with low HER2 expression. These observations may open the way to the use of these two mAbs in a large panel of carcinomas expressing different levels of the two HER receptors.
Measurements of the hopcount in internet (2001)

End-to-end quality of service is very likely to depend on the hopcount, the number of traversed routers. The hopcount also enhances our understanding of properties of the Internet topology. In this paper we present the results of the measurements of the hopcount from a source at Delft towards several destinations spread over three continents. Fitting the data with our theoretical model illustrates that the number of routers based on our measurements is around 98400. The dynamics in the change of the hopcount is investigated, it was found that though there is virtually no short-term change in the average hopcount the individual hopcounts do change significantly. When investigating the changes in the paths to the sites within these continents, rapid changes in the paths were observed to barely affect the hopcount.
In Vitro and in Vivo Studies of Benzisoquinoline Ligands for the Brain Synaptic Vesicle Monoamine Transporter (1996)

Tetrabenazine is a high-affinity inhibitor of the vesicular monoamine transporter in mammalian brain. As part of a program to develop in vivo imaging agents for these transporters in human brain, a series of 2-alkylated dihydrotetrabenazine ligands was synthesized and evaluated in vitro and in vivo for binding to the brain vesicular monoamine transporter. Additions of organometallic reagents to tetrabenazine produced 2-methyl, 2-ethyl, 2-n-propyl, 2-isopropyl, and 2-isobutyl derivatives of dihydrotetrabenazine. The stereochemistry and conformation of the addition products were thoroughly verified by two-dimensional NMR techniques. All of these alkyl derivatives displayed in vitro affinity for the vesicular monoamine transporter binding site in rat brain using competitive assays with the radioligand [3H]methoxytetrabenazine. Except for the isopropyl derivative, all compounds when tested at 10 mg/kg iv showed an ability to inhibit in vivo accumulation of the radioligand [11C]methoxytetrabenazine in the mouse brain striatum. Derivatives with small alkyl groups (methyl, ethyl) were more effective than those with large groups (propyl, isobutyl). These studies suggest that large groups in the 2-position of the benzisoquinoline structure will significantly diminish both in vitro and in vivo binding of these compounds to the vesicular monoamine transporter.
Structural Considerations of Layered and Spinel Lithiated Oxides for Lithium Ion Batteries (1995)

Rechargeable lithium batteries that can be assembled in the discharged state with lithiated metal oxide cathodes and carbon anodes are being developed to minimize the safety hazards associated with batteries that use pure metallic lithium anodes. This paper reviews crystallographic aspects of insertion electrodes with layered and spinel structures . The use of (spinel) instead of lithiated carbon as the anode is briefly discussed. Emphasis is placed on the structural properties of insertion electrodes that control their stability during electrochemical cycling.
Chiral synthon obtained with pig liver esterase: Introduction of chiral centers into cyclohexene skeleton. (1990)

A versatile chiral synthon, (1R,6S)-6-methoxycarbonyl-3-cyclohexene-1-carboxylic acid, was obtained by an enantioselective hydrolysis of the corresponding meso diester with pig liver esterase. This enzymatic hydrolysis can easily be carried out on a multi-hundred gram scale. The chiral monoester thus obtained can be further converted into all stereoisomers of 1-amino-2-alkoxycarbonyl-4-cyclohexene derivatives in an enantio- and stereocontrolled manner. These derivatives are considered as potential key intermediates for synthesizing a variety of biologically interesting compounds such as aminocyclitol and carbapenem antibiotics.
In Vitro and In Vivo Characterization of MicroRNA-Targeted Alphavirus Replicon and Helper RNAs (2010)

Alphavirus-based replicon vector systems (family Togaviridae) have been developed as expression vectors with demonstrated potential in vaccine development against both infectious diseases and cancer. The single-cycle nature of virus-like replicon particles (VRP), generated by supplying the structural proteins from separate replicable helper RNAs, is an attractive safety component of these systems. MicroRNAs (miRNAs) have emerged as important cellular RNA regulation elements. Recently, miRNAs have been employed as a mechanism to attenuate or restrict cellular tropism of replication-competent viruses, such as oncolytic adenoviruses, vesicular stomatitis virus, and picornaviruses as well as nonreplicating lentiviral and adenoviral vectors. Here, we describe the incorporation of miRNA-specific target sequences into replicable alphavirus helper RNAs that are used in trans to provide the structural proteins required for VRP production. VRP were found to be efficiently produced using miRNA-targeted helper RNAs if miRNA-specific inhibitors were introduced into cells during VRP production. In the absence of such inhibitors, cellular miRNAs were capable of downregulating helper RNA replication in vitro. When miRNA targets were incorporated into a replicon RNA, cellular miRNAs were capable of downregulating replicon RNA replication upon delivery of VRP into animals, demonstrating activity in vivo. These data provide the first example of miRNA-specific repression of alphavirus replicon and helper RNA replication and demonstrate the feasibility of miRNA targeting of expression vector helper functions that are provided in trans.
Magnetism in SQUIDs at Millikelvin Temperatures (2008)

We have characterized the temperature dependence of the flux threading dc SQUIDs cooled to millikelvin temperatures. The flux increases as 1/T as temperature is lowered; moreover, the flux change is proportional to the density of trapped vortices. The data are compatible with the thermal polarization of surface spins in the trapped fields of the vortices. In the absence of trapped flux, we observe evidence of spin-glass freezing at low temperature. These results suggest an explanation for the universal 1/f flux noise in SQUIDs and superconducting qubits.
Inactivation-reactivation of aconitase in Escherichia coli. A sensitive measure of superoxide radical. (1992)

The rapid inactivation of aconitase by O2-, previously seen to occur in vitro, was explored in vivo. A fraction of the aconitase in growing, aerobic, Escherichia coli is inactive at any instant but can be activated by imposition of anaerobic conditions. This reactivation occurred in the absence of protein synthesis and was inhibited by the ferrous chelator alpha,alpha'-dipyridyl. This fraction of inactive, but activatable, aconitase was increased by augmenting O2- production with paraquat, decreased by elevation of superoxide dismutase, and increased by inhibiting reactivation with alpha,alpha'-dipyridyl. The balance between inactive and active aconitase thus represented a pseudoequilibrium between inactivation by O2- and reactivation by restoration of Fe(II), and it provided, for the first time, a measure of the steady-state concentration of O2- within E. coli. On this basis, [O2-] was estimated to be approximately 20-40 pM in aerobic log phase E. coli containing wild type levels of superoxide dismutase and approximately 300 pM in a mutant strain lacking superoxide dismutase.
A Framework for Modelling Trojans and Computer Virus Infection (1998)

It is not possible to view a computer operating in the real world, including the possibility of Trojan horse programs and computer viruses, as simply a finite realisation of a Turing machine. We consider the actions of Trojan horses and viruses in real computer systems and suggest a minimal framework for an adequate formal understanding of the phenomena. Some conventional approaches, including biological metaphors, are shown to be inadequate; some suggestions are made towards constructing virally-resistant systems.
Nano to Macro Mechanical Characterization of Shale (2012)

Abstract We report on a nano-indentation study of shales from the Barnett, Woodford, Ordovician, Eagle Ford and Haynesville plays. Careful selection of load and displacement during nano-indentation testing yields micro to macro-mechanical properties, Young's modulus and hardness, of shale. Scanning Electron Microscope coupled and nano-indentation were used to study the mechanical behavior of kerogen. The measured Young's modulus of kerogen varied from 5 to 9 GPa. Mineralogy is found to play an important role in controlling mechanical properties of shales; an increase in carbonate and quartz content is correlated with an increase in Young's modulus whereas, an increase in TOC, clay content and porosity decreases Young's modulus. Close agreement is found between indentation moduli measured on small samples (mm scale) and dynamic moduli calculated from velocity and density measurements made on larger samples (centimeter scale). Tests conducted on cuttings provided results comparable to measurements made on larger core samples. Nano-indentation can provide a viable means of assessing quantitative measure of shale "fraccability."
Use of a novel human immunodeficiency virus type 1 reporter virus expressing human placental alkaline phosphatase to detect an alternative viral receptor (1995)

We report here on the construction and use of a novel human immunodeficiency virus (HIV) type 1 reporter vector, HIV-AP, that encodes human placental alkaline phosphatase. Upon staining with chromogenic alkaline phosphatase substrates 24 to 36 h postinfection, cells infected with HIV-AP develop an intense purple color and can then be counted under a dissecting microscope. Alternatively, HIV-AP infectivity can be quantitated and infected cells can be sorted by a fluorescence-activated cell sorter after staining with a fluorescent alkaline phosphatase substrate. The assay is rapid and accurate, has very low background in a variety of cell lines and primary cells, and is not restricted to use in human cells. Infectious HIV-AP can be pseudotyped by various HIV or murine leukemia virus envelope glycoproteins. Using this virus, we have addressed the long-standing question of CD4-independent infection of cells by HIV. Our results confirm the presence on a human osteosarcoma cell line of an alternative receptor for HIV infection that functions with an efficiency approximately 1/20 that of CD4.
Two Types of Nonlinear Optical Polyurethanes Containing the Same Isolation Groups: Syntheses, Optical Properties, and Influence of Binding Mode (2009)

In this paper, two new series of main-chain and side-chain second-order nonlinear optical (NLO) polyurethanes have been successfully prepared, in which isolation groups with different sizes were introduced to adjust the NLO property of the resultant polymers, according to the concept of "suitable isolation groups". The second harmonic generation (SHG) experiments demonstrated that all the polymers exhibited large second harmonic generation (SHG) coefficients of d33 values (up to 105.6 pm/V) with excellent thermal stability and film-forming ability, indicating that the introduction of isolation groups could alleviate the "nonlinearity-stability trade off" efficiently. In addition, for both main-chain and side-chain polymers, BOP acted as the suitable isolation group. It was also found that the positive influence of the linked suitable isolation spacer was more obvious in the main-chain polymers, in comparison with those in the side-chain polymers.
A biologically active peptide mimetic of N-acetylgalactosamine/galactose (2009)

The data indicate that the quadravalent peptide has biological activity with a degree of specificity. These effects occurred at concentrations in the nanomolar range, in contrast to free sugars that generally bind to proteins in the micro- to millimolar range.
Carbon Monoxide and Cyanide as Intrinsic Ligands to Iron in the Active Site of [NiFe]-Hydrogenases (1999)

Infrared-spectroscopic studies on the [NiFe]-hydrogenase of Chromatium vinosum-enriched in 15N or 13C, as well as chemical analyses, show that this enzyme contains three non-exchangeable, intrinsic, diatomic molecules as ligands to the active site, one carbon monoxide molecule and two cyanide groups. The results form an explanation for the three non-protein ligands to iron detected in the crystal structure of the Desulfovibrio gigas hydrogenase (Volbeda, A., Garcin, E., Piras, C., De Lacey, A. I., Fernandez, V. M., Hatchikian, E. C., Frey, M., and Fontecilla-Camps, J. C. (1996) J. Am. Chem. Soc. 118, 12989-12996) and for the low spin character of the lone ferrous iron ion observed with Mössbauer spectroscopy (Surerus, K. K., Chen, M., Van der Zwaan, W., Rusnak, F. M., Kolk, M. , Duin, E. C., Albracht, S. P. J., and Münck, E. (1994) Biochemistry 33, 4980-4993). The results do not support the notion, based upon studies of Desulfovibrio vulgaris [NiFe]-hydrogenase (Higuchi, Y., Yagi, T., and Noritake, Y. (1997) Structure 5, 1671-1680), that SO is a ligand to the active site. The occurrence of both cyanide and carbon monoxide as intrinsic constituents of a prosthetic group is unprecedented in biology.
SAXS and USAXS Investigation on Nanometer-Scaled Precursors in Organic-Mediated Zeolite Crystallization from Gelating Systems (1998)

The formation of precursor particles in the crystallization of zeolites from gelating systems has been studied using X-ray scattering at small angles. The crystallization of Si−MFI using trimethylene-bis(N-hexyl, N-methyl-piperidinium) as the structure-directing agent shows the formation of two categories of precursors: gel particles and nanometer-scaled primary units. The size of the primary units for the crystallization of Si−MFI is found to be 2.8 nm both for gelating and nongelating systems using different structure-directing agents. Zeolites Si−BEA and Si−MTW have been prepared using the same organic (trimethylene-bis(N-benzyl, N-methyl-piperidinium)) at different concentrations. Primary units with a size of 2.6 nm are found to be present in the synthesis of Si−BEA, while their size is 1.5 nm in the synthesis mixture directing to Si−MTW. Our data suggest that the nanometer-scaled primary units are specific for the zeolite topology formed.
Tumor Growth and Neovascularization: An Experimental Model Using the Rabbit Cornea 2 (1974)

By intracorneal implantation of tumors in the eyes of rabbits, the early neovascular response to solid tumor growth could be directly observed. Fragments of homologous tumors—Brown-Pearce epithelioma and V2 carcinoma—were implanted into the avascular corneal stroma of rabbits at various distances from the limbus. Tumor growth and neovascular response of llmbal vessels were studied by: 1) Slit Lamp Stereomicroscopy, 2) histologic examination, 3) filling of vasculature with colloidal carbon, and 4) autoradiography after exposure to 3Hthymidine. Centrally placed tumors spread as thin plates until they reached within 2.5 ± 0.5 mm of the limbus, when new vessels began to grow from the limbal plexus toward the tumor edge. When tumors became vascularized, they grew rapidly into exophytic masses. Peripherally placed tumors evoked early neovascularization. The prevascular growth of incompatible rabbit homograft and mouse xenograft tumors suggested that the cornea, before its vascularization, was an immunologically privileged site for tumor growth. Intracorneal polyacrylamide gel implants containing tumor extracts elicited a specific pattern of corneal vascularization not observed with nonmalignant cell extracts. These experiments provide a new model for study of tumor growth and neovascularization in a site where there is anatomic separation of tumor cell stimulus from host vascular response; the technique of corneal gel implantation may be useful in the characterization of mediators of neovascularization.
Determination of Pressure Dependent Leakoff and its Effect on Fracture Geometry (1996)

Abstract The effects of natural fissure opening, or pressure dependent leakoff, on the pressure behavior observed during fracturing are significant. Previous work has suggested that this behavior can be identified from pressure diagnostic plots during pumping, or from pressure falloff analysis. However, these techniques lead to ambiguous conclusions regarding the magnitude, and even existence, of pressure dependent leakoff. This paper presents a method of pressure falloff analysis which removes this ambiguity and allows an accurate determination of the magnitude of pressure dependent leakoff. The effects of fracture tip extension and recession, height recession, and transient flow in the fracture are also identified. The effect of pressure dependent fracture compliance, which has not been previously published, is also described.