gebhart/patrepeval huggingface dataset:
Charge regulation in nanopore ionic field-effect transistors (2011)

We studied the ionic conductance through Al₂O₃ nanopore transistors to probe the surface charge density and its dependence on the applied gate field. The observed conductance modulations are entirely attributable to the electrostatic field effect, and their dependence on pH, ionic strength, and gate voltage is described by a quantitative model. Importantly, these experiments revealed how reactive surface groups dominate the response of nanofluidic field-effect devices via a chemical effect called charge regulation. A quantitative understanding of this effect enables the development of new nanofluidic technologies.
Palladium-Catalyzed Intramolecular C−O Bond Formation (2001)

A number of oxygen heterocycles were synthesized using the palladium-catalyzed intramolecular etherification of aryl halides by employing di-tert-butylphosphinobiaryl ligands. The reaction proceeds under mild conditions using weak bases such as Cs(2)CO(3) or K(3)PO(4). A variety of functional groups are tolerated in the reaction, and enantioenriched alcohols can be coupled without erosion of optical purity. The mildness of the reaction conditions allows for the use of polyfunctionalized substrates. This method was used as the key step in the synthesis of MKC-242, an antidepressant currently in clinical trials. The synthesis of MKC-242 was achieved in 40% overall yield from commercially available sesamol and acrylonitrile.
Formation of a FGF-2 and calcium phosphate composite layer on a hydroxyapatite ceramic for promoting bone formation (2007)

Fibroblast growth factor-2 (FGF-2) was immobilized on a hydroxyapatite (HAP) ceramic in supersaturated calcium phosphate solution prepared using solutions corresponding to clinically approved infusion fluids. To avoid the risk of FGF-2 denaturation, FGF-2 immobilization was carried out at 25 degrees C. FGF-2 was successfully immobilized on HAP ceramic surfaces by deposition with calcium phosphate to form a FGF-2 and calcium phosphate composite layer. A maximum of 2.72 +/- 0.01 microg cm(-2) of FGF-2 was immobilized in the composite layer formed on the HAP ceramic under the optimum condition. A FGF-2-immobilized HAP ceramic is likely to have the ability to release a sufficient amount of FGF-2 to promote bone formation. FGF-2 released from a FGF-2-immobilized HAP ceramic maintained its biological activity, since the proliferation of fibroblastic NIH3T3 was promoted. Therefore, the FGF-2-immobilized HAP ceramic is expected to be a useful material for promoting new bone formation.
Expression and Immune Function of Tenascin-C (2011)

Our immune system is designed to protect us from danger. Upon pathogen invasion and tissue injury, activation of both innate and adaptive immunity enables us to combat infection and to repair tissue damage. Tenascin-C is a large, extracellular matrix glycoprotein that has a very tightly controlled pattern of expression. Little or no tenascin-C is expressed in most healthy adult tissues; however, it is rapidly and transiently induced at sites of tissue injury and infection. Persistent tenascin-C expression is associated with pathologies such as chronic, non-healing wounds, autoimmune diseases, cancer, and fibrotic diseases. We discuss the myriad roles that this multifunctional molecule plays during the immune response, with a focus on how tissue levels of tenascin-C are regulated and the consequences of misregulated tenascin-C expression in immune regulated disease pathogenesis.
Synthesis and Structure−Activity Profiles of A-Homoestranes, the Estratropones (1997)

2-Methoxyestradiol, a mammalian metabolite of estradiol, has reported antiangiogenic activity which has been proposed to be mediated through interaction at the colchicine binding site on the tubulin monomer. Subsequent structure−activity studies of 2-methoxyestradiol have yielded highly potent steroidal inhibitors of tubulin polymerization. In an effort to probe the scope of binding at the colchicine binding site and the nature of the relationship between 2-methoxyestradiol and colchicine, a series of colchicine/2-methoxyestradiol hybrids was synthesized. These A-homoestrane hybrid systems, collectively termed estratropones, possessed an A-ring tropone system with the keto functionality at either the C-2, C-3, or C-4 position of the steroid nucleus. The estratropones were evaluated for their ability to inhibit the polymerization of tubulin using an in vitro purified bovine brain assay. Most of these hybrids inhibit polymerization with greater potency than either of the natural products. The most potent of these congeners possessed an approximate 5-fold enhancement of the activity of colchicine for the inhibition of tubulin polymerization. α-Substituents on the tropone ring showed varied effects on the activities for the two classes of estratropones studied in this regard, the C-3 oxo and the C-4 oxo species. The 3-substituted 4-oxoestratropones exhibited antitubulin activity according to Cl ≈ Br > OCH3, whereas the 4-substituted 3-oxoestratropones exhibited activity according to OCH3 > Br ≈ Cl. It is unclear if these substituent factors are purely electronic or steric effects or if the substituent operates indirectly by altering the conformation of the nonplanar troponoid ring. The estratropones represent a new class of tubulin binding agents with potential antiangiogenic utility.
Energy-Optimal Electrical Excitation of Nerve Fibers (2005)

We derive, based on an analytical nerve membrane model and optimal control theory of dynamical systems, an energy-optimal stimulation current waveform for electrical excitation of nerve fibers. Optimal stimulation waveforms for nonleaky and leaky membranes are calculated. The case with a leaky membrane is a realistic case. Finally, we compare the waveforms and energies necessary for excitation of a leaky membrane in the case where the stimulation waveform is a square-wave current pulse, and in the case of energy-optimal stimulation. The optimal stimulation waveform is an exponentially rising waveform and necessitates considerably less energy to excite the nerve than a square-wave pulse (especially true for larger pulse durations). The described theoretical results can lead to drastically increased battery lifetime and/or decreased energy transmission requirements for implanted biomedical systems.
Mechanisms of Graft Rejection in the Transplantation of Retinal Pigment Epithelial Cells (1997)

In culture, some of the adult RPE cells are activated. These cells may accelerate the rejection cascade after transplantation. An elimination of activated RPE cells from the transplant should be recommended before transplantation.
Mosaic and the World Wide Web (1994)

The World-Wide Web, an information service on the Internet, uses hypertext links to other textual documents or files. Users can click on a highlighted word or words in the text to provide additional information about the selected word(s). Users can also access graphic pictures, images, audio clips, or even full-motion video through hypermedia, an extension of hypertext. One of the most popular graphics-oriented browsers is Mosaic, which was developed at the National Center for Supercomputing Applications (NCSA) as a way to graphically-navigate the WWW. Mosaic browsers are currently available for Unix workstations running X Windows, PCs running Microsoft Windows, and Macintosh computers. Mosaic can access data in WWW servers, Wide Area Information Servers (WAIS), Gopher servers, Archie servers, and several others. The World-Wide Web is still evolving at a rapid pace. Distributed hypermedia systems on the Internet will continue to be an active area of development in the future. The flexibility of the WWW design, its use of hyperlinks, and the integration of existing WAIS and Gopher information resources, make the WWW ideal for future research and study. Highly interactive multimedia applications will require more sophisticated tools than currently exist. The most significant issue that needs to be resolved is the mismatch between WWW system capabilities and user requirements in the areas of presentation and quality of service.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Molecular Model for Astringency Produced by Polyphenol/Protein Interactions (2004)

Polyphenols are responsible for the astringency of many beverages and foods. This is thought to be caused by the interaction of polyphenols with basic salivary proline-rich proteins (PRPs). It is widely assumed that the molecular origin of astringency is the precipitation of PRPs following polyphenol binding and the consequent change to the mucous layer in the mouth. Here, we use a variety of biophysical techniques on a simple model system, the binding of beta-casein to epigallocatechin gallate (EGCG). We show that at low EGCG ratios, small soluble polydisperse particles are formed, which aggregate to form larger particles as EGCG is added. There is an initial compaction of the protein as it binds to the polyphenol, but the particle subsequently increases in size as EGCG is added because of the incorporation of EGCG and then to aggregation and precipitation. These results are shown to be compatible with what is known of astringency in foodstuffs.
Rituximab treatment results in impaired secondary humoral immune responsiveness (2002)

In lymphoma patients, treatment with chimeric CD20 monoclonal antibodies (rituximab) results in a depletion of normal and malignant B cells, persisting for 6 to 9 months. This B-cell depletion leads neither to a decrease in immunoglobulin levels nor an increase in the number of infectious complications. However, the effect of rituximab treatment on the immune responsiveness is unknown. In 11 patients with relapsed, low-grade lymphoma, we investigated the effect of rituximab treatment on the humoral immune response to 2 primary antigens and 2 recall antigens. After rituximab treatment, the humoral immune response to the recall antigens was significantly decreased when compared with the response before treatment. Already before rituximab treatment, none of these patients was able to mount a response to the primary antigens. These findings are relevant regarding the feasibility of rituximab in maintenance treatment and may also offer a rationale for the treatment of antibody-mediated autoimmune diseases with rituximab.
Improving generalization of constructive neural networks using ensembles (1999)

Ensemble networks have been receiving considerable attention within the last few years. Most existing models are created with linear networks. Ensembles of linear networks have demonstrated improved performance over individual networks, but linear models have limited capacity problems. Ensembles of more complex well-trained networks offer a promising alternative. Unfortunately, the computational expense involved in training large numbers of well-trained networks may be prohibitive. 
An ensemble of non-linear feed-forward neural networks generated by a constructive algorithm is presented. The ensemble method presented exhibits better generalization than linear ensembles, and shows promise toward a reduction in time-complexity over well-trained ensembles. The problems addressed in this research are: generalization of non-linear data, time-complexity, structural dilemmas, model creation, and model combination. The Neural Network Ensemble Simulator (NNES) is also introduced as a simulation tool for managing ensemble experiments. NNES provides routines for ensemble creation, selection, combination, and analysis.
Antimicrobial action of .EPSILON.-poly-L-lysine. (1984)

The antimicrobial spectrum of epsilon-poly-L-lysine (n = 25-30, epsilon-PL) was investigated by comparison with alpha-poly-L-lysine (n = 50, alpha-PL). epsilon-PL showed antimicrobial activity against Gram-positive and -negative bacteria at concentrations of 1-8 micrograms/ml. alpha-PL was less active than epsilon-PL. A chain length of at least 10 L-lysine monomers was found to be optimum for antimicrobial activity. Chemical modification of the amino groups of epsilon-PL lowered its antibacterial activity. Studies on the mode of action of epsilon-PL suggest that absorption of epsilon-PL to the bacterial cell surface plays an important role in its antibacterial activity.
Accessibility of nuclear DNA to triplex-forming oligonucleotides: The integrated HIV-1 provirus as a target (1997)

The control of gene transcription by antigene oligonucleotides rests upon the specific recognition of double-helical DNA by triplex-forming oligonucleotides. The development of the antigene strategy requires access to the targeted DNA sequence within the chromatin structure of the cell nucleus. In this sudy we have used HIV-1 chronically infected cells containing the HIV provirus as endogenous genes to demonstrate that the integrated HIV-1 proviral genome is accessible to triplex-forming oligonucleotides within cell nuclei. An oligonucleotide-psoralen conjugate targeted to the polypurine tract (PPT) of the HIV-1 proviral sequence was used as a tool to convert the noncovalent triple-helical complex into a covalent lesion on genomic DNA after UV irradiation of cells. Triplex-derived adducts were analyzed using two different methods. The photo-induced psoralen cross-link prevented cleavage of the target sequence by DraI restriction endonuclease, and the sequence-specific inhibition of cleavage was revealed and quantitated by Southern blot analysis. A quantitative analysis of cross-linking efficiency was also carried out by a competitive PCR-based assay. These two approaches allowed us to demonstrate that a triplex-forming oligonucleotide can recognize and bind specifically to a 15-bp sequence within the chromatin structure of cell nuclei.
Wiskott-Aldrich syndrome protein regulates podosomes in primary human macrophages (1999)

Wiskott-Aldrich syndrome protein (WASp) is a hematopoietic-specific, multidomain protein whose mutation is responsible for the immunodeficiency disorder Wiskott-Aldrich syndrome. WASp contains a binding motif for the Rho GTPase CDC42Hs as well as verprolin/cofilin-like actin-regulatory domains, but no specific actin structure regulated by CDC42Hs-WASp has been identified. We found that WASp colocalizes with CDC42Hs and actin in the core of podosomes, a highly dynamic adhesion structure of human blood-derived macrophages. Microinjection of constitutively active V12CDC42Hs or a constitutively active WASp fragment consisting of the verprolin/cofilin-like domains led to the disassemly of podosomes. Conversely, macrophages from patients expressing truncated forms of WASp completely lacked podosomes. These findings indicate that WASp controls podosome assembly and, in cooperation with CDC42Hs, podosome disassembly in primary human macrophages.
Isolation and characterization of human CD34−Lin− and CD34+Lin− hematopoietic stem cells using cell surface markers AC133 and CD7 (2000)

Recent evidence indicates that human hematopoietic stem cell properties can be found among cells lacking CD34 and lineage commitment markers (CD34−Lin−). A major barrier in the further characterization of human CD34− stem cells is the inability to detect this population using in vitro assays because these cells only demonstrate hematopoietic activity in vivo. Using cell surface markers AC133 and CD7, subfractions were isolated within CD34−CD38−Lin− and CD34+CD38−Lin− cells derived from human cord blood. Although the majority of CD34−CD38−Lin− cells lack AC133 and express CD7, an extremely rare population of AC133+CD7− cells was identified at a frequency of 0.2%. Surprisingly, these AC133+CD7− cells were highly enriched for progenitor activity at a frequency equivalent to purified fractions of CD34+ stem cells, and they were the only subset among the CD34−CD38−Lin− population capable of giving rise to CD34+ cells in defined liquid cultures. Human cells were detected in the bone marrow of non-obese/severe combined immunodeficiency (NOD/SCID) mice 8 weeks after transplantation of ex vivo–cultured AC133+CD7− cells isolated from the CD34−CD38−Lin− population, whereas 400-fold greater numbers of the AC133−CD7− subset had no engraftment ability. These studies provide novel insights into the hierarchical relationship of the human stem cell compartment by identifying a rare population of primitive human CD34− cells that are detectable after transplantation in vivo, enriched for in vitro clonogenic capacity, and capable of differentiation into CD34+ cells.
Cometin is a novel neurotrophic factor that promotes neurite outgrowth and neuroblast migration in vitro and supports survival of spiral ganglion neurons in vivo (2011)

Neurotrophic factors are secreted proteins responsible for migration, growth and survival of neurons during development, and for maintenance and plasticity of adult neurons. Here we present a novel secreted protein named Cometin which together with Meteorin defines a new evolutionary conserved protein family. During early mouse development, Cometin is found exclusively in the floor plate and from E13.5 also in dorsal root ganglions and inner ear but apparently not in the adult nervous system. In vitro, Cometin promotes neurite outgrowth from dorsal root ganglion cells which can be blocked by inhibition of the Janus or MEK kinases. In this assay, additive effects of Cometin and Meteorin are observed indicating separate receptors. Furthermore, Cometin supports migration of neuroblasts from subventricular zone explants to the same extend as stromal cell derived factor 1a. Given the neurotrophic properties in vitro, combined with the restricted inner ear expression during development, we further investigated Cometin in relation to deafness. In neomycin deafened guinea pigs, two weeks intracochlear infusion of recombinant Cometin supports spiral ganglion neuron survival and function. In contrast to the control group receiving artificial perilymph, Cometin treated animals retain normal electrically-evoked brainstem response which is maintained several weeks after treatment cessation. Neuroprotection is also evident from stereological analysis of the spiral ganglion. Altogether, these studies show that Cometin is a potent new neurotrophic factor with therapeutic potential.
Avoiding Pitfalls in Fault-Injection Based Comparison of Program Susceptibility to Soft Errors (2015)

Since the first identification of physical causes for soft errors in memory circuits, fault injection (FI) has grown into a standard methodology to assess the fault resilience of computer systems. A variety of FI techniques trying to mimic these physical causes has been developed to measure and compare program susceptibility to soft errors. In this paper, we analyze the process of evaluating programs, which are hardened by software-based hardware fault-tolerance mechanisms, under a uniformly distributed soft-error model. We identify three pitfalls in FI result interpretation widespread in the literature, even published in renowned conference proceedings. Using a simple machine model and transient single-bit faults in memory, we find counterexamples that reveal the unfitness of common practices in the field, and substantiate our findings with real-world examples. In particular, we demonstrate that the fault coverage metric must be abolished for comparing programs. Instead, we propose to use extrapolated absolute failure counts as a valid comparison metric.
Portal dosimetry using a liquid ion chamber matrix: Dose response studies (1995)

Current intensive investigations of electronic portal imaging devices (EPIDs) have prompted their potential application to portal dosimetry. In this paper, the progress made in using a commercial liquid ion chamber matrix EPID for portal dosimetry is discussed. The pixel value of the liquid ion chamber element was calibrated against dose by exposing the imager to 6-MV x-ray beams of various intensities obtained with various thicknesses of lead attenuators and a range of source to detector distances. Absolute dose values were determined using an ion chamber on the central axis at the depth of maximum dose in a solid water phantom. The pixel values of the matrix were determined for various field sizes in order to evaluate the dependence of pixel value on dose at those field sizes. It was confirmed that the pixel value was proportional to the square root of the dose rate and was nearly independent of the field size. The 2D pixel values were converted to 2D dose maps in the water phantom after applying a correction for the effect of horns in the flood calibration field. The flood calibration field was used to obtain the relative sensitivity of each pixel. Good agreement was observed (normally better than 1% in relative standard deviation) between the converted dose distribution obtained from the pixel matrix and the direct dose measurement using an ion chamber scanned in a water phantom in regions of shallow dose gradient. For application to on-line portal dosimetry, both the short- and long-term stability of this EPID system were found to be within 1% relative standard deviation.(ABSTRACT TRUNCATED AT 250 WORDS)
BDAM — Batched Dynamic Adaptive Meshes for High Performance Terrain Visualization (2003)

Abstract This paper describes an efficient technique for out‐of‐core rendering and management of large textured terrainsurfaces. The technique, called Batched Dynamic Adaptive Meshes (BDAM), is based on a paired tree structure:a tiled quadtree for texture data and a pair of bintrees of small triangular patches for the geometry. These smallpatches are TINs and are constructed and optimized off‐line with high quality simplification and tristrippingalgorithms. Hierarchical view frustum culling and view‐dependent texture and geometry refinement is performedat each frame through a stateless traversal algorithm. Thanks to the batched CPU/GPU communication model,the proposed technique is not processor intensive and fully harnesses the power of current graphics hardware.Both preprocessing and rendering exploit out‐of‐core techniques to be fully scalable and to manage large terraindatasets. Categories and Subject Descriptors (according to ACM CCS): I.3.3 [Computer Graphics]: Picture and Image Generation;I.3.7 [Computer Graphics]: Three‐Dimensional Graphics and Realism.
Possible Function of the ADAM1a/ADAM2 Fertilin Complex in the Appearance of ADAM3 on the Sperm Surface (2004)

In mouse, two different isoforms of ADAM1 (fertilin alpha), ADAM1a and ADAM1b, are produced in the testis. ADAM1a is localized within the endoplasmic reticulum of testicular germ cells, whereas epididymal sperm contain only ADAM1b on the plasma membrane. In this study, we show that the loss of ADAM1a results in the male infertility because of the severely impaired ability of sperm to migrate from the uterus into the oviduct through the uterotubal junction. However, epididymal sperm of ADAM1a-deficient mice were capable of fertilizing cumulus-intact, zona pellucida-intact eggs in vitro despite the delayed dispersal of cumulus cells and the reduced adhesion/binding to the zona pellucida. Among testis (sperm)-specific proteins examined, only the level of ADAM3 (cyritestin) was strongly reduced in ADAM1a-deficient mouse sperm. Moreover, the appearance of ADAM3 on the sperm surface was dependent on the formation of a fertilin protein complex between ADAM1a and ADAM2 (fertilin beta) in testicular germ cells, although no direct interaction between the fertilin complex and ADAM3 was found. These results suggest that ADAM1a/ADAM2 fertilin may be implicated in the selective transport of specific sperm proteins including ADAM3 from the endoplasmic reticulum of testicular germ cells onto the cell surface. These proteins then can participate in sperm migration into the oviduct, the dispersal of cumulus cells, and sperm binding to the zona pellucida.