gebhart/patrepeval huggingface dataset:
Synthesis of Monodisperse Spherical Nanocrystals (2007)

Much progress has been made over the past ten years on the synthesis of monodisperse spherical nanocrystals. Mechanistic studies have shown that monodisperse nanocrystals are produced when the burst of nucleation that enables separation of the nucleation and growth processes is combined with the subsequent diffusion-controlled growth process through which the crystal size is determined. Several chemical methods have been used to synthesize uniform nanocrystals of metals, metal oxides, and metal chalcogenides. Monodisperse nanocrystals of CdSe, Co, and other materials have been generated in surfactant solution by nucleation induced at high temperature, and subsequent aging and size selection. Monodisperse nanocrystals of many metals and metal oxides, including magnetic ferrites, have been synthesized directly by thermal decomposition of metal-surfactant complexes prepared from the metal precursors and surfactants. Nonhydrolytic sol-gel reactions have been used to synthesize various transition-metal-oxide nanocrystals. Monodisperse gold nanocrystals have been obtained from polydisperse samples by digestive-ripening processes. Uniform-sized nanocrystals of gold, silver, platinum, and palladium have been synthesized by polyol processes in which metal salts are reduced by alcohols in the presence of appropriate surfactants.
Template-based Composition of Semantic Web Services. (2005)

Workflow templates are necessary for various different Web Service related tasks such as encoding business rules in a B2B application, specifying domain knowledge in a scien-tific Grid application, and defining preferences for users that interact with Web Services. Abstract activities in templates can be used to specify the features of a required service and concretes service can be discovered and used to generate ex-ecutable workflows. In this paper, we examine how Web on-tologies can be used to write such template descriptions that will allow flexible matchmaking of services. We discuss the importance of expressing preferences in templates and pro-vide a ranking algorithm based on DL inference services. We then present the HTN-DL formalism – an extension to the HTN planning formalism to generate compositions of Web Services based on these templates. Finally we present the experimental evaluation for the composition system we pro-posed.
Learning to Interpret Natural Language Navigation Instructions from Observations (2011)

The ability to understand natural-language instructions is critical to building intelligent agents that interact with humans. We present a system that learns to transform natural-language navigation instructions into executable formal plans. Given no prior linguistic knowledge, the system learns by simply observing how humans follow navigation instructions. The system is evaluated in three complex virtual indoor environments with numerous objects and landmarks. A previously collected realistic corpus of complex English navigation instructions for these environments is used for training and testing data. By using a learned lexicon to refine inferred plans and a supervised learner to induce a semantic parser, the system is able to automatically learnto correctly interpret a reasonable fraction of the complex instructions in this corpus.
Correction of a mouse model of sickle cell disease: lentiviral/antisickling β-globin gene transduction of unmobilized, purified hematopoietic stem cells (2003)

Although sickle cell anemia was the first hereditary disease to be understood at the molecular level, there is still no adequate long-term treatment. Allogeneic bone marrow transplantation is the only available cure, but this procedure is limited to a minority of patients with an available, histocompatible donor. Autologous transplantation of bone marrow stem cells that are transduced with a stably expressed, antisickling globin gene would benefit a majority of patients with sickle cell disease. Therefore, the development of a gene therapy protocol that corrects the disease in an animal model and is directly translatable to human patients is critical. A method is described in which unmobilized, highly purified bone marrow stem cells are transduced with a minimum amount of self-inactivating (SIN) lentiviral vector containing a potent antisickling beta-globin gene. These cells, which were transduced in the absence of cytokine stimulation, fully reconstitute irradiated recipients and correct the hemolytic anemia and organ pathology that characterize the disease in humans. The mean increase of hemoglobin concentration was 46 g/L (4.6 g/dL) and the average lentiviral copy number was 2.2; therefore, a 21-g/L /vector copy increase (2.1-g/dL) was achieved. This transduction protocol may be directly translatable to patients with sickle cell disease who cannot tolerate current bone marrow mobilization procedures and may not safely be exposed to large viral loads.
Oxidation of Cysteine 645 of Cobalamin-Independent Methionine Synthase Causes a Methionine Limitation in Escherichia coli (2009)

Cobalamin-independent methionine synthase (MetE) catalyzes the final step in Escherichia coli methionine biosynthesis but is inactivated under oxidative conditions, triggering a methionine deficiency. This study demonstrates that the mutation of MetE cysteine 645 to alanine completely eliminates the methionine auxotrophy imposed by diamide treatment, suggesting that modulation of MetE activity via cysteine 645 oxidation has significant physiological consequences for oxidatively stressed cells.
Invariant chain targets HLA class II molecules to acidic endosomes containing internalized influenza virus. (1991)

The role of the HLA class II-associated invariant chain in the intracellular trafficking of HLA-DR molecules was examined in a transient expression system using HeLa cells. In the absence of alpha and beta polypeptides, invariant chain was retained in the endoplasmic reticulum (ER). In the absence of invariant chain, intracellular alpha beta heterodimers could be detected only in the ER and the Golgi apparatus. However, when alpha and beta subunits were coexpressed with invariant chain, HLA-DR molecules were detectable in peripheral cytoplasmic vesicles, which also contained invariant chain. In addition, an antibody directed to an acid-induced conformational determinant on the influenza hemagglutinin molecule detected internalized influenza virus in the HLA-DR-containing vesicles. These findings provide direct evidence that the invariant chain targets class II molecules to an acidic endosomal compartment and that this compartment, long suspected to be the site of antigen processing, is the site where class II molecules interact with natural antigen.
Bulk viscosity and compressibility measurement using acoustic spectroscopy (2009)

Bulk viscosity is a somewhat obscure parameter that appears in the hydrodynamic equations for Newtonian liquids when compressibility is important and, together with the dynamic viscosity, controls sound attenuation. Whereas dynamic viscosity reflects only "translational" molecular motion, in contrast the bulk viscosity reflects the relaxation of both "rotational" and "vibrational" degrees of molecular freedom. Several molecular theories yield predictive expressions for both bulk and dynamic viscosities, but experimentally the situation is quite out of balance, in that there is extensive data for the dynamic viscosity of all sorts of liquids, but a paucity of data for bulk viscosity, just a few values for water and a handful of exotic liquids. We compare three possible experimental techniques for measuring bulk viscosity, namely, Brillouin spectroscopy, Laser transient grating spectroscopy, and acoustic spectroscopy. We then formulate some arguments suggesting that acoustic spectroscopy is not only the most suitable for measuring bulk viscosity, but that it also offers a verification procedure that can confirm that the measured parameter agrees with theoretical definition of bulk viscosity for a Newtonian liquid. In addition, acoustic spectroscopy provides a measurement of sound speed, which cannot only improve the attenuation measurement but as a side benefit can also be used to calculate liquid compressibility. We apply this technique for measuring the bulk viscosity and compressibility of twelve commonly assumed Newtonian liquids, two of which surprisingly fails to pass a verification test described here to test the Newtonian hypothesis. Then, we test correlation between measured bulk viscosity and several other intensive properties of these liquids, such as density, dynamic viscosity, dielectric permittivity, and compressibility. We have not discovered any meaningful correlation. This suggests that bulk viscosity is an independent parameter that reflects peculiar properties of liquids and can be used in the set of independent equations describing molecular interaction in liquids.
Analytical Electron Microscope Analysis of the Formation of BaO · 6Al 2 O 3 (1988)

The formation process of barium hexaaluminate (BaO 6Al 2 O 3 ) from BaCO 3 /γ‐Al 2 O 3 powders or hydrolyzed alkoxides was studied by analytical electron microscopy. Barium hexaaluminate is produced by a two‐step solid‐state reaction from BaCO 3 and Al 2 O 3 via formation of BaO·Al 2 O 3 . Marked grain growth and inclusion of nonequilibrium phase were inevitable in this powder mixture process. However, in an alkoxide‐derived precursor, homogeneous mixing of components is attained and hence the formation of BaO·6Al 2 O 3 proceeds readily. Powders obtained by this latter route consisted of fine planar particles with a uniform size and retained a large surface area (20.2 m 2 /g) even after heating at 1300°C. Electron diffraction results implied that suppression of crystal growth along the c axis is the reason for the large surface area of BaO·6Al 2 O 3 .
Autoimmune Encephalopathies (2007)

Autoimmune encephalopathies are an important cause of rapidly progressive cognitive and behavioral decline that probably remain under recognized. Electroencephalography, brain MRI, cerebrospinal fluid examination and serological tests are useful diagnostic tools. With increased clinical suspicion, these diseases may be diagnosed and treated successfully.
Efficient multi-scale 3D CNN with fully connected CRF for accurate brain lesion segmentation (2016)

We propose a dual pathway, 11-layers deep, three-dimensional Convolutional Neural Network for the challenging task of brain lesion segmentation. The devised architecture is the result of an in-depth analysis of the limitations of current networks proposed for similar applications. To overcome the computational burden of processing 3D medical scans, we have devised an efficient and effective dense training scheme which joins the processing of adjacent image patches into one pass through the network while automatically adapting to the inherent class imbalance present in the data. Further, we analyze the development of deeper, thus more discriminative 3D CNNs. In order to incorporate both local and larger contextual information, we employ a dual pathway architecture that processes the input images at multiple scales simultaneously. For post-processing of the network's soft segmentation, we use a 3D fully connected Conditional Random Field which effectively removes false positives. Our pipeline is extensively evaluated on three challenging tasks of lesion segmentation in multi-channel MRI patient data with traumatic brain injuries, brain tumours, and ischemic stroke. We improve on the state-of-the-art for all three applications, with top ranking performance on the public benchmarks BRATS 2015 and ISLES 2015. Our method is computationally efficient, which allows its adoption in a variety of research and clinical settings. The source code of our implementation is made publicly available.
Molecular plant pathology : a practical approach (1992)

Part 1 Defence response (gene products): callose and callose synthase, H. Kauss lignin and associated phenolic acids in cell walls, J. Friend preparation and analysis of intercellular fluid, K.E. Hammond-Kosack biochemical analysis of chitinases and beta-1,3- glucanases, T. Boller localization of proteins and carbohydrates using immunogold labelling in light and electron microscopy, K.A. Van den Bosch isoflavonoid phytoalexins and their biosynthetic enzymes, R. Edwards and H. Kessmann analysis of terpernoid phytoalexins and their biosynthetic enzymes, D.R. Threlfall and I.M. Whitehead. Part 2 Elicitors: preparation and characterization of oligosaccharide elicitors of phytoalexin accumulation, M.G. Hahn et al xyloglucan oligosaccharides, S.C. Fry. Part 3 Signal transduction pathways: analysis of calcium involvement in host-pathogen interactions, B.K. Drobak et al analysis of components of the plant phosphoinositide system, B.K. Drobak and K. Roberts metabolic changes following infection of leaves by fungi and viruses, R.C. Leegood and J.D. Scholes. Part 4 Disease resistance genes: strategies for cloning disease resistance genes, R.W. Michelmore et al.
Randomized Phase III Trial of Docetaxel Versus Vinorelbine or Ifosfamide in Patients With Advanced Non–Small-Cell Lung Cancer Previously Treated With Platinum-Containing Chemotherapy Regimens (2000)

This first randomized trial in this setting demonstrates that D75 every 3 weeks can offer clinically meaningful benefit to patients with advanced NSCLC whose disease has relapsed or progressed after platinum-based chemotherapy.
Tumor growth suppression by a mouse/human chimeric anti-CEA antibody and lymphokine-activated killer cells in vitro and in SCID mouse xenograft model. (1998)

The mouse/human chimeric antibody Ch F11-39, recently generated by ourselves, shows the same high specificity and affinity for carcinoembryonic antigen (CEA) as those of its parental mouse monoclonal antibody. Ch F11-39 is capable of mediating antibody-dependent cell-mediated cytotoxicity (ADCC) with human peripheral blood lymphocytes (PBL). Interleukin-2 (IL-2) modulates the function of immunocytes, in particular inducing lymphokine-activated killer (LAK) cells and enhancing ADCC. In the present study, we therefore tested the combination immunotherapy of Ch F11-39 with LAK cells in vitro and in severe combined immunodeficiency (SCID) mice bearing human CEA-producing tumors. In vitro experiments using human gastric tumor cell lines, Ch F11-39 effectively mediated ADCC against CEA-positive MKN-45 cells, but not against CEA-negative cells. The specificity of ADCC for Ch F11-39 was demonstrated by experiments with irrelevant target cells or irrelevant antibody. ADCC activity of PBL with Ch F11-39 was enhanced by double after preincubation with IL-2 at 10 U/ml. The concentration of Ch F11-39 required for 50% maximal cell killing was about 0.25 microgram/ml at 10 U/ml of IL-2. Increasing ADCC was triggered by IL-2 earlier (1 day) than the generation of LAK cells (3 days). Control human IgG blocked the ADCC, suggesting that the enhancement of ADCC by IL-2 may be caused by activation of effector cells expressing Fc receptors. In vivo anti-tumor activity of combined immunotherapy was estimated using SCID mice inoculated s.c. with 1 x 10(7) MKN-45 cells. The i.v. administration of LAK cells and i.p. administration of Ch F11-39 and IL-2 produced a marked growth inhibition of MKN-45 tumors in SCID mice (about 50% reduction in tumor size as compared to the control untreated group, measured 15 days after treatment). In summary, the enhanced antitumor activity of Ch F11-39 with LAK cells suggests that it might be a useful immunotherapeutic reagent for CEA-expressing tumors.
Human embryonic stem cells and liver diseases: From basic research to future clinical application (2008)

Human embryonic stem cells (hESC) provide access to the earliest stages of human development and because of their high proliferation capability, pluripotency and low immunogenicity may serve as a potential source of specialized cells for regenerative medicine. hESC-derived hepatocyte-like cells exhibit characteristic hepatocyte morphology, express hepatocyte markers and are capable of executing a range of hepatocyte functions. However, there are many challenges and obstacles to be overcome before the use of hESC and hESC-derived hepatocyte-like cells in clinical practice can be realized. Here, we highlight some of the recent efforts in this area, in hope of providing insights toward this complex yet important area of therapeutical modality for treating patients with liver disease.
Metal-Clad Optical Waveguides: Analytical and Experimental Study (1974)

Planar optical waveguides consisting of thin dielectric films with metal cladding have been investigated theoretically and experimentally. A computer program was devised to provide the phase and attenuation constants and wavefunctions for TE and TM modes in symmetric and asymmetric guides. Approximate expressions suitable for slide-rule calculation were also derived. Numerical results and illustrations are given for films of photoresist with Al, Ag, and Au cladding. Direct measurements of the attenuation and phase constants at 0.633 microm of numerous experimental waveguides are in reasonable agreement with theory. Attenuations <1 dB/cm, which is sufficiently small for application in devices, were measured. Calculated wavefunctions illustrate the mismatch of modes at transitions between unclad and metal-clad waveguides. Experimentally, we find substantial losses at such abrupt junctions. They can be overcome by simple tapered transitions.
A survey of encryption standards (1993)

The author reviews encryption algorithms and standards, how they compare, how they differ, and where they are headed. Attention is given to secret-key cryptosystems, public-key cryptosystems, digital signature schemes, key-agreement algorithms, cryptographic hash functions, and authentication codes. Applications considered are secure electronic mail, secure communications, directory authentication and network management, banking, and escrowed encryption.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
The Arabidopsis MALE MEIOCYTE DEATH1 Gene Encodes a PHD-Finger Protein That Is Required for Male Meiosis (2003)

In plants, reproductive development requires normal meiosis, which involved several highly coordinated events. Such meiotic events are regulated in a number of ways in yeast and animal systems, including transcriptional and checkpoint control mechanisms. Although a number of mutations that affect different aspects of meiosis have been characterized in plants, very little is known about the regulation of plant meiosis at the molecular level. In particular, no meiosis-specific transcriptional regulators have been identified in plants, and checkpoint control has not been observed during plant meiosis. We report here the isolation and characterization of a new Arabidopsis male-sterile mutant that exhibits meiotic defects. Meiocytes from mutant plants appeared normal up to diakinesis, when they exhibited signs of apoptosis, including defects in chromosome behavior, cytoplasmic shrinkage, and chromatin fragmentation, followed by cell death before cytokinesis. Therefore, the mutant was named male meiocyte death1 (mmd1). The MMD1 gene was cloned using Dissociation transposon tagging and encodes a plant homeo domain domain-containing protein. MMD1 is expressed preferentially during male meiosis. Our results suggest that MMD1 may be involved in the regulation of gene expression during meiosis and that the mmd1 mutation triggers cell death in male meiocytes.
PCB-Based Prototyping of 3-D Micromachined RF Subsystems (2013)

A stacked printed circuit board (PCB) approach for prototyping 3-D microfabrication enabled millimeter and submillimeter wave components and subsystems is proposed. To demonstrate this approach, a 4 to 8 GHz two element tapered slot antenna array with integrated rectangular coaxial 90 ° hybrid, and its stand-alone elements, are designed and fabricated. Measured subsystem results show properly formed radiation patterns, realized gain from 9 to 11 dBi, and 3-dB beamwidth from 30 ° to 45 °. Excellent agreement between simulations and measurements of individual components and the full subsystem as well as outcomes of a tolerance study and comparison to a Ka band micromachined subsystem confirm suitability of the proposed approach for fast, low-cost prototyping of 3-D micromachined rectangular coaxial components and subsystems.
Real time user context modeling for information retrieval agents (2001)

The success of personal information agents depends on their ability to provide task-relevant information. This paper presents WordSieve, a new algorithm that generates context descriptions to guide document indexing and retrieval. WordSieve exploits information about the sequence of accessed documents to identify words which indicate a shift in context. We have tested WordSieve in a personal information agent, Calvin, which monitors a user's document access, generates a representation of the user's task context, indexes the resources consulted, and presents recommendations for other resources that were consulted in similar prior contexts. In initial experiments, WordSieve outperforms term frequency/inverse document frequency at matching documents to hand-coded vector representations of the task contexts in which they were originally consulted, where the task context representations are term vectors representing a specific search task given to the user.
Pediatric Selective IgM Immunodeficiency (2008)

The prevalence of SIgMID in our pediatric population was 0.03%. In general, respiratory infections are the common comorbid conditions. Death and autoimmune disease are uncommon complications of pediatric SIgMID.
Real-time single-molecule electronic DNA sequencing by synthesis using polymer-tagged nucleotides on a nanopore array (2016)

DNA sequencing by synthesis (SBS) offers a robust platform to decipher nucleic acid sequences. Recently, we reported a single-molecule nanopore-based SBS strategy that accurately distinguishes four bases by electronically detecting and differentiating four different polymer tags attached to the 5'-phosphate of the nucleotides during their incorporation into a growing DNA strand catalyzed by DNA polymerase. Further developing this approach, we report here the use of nucleotides tagged at the terminal phosphate with oligonucleotide-based polymers to perform nanopore SBS on an α-hemolysin nanopore array platform. We designed and synthesized several polymer-tagged nucleotides using tags that produce different electrical current blockade levels and verified they are active substrates for DNA polymerase. A highly processive DNA polymerase was conjugated to the nanopore, and the conjugates were complexed with primer/template DNA and inserted into lipid bilayers over individually addressable electrodes of the nanopore chip. When an incoming complementary-tagged nucleotide forms a tight ternary complex with the primer/template and polymerase, the tag enters the pore, and the current blockade level is measured. The levels displayed by the four nucleotides tagged with four different polymers captured in the nanopore in such ternary complexes were clearly distinguishable and sequence-specific, enabling continuous sequence determination during the polymerase reaction. Thus, real-time single-molecule electronic DNA sequencing data with single-base resolution were obtained. The use of these polymer-tagged nucleotides, combined with polymerase tethering to nanopores and multiplexed nanopore sensors, should lead to new high-throughput sequencing methods.