gebhart/patrepeval huggingface dataset:
Delta-like 4 is indispensable in thymic environment specific for T cell development (2008)

The thymic microenvironment is required for T cell development in vivo. However, in vitro studies have shown that when hematopoietic progenitors acquire Notch signaling via Delta-like (Dll)1 or Dll4, they differentiate into the T cell lineage in the absence of a thymic microenvironment. It is not clear, however, whether the thymus supports T cell development specifically by providing Notch signaling. To address this issue, we generated mice with a loxP-flanked allele of Dll4 and induced gene deletion specifically in thymic epithelial cells (TECs). In the thymus of mutant mice, the expression of Dll4 was abrogated on the epithelium, and the proportion of hematopoietic cells bearing the intracellular fragment of Notch1 (ICN1) was markedly decreased. Corresponding to this, CD4 CD8 double-positive or single-positive T cells were not detected in the thymus. Further analysis showed that the double-negative cell fraction was lacking T cell progenitors. The enforced expression of ICN1 in hematopoietic progenitors restored thymic T cell differentiation, even when the TECs were deficient in Dll4. These results indicate that the thymus-specific environment for determining T cell fate indispensably requires Dll4 expression to induce Notch signaling in the thymic immigrant cells.
Membrane sialoglycolipids regulate the activation of alternative complement pathway by liposomes containing trinitrophenylaminocaproyldipalmitoylphosphatidylethaolamine. (1983)

We found that liposomes associated with trinitrophenylaminocaproyldipalmitoylphosphatidylethanolamine (TNP-Cap-DDPE) activate the alternative complement pathway (ACP) of guinea-pig. The complement-activating capacity (CAC) of liposomes with TNP-Cap-DPPE (TNP-Cap-liposomes) was found to be inhibited by the insertion of sialoglycolipids such as GM3 onto the membrane. However, neutral glycolipids tested had no inhibitory effect on the CAC of the TNP-Cap-liposomes. The minimum amount of sialoglycolipids required for the inhibition of the ACP-activating capacity of TNP-Cap-liposomes was 0.01 or less in molar ratio to dimyristoylphosphatidylcholine in the liposomes. Since the insertion of charged amphiphiles did not affect the status of TNP-Cap-liposomes containing glycolipids with respect to their ACP-activating capacity, the surface potential caused by sialoglycolipids was disregarded as being the factor responsible for restriction of the complement-activating effect. For the inhibitory effect to be manifested, it was demonstrated that the presence of GM3 was required on the same liposome membrane as where the TNP-Cap-triggered ACP activation is taking place. Therefore, sialoglycolipids may inhibit ACP activation by reacting directly on certain nascently activated complement proteins. However, insertion of GM3 could not inhibit liposome lysis via the classical complement pathway. Furthermore, the presence of antibody reaction significantly reduced the inhibitory capacity of GM3 indicating that natural antibody may be responsible for discriminating between self and heterologous surfaces, thus cancelling the glycolipid-mediated restriction of ACP activation in the case of heterologous cell surface, bringing about lysis by the cancellation of the glycolipid-mediated restriction of ACP activation on heterologous cell surfaces.
Kotai Antibody Builder: automated high-resolution structural modeling of antibodies (2014)

standley@ifrec.osaka-u.ac.jp.
Experimental study of the characteristics of top-loaded microstrip monopoles (1983)

The characteristics of microstrip monopoles fed at the center with antiphase currents are investigated experimentally. First the impedance is measured as a function of frequency. It is found that the radiation resistance at the resonance near <tex xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">L \simeq 05 \lambda</tex> , is very low while the radiation resistance at the resonance near <tex xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">L \simeq \lambda</tex> is very high. For a given physical length of the monopole, the resonant frequency is dependent on the strip width and the substrate thickness. The effect of substrate thickness and strip width on the input impedance and bandwidth has also been studied. Finally the <tex xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">E</tex> -plane radiation pattern is found to contain two maxima, occurring at approximately <tex xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">\pm 40\deg</tex> from broadside.
Syntrophin binds to an alternatively spliced exon of dystrophin. (1995)

Dystrophin, the protein product of the Duchenne muscular dystrophy locus, is a protein of the membrane cytoskeleton that associates with a complex of integral and membrane-associated proteins. Of these, the 58-kD intracellular membrane-associated protein, syntrophin, was recently shown to consist of a family of three related but distinct genes. We expressed the cDNA of human beta 1-syntrophin and the COOH terminus of human dystrophin in reticulocyte lysates using an in vitro transcription/translation system. Using antibodies to dystrophin we immunoprecipitated these two interacting proteins in a variety of salt and detergent conditions. We demonstrate that the 53 amino acids encoded on exon 74 of dystrophin, an alternatively spliced exon, are necessary and sufficient for interaction with translated beta 1-syntrophin in our assay. On the basis of its alternative splicing, dystrophin may thus be present in two functionally distinct populations. In this recombinant expression system, the dystrophin relatives, human dystrophin related protein (DRP or utrophin) and the 87K postsynaptic protein from Torpedo electric organ, also bind to translated beta 1-syntrophin. We have found a COOH-terminal 37-kD fragment of beta 1-syntrophin sufficient to interact with translated dystrophin and its homologues, suggesting that the dystrophin binding site on beta 1-syntrophin occurs on a region that is conserved among the three syntrophin homologues.
Concave diffraction gratings fabricated with planar lithography (2008)

This paper reports on the development and validation of a new technology for the fabrication of variable line-spacing non-planar diffraction gratings to be used in compact spectrometers. The technique is based on the standard lithographic process commonly used for pattern transfer onto a flat substrate. The essence of the technology presented here is the lithographic fabrication of a planar grating structure on top of a flexible membrane on a glass or silicon wafer and the subsequent deformation of the membrane using a master shape. For the validation of the proposed technology we fabricated several reflection concave diffraction gratings with the f-numbers varying from 2 to 3.8 and a diameter in the 4 - 7 mm range. A glass wafer with circular holes was laminated by dry-film resist to form the membranes. Subsequently, standard planar lithography was applied to the top part of the membranes for realizing grating structures. Finally the membranes were deformed using plano-convex lenses in such a way that precise lens alignment is not required. A permanent non-planar structure remains after curing. The imaging properties of the fabricated gratings were tested in a three-component spectrograph setup in which the cleaved tip of an optical fiber served as an input slit and a CCD camera was used as a detector. This simple spectrograph demonstrated subnanometer spectral resolution in the 580 - 720 nm range.
Classification of Sensitivity or Resistance of Cervical Cancers to Ionizing Radiation According to Expression Profiles of 62 Genes Selected by cDNA Microarray Analysis (2002)

To identify a set of genes related to radiosensitivity of cervical squamous cell carcinomas and to establish a predictive method, we compared expression profiles of 9 radiosensitive and 10 radioresistant tumors obtained by biopsy before treatment, on a cDNA microarray consisting of 23,040 human genes. We identified 121 genes whose expression was significantly greater in radiosensitive cells than in radioresistant cells, and 50 genes that showed higher levels of expression in radioresistant cells than in radiosensitive cells. Some of these genes had already known to be associated with the radiation response, such as aldehyde dehydrogenase 1 (ALDH1) and X-ray repair cross-complementing 5 (XRCC5) (P<.05, Mann-Whitney test). The validity of the total of 171 genes as radiosensitivity related genes were certified by permutation test (P<.05). Furthermore, we selected 62 genes on the basis of a clustering analysis, and confirmed the validity of these genes with cross-validation test. The cross-validation test also indicates the possibility of making prediction of radiosensitivity for discriminating radiation-sensitive from radiation resistant biopsy samples by predicting score (PS) values calculated from expression values of 62 genes in 19 samples, because the prediction successfully and unequivocally discriminated the radiosensitive phenotype from the radioresistant phenotype in our test panel of 19 cervical carcinomas. The extensive list of genes identified in these experiments provides a large body of potentially valuable information for studying the mechanism(s) of radiosensitivity, and selected 62 genes opens the possibility of providing appropriate and effective radiotherapy to cancer patients.
CFW: A Collaborative Filtering System Using Posteriors Over Weights Of Evidence (2012)

We describe CFW, a computationally efficient algorithm for collaborative filtering that uses posteriors over weights of evidence. In experiments on real data, we show that this method predicts as well or better than other methods in situations where the size of the user query is small. The new approach works particularly well when the user s query CONTAINS low frequency(unpopular) items.The approach complements that OF dependency networks which perform well WHEN the size OF the query IS large.Also IN this paper, we argue that the USE OF posteriors OVER weights OF evidence IS a natural way TO recommend similar items collaborative - filtering task.
Polycrystalline Graphene Ribbons as Chemiresistors (2011)

Polycrystalline graphene sensors easily obtained through chemical vapor deposition (CVD) have been developed for chemical sensing. We show that linear defects or continuous lines of point defects on these sensors result in significantly higher sensitivity than that of pristine graphene and carbon nanotube film sensors. Further sensitivity enhancement is obtained by cutting the graphene into ribbons of width comparable to the linear defect dimensions (micrometers).
Factors Influencing the Luminescence Quantum Efficiency of Nanocrystalline ZnS:Mn2+ (2001)

The influence of the Mn2+ concentration, the nature of the passivating polymer and UV irradiation on the luminescence efficiency of nanocrystalline ZnS:Mn2+ is investigated. With increasing Mn2+ concentration the quantum efficiency increases, until it reaches a stable value. No drastic decrease in quantum efficiency is observed at high Mn2+ concentrations, as was found earlier for both bulk and nanocrystalline ZnS:Mn2+. By altering the passivating polymer many other factors influencing the quantum efficiency are changed, such as the particle diameter and Mn content. This makes it hard to study the influence of the passivating behaviour of the various polymers on the quantum efficiency. The UV enhancement of the quantum efficiency of the various samples could be explained by two mechanisms: UV curing of the passivating polymer and passivation by a photo-oxidation of the surface of the nanoparticles during the irradiation. The highest quantum efficiency obtained was about 15%.
HYPOGLYCEMIA IN PATIENTS WITH RENAL FAILURE (2000)

Of a total of 1545 admissions of end stage renal failure (ESRD) patients, fifty-six (3.6%) were admitted during a ten-year period with hypoglycemia. Thirty-eight of them were diabetic while the others were non-diabetic patients. The most common etiology found to be drug-induced hypoglycemia in 26 (46%) patients. In 22 (39%) cases, sepsis was the contributing cause of hypoglycemia. Severe malnutrition caused 7% of hypoglycemic episodes. Of the patients, 18 (32%) with ESRD eventually died, none of them were from the drug induced group. However, mortality rate in the sepsis induced hypoglycemia group was 66%, and of the malnutrition group 17% of the deaths. Thus, hypoglycemia is frequent in ESRD patients, and is fatal if associated with either sepsis or malnutrition.
Affine differential geometry analysis of human arm movements (2007)

Humans interact with their environment through sensory information and motor actions. These interactions may be understood via the underlying geometry of both perception and action. While the motor space is typically considered by default to be Euclidean, persistent behavioral observations point to a different underlying geometric structure. These observed regularities include the "two-thirds power law", which connects path curvature with velocity, and "local isochrony", which prescribes the relation between movement time and its extent. Starting with these empirical observations, we have developed a mathematical framework based on differential geometry, Lie group theory and Cartan's moving frame method for the analysis of human hand trajectories. We also use this method to identify possible motion primitives, i.e., elementary building blocks from which more complicated movements are constructed. We show that a natural geometric description of continuous repetitive hand trajectories is not Euclidean but equi-affine. Specifically, equi-affine velocity is piecewise constant along movement segments, and movement execution time for a given segment is proportional to its equi-affine arc-length. Using this mathematical framework, we then analyze experimentally recorded drawing movements. To examine movement segmentation and classification, the two fundamental equi-affine differential invariants-equi-affine arc-length and curvature are calculated for the recorded movements. We also discuss the possible role of conic sections, i.e., curves with constant equi-affine curvature, as motor primitives and focus in more detail on parabolas, the equi-affine geodesics. Finally, we explore possible schemes for the internal neural coding of motor commands by showing that the equi-affine framework is compatible with the common model of population coding of the hand velocity vector when combined with a simple assumption on its dynamics. We then discuss several alternative explanations for the role that the equi-affine metric may play in internal representations of motion perception and production.
Self-Assembling Amphiphilic Siderophores from Marine Bacteria (2000)

Most aerobic bacteria secrete siderophores to facilitate iron acquisition. Two families of siderophores were isolated from strains belonging to two different genera of marine bacteria. The aquachelins, from Halomonas aquamarina strain DS40M3, and the marinobactins, from Marinobacter sp. strains DS40M6 and DS40M8, each contain a unique peptidic head group that coordinates iron(III) and an appendage of one of a series of fatty acid moieties. These siderophores have low critical micelle concentrations (CMCs). In the absence of iron, the marinobactins are present as micelles at concentrations exceeding their CMC; upon addition of iron(III), the micelles undergo a spontaneous phase change to form vesicles. These observations suggest that unique iron acquisition mechanisms may have evolved in marine bacteria.
Wireless polar receiver using two injection-locked oscillator stages for green radios (2011)

Direct-conversion receiver is the most prevalent receiver architecture today for wireless communications. However, it requires coherent demodulation using the phase-locked loop (PLL)-based carrier recovery techniques, which increases circuit complexity and power consumption of the receiver. This paper presents a novel polar receiver that utilizes two injection-locked oscillators (ILO) stages to extract the modulation envelope and phase components from a received non-constant envelope modulation signal without using carrier recovery circuitry. The implemented prototype can perform π/4 DQPSK and QPSK demodulation with error vector magnitudes (EVM) of 7.5% and 8.2%, respectively, both at 2 Msps and a received power of -40 dBm. Owing to its simplicity, the proposed receiver has great potential as an energy-efficient architecture with low cost for green radio applications.
The tagGH operon of Bacillus subtilis 168 encodes a two‐component ABC transporter involved in the metabolism of two wall teichoic acids (1995)

We report the nucleotide sequence and the characterization of the Bacillus subtilis tagGH operon. The latter is controlled by a sigma A-dependent promoter and situated in the 308 degrees chromosomal region which contains genes involved in teichoic acid biosynthesis. TagG is a hydrophobic 32.2 kDa protein which resembles integral membrane proteins belonging to polymer-export systems of Gram-negative bacteria. Gene tagH encodes a 59.9 kDa protein whose N-moiety contains the ATP-binding motif and shares extensive homology with a number of ATP-binding proteins, particularly with those associated with the transport of capsular polysaccharides and O-antigens. That the tagGH operon is essential for cell growth was established by the failure to inactivate tagG and the 5'-moiety of tagH by insertional mutagenesis. During limited tagGH expression, cells exhibited a cocoid morphology while their walls contained reduced amounts of phosphate as well as galactosamine. These observations, revealing impaired metabolism of both wall teichoic acids of B. subtilis 168, i.e. poly(glycerol phosphate), and poly(glucose galactosamine phosphate), combined with sequence homologies, suggest that TagG and TagH are involved in the translocation through the cytoplasmic membrane of the latter teichoic acids or their precursors.
Further Approaches for Optimizing Polysaccharide-Protein Conjugate Vaccines for Prevention of Invasive Bacterial Disease (1992)

The design of conjugate vaccines to optimize their immunologic performance has not been studied extensively. Immunologic performance in relation to changing specific structural parameters in a conjugate can most effectively be analyzed using conjugate syntheses involving terminally activated polysaccharide fragments. Random activation of fragments before conjugation results in more complex and poorly defined conjugates. This is especially true when the length of polysaccharide fragments in polysaccharide-protein conjugates is varied. Both the antigenicity and immunogenicity of saccharide fragments are length-dependent, and antigenicity traditionally has been associated with oligosaccharide epitopes no larger than an antibody site. However, the recent identification of length-stabilized conformational saccharide epitopes has added a new dimension to this concept. The immunologic performance of polysaccharide-protein conjugates is also length-dependent, probably requiring multiple epitopes for optimization.
Retrovirus activation in embryonal carcinoma cells by cellular promoters. (1989)

Retrovirus expression in embryonal carcinoma (EC) cells is blocked at a postintegration stage of the viral life cycle, because of the inadequate function of the viral long terminal repeat (LTR) promoter in this cell type. However, rare sites in the EC cell genome permit provirus expression by undefined mechanisms. Our analysis of three expressed proviruses indicates that they have inserted into actively transcribed regions. Two of the three, examined in detail, integrated into the first introns of cellular transcription units in close proximity to active cellular promoters. One of these cellular genes is the probable murine homolog of the yeast ribosomal protein L3, responsible for trichodermin resistance. In all cases, virus activation appears to involve production of viral transcripts that are initiated in the 5'-flanking region, transcribed through the viral LTR, and subsequently spliced from a cellular donor to a viral acceptor. Our results suggest a general procedure for the isolation of active genes and promoters in different tissues.
A phase I trial of an interleukin‐12/23 monoclonal antibody in relapsing multiple sclerosis (2006)

Single subcutaneous administrations of IL-12/23 mAb in this first study of relapsing MS were generally well tolerated. Safety of the agent will need to be tested in a study of longer duration and involving a larger cohort of subjects.
Abnormal plant development and down-regulation of phenylpropanoid biosynthesis in transgenic tobacco containing a heterologous phenylalanine ammonia-lyase gene. (1990)

Biosynthesis of phenylpropanoid natural products in tobacco was perturbed by introduction of a heterologous (bean) phenylalanine ammonia-lyase (PAL; L-phenylalanine ammonia-lyase, EC 4.3.1.5) gene, modified by inclusion of cauliflower mosaic virus 35S enhancer sequences in its promoter. These transgenic plants can exhibit a series of unusual phenotypes including localized fluorescent lesions, altered leaf shape and texture, reduced signification in xylem, stunted growth, reduced pollen viability, and altered flower morphology and pigmentation. Genetic analysis of a transformant with severe symptoms showed that symptom development was inherited as a single, partially dominant trait and cosegregated with reduced levels of PAL activity and soluble phenylpropanoid products. Accumulation of transcripts encoded by the endogenous tobacco PAL genes was suppressed. We conclude that the transgene disrupts PAL regulation and that some of the phenotypes reflect interference with putative signals dependent on phenylpropanoid biosynthesis.
Partnership Selection Involving Mixed Types of Uncertain Preferences (2013)

Partnership selection is an important issue in management science. This study proposes a general model based on mixed integer programming and goal-programming analytic hierarchy process (GP-AHP) to solve partnership selection problems involving mixed types of uncertain or inconsistent preferences. The proposed approach is designed to deal with crisp, interval, step, fuzzy, or mixed comparison preferences, derive crisp priorities, and improve multiple solution problems. The degree of fulfillment of a decision maker’s preferences is also taken into account. The results show that the proposed approach keeps more solution ratios within the given preferred intervals and yields less deviation. In addition, the proposed approach can treat incomplete preference matrices with flexibility in reducing the number of pairwise comparisons required and can also be conveniently developed into a decision support system.
NLP Applications Based on Weighted Multi-Tape Automata (2004)

This article describes two practical applications of weighted multi-tape automata (WMTAs) in Natural Language Processing, that demonstrate the augmented descriptive power of WMTAs compared to weighted 1-tape and 2-tape automata. The two examples concern the preservation of intermediate results in transduction cascades and the search for similar words in two languages. As a basis for these applications, the article proposes a number of operations on WMTAs. Among others, it (re-)defines multi-tape intersection, where a number of tapes of one WMTA are intersected with the same number of tapes of another WMTA. In the proposed approach, multi-tape intersection is not an atomic operation but rather a sequence of more elementary ones, which facilitates its implementation.