gebhart/patrepeval huggingface dataset:
Construction of a Genetic Linkage Map of the Model Legume Lotus japonicus Using an Intraspecific F2 Population (2001)

Among leguminous plants, the model legume Lotus japonicus (Regel) Larsen has many biological and genetic advantages. We have developed a genetic linkage map of L. japonicus based on amplified fragment length polymorphism (AFLP), simple sequence repeat polymorphism (SSRP) and derived cleaved amplified polymorphic sequence (dCAPS). The F2 mapping population used was derived from a cross between two L. japonicus accessions Gifu B-129 and Miyakojima MG-20. These parental accessions showed remarkable cytological differences, particularly with respect to size and morphology of chromosomes 1 and 2. Using fluorescence in situ hybridization (FISH) with BAC clones from Gifu B-129 and TAC (Transformation-competent Artificial Chromosome) clones from Miyakojima MG-20, a reciprocal translocation was found to be responsible for the cytological differences between chromosomes 1 and 2. The borders of the translocations were identified by FISH and by alignment toward the L. filicaulis x L. japonicus Gifu B-129 linkage map. The markers from the main translocated region were located on linkage groups 1 and 2 of the two accessions, Gifu B-129 and Miyakojima MG-20, respectively. The framework of the linkage map was constructed based on codominant markers, and then dominant markers were integrated separately in each linkage group of the parents. The resulting linkage groups correspond to the six pairs of chromosomes of L. japonicus and consist of 287 markers with 487.3 cM length in Gifu B-129 and 277 markers with 481.6 cM length in Miyakojima MG-20. The map and marker information is available through the World Wide Web at http://www.kazusa.or.jp/lotus/.
Adrenal medulla imaging agents: a structure-distribution relationship study of radiolabeled aralkylguanidines (1984)

Fourteen 125I-labeled aralkylguanidines were synthesized and evaluated as potential imaging agents for the adrenal medullae and tumors of adrenomedullary origin. These guanidines are radiotracer analogues of guanethidine, an antihypertensive agent thought to mediate neuron blockade by uptake into adrenergic nerves. Dog adrenal medullae were used as a model to test radiotracer affinity for catecholamine storage tissue. Tissue distribution studies revealed that a number of radioiodinated guanidines showed pronounced localization in the adrenal medullae following intravenous injection, in certain cases exceeding that of either (-)-[3H]norepinephrine or [14C]guanethidine. (m-[125I]Iodobenzyl)guanidine (m-IBG, 2b) gave the best combination of high concentration and selectivity. The low adrenomedullary affinity observed with [14C]guanidine and m-[125I]iodobenzylamine demonstrates the uniqueness of the aralkylguanidine structure. Preliminary evidence suggests that 2b is a storage analogue of norepinephrine. [125I]2a is now being used clinically in imaging and radiotherapy of catecholamine tumors, such as pheochromocytoma.
Paraconiothyrium, a new genus to accommodate the mycoparasite Coniothyrium minitans, anamorphs of Paraphaeosphaeria, and four new species (2004)

Coniothyrium-like coelomycetes are drawing attention as biological control agents, potential bioremediators, and producers of antibiotics. Four genera are currently used to classify such anamorphs, namely, Coniothyrium, Microsphaeropsis, Cyclothyrium, and Cytoplea. The morphological plasticity of these fungi, however, makes it difficult to ascertain their best generic disposition in many cases. A new genus, Paraconiothyrium is here proposed to accommodate four new species, P. estuarinum, P. brasiliense, P. cyclothyrioides, and P. fungicola. Their formal descriptions are based on anamorphic characters as seen in vitro. The teleomorphs of these species are unknown, but maximum parsimony analysis of ITS and partial SSU nrDNA sequences showed that they belong in the Pleosporales and group in a clade including Paraphaeosphaeria s. str., the biocontrol agent Coniothyrium minitans, and the ubiquitous soil fungus Coniothyrium sporulosum. Coniothyrium minitans and C. sporulosum are therefore also combined into the genus Paraconiothyrium. The anamorphs of Paraphaeosphaeria michotii and Paraphaeosphaeria pilleata are regarded representative of Paraconiothyrium, but remain formally unnamed. Paraconiothyrium species are phylogenetically distant from typical members of the other coelomycete genera mentioned above
Ether Sulfones with Additives as Electrolytes for Applications in Rechargeable Lithium Ion Batteries (2008)

Abstract not Available.
Fully automatic left ventricular boundary extraction in echocardiographic images (2002)

Describes a fully automatic, radial search based LV boundary extraction algorithm for echocardiographic images. Neural network classifiers are used with new input feature vectors to detect the LV centre and LV edge points. The centre detection stage combines these neural classifiers with knowledge based techniques to refine the centre estimate. Knowledge guided snakes are developed to extract the epicardial and endocardial boundaries by linking candidate edge points. The snakes' energy functions are minimised using a new two stage dynamic programming method, which is several times faster than the existing method. Knowledge is used to guide the snakes through the edge points improving their accuracy and robustness.
12× pulse compression using optical fibers (1983)

We report a factor of 12 compression of the 5.4-ps, 1-kW pulses from a mode-locked dye laser. The pulses were frequency broadened and linearly chirped by the combined action of self-phase modulation and group velocity dispersion during passage through a 30-m single-mode optical fiber. The fiber output pulses were then compressed to 450-fs, 3-kW pulses by passage through a diffraction grating based dispersive delay line. These short pulses were tunable over the 300-Å range of the laser dye.
The Addition of Epinephrine to Tetracaine Injected Intrathecally Sustains an Increase in Glutamate Concentrations in the Cerebrospinal Fluid and Worsens Neuronal Injury (2001)

Sustained increase of glutamate concentrations produced by the addition of epinephrine to intrathecal tetracaine can cause neuronal injury.
Let Visuals Tell the Story: Medication Adherence in Patients with Type II Diabetes Captured by a Novel Ingestion Sensor Platform (2015)

Visualizations integrating medication ingestion and physiological data from the DHFS over varying time intervals captured detailed individual longitudinal patterns of medication adherence and self-management in the natural setting. Visualizing multiple data streams simultaneously, providing a data-rich representation, revealed information that would not have been shown by plotting data streams individually. Such analyses provided data far beyond traditional adherence summary statistics and may form the foundation of future personalized predictive interventions to drive longitudinal adherence and support optimal self-management in chronic diseases such as diabetes.
Families of zinc metalloproteases (1994)

A scheme based on the zinc binding site [1992, FEBS Lett. 312, 110-114] has been extended to classify zinc metalloproteases into distinct families. The gluzincins, defined by the HEXXH motif and a glutamic acid as the third zinc ligand, include the thermolysin, endopeptidase-24.11, aminopeptidase, angiotensin converting enzyme, endopeptidase-24.15, and tetanus and botulinum neurotoxin families. The metzincins, defined by the HEXXH motif, a histidine as the third zinc ligand and a Met-turn, include the astacin, serralysin, reprolysin and matrixin families. The inverted zincin motif, HXXEH, defines the inverzincin family of insulin-degrading enzymes, the HXXE motif defines the carboxypeptidase family, and the HXH motif DD-carboxypeptidase.
Stem cell conditioned medium improves acute lung injury in mice: in vivo evidence for stem cell paracrine action (2012)

Mortality and morbidity of acute lung injury and acute respiratory distress syndrome remain high because of the lack of pharmacological therapies to prevent injury or promote repair. Mesenchymal stem cells (MSCs) prevent lung injury in various experimental models, despite a low proportion of donor-derived cell engraftment, suggesting that MSCs exert their beneficial effects via paracrine mechanisms. We hypothesized that soluble factors secreted by MSCs promote the resolution of lung injury in part by modulating alveolar macrophage (AM) function. We tested the therapeutic effect of MSC-derived conditioned medium (CdM) compared with whole MSCs, lung fibroblasts, and fibroblast-CdM. Intratracheal MSCs and MSC-CdM significantly attenuated lipopolysaccharide (LPS)-induced lung neutrophil influx, lung edema, and lung injury as assessed by an established lung injury score. MSC-CdM increased arginase-1 activity and Ym1 expression in LPS-exposed AMs. In vivo, AMs from LPS-MSC and LPS-MSC CdM lungs had enhanced expression of Ym1 and decreased expression of inducible nitric oxide synthase compared with untreated LPS mice. This suggests that MSC-CdM promotes alternative macrophage activation to an M2 "healer" phenotype. Comparative multiplex analysis of MSC- and fibroblast-CdM demonstrated that MSC-CdM contained several factors that may confer therapeutic benefit, including insulin-like growth factor I (IGF-I). Recombinant IGF-I partially reproduced the lung protective effect of MSC-CdM. In summary, MSCs act through a paracrine activity. MSC-CdM promotes the resolution of LPS-induced lung injury by attenuating lung inflammation and promoting a wound healing/anti-inflammatory M2 macrophage phenotype in part via IGF-I.
Thermal and Hydraulic Design and Characterization of a Liquid-Cooled 3D Silicon Module (2008)

Thermal management in 3D packaging is a critical factor to be considered in enabling this technology to be exploited further. Heat density in excess of 100 W/cm <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> can be achieved due to the smaller footprint of such packages. Liquid cooling through microchannels embedded within the package had been shown to improve the thermal characteristics of packages. In this work, a liquid cooling solution is designed with emphasis on the flow distribution through the microchannels. The use of a reducing plenum design had been shown to lower the pressure drop requirement while improving the thermal characteristics. The thermal implication with achieving deep channels through the DRIE process is an introduction of a significant thermal resistance to the overall thermal network. Numerical modeling of the actual physical components in the cooling module had also being done to evaluate the system operating points and hence sizing the pump. The approach taken in this work identified the issues faced when embedding heat transfer features within the package and in a cooling solution. The system modeling had also been shown to provide a good estimate of the operating conditions within the physical module.
IL-1 Receptor-Associated Kinase Modulates Host Responsiveness to Endotoxin (2000)

Endotoxin triggers many of the inflammatory, hemodynamic, and hematological derangements of Gram-negative septic shock. Recent genetic studies in mice have identified the Toll-like receptor 4 as the transmembrane endotoxin signal transducer. The IL-1 intracellular signaling pathway has been implicated in Toll-like receptor signal transduction. LPS-induced activation of the IL-1 receptor-associated kinase (IRAK), and the influence of IRAK on intracellular signaling and cellular responses to endotoxin has not been explored in relevant innate immune cells. We demonstrate that LPS activates IRAK in murine macrophages. IRAK-deficient macrophages, in contrast, are resistant to LPS. Deletion of IRAK disrupts several endotoxin-triggered signaling cascades. Furthermore, macrophages lacking IRAK exhibit impaired LPS-stimulated TNF-alpha production, and IRAK-deficient mice withstand the lethal effects of LPS. These findings, coupled with the critical role for IRAK in IL-1 and IL-18 signal transduction, demonstrate the importance of this kinase and the IL-1/Toll signaling cassette in sensing and responding to Gram-negative infection.
Plasma vitamin D-binding protein (Gc-globulin): Multiple tasks (1995)

The transporter of vitamin D and its metabolites in blood has received increasing attention in recent years, and is recognized to be a member of a gene family that includes albumin and alpha-fetoprotein. Identical to the group specific component (Gc-globulin) of serum, the protein is a single-chain polypeptide constitutively synthesized in liver that circulates in amounts in far excess of normal vitamin D metabolite concentrations in blood. It plays the major role in the egress of endogenously synthesized vitamin D, from skin and appears to restrain D-sterols from too rapid/excessive cell entry. Along with plasma gelsolin, it comprises the plasma actin-scavenger system that facilitates removal of actin, liberated from lysed cells, by depolymerization and prevention of polymerization. Recently, the protein has been shown to behave as a co-chemotaxin specific for the complement peptide C5a, and its sialic acid-free form has been reported to play a role in macrophage activation. The latter functions strongly implicate its participation in inflammation responses. A unifying hypothesis might also suggest the protein to provide focal D-sterol delivery to cells that are important to the resolution of tissue injuries.
An optical method for measurement of dioxygen concentration based upon quenching of phosphorescence. (1987)

An optical method for measuring oxygen concentrations in aqueous solutions is described. This method is based upon the oxygen-dependent quenching of phosphorescence. Phosphorescence excitation and emission spectra and lifetimes of some of the probe molecules suitable for measurement of oxygen in aqueous solutions are given. The probes include fluorescein derivatives, 4'5'-diiodofluorescein, eosin Y, 5(and 6)-carboxyeosin, erythrosin, and 5(and 6)-carboxyerythrosin as well as the Zn(II), Y(III), Sn(IV), Lu(III), and Pd(II) derivatives of meso-tetra-(4-sulfonatophenyl)-porphine, meso-tetra-(N-methyl-4-pyridyl)-porphine and coproporphyrin. The phosphorescence lifetimes of the given probes were found to depend upon the oxygen concentration by a simple Stern-Volmer relationship with a quenching constant of approximately 10(9) M-1 S-1. Binding of the molecules to bovine serum albumin decreased the quenching constant for oxygen by approximately an order of magnitude and also inhibited probe self-quenching, indicating that at the protein binding site the probes are somewhat protected from collision with quenchers. The use of this optical method for measuring oxygen is demonstrated for reactions catalyzed by glucose oxidase and by cytochrome c oxidase. It is shown that, using this method oxygen concentrations can be measured from approximately 250 microM (air saturation) down to the nanomolar range.
Potential and role of a prototype amorphous silicon array electronic portal imaging device in breathing synchronized radiotherapy (1999)

Current electronic portal imaging devices (EPID) are limited in their ability to provide direct and quick verification and monitoring of patients during both setup and treatment of breathing synchronized radiotherapy (BSRT, including breathing gated, voluntary and forced breath-hold radiotherapy treatment.) These limitations are largely due to their slow image capture rate and poor image quality. An amorphous silicon array flat panel electronic portal imaging device (si-EPID) is emerging to meet the challenge. The purpose of this study is threefold: (1) to characterize the performance of a prototype si-EPID; (2) to compare image quality against that of digitized films; and (3) to evaluate the device in terms of verification of patient setup and monitoring during BSRT. In this study a Varian prototype si-EPID detector array and Clinic accelerator at the University of California Davis Cancer Center were used for imaging. Three quality assurance phantoms: a Lutz PVC phantom, a modified "Las Vegas" phantom, and a RMI model 1151 phantom, were used to characterize the imaging system. A Rando head phantom was used for anthropomorphic imaging tests. Images were obtained with the si-EPID and a Fuji RX film in a Kodak X-Omatic cassette. To investigate the clinical application, two sets of si-EPID images were collected from a lung cancer patient during a 22 s breath-hold and normal breathing. The quality of images obtained with the fast mode was found to be comparable to that obtained with the digitized films. The images with the standard mode were found to be better than the digitized film images. With this prototype si-EPID, it is possible to collect the images at the beginning, middle, and end of each breath-hold for those patients who can hold their breath for longer than 15 s. The si-EPID images can provide a quick verification of the initial patient setup and subsequent treatment position throughout the daily fractionation.
Active music therapy and Parkinson's disease: methods. (1998)

Music therapy (MT) is an unconventional, multisensorial therapy poorly assessed in medical care but widely used to different ends in a variety of settings. MT has two branches: active and passive. In active MT the utilisation of instruments is structured to correspond to all sensory organs so as to obtain suitable motor and emotional responses. We conducted a prospective study to evaluate the effects of MT in the neurorehabilitation of patients with Parkinson's Disease (PD), a common degenerative disorder involving movement and emotional impairment. Sixteen PD patients took part in 13 weekly sessions of MT each lasting 2 hours. At the beginning and at the end of the session, every 2 weeks, the patients were evaluated by a neurologist, who assessed PD severity with UPDRS, emotional functions with Happiness Measures (HM) and quality of life using the Parkinson's Disease Quality of Life Questionnaire (PDQL). After every session a significant improvement in motor function, particularly in relation to hypokinesia, was observed both in the overall and in the pre-post session evaluations. HM, UPDRS-ADL and PDQL changes confirmed an improving effect of MT on emotional functions, activities of daily living and quality of life. In conclusion, active MT, operating at a multisensorial level, stimulates motor, affective and behavioural functions. Finally, we propose active MT as new method to include in PD rehabilitation programmes. This article describes the methods adopted during MT sessions with PD patients.
Iron Induced Oxidative Damage As a Potential Factor in Age-Related Macular Degeneration: The Cogan Lecture (2006)

Iron is a potent generator of oxidative damage whose levels increase with age, potentially exacerbating age-related diseases. Several lines of evidence suggest that iron accumulation may be a factor in age-related macular degeneration (AMD). AMD retinas have more iron within the photoreceptors, RPE, and drusen than do age-matched control retinas. Accelerated AMD-like maculopathy develops in patients with retinal iron overload from the hereditary disease aceruloplasminemia. Mice with retinal iron overload resulting from knockout of ceruloplasmin and its homologue hephaestin exhibit retinal degeneration with some features of AMD, including subretinal neovascularization, accumulation of RPE lipofuscin and sub-RPE deposits, and RPE/photoreceptor death. Increased understanding of the mechanisms of retinal iron homeostasis may help in the development of therapies to prevent iron overload. For example, herein it is shown that one regulator of systemic iron homeostasis, HFE, is expressed in the RPE. Thus, patients with the common disease hereditary hemochromatosis, which is often caused by an HFE mutation, may have retinal iron overload predisposing to AMD. Preliminary data suggest that iron chelation can reduce RPE iron overload in mice and protect them from degeneration, suggesting that iron-binding drugs may one day prove useful in reducing RPE oxidative stress and decreasing the risk of AMD progression.
Developing and deploying corporate cryptographic systems (1995)

The MITRE Corporation has developed a number of cryptographic systems that provide security-related capabilities for its growing electronic information environment. These cryptographic systems were developed using commercial off-the-shelf products and widely accepted standards. Standards were adhered to in order to assure interoperability with emerging products such as those used to conduct electronic commerce on the Internet. However, there are many shortcomings within the marketplace and the Internet community that are limiting the extent to which interoperability can be achieved. Products are not as open as we need them to be, infrastructures are not in place, and standards are still evolving. This paper presents many of the issues with which we are faced and, in some cases, provides solutions. MITRE's needs are not unique. They are the needs of any enterprise wishing to provide an integrated security solution for the access and exchange of valuable electronic information.

This paper first introduces The MITRE Corporation and describes its corporate cryptographic systems and information infrastructure. The paper then discusses issues associated with integrating MITRE's cryptographic systems with emerging electronic commerce products both for use within the corporation and for conducting electronic commerce externally. The paper concludes with recommendations and lends some insight into where The MITRE Corporation is headed in terms of its corporate cryptographic systems and electronic commerce.
Application of Arrhenius kinetic theory to viral eclipse: selection of bacteriophage phi X174 mutants (1981)

Analysis of the bacteriophage phi X174 eclipse period in terms of Arrhenius kinetic theory suggests the following hypothesis: mutants should exist with two concomitant physiological characteristics as their phenotype. These are an eclipse rate lower than that of the wild type at permissive temperatures for plaque formation and an eclipse rate too low at lower temperatures to permit plaque development. Thus, enrichment of a mutagenized virus population for mutants that fail to eclipse during a short period at permissive temperatures should yield eclipse mutants with the cold-sensitive (cs; nonpermissive temperature, 25 degrees C), and not the temperature-sensitive (ts; nonpermissive temperature, 42 degrees C), plaque phenotype. In several trials, the frequency of the cs phenotype in the population increased from less than 0.2% to between 2 and 4% after the enrichment step, whereas the frequency of the ts phenotype remained unchanged (less than 0.2%). Moreover, 80% of these cs mutants have eclipse rates that are 3- to 40-fold lower than that of the wild type at both 37 degrees C and 25 degrees C. The successful application of the Arrhenius theory to phi X eclipse may provide insights into the molecular mechanism whereby the phi X174 genome is delivered into the host cell. Since the eclipse kinetics of other nonenveloped viruses are similar to those of phi X174, kinetic theory may be broadly applicable in the selection and characterization of viral eclipse mutants.