gebhart/patrepeval huggingface dataset:
Tandem Mass Spectrometry of Lipids (2014)

The emerging field of lipidomics has been made possible because of advances in mass spectrometry, and in particular tandem mass spectrometry of lipid ions generated by electrospray ionization. The ability to carry out basic biochemical studies of lipids using electrospray ionization is predicated upon understanding the behaviour of lipid derived ions following collision induced decomposition and mechanisms of product ion formation. During the past 20 years, a wealth of information has been generated about lipid molecules that are now analysed by mass spectrometry, however there is no central source where one can obtain basic information about how these very diverse biomolecules behave following collisional activation. This book brings together, in one volume, this information so that investigators considering using tandem mass spectrometry to structurally characterize lipids or to quantitate their occurrence in a biological matrix, will have a convenient source to review mechanism of decomposition reactions related to the diversity of lipid structures. A separate chapter is devoted to each of seven major lipid classes including fatty acids, eicosanoids and bioactive lipid mediators, fatty acyl esters and amides, glycerol esters, glycerophospholipids, sphingolipids, and steroids. Mechanistic details are provided for understanding the pathways of formation of major product ions and ions used for structural characterization. In most cases specific ancillary information has been critical to understand the pathways, including isotope labeling and high resolution analysis of precursor and product ions. For a few specific examples such data is missing and pathways are proposed as a means to initiate further mass spectral experiments to prove or disprove pathway hypotheses. While this work largely centres on the lipid biochemistry of animal (mammalian) systems, general principles can be taken from the specific examples and applied to lipid biochemistry found in plants, fungi, prokaryotes and archeal organisms.
Detection of endotoxin in human blood and demonstration of an inhibitor. (1970)

Abstract Gelation of a lysate of amebocytes of Limulus, the horseshoe crab, is a sensitive indicator of the presence of a variety of endotoxins. Amebocyte lysate is stable. The reaction between lysate and endotoxin is reproducible and easy to measure. The rate of the reaction between amebocyte lysate and endotoxin is dependent upon the concentration of endotoxin. The reaction is capable of detecting as little as 0.0005 μg per milliliter of endotoxin in human blood plasma and serum. Addition of endotoxin to normal blood resulted in loss of detectable endotoxin activity when undiluted plasma or serum prepared from such blood samples was compared with saline controls. Coagulation resulted in additional loss of endotoxin activity. Preincubation of endotoxin with blood or a low calcium ion concentration was not necessary for the demonstration of inhibition. The inhibitory effect could be eliminated almost completely by dilution of serum or plasma to 1 to 10 per cent. Extraction of plasma with chloroform for 60 minutes permitted essentially total recovery of endotoxin which had been added to whole blood or plasma. The increase in positive tests, following dilution or chloroform extraction of serum or plasma, suggested that the inhibitory nature of blood is primarily the result of reversible binding between endotoxin and serum protein(s), rather than destruction of endotoxin. This test is the most sensitive in vitro assay for endotoxin which has been reported. The technique should have application both for clinical and experimental studies of endotoxin and endotoxemia.
A self-normalizing gradient search adaptive array algorithm (1991)

A method is described to normalize the step parameter and perturbation amount used for gradient search adaptive algorithms. The step normalization assures rapid stable convergence. The perturbation normalization also assures rapid stable convergence and limits the output perturbation noise to a level below thermal noise. The normalizations are computationally simple and are consistent with the use of a single receiver at the adaptive array output. Results are presented to verify the robustness of the technique.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Flow sensor using micromachined pressure sensor (2008)

A flow sensor capable of measuring flow rate, fluid type, fluid pressure, fluid presence, and flow direction has been demonstrated. This research activity demonstrates a very simple cap fabrication and assembly process that enabled the realization of a flow sensor with multiple sensing capabilities. A surface micromachined process is employed to fabricate the pressure sensors as well as the cap that defines the fluid channel. The sensor was configured in a way to successfully demonstrate two differential pressure sensing modes (i.e. sensors within the cavity and sensors in the flow channel). Both flow rate and viscosity measurements are based on the differential pressure sensing principle. Fluid presence is determined using an interdigitated structure which can also sense the fluid type based on permittivity of the fluid. The flow rate measured successfully has been as low as 0.01 ml/hr and showed very good linearity when compared to the theoretical model. The diameter of the pressure sensor diaphragm utilized was as low as 100 microns and depended on the flow rate required to measure.
Structure-Activity Relationships of 2-Aminothiazole Derivatives as Inducible Nitric Oxide Synthase Inhibitor (2004)

Nitric oxide synthase (NOS) has been divided into two major sub-enzymes, i.e. inducible NOS (iNOS) and constitutive NOS (cNOS). Although nitric oxide (NO) plays an important role as host defense mediator, excessive production of NO by iNOS has been involved in the pathology of many inflammatory diseases. Recently, we reported that the 2-imino-1,3-oxazolidine (1a) weakly inhibits iNOS and that introduction of an alkyl moiety on the oxazolidine ring of 1a enhances the inhibitory activity and selectivity for iNOS. In our search for better iNOS inhibitors, we focused our efforts on the 2-aminothiazole scaffold 3 as it possesses a ring similar to that of 1a. In this study, we evaluated the inhibitory activity of a series of 2-aminothiazole derivatives against both iNOS and neuronal NOS (nNOS). Our results show that introduction of appropriately-sized substituents at the 4- and 5-position of the 2-aminothiazole ring improves the inhibitory activity and selectivity for iNOS. We also found that the selectivity of 5a [5-(1-methyl)ethyl-4-methylthiazol-2-ylamine] and 5b [5-(1,1-dimethyl)ethyl-4-methylthiazol-2-ylamine] for iNOS was similar to that of oxazolidine derivative 1b (4-methyl-5-propyl-2-imino-1,3-oxazolidine) and much higher than that of L-NAME. However, we could not enhance the inhibitory activity against iNOS by introducing an alkyl substituent into the 2-aminothiazole ring as we could in the case of oxazolidine one. On the other hand, introduction of bulky or hydrophilic substituent at any position of the 2-aminothiazole ring remarkably decreased or even abolished the inhibitory activity against NOS.
Joint Learning of the Embedding of Words and Entities for Named Entity Disambiguation (2016)

Named Entity Disambiguation (NED) refers to the task of resolving multiple named entity mentions in a document to their correct references in a knowledge base (KB) (e.g., Wikipedia). In this paper, we propose a novel embedding method specifically designed for NED. The proposed method jointly maps words and entities into the same continuous vector space. We extend the skip-gram model by using two models. The KB graph model learns the relatedness of entities using the link structure of the KB, whereas the anchor context model aims to align vectors such that similar words and entities occur close to one another in the vector space by leveraging KB anchors and their context words. By combining contexts based on the proposed embedding with standard NED features, we achieved state-of-the-art accuracy of 93.1% on the standard CoNLL dataset and 85.2% on the TAC 2010 dataset.
Control of the necrosed tissue volume during noninvasive ultrasound surgery using a 16‐element phased array (1995)

Focused high-power ultrasound beams are well suited for noninvasive local destruction of deep target volumes. In order to avoid cavitation and to utilize only thermal tissue damage, high frequencies (1-5 MHz) are used in ultrasonic surgery. However, the focal spots generated by sharply focused transducers become so small that only small tumors can be treated in a reasonable time. Phased array ultrasound transducers can be employed to electronically scan a focal spot or to produce multiple foci in the desired region to increase the treated volume. In this article, theoretical and experimental studies of spherically curved square-element phased arrays for use in ultrasonic surgery were performed. The simulation results were compared with experimental results from a 16-element array. It was shown that the phased array could control the necrosed tissue volume by using closely spaced multiple foci. The phased array can also be used to enlarge a necrosed tissue volume in only one direction at a time, i.e., lateral or longitudinal. The spherically curved 16 square-element phased array can produce useful results by varying the phase and amplitude setting. Four focal points can be easily generated with a distance of two or four wavelengths between the two closest peaks. The maximum necrosed tissue volume generated by the array can be up to sixteen times the volume induced by a similar spherical transducer. Therefore the treatment time could be reduced compared with single transducer treatment.
A survey of applications of mathematical programming to circuit‐switched network planning problems (1992)

Abstract In the planning of circuit‐switched networks the decisions regarding the capacity of transmission and switching equipments, the location of exchanges and the routing principles are of primary importance. Traditionally planning methods were based on heuristic type algorithms using sometimes simple mathematical programming algorithms for particular sub‐problems. However in the 70's and 80's, new approaches based on mathematical programming algorithms (namely non‐linear programming, integer programming and dynamic programming algorithms) have been put forward for solving some key telecommunication network planning problems. The main objective of the paper is to identify the main characteristics of problems where mathematical programming has been applied (in the context of circuit‐switched network planning) and referring to relevant works in these areas. A system of taxonomic classification of circuit‐switched network planning problems is proposed and applied to an extensive list of relevant publications complemented with a list of correlated papers and other publications. The core of the overview of contributions, presented in the paper, will be limited to models of operational planning of circuit‐switched networks. Finally the authors, based on their own experience in specific problems, will try to put forward some general conclusions of a broad methodological nature.
An interface for liquid chromatograph/mass spectrometer using atmospheric pressure ionization coupled with a nebulizing sample introduction system. (1983)

An interface for liquid chromatograph/mass spectrometer (LC/MS) using atmospheric pressure ionization (API) coupled with a nebulizing sample introduction system is mounted on a single focusing mass spectrometer. Many kinds of nonvolatile compounds are investigated. Comparison between API and chemical ionization (CI) and/or molecular secondary ion mass spectra are carried out. It is demonstrated that a few ng sample can be detected in this LC/APIMS system.
The Prevalence of Mitochondrial Gene Mutations in Childhood Diabetes in Japan (1999)

To investigate the prevalence of mitochondrial DNA mutations among Japanese children with IDDM as well as in those with NIDDM, a total of 155 patients with IDDM and 30 patients with NIDDM who were younger than 15 years of age at onset were studied for the following mtDNA mutations: 1) the A-->G mutation at position 3243 of mitochondrial leucine transfer RNA (3243 mutation); 2) the G-->A mutation at position 3316 of mitochondrial leucine transfer RNA (3316 mutation), and 3) The T-->C mutation at position 3394 of the mitochondrial NADH dehydrogenase subunit (3394 mutation). None of the 155 IDDM patients had the 3243 mutation. Although two of the 155 IDDM patients had homoplasmy of 3316 and five had 3394 mutations, these frequencies were not significant compared with healthy controls. None of the 30 NIDDM patients had the 3243, 3316 or 3394 mutation. The presence of these mutations even in control subjects suggests that the effect of the 3316 or 3394 mutation on mitochondrial function is relatively mild. It seems that 3316 and 3394 mutations contribute to the manifestation of diabetes together with other genetic and/or environmental factors.
Isotope-selective photoionization for calcium ion trapping (2004)

We present studies of resonance-enhanced photoionization for isotope-selective loading of ${\mathrm{Ca}}^{+}$ into a Paul trap. The ${4s}^{2}{}^{1}{S}_{0}\ensuremath{\leftrightarrow}4s4p{}^{1}{P}_{1}$ transition of neutral calcium is driven by a 423 nm laser and the atoms are photoionized by a second laser at 389 nm. Isotope selectivity is achieved by using crossed atomic and laser beams to reduce the Doppler width significantly below the isotope shifts in the 423 nm transition. The loading rate of ions into the trap is studied under a range of experimental parameters for the abundant isotope ${}^{40}{\mathrm{Ca}}^{+}.$ Using the fluorescence of the atomic beam at 423 nm as a measure of the Ca number density, we estimate a lower limit for the absolute photoionization cross section of 170(60) Mb. We achieve loading and laser cooling of all the naturally occurring isotopes, without the need for enriched sources. Laser heating/cooling is observed to enhance the isotope selectivity. In the case of the rare species ${}^{43}{\mathrm{Ca}}^{+}$ and ${}^{46}{\mathrm{Ca}}^{+},$ which have not previously been laser cooled, the loading is not fully isotope selective, but we show that pure crystals of ${}^{43}{\mathrm{Ca}}^{+}$ may nevertheless be obtained. We find that for loading ${}^{40}{\mathrm{Ca}}^{+}$ the 389 nm laser may be replaced by an incoherent source.
Postexposure rabies prophylaxis and preexposure rabies vaccination failure in domestic animals. (1996)

An effective PEX schedule for domestic animals includes immediate rabies vaccination, with a minimum of 1 booster vaccination, and 90 days' strict isolation.
Reversibly Light-Modulated Dirac Point of Graphene Functionalized with Spiropyran (2012)

Graphene has been functionalized with spiropyran (SP), a well-known photochromic molecule. It has been realized with pyrene-modified SP, which has been adsorbed on graphene by π-π interaction between pyrene and graphene. The field-effect transistor (FET) with SP-functionalized graphene exhibited n-doping effect and interesting optoelectronic behaviors. The Dirac point of graphene in the FET could be controlled by light modulation because spiropyran can be reversibly switched between two different conformations, a neutral form (colorless SP) and a charge-separated form (purple colored merocyanine, MC), on UV and visible light irradiation. The MC form is produced during UV light irradiation, inducing the shift of the Dirac point of graphene toward negative gate voltage. The reverse process back to the neutral SP form occurred under visible light irradiation or in darkness, inducing a shift of the Dirac point toward positive gate voltage. The change of the Dirac point by UV and visible light was reproducibly repeated. SP molecules also improved the conductance change in the FET device. Furthermore, dynamics on conversion from MC to SP on graphene was different from that in solution and solid samples with SP-grafted polymer or that on gold nanoparticles.
Primary structure of glucagon from the gut of the common dogfish (<i>Scyliorhinus canicula</i>) (1987)

The primary structure of glucagon isolated from the intestine of the common dogfish, Scyliorhinus canicula, was established as H S E G T F T S D Y S K Y M D N R R A K D F V Q W L M N T. The peptide shows four substitutions compared with human glucagon: Glu-3 for Gln, Met-14 for Leu, Asn-16 for Ser and Lys-20 for Gln. Glucagon represented the predominant molecular form of the glucagon-like immunoreactivity in the dogfish gut extracts demonstrating that the pathway of posttranslational processing of proglucagon in the gut of this fish differs markedly from the pathway in the mammalian gut.
Local Maximum Likelihood Estimation and Inference (1998)

Summary Local maximum likelihood estimation is a nonparametric counterpart of the widely used parametric maximum likelihood technique. It extends the scope of the parametric maximum likelihood method to a much wider class of parametric spaces. Associated with this nonparametric estimation scheme is the issue of bandwidth selection and bias and variance assessment. This paper provides a unified approach to selecting a bandwidth and constructing confidence intervals in local maximum likelihood estimation. The approach is then applied to least squares nonparametric regression and to nonparametric logistic regression. Our experiences in these two settings show that the general idea outlined here is powerful and encouraging.
The morphoelectrotonic transform: a graphical approach to dendritic function (1995)

Electrotonic structure of dendrites plays a critical role in neuronal computation and plasticity. In this article we develop two novel measures of electrotonic structure that describe intraneuronal signaling in dendrites of arbitrary geometry. The log-attenuation Lij measures the efficacy, and the propagation delay Pij the speed, of signal transfer between any two points i and j. These measures are additive, in the sense that if j lies between i and k, the total distance Lik is just the sum of the partial distances: Lik = Lij + Ljk, and similarly Pik = Pij + Pjk. This property serves as the basis for the morphoelectrotonic transform (MET), a graphical mapping from morphological into electrotonic space. In a MET, either Pij or Lij replace anatomical distance as the fundamental unit and so provide direct functional measures of intraneuronal signaling. The analysis holds for arbitrary transient signals, even those generated by nonlinear conductance changes underlying both synaptic and action potentials. Depending on input location and the measure of interest, a single neuron admits many METs, each emphasizing different functional consequences of the dendritic electrotonic structure. Using a single layer 5 cortical pyramidal neuron, we illustrate a collection of METs that lead to a deeper understanding of the electrical behavior of its dendritic tree. We then compare this cortical cell to representative neurons from other brain regions (cortical layer 2/3 pyramidal, region CA1 hippocampal pyramidal, and cerebellar Purkinje). Finally, we apply the MET to electrical signaling in dendritic spines, and extend this analysis to calcium signaling within spines. Our results demonstrate that the MET provides a powerful tool for obtaining a rapid and intuitive grasp of the functional properties of dendritic trees.
Ambrisentan for the Treatment of Pulmonary Arterial Hypertension (2008)

Ambrisentan improves exercise capacity in patients with pulmonary arterial hypertension. Improvements were observed for several secondary end points in each of the studies, although statistical significance was more variable. Ambrisentan is well tolerated and is associated with a low risk of aminotransferase abnormalities.
Tracking genetically engineered lymphocytes long-term reveals the dynamics of T cell immunological memory (2015)

Long-lasting immune protection from pathogens and cancer requires the generation of memory T cells able to survive long-term. To unravel the immunological requirements for long-term persistence of human memory T cells, we characterized and traced, over several years, T lymphocytes genetically modified to express the thymidine kinase (TK) suicide gene that were infused in 10 patients after haploidentical hematopoietic stem cell transplantation (HSCT). At 2 to 14 years after infusion and in the presence of a broad and resting immune system, we could still detect effectors/effector memory (TEM/EFF), central memory (TCM), and stem memory (TSCM) TK(+) cells, circulating at low but stable levels in all patients. Longitudinal analysis of cytomegalovirus (CMV)- and Flu-specific TK(+) cells indicated that antigen recognition was dominant in driving in vivo expansion and persistence at detectable levels. The amount of infused TSCM cells positively correlated with early expansion and with the absolute counts of long-term persisting gene-marked cells. By combining T cell sorting with sequencing of integration (IS), TCRα and TCRβ clonal markers, we showed that T cells retrieved long-term were enriched in clones originally shared in different memory T cell subsets, whereas dominant long-term clonotypes appeared to preferentially originate from infused TSCM and TCM clones. Together, these results indicate that long-term persistence of gene-modified memory T cells after haploidentical HSCT is influenced by antigen exposure and by the original phenotype of infused cells. Cancer adoptive immunotherapy might thus benefit from cellular products enriched in lymphocytes with an early-differentiated phenotype.
Performance of wideband CDMA with TDD scheme (2002)

This paper overviews the performance of wideband CDMA with time division duplex for the third generation mobile communication systems. The W-CDMA-TDD system is attractive for the application to the FPLMTS frequency band, since the TDD scheme has flexibility of spectrum allotment and the improved transmission performance with base station antenna diversity and simplified open loop transmitter power control.
Influence of mouthguard on temporomandibular joint (2008)

The aim of this study is to examine whether wearing a mouthguard (MG) has an influence on temporomandibular joint (TMJ) components (i.e., the condyle and the articular disk) and whether clenching with a resilient MG has an effect on the same components. Twenty-six healthy volunteers (15 females, 11 males) with an age range of 26-42 years old (median 28 years) participated in this study. Among all 52 joints in the 26 subjects, anterior disk displacement (AntDD) was recognized in 15. Thus, we classified the 52 joints into two groups, the AntDD group and the Normal group. Resilient thermoplastic materials were used to fabricate two types of MG, one that raised the vertical dimension height by 3 mm and another that raised it by 6 mm. Subjects were scanned with/without two types of MG with/without clenching by magnetic resonance imaging (MRI). The movement of the condylar head and articular disk was measured in the magnetic resonance images using the special subtraction technique. Wearing the MG without clenching did not have a negative influence on the TMJ and clenching in the Normal group. In the AntDD group, however, the relationship between the disk and condyle was affected by clenching and the degree of disk displacement was worsened by clenching with the thicker MG. From our results, we recommend that athletes with an internal derangement of the TMJ not wear the thicker MG and attention should be paid to its setting. And the subtraction technique using MRI was thought as a good tool for detecting a slight change in the TMJ.
Modulation of cellular redox state underlies antagonism between oxaliplatin and cetuximab in human colorectal cancer cell lines (2009)

Cetuximab limited oxaliplatin efficiency by affecting the redox status of cancer cells through Nox1. Such combined therapy might be improved by controlling H(2)O(2) elimination.