gebhart/patrepeval huggingface dataset:
Metabolism of cyclic carotenoids: a model for the alteration of this biosynthetic pathway in Capsicum annuum chromoplasts (1995)

The biosynthetic pathway of cyclic carotenoid is known to be quantitatively and qualitatively different in the non-green plastids of Capsicum annuum fruits compared with chloroplasts. Here, the cloning is described of a novel cDNA from this organism, which encodes an enzyme catalyzing the cyclization of lycopene to beta-carotene when expressed in Escherichia coli. The corresponding gene is constitutively expressed during fruit development. Significant amino acid sequence identity was observed between this enzyme and capsanthin/capsorubin synthase which is involved in the synthesis of the species-specific red carotenoids of C. annuum fruits. The latter enzyme was found also to possess a lycopene beta-cyclase activity when expressed in E. coli. A model is proposed for the origin of the capsanthin/capsorubin synthase gene and the role of this enzyme, together with the newly cloned lycopene cyclase, in the specific re-channeling of linear carotenoids into beta-cyclic carotenoids in C. annuum ripening fruits.
Active Server Pages開発テクニック (1998)

１ Ａｃｔｉｖｅ Ｓｅｒｖｅｒ開発の下準備 ２ ＶＢＳｃｒｉｐｔによるＡｃｔｉｖｅ Ｓｅｒｖｅｒ Ｐａｇｅｓのプログラミング ３ Ａｃｔｉｖｅ Ｓｅｒｖｅｒオブジェクトとコンポーネント ４ Ａｃｔｉｖｅ Ｓｅｒｖｅｒ Ｐａｇｅｓによるデータベース管理
Prevention of liver damage by aged garlic extract and its components in mice (1989)

Abstract The hepato‐protective effects of aged garlic extract (GE), S‐allyl cysteine (SAC) and S‐allylmercapto cysteine (SAMC) were evaluated, using mice with acute hepatitis, induced by hepatotoxins. These substances reduced the rise of serum enzyme levels and liver necrosis caused by paracetamol or carbon tetrachloride. It was found that the protective effect of SAMC upon the liver cells were far superior than that of SAC and the other chemicals tested.
Growth and Dissolution of Organic Crystals with “Tailor‐Made” Inhibitors—Implications in Stereochemistry and Materials Science (1985)

Abstract When crystals of organic compounds are grown in the presence of growth inhibitors, there is a change in crystal morphology. A stereochemical correlation exists between the crystal structure, its modified morphology, and the molecular structure of the inhibitor. This correlation has been successfully exploited for the efficient resolution of conglomerates, the engineering of organic crystals with desired morphologies, the direct and relative assignment of the absolute configurations of chiral molecules and crystals, and for the design of a new model for the spontaneous generation of optical activity. In an analogous way dissolution of organic crystals in the presence of these growth inhibitors induces etch pits at preselected faces. The effect of solvent on crystal growth has been analyzed in some model systems. The experimental results are complemented by atom‐atom potential energy calculations.
Comparative Serological Study for the Prevalence of Anti-MERS Coronavirus Antibodies in High- and Low-Risk Groups in Qatar (2019)

Infection with Middle East respiratory syndrome coronavirus (MERS-CoV) could be asymptomatic or cause mild influenza-like illness. Therefore, the prevalence of MERS-CoV infections in the general population could be underestimated, which necessitates active surveillance to determine the epidemiological importance of asymptomatic cases. The aim of this study is to evaluate the performance of various serological assays and to estimate the seroprevalence of anti-MERS-CoV antibodies in high- and low-risk groups in Qatar. A total of 4858 samples were screened, including 4719 samples collected from healthy blood donors (BD) over a period of five years (2012-2016), 135 samples from baseline case contacts (CC) collected from individuals in close contact with three positive PCR-confirmed patients (CP), and four samples from MERS-CoV CP. Initial screening using anti-MERS-CoV IgG (IgG rS1-ELISA kit) revealed ten reactive samples from BD (10/4719, 0.21%), one from CC (1/135, 0.74%), and three from CP (3/4, 75%). Samples from CP but not from BD were also reactive by whole-virus anti-MERS-CoV IgG (<i>n</i> = 3/4) and IgM (<i>n</i> = 1/4) indirect immunefluorescent tests (IIFT) and pseudoparticle neutralization test (ppNT). The reactive sample from CC was also confirmed by ppNT. Surprisingly, one out of thirteen (7.7%) randomly selected IgG rS1-ELISA-negative BD samples from the initial screening was reactive by the IgM-IIFT (but not by the IgG-IIFT) and was subsequently confirmed by ppNT. All IgG rS1-ELISA-reactive samples from BD exhibited considerable reactivity to the four circulating human coronaviruses (HKU1, OC43, 229E, and NL63). Cross-reactivity with SARS was only reported for samples from CP using IgG and IgM-IIFT. In conclusion, we report a low prevalence of anti-MERS antibodies in the general population, which coincides with the low number of all reported cases by the time of our study (2017) in Qatar (<i>n</i> = 21). The false-positive results and the observed cross-reactivity between MERS-CoV and other circulating human coronavirus necessitate more detailed evaluation of available serological assays.
The influence of the hinge region length in binding of human IgG to human Fcγ receptors (1998)

Interactions between human IgG with human FcgammaRI and FcgammaRIIa (R131) were studied to investigate the role of the hinge region of IgG3 and IgG1 in the binding of the antibodies to FcgammaR. It was found that a hinge deletion mutant of IgG3 (IgG3 m15) was reduced in its ability to bind to FcgammaRI and FcgammaRIIa but was more potent at activating ADCC by activated lymphocytes (FcgammaRIIIa-mediated), compared to the wild-type version of IgG3. The human IgG1 allotype G1m(a,z) was more efficient at binding to FcgammaRI than the two IgG3 antibodies tested. The IgG1 and IgG3 wild type antibodies were better able to bind to FcgammaRII than the hinge deletion mutant version of IgG3. The data suggest a role for the hinge region in influencing FcgammaR mediated effector functions in IgG3.
A highly polymorphic locus in human DNA revealed by cosmid-derived probes. (1985)

Human gene mapping would be greatly facilitated if marker loci with sufficient heterozygosity were generally available. As a source of such markers, we have used cosmids from a human genomic library. We have developed a rapid method for screening random cosmids to identify those that are homologous to genomic regions especially rich in restriction fragment length polymorphisms. This method allows whole cosmids to be used as probes against Southern transfers of genomic DNA; regions of cosmid probes homologous to repeated genomic sequences are rendered unable to hybridize with Southern transfers by prehybridization of the probes with a vast excess of nonradioactive genomic DNA. From one cosmid identified by this procedure, we have isolated three single-copy probes that collectively identify seven polymorphic loci. Of 56 unrelated individuals, 52 were heterozygous at one or more of these marker loci.
The Effect of Ventricular Activation Sequence on Cardiac Performance During Pacing (1996)

The aim of this study was to evaluate the importance of a normal ventricular activation pattern for cardiac performance. In nine mongrel dogs, atrial pacing was compared to AV synchronous pacing at three different AV delays (150, 100, and 60 ms). In six dogs, proximal septal AV synchronous pacing was compared to apical AV synchronous pacing at three different AV delays. AV synchronous pacing was performed after RF induced complete heart block. Hemodynamics were evaluated by assessment of positive and negative dP/dt, cardiac output, and left ventricular and pulmonary pressures. Atrial pacing was superior to AV synchronous pacing with respect to positive and negative dP/dt and cardiac output. This difference was present at all AV delays. Proximal septal pacing was associated with a higher positive and negative dP/dt compared to apical pacing at all AV delays. Left ventricular activation time was significantly shorter during proximal septal pacing than during apical pacing (88 +/- 4 vs 115 +/- 4 ms, P < 0.001). We conclude that atrial and proximal septal pacing improves cardiac function and shortens the ventricular activation time compared to apical AV synchronous pacing independent of the AV interval.
cDNA sequence of a Drosophila melanogaster gene, Dfur1, encoding a protein structurally related to the subtilisin‐like proprotein processing enzyme furin (1991)

Screening a genomic library of Drosophila melanogaster DNA with a human fur cDNA probe resulted in the isolation of DNA clones that apparently belonged to two different DNA regions of the Drosophila genome. Subsequently, corresponding Drosophila cDNA clones were isolated. Nucleotide sequence analysis indicated that these cDNA clones originated from two different genes, which were called Dfur1 and Dfur2. From overlapping Dfur1 cDNA clones, a composite cDNA could be constructed and analysis of its nucleotide sequence revealed the coding sequence for a protein of 899 amino acid residues. This protein, designated Dfurin1, exhibited striking sequence homology to human furin and contained the same protein domains except for the cysteine-rich region. Furthermore, unlike human furin, Dfurin1 possessed an extended amino-terminal region in which a potential transmembrane anchor was present.
Seamless correction of the sickle cell disease mutation of the HBB gene in human induced pluripotent stem cells using TALENs (2013)

Sickle cell disease (SCD) is the most common human genetic disease which is caused by a single mutation of human β-globin (HBB) gene. The lack of long-term treatment makes the development of reliable cell and gene therapies highly desirable. Disease-specific patient-derived human induced pluripotent stem cells (hiPSCs) have great potential for developing novel cell and gene therapies. With the disease-causing mutations corrected in situ, patient-derived hiPSCs can restore normal cell functions and serve as a renewable autologous cell source for the treatment of genetic disorders. Here we successfully utilized transcription activator-like effector nucleases (TALENs), a recently emerged novel genome editing tool, to correct the SCD mutation in patient-derived hiPSCs. The TALENs we have engineered are highly specific and generate minimal off-target effects. In combination with piggyBac transposon, TALEN-mediated gene targeting leaves no residual ectopic sequences at the site of correction and the corrected hiPSCs retain full pluripotency and a normal karyotype. Our study demonstrates an important first step of using TALENs for the treatment of genetic diseases such as SCD, which represents a significant advance toward hiPSC-based cell and gene therapies.
Epitaxial Layers Grown with HCl Addition: A Comparison with the Standard Process (2006)

The growth rate of 4H-SiC epi layers has been increased by a factor 3 (up to 18μm/h) with respect to the standard process with the introduction of HCl in the deposition chamber. The epitaxial layers grown with the addition of HCl have been characterized by electrical, optical and structural characterization methods. An optimized process without the addition of HCl is reported for comparison. The Schottky diodes, manufactured on the epitaxial layer grown with the addition of HCl at 1600 °C, have electrical characteristics comparable with the standard epitaxial process with the advantage of an epitaxial growth rate three times higher.
Relative Changes in Regional Cerebral Blood Flow During Spinal Cord Stimulation in Patients with Refractory Angina Pectoris (1997)

Spinal cord stimulation applied at thoracic level 1 (T1) has a neurally mediated anti-anginal effect based on anti-ischaemic action in the myocardium. Positron emission tomography was used to study which higher brain centres are influenced by spinal cord stimulation. Nine patients with a spinal cord stimulator for angina pectoris were studied using H(2)(15)O as a flow tracer. Relative changes in regional cerebral blood flow related to stimulation compared with non-stimulation were assessed and analysed using the method of statistical parametric mapping. Increased regional cerebral blood flow was observed in the left ventrolateral periaqueductal grey, the medial prefrontal cortex [Brodmann area (BA) 9/10], the dorsomedial thalamus bilaterally, the left medial temporal gyrus (BA 21), the left pulvinar of the thalamus, bilaterally in the posterior caudate nucleus, and the posterior cingulate cortex (BA 30). Relative decreases in rCBF were noticed bilaterally in the insular cortex (BA 20/21 and BA 38), the right inferior temporal gyrus (BA 19/37), the right inferior frontal gyrus (BA 45), the left inferior parietal lobulus (BA 40), the medial temporal gyrus (BA 39) and the right anterior cingulate cortex (BA 24). It is concluded that spinal cord stimulation used as an additional treatment for angina applied at T1 modulates regional cerebral blood flow in brain areas known to be associated with nociception and in areas associated with cardiovascular control.
Combinatorial Recombination of Gene Fragments to Construct a Library of Chimeras (2010)

Abstract Recombination of distantly related and nonrelated genes is difficult using traditional PCR‐based techniques, and truncation‐based methods result in a large proportion of nonviable sequences due to frame shifts, deletions, and insertions. This unit describes a method for creating libraries of chimeras through combinatorial assembly of gene fragments. It allows the experimenter to recombine genes of any identity and to select the sites where recombination takes place. Combinatorial recombination is achieved by generating gene fragments with specific overhangs, or sticky ends. The overhangs permit the fragments to be ligated in the correct order while allowing independent assortment of blocks with identical overhangs. Genes of any identity can be recombined so long as they share 3 to 5 base pairs of identity at the desired recombination sites. Simple adaptations of the method allow incorporation of specific gene fragments. Curr. Protoc. Protein Sci . 61:26.2.1‐26.2.20. © 2010 by John Wiley &amp; Sons, Inc.
Influence of plasma and inflammatory proteins on the ultrastructure of exogenous surfactant (2004)

We tested the hypothesis that albumin, fibrinogen and eosinophilic cationic protein (ECP) alter not only the function but also the ultrastructural composition of natural bovine surfactant (Alveofact). Therefore, natural bovine surfactant was mixed with equimolar concentrations of these proteins for 2 h and prepared for electron microscopical examination. Volume fractions, the volume to surface ratio and the volume-weighted mean volume were determined by using various stereological methods. Alveofact surface activity was tested with the capillary surfactometer. Native Alveofact-suspension contained mainly multilamellar bodies (numerous concentric predominantly fused compact phospholipid lamellae) and small fractions of multilamellar vesicles (several concentrically arranged lamellae with a less dense order) and unilamellar vesicles (one to two concentrically arranged phospholipid lamellae), but no tubular myelin. Addition of proteins to Alveofact led to a protein-dependent alteration in the distribution patterns of surfactant subtypes. The significant highest decrease in the volume fraction of multilamellar bodies was found in Alveofact-fibrinogen preparations and the lowest decrease was in Alveofact-albumin preparations. Interaction of Alveofact with ECP resulted in a significant decrease in the size of multilamellar bodies and a significant increase in the volume fraction of very small unilamellar and electron-dense vesicles. Alveofact with ECP kept test capillaries open for the shortest time, while Alveofact with albumin had little inhibitory effect. There was a significant correlation between percentage of capillary openness and the volume fraction quotient of inactive to active surfactant subtypes. Thus, equimolar concentrations of different proteins in Alveofact induce a conversion of multilamellar bodies combined with a decrease in surface activity. The most impressive structural alterations were found after mixture with ECP.
Quantitative fluorescence microscopy (1991)

Preface Abbreviations and symbols 1. Principles of fluorescence microscopy 2. Instrumentation for microfluorometry 3. Microfluorometric technique 4. Microfluorometry: errors, standardization and data processing 5. Applications of microfluorometry 6. Principles of microspectrofluorometry 7. Instrumentation: microspectrofluorometers 8. Microspectrofluorometric technique 9. Microspectrofluorometry: errors, standardization and data processing 10. Applications of microspectrofluorometry 11. Photobleaching, photoactivation and quenching 12. Time-resolved fluorescence, phosphorescence and polarization 13. Quantitative enzyme studies 14. Flow cytometry Hans J. Tanke 15. Scanning, video intensification and image processing 16. History of quantitative fluorescence microscopy Appendices References Index.
Lidocaine Action on Na+Currents in Ventricular Myocytes From the Epicardial Border Zone of the Infarcted Heart (1998)

Myocytes overlying a zone of infarction form the primary substrate for serious reentrant ventricular arrhythmias. In vitro and in vivo studies suggest that antiarrhythmic agents affect Na+ channels of cells from the epicardial border zone (EBZ) of the 5-day infarcted heart differently than they affect those of normal muscle. However, the mechanisms responsible for this difference remain unclear. Previous studies have revealed differences in Na+ current (INa) density and inactivation gating kinetics in myocytes dispersed from the EBZ (IZs). Since changes in inactivation gating could influence lidocaine action, we examined the effects of lidocaine on INa of IZs (n=38) and epicardial myocytes from the noninfarcted heart (NZs) (n=50) using the whole-cell variation of the patch-clamp technique. In drug-free conditions, the voltage dependence of steady-state inactivation of IZs was shifted negative to that of NZs, causing greater inactivation of IZ channels at depolarized (> or = -100-mV) holding potentials. Consistent with a high affinity for the inactivated channel conformation, lidocaine produced more tonic block in IZs than NZs at depolarized holding potentials. Additionally, in drug-free conditions, IZ INa exhibited an enhanced rate of inactivation from closed states, a delay in recovery from inactivation, and increased use-dependent reduction in amplitude during rapid (1- to 3-Hz) pulse trains. In both IZs and NZs, lidocaine (20 to 120 micromol/L) accelerated the rate of time-dependent loss of availability and markedly delayed recovery from availability, inducing significant use-dependent reduction of INa. However, at drug concentrations > or =60 micromol/L, the difference in use-dependent current reduction between IZs and NZs was minimized. The action of lidocaine to render Na+ channel inactivation in NZs more similar to that of IZs may be central to its (pro)antiarrhythmic effects.
The D136A mutation of the V2 vasopressin receptor induces a constitutive activity which permits discrimination between antagonists with partial agonist and inverse agonist activities (1998)

The substitution, in the human V2 vasopressin receptor, of the aspartate at position 136 by alanine leads to agonist-independent activation of this mutant V2 receptor. Pharmacological studies of the D136A V2 receptor helped us in characterizing different V2 receptor antagonists. SR-121463A and OPC-31260, two non-peptide antagonists, behaved as inverse agonists, while two cyclic peptides d(CH2)5[D-Tyr(Et)2,-Val4,Tyr-NH(2)9]AVP and d(CH2)5[D-Ile2,Ile4,Tyr-NH(2)9]AVP known to be V2 antagonists, demonstrated clear partial agonist properties. The finding of a constitutively activated human V2 receptor represents a useful tool in characterizing V2 receptor antagonist ligands.
Potential of a Compton camera for high performance scintimammography (2004)

In this paper, we present a novel approach to scintimammography that is based on the Compton camera principle. We analyse the performance of our scheme using Monte Carlo simulations. In particular, we evaluate the detection efficiency, spatial resolution and lesion visibility of the system at several gamma photon energies. The simulation results show that the proposed technique achieves an absolute detection efficiency of 0.03 and a full width at half maximum resolution of 3.8 mm at 141 keV photon energy for point sources 2.5 cm deep in a 5 cm thick breast phantom using 5 mm thick silicon detectors. Furthermore, our approach shows good performance in lesion detection, especially at high gamma photon energies, where mechanically collimated systems perform poorly due to severe septal penetration. With total collected counts of 1.35 million, equivalent to a 30 s acquisition time for an activity concentration level of 3.7 kBq ml(-1) (100 nCi cm(-3)) in normal breast tissue, and a tumour-to-background ratio of 8:1, our system can clearly reveal an 8 mm diameter tumour that is located 2.5 cm deep in a 500 ml breast phantom. We also present a simulation-based quantitative performance comparison between the proposed scintimammographic system and the compact collimated scintimammographic system in the task of lesion detection under a clinical imaging situation using a non-prewhitening matched filter observer model. Our comparison demonstrates that for the same imaging time, the two systems have a comparable performance in detecting an 8 mm tumour at 141 keV, with the proposed system performing marginally better. However, the proposed scintimammographic system clearly outperforms the compact collimated counterpart in the detection of a 5 mm tumour. We also investigate the contribution of scatter and direct radiation from adjacent organs. We find that the background contribution of liver to the right breast is 30% at 141 keV, which can be reduced to 4.8% with shielding.
Regulation of Silk Material Structure by Temperature-Controlled Water Vapor Annealing (2011)

We present a simple and effective method to obtain refined control of the molecular structure of silk biomaterials through physical temperature-controlled water vapor annealing (TCWVA). The silk materials can be prepared with control of crystallinity, from a low content using conditions at 4 °C (α helix dominated silk I structure), to highest content of ∼60% crystallinity at 100 °C (β-sheet dominated silk II structure). This new physical approach covers the range of structures previously reported to govern crystallization during the fabrication of silk materials, yet offers a simpler, green chemistry, approach with tight control of reproducibility. The transition kinetics, thermal, mechanical, and biodegradation properties of the silk films prepared at different temperatures were investigated and compared by Fourier transform infrared spectroscopy (FTIR), differential scanning calorimetry (DSC), uniaxial tensile studies, and enzymatic degradation studies. The results revealed that this new physical processing method accurately controls structure, in turn providing control of mechanical properties, thermal stability, enzyme degradation rate, and human mesenchymal stem cell interactions. The mechanistic basis for the control is through the temperature-controlled regulation of water vapor to control crystallization. Control of silk structure via TCWVA represents a significant improvement in the fabrication of silk-based biomaterials, where control of structure-property relationships is key to regulating material properties. This new approach to control crystallization also provides an entirely new green approach, avoiding common methods that use organic solvents (methanol, ethanol) or organic acids. The method described here for silk proteins would also be universal for many other structural proteins (and likely other biopolymers), where water controls chain interactions related to material properties.