gebhart/patrepeval huggingface dataset:
Insertion of Tn916 in Neisseria meningitidis resulting in loss of group B capsular polysaccharide (1991)

We recently found that the 16.4-kb conjugative transposon Tn916 could be introduced into Neisseria meningitidis by transformation and that it appeared to transpose to many different sites in the chromosome of recipient meningococci. In order to identify transposon-induced alterations of specific meningococcal virulence determinants, a library of meningococcal Tetr transformants containing Tn916 was made and screened for those altered in the production of group B capsular polysaccharide. A capsule-defective mutant, M7, was identified by using monoclonal and polyclonal antisera to group B polysaccharide in immunoblot and agar antiserum procedures. Growth of M7 was similar to that of the parent strain. M7 produced no group B capsular polysaccharide by rocket immunoelectrophoresis, and the mutation was stable during laboratory passage. The capsule-defective phenotype was linked to Tetr, as demonstrated by immunoblot and Southern blot analysis of progeny Tetr transformants (transformants of the parent strain obtained with DNA from M7). A capsule-deficient mutant, O8, was identified by using a similar approach. Analysis of the Tn916 insertions in M7 and O8 indicated that a significant portion of the transposon on either side of the tetM determinant had been lost. The ability of Tn916 to generate defined, stable mutations in meningococcal virulence determinants is demonstrated by our study.
Human hydrometry: comparison of multifrequency bioelectrical impedance with2H2O and bromine dilution (1998)

The traditional method of assessing total body water (TBW), extracellular water (ECW), and intracellular water (ICW) has been the use of isotopes, on the basis of the dilution principle. Although the development of bioelectrical impedance techniques has eliminated many of the measurement constraints associated with the dilution methods, the degree of interchangeability between the two methods remains uncertain. We used multifrequency bioelectrical impedance spectroscopy (BIS), 2H2O dilution, and bromine dilution to assess TBW, ECW, and ICW in 469 healthy subjects (248 males, 221 females) aged 3-29 yr. We found that the TBW, ECW, and ICW estimates for the BIS and dilution methods were significantly correlated (r2 = 0.80-0.96, P < 0.0001, SE of the estimate = 2.3-2.7 liters). On the basis of population, the constants used in the BIS analysis could be adjusted so that the mean differences with the dilution methods would become zero. The SD values for the mean differences between the dilution and BIS methods, however, remained significant for both males and females: TBW (+/-2.1-2.8 liters), ECW (+/-1.4-1.6 liters), and ICW (2.0-3.1 liters). To improve the accuracy of the BIS measurement for an individual within the age range we have examined, further refinement of the constants used in the BIS analysis is needed.
Image-space modal bases for plausible manipulation of objects in video (2015)

We present algorithms for extracting an image-space representation of object structure from video and using it to synthesize physically plausible animations of objects responding to new, previously unseen forces. Our representation of structure is derived from an image-space analysis of modal object deformation: projections of an object's resonant modes are recovered from the temporal spectra of optical flow in a video, and used as a basis for the image-space simulation of object dynamics. We describe how to extract this basis from video, and show that it can be used to create physically-plausible animations of objects without any knowledge of scene geometry or material properties.
Suppression of bulk wave radiation from surface acoustic wave devices (1977)

It is well known that interdigital transducers usually launch a substantial amount of bulk wave radiation as well as the required surface wave. This dual effect is hardly surprising, since some of the first acoustic applications of such structures were specifically as sources of bulk wave radiation. The standard interdigital structure was used for this purpose by Mortley in 1965, and the interdigitally poled version described by Thomann in 1970 had already been described as a bulk wave transducer by van der Pauw in 1966. Furthermore, arrays of grooves were used as a means of converting bulk wave signals to surface waves, and vice versa , long before their use in reflective array compressors. Bulk wave radiation is therefore an expected rather than a surprising phenomenon in all these devices.
Characteristics and Autoradiographic Localization of 2-[125I]Iodomelatonin Binding Sites in Djungarian Hamster Brain* (1989)

These studies investigated the characteristics and regional distribution of 2-[125I]iodomelatonin binding in Djungarian hamster brain. The results showed that 2-[125I]iodomelatonin labels two types of binding sites, which resemble the ML-1 and ML-2 melatonin subtypes previously described in other tissues. The 2-[125I]iodomelatonin binding site identified in whole brain membranes has a nanomolar affinity (Kd = 1.48 +/- 0.26 nM) and biochemical and pharmacological characteristics identical to those of the ML-2 site of Syrian hamster whole brain. The 2-[125I]iodomelatonin site in the hypothalamus has a picomolar affinity (Kd = 43.4 +/- 5.1 pM) and resembles the ML-1 site of chicken retina. The localization of 2-[125I]iodomelatonin labeling in autoradiographic studies of the Djungarian hamster brain includes the suprachiasmatic nuclei, the median eminence, the reuniens nucleus, and the paraventricular nucleus of the thalamus.
Bacteroides pectinophilus sp. nov. and Bacteroides galacturonicus sp. nov.: two pectinolytic bacteria from the human intestinal tract (1986)

Studies on the physiological characteristics of two obligately anaerobic, rod-shaped bacteria from the human intestinal tract indicated that the organisms represented two previously undescribed species of Bacteroides, for which we propose the names Bacteroides pectinophilus (type strain, N3) and Bacteroides galacturonicus (type strain, N6). Both strains were pectinophilic; that is, they utilized as fermentable substrates for growth only pectin and a few related compounds. The two species differed significantly from each other in guanine plus cytosine content of the DNA, in substrate utilization patterns, and in other phenotypic characteristics. Both species deesterified pectin by means of an extracellular pectinesterase (EC 3.1.1.11) activity. Polygalacturonate (the main component of deesterified pectin) was depolymerized extracellularly with formation of unsaturated products by both species. The depolymerizing activity required Ca2+, functioned at a higher rate when polygalacturonate was the substrate as compared with pectin, and had an alkaline pH optimum. These data, as well as viscosity decrease studies and identification of products formed from polygalacturonate, indicated that the extracellular depolymerizing activity of either species was characteristic of an exopectate (exopolygalacturonate) lyase. The exopectate lyase activity had an unusual action pattern that resulted in terminal cleavage of unsaturated trigalacturonic acid units from polygalacturonate. An unsaturated trimer was the major product that accumulated in cell-free reaction mixtures, where it was not cleaved further. Growing cells of both Bacteroides species released the exopectate lyase into the external environment by processes that did not involve cell lysis to any significant extent.(ABSTRACT TRUNCATED AT 250 WORDS)
Signal transduction via CD40 involves activation of lyn kinase and phosphatidylinositol-3-kinase, and phosphorylation of phospholipase C gamma 2. (1994)

CD40 is a 50-kD glycoprotein that plays an important role in B cell survival, memory, and immunoglobulin isotype switch. Engagement of the CD40 antigen by monoclonal antibodies (mAbs) results in increased protein tyrosine kinase (PTK) activity, which plays an important role in mediating the biologic effects of CD40. We demonstrate, using an in situ phosphorylation technique, that CD40 cross-linking by the anti-CD40 mAb 626.1 resulted within 1 min in increased phosphorylation of the src type kinase, lyn, in Daudi B cell lines and remained sustained for up to 20 min. The activity of lyn kinase, as measured by immune complex kinase assay, was also increased after CD40 engagement, with similar kinetics. In contrast, the phosphorylation and activity of fyn, fgr, and lck kinases demonstrated minimal changes following stimulation of Daudi cells with mAb 626.1 over this same time period. CD40 engagement also resulted in phosphorylation of phospholipase C gamma 2 of phosphatidylinositol (PLC gamma 2) and phosphatidylinositol (PI)-3-kinase. Phosphorylation of PI-3-kinase was shown to be associated with an increase in its enzymatic activity. These results suggest that lyn plays an important role in CD40-mediated PTK activation and identify PLC gamma 2 and PI-3-kinase targets for CD40-mediated phosphorylation, suggesting a role for these two enzymes in CD40 signal transduction.
Purification and Characterization of S‐adenosyl‐l‐methionine:norcoclaurine 6‐O‐Methyltransferase from Cultured Coptis japonica Cells (1994)

S-adenosyl-L-methionine:norcoclaurine 6-O-methyltransferase (norcoclaurine 6-O-methyltransferase), which catalyzes the transfer of the S-methyl group of S-adenosyl-L-methionine to the 6-hydroxyl group of 1,2,3,4-tetrahydro-1-[(4-hydroxyphenyl)methyl]-6,7- isoquinolinediol (norcoclaurine), was purified from cultured Coptis japonica cells and its enzymic properties were characterized. Purified norcoclaurine 6-O-methyltransferase had apparent pI 4.7, a native molecular mass of 95 kDa (determined by gel filtration) and subunit molecular mass of 40 kDa (SDS/PAGE). The enzyme did not require a divalent cation for activity, and the addition of Fe2+, Cu2+, Co2+, Zn2+, Mn2+, or Ni2+ at 5 mM severely inhibited enzyme activity. Neither p-chloromercuribenzoate, N-methylmaleimide nor iodoacetamide inhibited enzyme activity at 1 mM. 5,6-Dihydro-9,10-dimethoxybenzo[g]-1,3-benzodioxolo[5,6-a]qu inolizinium (berberine, the end-product of the biosynthetic pathway in which norcoclurine 6-O-methyltransferase catalyzes an intermediate step) also inhibited the activity by 50% at 10 mM. Norcoclaurine 6-O-methyltransferase methylated both (S)-norcoclaurine and (R)-norcoclaurine and (R,S)-norlaudanosoline. Further characterization of substrate-saturation kinetics and product inhibition of the purified enzyme indicated that norcoclaurine 6-O-methyltransferase follows a bi-bi ping-pong mechanism with Km values of 2.23 mM and 3.95 mM for (R,S)-norlaudanosoline and S-adenosyl-L-methionine, respectively, while Ki values for S-adenosylhomocysteine versus S-adenosyl-L-methionine and (R,S)-norlaudanosoline were 2.1 mM and 0.18 mM, respectively.
Immunochemical Proof That a Novel Rearranging Gene Encodes the T Cell Receptor δ Subunit (1987)

The T cell receptor (TCR) delta protein is expressed as part of a heterodimer with TCR gamma, in association with the CD3 polypeptides on a subset of functional peripheral blood T lymphocytes, thymocytes, and certain leukemic T cell lines. A monoclonal antibody directed against TCR delta was produced that binds specifically to the surface of several TCR gamma delta cell lines and immunoprecipitates the TCR gamma delta as a heterodimer from Triton X-100 detergent lysates and also immunoprecipitates the TCR delta subunit alone after chain separation. A candidate human TCR delta complementary DNA clone (IDP2 O-240/38), reported in a companion paper, was isolated by the subtractive library approach from a TCR gamma delta cell line. This complementary DNA clone was used to direct the synthesis of a polypeptide that is specifically recognized by the monoclonal antibody to TCR delta. This complementary DNA clone thus corresponds to the gene that encodes the TCR delta subunit.
Improved Antitumor Activity and Tumor Targeting of NH2-Terminal–Specific PEGylated Tumor Necrosis Factor–Related Apoptosis-Inducing Ligand (2010)

Tumor necrosis factor-related apoptosis-inducing ligand (TRAIL) is considered an attractive anticancer agent due to its tumor cell-specific cytotoxicity. However, its low stability, solubility, unexpected side effects, and weak pharmacokinetic profiles restrict its successful clinical application. To develop efficient TRAIL-based anticancer biotherapeutics, a new version of trimeric TRAIL was constructed by incorporating trimer-forming zipper sequences (HZ-TRAIL), and then NH(2)-terminal-specific PEGylation was done to produce PEGylated TRAIL (PEG-HZ-TRAIL). The biological, physicochemical, and pharmaceutical characteristics of PEG-HZ-TRAIL were then investigated using various in vitro and in vivo experiments, including a cell-based cytotoxicity test, a solubility test, pharmacokinetic analysis, and antitumor efficacy evaluations. Although slight activity loss occurred after PEGylation, PEG-HZ-TRAIL showed excellent tumor cell-specific cytotoxic effects via apoptotic pathways with negligible normal cell toxicity. The stability and pharmacokinetic problems of HZ-TRAIL were successfully overcome by PEGylation. Furthermore, in vivo antitumor tests revealed that PEG-HZ-TRAIL treatment enhanced therapeutic potentials compared with HZ-TRAIL in tumor xenograft animal models, and these enhancements were attributed to its better pharmacokinetic properties and tumor-targeting performance. These findings show that PEG-HZ-TRAIL administration provides an effective antitumor treatment, which exhibits superior tumor targeting and better inhibits tumor growth, and suggest that PEG-HZ-TRAIL should be considered a potential candidate for antitumor biotherapy.
Customized eye models for determining optimized intraocular lenses power (2011)

We have developed a new optical procedure to determine the optimum power of intraocular lenses (IOLs) for cataract surgery. The procedure is based on personalized eye models, where biometric data of anterior corneal shape and eye axial length are used. A polychromatic exact ray-tracing through the surfaces defining the eye model is performed for each possible IOL power and the area under the radial MTF is used as a metric. The IOL power chosen by the procedure maximizes this parameter. The IOL power for 19 normal eyes has been determined and compared with standard regression-based predictions. The impact of the anterior corneal monochromatic aberrations and the eye's chromatic aberration on the power predictions has been studied, being significant for those eyes with severe monochromatic aberrations, such as post-LASIK cataract patients, and for specific IOLs with low Abbe numbers.
Co-aggregation of FcγRII with FcϵRI on Human Mast Cells Inhibits Antigen-induced Secretion and Involves SHIP-Grb2-Dok Complexes (2004)

Signaling through the high affinity IgE receptor FcepsilonRI on human basophils and rodent mast cells is decreased by co-aggregating these receptors to the low affinity IgG receptor FcgammaRII. We used a recently described fusion protein, GE2, which is composed of key portions of the human gamma1 and the human epsilon heavy chains, to dissect the mechanisms that lead to human mast cell and basophil inhibition through co-aggregation of FcgammaRII and FcepsilonRI. Unstimulated human mast cells derived from umbilical cord blood express the immunoreceptor tyrosine-based inhibitory motif-containing receptor FcgammaRII but not FcgammaRI or FcgammaRIII. Interaction of the mast cells with GE2 alone did not cause degranulation. Co-aggregating FcepsilonRI and FcgammaRII with GE2 1) significantly inhibited IgE-mediated histamine release, cytokine production, and Ca(2+) mobilization, 2) reduced the antigen-induced morphological changes associated with mast cell degranulation, 3) reduced the tyrosine phosphorylation of several cellular substrates, and 4) increased the tyrosine phosphorylation of the adapter protein downstream of kinase 1 (p62(dok); Dok), growth factor receptor-bound protein 2 (Grb2), and SH2 domain containing inositol 5-phosphatase (SHIP). Tyrosine phosphorylation of Dok was associated with increased binding to Grb2. Surprisingly, in non-stimulated cells, there were complexes of phosphorylated SHIP-Grb2-Dok that were lost upon IgE receptor activation but retained under conditions of Fcepsilon-Fcgamma co-aggregation. Finally, studies using mast cells from Dok-1 knock-out mice showed that IgE alone triggers degranulation supporting an inhibitory role for Dok degranulation. Our results demonstrate how human FcepsilonRI-mediated responses can be inhibited by co-aggregation with FcgammaRIIB and implicate Dok, SHIP, and Grb2 as key intermediates in regulating antigen-induced mediator release.
Generation and reactions of some dimethyl benzylphosphonate carbanions: synthesis of trans-diaryl-substituted ethylenes (1976)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTGeneration and reactions of some dimethyl benzylphosphonate carbanions: synthesis of trans-diaryl-substituted ethylenesRam S. Tewari, Nirmal Kumari, and Purshottam S. KendurkarCite this: J. Chem. Eng. Data 1976, 21, 1, 125–131Publication Date (Print):January 1, 1976Publication History Published online1 May 2002Published inissue 1 January 1976https://pubs.acs.org/doi/10.1021/je60068a006https://doi.org/10.1021/je60068a006research-articleACS PublicationsRequest reuse permissionsArticle Views364Altmetric-Citations10LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-Alertsclose Get e-Alerts
MicroRNA Target Identification—Experimental Approaches (2013)

MicroRNAs (miRNAs) are small non-coding RNA molecules of 21-23 nucleotides that control gene expression at the post-transcriptional level. They have been shown to play a vital role in a wide variety of biological processes and dysregulated expression of miRNAs is observed in many pathologies. Understanding the mechanism of action and identifying functionally important mRNA targets of a specific miRNA are essential to unravelling its biological function and to assist miRNA-based drug development. This review summarizes the current understanding of the mechanistic aspects of miRNA-mediated gene repression and focuses on the different approaches for miRNA target identification that have been proposed in recent years.
Arkesilaos of Pitane (2017)

Abstract Arkesilaos was the first skeptical head of the Academy. He claimed to revive a Socratic practice of question and answer, with a view to generating skeptical suspension of judgment ( epochê ). But he is also reported to have claimed that nothing could be known, which is inconsistent with epochê , and to have promoted epochê itself as a positive good, which again looks like a definite position. One may interpret these remarks “dialectically”: that is, as showing other philosophers what they are committed to, rather than as positions adopted by Arkesilaos himself. However, while some of his activity (especially against the Stoics) seems to support this interpretation, his widely reported enthusiasm for epochê seems hard to square with it. But perhaps this enthusiasm can be understood as a preference deriving from a basic concern for intellectual integrity. Arkesilaos also appealed to "the reasonable" as a way of making choices while suspending judgment.
Use of Tetrahydropterins in the Treatment of Hyperphenylalaninemia due to Defective Synthesis of Tetrahydrobiopterin: Evidence that Peripherally Administered Tetrahydropterins Enter the Brain (1982)

Substantial amounts of tetrahydrobiopterin and 6-methyltetrahydropterin can be detected in CSF when these pterins are given peripherally to patients with hyperphenylalaninemia due to defective biopterin synthesis. Results of this study suggest that administration of either of these pterins in proper doses may prove to be a treatment not only for the impaired peripheral phenylalanine metabolism, but also for the neurologic disorders that are characteristic of the variant forms of hyperphenylalaninemia due to defective tetrahydrobiopterin synthesis or metabolism.
The Effect of Carbimazole on Thyroid Autoantibody Synthesis by Thyroid Lymphocytes* (1985)

Thyroid autoantibody synthesis was investigated in cultures of lymphocytes isolated from several sources, including thyroid and lymph nodes from patients with hyperthyroid Graves' disease treated preoperatively with carbimazole or propranolol. The ability of thyroid lymphocytes to secrete immunoglobulins, including thyroid microsomal or thyroglobulin autoantibodies, was markedly reduced in lymphocyte suspensions obtained from patients treated with carbimazole compared with suspensions from patients treated with propranolol. This effect (which was greater in individuals treated with carbimazole for longer periods) was attributable to a significant reduction in the number of viable lymphocytes present after the 14-day culture interval. In contrast, the type of preoperative therapy had little effect on cultures of lymphocytes obtained from lymph nodes draining the thyroid. Although it is not yet clear whether carbimazole exerts its effects in vivo by direct immunosuppression or indirectly by altering the thyroid microenvironment, our observations indicate that the fall in serum levels of thyroid autoantibodies that occurs during carbimazole therapy is related to an effect of the drug on lymphocytes within the thyroid.
Hardware acceleration of transactional memory on commodity systems (2011)

The adoption of transactional memory is hindered by the high overhead of software transactional memory and the intrusive design changes required by previously proposed TM hardware. We propose that hardware to accelerate software transactional memory (STM) can reside outside an unmodified commodity processor core, thereby substantially reducing implementation costs. This paper introduces Transactional Memory Acceleration using Commodity Cores (TMACC), a hardware-accelerated TM system that does not modify the processor, caches, or coherence protocol. We present a complete hardware implementation of TMACC using a rapid prototyping platform. Using this hardware, we implement two unique conflict detection schemes which are accelerated using Bloom filters on an FPGA. These schemes employ novel techniques for tolerating the latency of fine-grained asynchronous communication with an out-of-core accelerator. We then conduct experiments to explore the feasibility of accelerating TM without modifying existing system hardware. We show that, for all but short transactions, it is not necessary to modify the processor to obtain substantial improvement in TM performance. In these cases, TMACC outperforms an STM by an average of 69% in applications using moderate-length transactions, showing maximum speedup within 8% of an upper bound on TM acceleration. Overall, we demonstrate that hardware can substantially accelerate the performance of an STM on unmodified commodity processors.
Enzymatic Hydrazinolysis of Diesters and Synthesis ofN-Aminosuccinimide Derivatives (1993)

Selective hydrazinolysis of diesters is catalyzed by PS lipase. This enzyme is an efficient catalyst for the preparation of N-aminosuccinimide derivatives.