gebhart/patrepeval huggingface dataset:
Biosynthesis of anthraquinones by interspecies cloning of actinorhodin biosynthesis genes in streptomycetes: clarification of actinorhodin gene functions (1990)

Streptomyces galilaeus ATCC 31133 and ATCC 31671, producers of the anthracyclines aclacinomycin A and 2-hydroxyaklavinone, respectively, formed an anthraquinone, aloesaponarin II, when they were transformed with DNA from Streptomyces coelicolor containing four genetic loci, actI, actIII, actIV, and actVII, encoding early reactions in the actinorhodin biosynthesis pathway. Subcloning experiments indicated that a 2.8-kilobase-pair XhoI fragment containing only the actI and actVII loci was necessary for aloesaponarin II biosynthesis by S. galilaeus ATCC 31133. Aloesaponarin II was synthesized via the condensation of 8 acetyl coenzyme A equivalents, followed by a decarboxylation reaction as demonstrated by [1,2-13C2]acetate feeding experiments. S. coelicolor B22 and B159, actVI blocked mutants, also formed aloesaponarin II as an apparent shunt product. Mutants of S. coelicolor blocked in several other steps in actinorhodin biosynthesis did not synthesize aloesaponarin II or other detectable anthraquinones. When S. galilaeus ATCC 31671 was transformed with the DNA carrying the actI, actIII, and actVII loci, the recombinant strain produced both aloesaponarin II and aklavinone, suggesting that the actinorhodin biosynthesis DNA encoded a function able to deoxygenate 2-hydroxyaklavinone to aklavinone. When S. galilaeus ATCC 31671 was transformed with a plasmid carrying only the intact actIII gene (pANT45), aklavinone was formed exclusively. These experiments indicate a function for the actIII gene, which is the reduction of the keto group at C-9 from the carboxy terminus of the assembled polyketide to the corresponding secondary alcohol. In the presence of the actIII gene, anthraquinones or anthracyclines formed as a result of dehydration and aromatization lack an oxygen function on the carbon on which the keto reductase operated. When S. galilaeus ATCC 31671 was transformed with the DNA carrying the actI, actVII, and actIV loci, the recombinant strain produced two novel anthraquinones, desoxyerythrolaccin, the 3-hydroxy analog of aloesaponarin II, and 1-O-methyldesoxyerythrolaccin. The results obtained in these experiments together with earlier data suggest a pathway for the biosynthesis of actinorhodin and related compounds by S. coelicolor.
Synthesis, Biological Activity and Decomposition Studies of Amino Acid Phosphomonoester Amidates of Acyclovir (1997)

Abstract Highly stable and water soluble amino acid phosphomonoester amidates of acyclovir (ACV) were synthesized and shown to function predominantly as prodrugs of AC V and not acyclovir monophosphate (AC V-MP) with activities within two fold of the amino acid prodrug of ACV, valaciclovir (VACV). Metabolism studies revealed that incubation of cell-free extracts of Vero cells with the L-leucine phosphomonoester amidate of ACV (3c), resulted in a burst of ACV-MP production followed by the rapid generation of ACV.
Essential Contribution of Germline-Encoded Lysine Residues in Jγ1.2 Segment to the Recognition of Nonpeptide Antigens by Human γδ T Cells (2001)

Abstract Human γδ T cells display unique repertoires of Ag specificities largely imposed by selective usages of distinct Vγ and Vδ genes. Among them, Vγ2/Vδ2+ T cells predominate in the circulation of healthy adults and respond to various microbial small molecular mass nonpeptide Ags. The present results indicate that the primary Vγ2/Vδ2+ T cells stimulated with the distinct groups of nonpeptide Ags, including monoethyl pyrophosphate, isobutyl amine, and aminobisphosphonate, invariably exhibit Jγ1.2 in the Vγ2+ TCR-γ chains. Gene transfer studies revealed that most of the randomly cloned Vγ2/Jγ1.2+ TCR-γ genes bearing diverse Vγ/Jγ junctional sequences could confer the responsiveness to all these nonpeptide Ags, while none of the Vγ2/Jγ1.1+ or Vγ2/Jγ1.3+ TCR-γ genes could do so. Furthermore, mutation of the lysine residues encoded by the Jγ1.2 gene, which are unique in human Jγ1.2 and absent in other human or mouse Jγ segments, completely abrogated the responsiveness to all the nonpeptide Ags without affecting the response to anti-CD3 mAb. These results strongly suggested that the positively charged lysine residues in the TCR-γ chain CDR3 region encoded by the germline Jγ1.2 gene play a key role in the recognition of diverse small molecular mass nonpeptide Ags.
The History of Storage Systems (2012)

This paper reviews the history of storage systems. The first section begins with the era of early mechanical calculators and the following four sections review historically major storage devices such as magnetic tapes, magnetic disks, optical devices, and solid-state devices. The final two sections focus on recent system technologies such as storage networking and cloud-based storage.
The Rapamycin and FKBP12 Target (RAFT) Displays Phosphatidylinositol 4-Kinase Activity (1995)

The immunosuppressant rapamycin prevents cell cycle progression in several mammalian cell lines and the yeast Saccharomyces cerevisiae. In mammalian cells, rapamycin binds to the small FK506-binding protein, FKBP12, allowing the drug-receptor complex to interact with the 289-kDa RAFT1/FRAP proteins. These proteins, along with their yeast homologs, TOR1/DRR1 and TOR2/DRR2, contain a C-terminal domain with amino acid homology to several phosphatidylinositol (PI) 4- and 3-kinases. However, no direct demonstration of kinase activity for this family of proteins has been reported. We now show that RAFT1, immunoprecipitated from rat brain and MG63 and HEK293 cells, contains PI 4-kinase activity and that rapamycin-FKBP12 has no effect on this activity. Thus, it is likely that, in vivo, rapamycin does not directly inhibit the PI 4-kinase activity and affects the RAFT1/FRAP protein through another mechanism.
Contact Lens‐Induced Discomfort and Protein Changes in Tears (2016)

Only the absolute concentration of prolactin-induced protein correlated with subjective comfort ratings. Taking into consideration that prolactin-induced protein can be associated with disruption in water transport in lacrimal glands, our findings may indicate that changes to aqueous secretion are associated with contact lens discomfort.
Evaluation of Teat Dips with Excised Teats (1984)

Thirty-eight teat dip formulations were evaluated for germicidal activity against Staphylococcus aureus and Streptococcus agalactiae with an excised teat model. Twenty-six of 27 iodophor products provided log reductions greater than 3 against Staphylococcus aureus, but only 13 against Streptococcus agalactiae. Log reductions obtained with two .2% quaternary ammonium and .5% cetylpyridium chloride products were greater than 4 against both organisms. A 1% benzyl alcohol formulation provided log reductions of 3.86 and 4.30 against Staphylococcus aureus and Streptococcus agalactiae. Germicidal activities of six novel formulations containing sodium chlorite were determined. Two products were effective against Staphylococcus aureus and Streptococcus agalactiae with log reductions greater than 4. One product provided a log reduction of 3; three products were ineffective.
PepDist: A New Framework for Protein-Peptide Binding Prediction based on Learning Peptide Distance Functions (2006)

The results obtained suggest that learning a single distance function over an entire family of proteins achieves higher prediction accuracy than learning a set of binary classifiers for each of the proteins separately. We also show the importance of obtaining information on experimentally determined non-binders. Learning with real non-binders generalizes better than learning with randomly generated peptides that are assumed to be non-binders. This suggests that information about non-binding peptides should also be published and made publicly available.
Knowing when you're wrong: Building fast and reliable approximate query processing systems (2014)

Modern data analytics applications typically process massive amounts of data on clusters of tens, hundreds, or thousands of machines to support near-real-time decisions.The quantity of data and limitations of disk and memory bandwidth often make it infeasible to deliver answers at interactive speeds. However, it has been widely observed that many applications can tolerate some degree of inaccuracy. This is especially true for exploratory queries on data, where users are satisfied with "close-enough" answers if they can come quickly. A popular technique for speeding up queries at the cost of accuracy is to execute each query on a sample of data, rather than the whole dataset. To ensure that the returned result is not too inaccurate, past work on approximate query processing has used statistical techniques to estimate "error bars" on returned results. However, existing work in the sampling-based approximate query processing (S-AQP) community has not validated whether these techniques actually generate accurate error bars for real query workloads. In fact, we find that error bar estimation often fails on real world production workloads. Fortunately, it is possible to quickly and accurately diagnose the failure of error estimation for a query. In this paper, we show that it is possible to implement a query approximation pipeline that produces approximate answers and reliable error bars at interactive speeds.
Sequential cytopunctures during preoperative chemotherapy for primary breast carcinoma. II. DNA flow cytometry changes during chemotherapy, tumor regression, and short-term follow-up (1992)

Between May 1986 and May 1987, 35 primary noninflammatory breast carcinomas (T3N0-N1M0) were studied by means of DNA flow cytometry (FCM-DNA) before and after each of three courses of preoperative chemotherapy (doxorubicin, vincristine, cyclophosphamide, methotrexate, and 5-fluorouracil) to assess initial nuclear DNA content, initial S-phase fraction (SPF), and the impact of chemotherapy on these parameters. Correlations were sought with objective regression and short-term follow-up. Four sequential cytopunctures were performed for cytologic examination and FCM-DNA analyses. Ten tumors were diploid and 25 aneuploid. No significant changes in FCM-DNA parameters during chemotherapy were observed in diploid tumors, and no regression was seen in nine of the ten cases. Among the 25 aneuploid tumors, 10 showed changes in DNA content and/or kinetic parameters. A significant correlation was observed between objective regression and initial FCM-DNA content (P = 0.008), initial SPF (P = 0.004), and changes in FCM-DNA patterns observed during chemotherapy (P = 0.00005). During the follow-up period (range, 27 to 41 months), 13 patients had relapses. Patients with aneuploid tumors were more likely to have relapses (n = 11) than patients with diploid tumors (n = 2), and patients with high SPF were more likely to have relapses than patients with low SPF, but the differences were not significant. Similarly, changes in FCM-DNA parameters were observed more often in patients who had relapses, but, again, the difference was not significant. In 5 of the 13 patients who had relapses, FCM-DNA analyses were performed on cytopunctures of the recurrences: patterns were identical to those observed before treatment even when the primary tumor regressed or showed changes in FCM-DNA parameters during chemotherapy.
Adaptor protein Lnk associates with Tyr568 in c-Kit (2008)

The adaptor protein Lnk is expressed in haemopoietic cells and plays a critical role in haemopoiesis. Animal model studies demonstrated that Lnk acts as a broad inhibitor of signalling pathways in haemopoietic lineages. Lnk belongs to a family of proteins sharing several structural motifs, including an SH2 (Src homology 2) domain which binds phosphotyrosine residues in various signal-transducing proteins. The SH2 domain is essential for Lnk-mediated negative regulation of several cytokine receptors [e.g. Mpl, EpoR (erythropoietin receptor), c-Kit]. Therefore inhibition of the binding of Lnk to cytokine receptors might lead to enhanced downstream signalling of the receptor and thereby to improved haemopoiesis in response to exposure to cytokines (e.g. erythropoietin in anaemic patients). This hypothesis led us to define the exact binding site of Lnk to the stem cell factor receptor c-Kit. Pull-down experiments using GST (glutathione transferase)-fusion proteins of the different domains of c-Kit showed that Lnk almost exclusively binds to the phosphorylated juxtamembrane domain. Binding of Lnk to the juxtamembrane domain was abolished by point mutation of Tyr(568) and was competed by peptides with a phosphotyrosine residue at position 568. Co-immunoprecipitation with full-length wild-type or Y568F mutant c-Kit and Lnk confirmed these results, thus showing the importance of this phosphorylated tyrosine residue. Lnk bound directly to c-Kit without requiring other interacting partners. The identification of the binding site of Lnk to c-Kit will be useful to discover inhibitory molecules that prevent the binding of these two proteins, thus making haemopoietic cells more sensitive to growth factors.
Electrophilic conversion of oxiranes to allylic alcohols with tert-butyldimethylsilyl iodide (1980)

ADVERTISEMENT RETURN TO ISSUEPREVArticleElectrophilic conversion of oxiranes to allylic alcohols with tert-butyldimethylsilyl iodideMichael R. DettyCite this: J. Org. Chem. 1980, 45, 5, 924–926Publication Date (Print):February 1, 1980Publication History Published online1 May 2002Published inissue 1 February 1980https://doi.org/10.1021/jo01293a034RIGHTS & PERMISSIONSArticle Views315Altmetric-Citations34LEARN 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 InReddit PDF (307 KB) Get e-Alerts Get e-Alerts
Membrane-Based Synthesis of Nanomaterials (1996)

This paper reviews a relatively new method for preparing nanomaterials: membrane-based synthesis. This method entails the synthesis of the desired material within the pores of a nanoporous membrane. Because the membranes employed contain cylindrical pores of uniform diameter, monodisperse nanocylinders of the desired material, whose dimensions can be carefully controlled, are obtained. These nanocylinders may be either hollow (a tubule) or solid (a fibril or nanowire). We call this approach the "template" method because the pores in the nanoporous membranes are used as templates for forming the desired material. This template method is a very general approach; it has been used to prepare nanotubules and fibrils of polymers, metals, semiconductors, carbons, and other materials.
Prolonged in-vivo half-life of factor VIIa by fusion to albumin (2008)

For the treatment of haemophilia patients with inhibitors, recombinant factor VIIa (rFVIIa) is available as a therapeutic option to control bleeding episodes with a good balance of safety and efficacy. However, the short in-vivo half-life of approximately 2.5 hours makes multiple injections necessary, which is inconvenient for both physicians and patients. Here we describe the generation of a recombinant FVIIa molecule with an extended half-life based on genetic fusion to human albumin. The recombinant FVII albumin fusion protein (rVII-FP) was expressed in mammalian cells and upon activation displayed a FVII activity close to that of wild type FVIIa. Pharmacokinetic studies in rats demonstrated that the half-life of the activated recombinant FVII albumin fusion protein (rVIIa-FP) was extended six- to seven-fold compared with wild type rFVIIa. The in-vitro and in-vivo efficacy was evaluated and was found to be comparable to a commercially available rFVIIa (NovoSeven((R))). The results of this study demonstrate that it is feasible to develop a half-life extended FVIIa molecule with haemostatic properties very similar to the wild-type factor.
Regulation of intracellular pH in cultured hippocampal neurons by an amiloride-insensitive Na+/H+ exchanger. (1991)

Regulation of intracellular pH (pHi) in single cultured rat hippocampal neurons was investigated using the fluorescent pHi indicator dye bis-carboxyethylcarboxyfluorescein. Resting pHi was dependent on the presence of bicarbonate and external Na+ but was not altered significantly by removal of Cl- or treatment with the anion exchange inhibitor diisothiocyanatostilbene-2,2'-disulfonate. Recovery of pHi from acute acid loading was due, in large part, to a pharmacologically distinct variant of the Na+/H+ antiporter. In nominally HCO3(-)-free solutions, this recovery exhibited a saturable dose dependence on extracellular Na+ (Km = 23-26 mM) or Li+. The antiporter was activated by decreasing pHi and was unaffected by collapse of the membrane potential with valinomycin. Like the Na+/H+ antiporter described in other cell systems, the hippocampal activity was inhibited by harmaline, but in sharp contrast, neither amiloride nor its more potent 5-amino-substituted analogues were able to prevent the recovery from an acid load. These data indicate that Na(+)-dependent mechanisms dominate pHi regulation in hippocampal neurons and suggest a role for a novel variant of the Na+/H+ antiporter.
A successful integrated project. (1994)

The experiences of the Juxian County Family Planning Committee of Shandong Province, China, were discussed in terms of the integration of family planning with income generation activities in rural areas. The integrated program was initiated in 1988 with pilot programs established by the Qiaoshan Family Planning Association to develop marketable skills in carpet weaving and grass braiding in Xiazhuang Town and Qiaoshan Township. The program gave priority of admission to women with only children and those who practiced family planning. 1400 women were recruited in these factories. Other income generation programs were developed for silkworm breeding and silk reeling, woolen embroidery, and printing. High ranking officials of the China Family Planning Association commended the work in income generation and family planning in Juxian County. This recognition spurred the second phase of development by the county family planning association: the establishment of village operated factories and mills for native products. By the end of 1991, there were 26 such projects in the county and per capita income to women increased by RMB 678 yuan. In the third stage of 1992, the number of association enterprises increased to 196 with recruitment of over 18,000 reproductive age women. The programs were initiated with collective funds from farmers and villages. The 170 projects in 1992 were developed with an investment of 9.6 million yuan, of which 2.26 million yuan was from individuals (23.5%). Emphasis was placed on self-reliance and recruitment of women with one child, women with 2 daughters and tubal ligations, and family planning motivators. The consequences of the integrated program were weakening traditional customs of marriage and childbearing, improvement in socioeconomic status of women, and effective service delivery of family planning and maternal and child health care services.
Development of shape memory polyurethane fiber with complete shape recoverability (2006)

To illustrate the shape memory properties of shape memory polyurethane (SMPU) fiber and the difference of thermal/mechanical properties between SMPU fiber and other various man-made fibers, series of shape memory polyurethane having various hard segment content were synthesized with the pre-polymerization method and spun with the wet spinning process. Differential scanning calorimetry (DSC), dynamic mechanical analysis (DMA), and mechanical testing were conducted to study the particular thermal/mechanical properties of shape memory polyurethane fiber in comparison with other man-made fibers such as nylon6, polyester, Lycra and XLA. In addition, in the preparation of shape memory polyurethane fiber, the effect of thermal setting temperature was systematically investigated by mechanical properties testing, DMA and cyclic tensile testing, suggesting that the thermal setting temperature has a huge influence on the mechanical properties and shape memory property due to the elimination of internal stress. Thermal setting with a higher temperature will give rise to a lower tensile modulus and tenacity and a higher elongation ratio at break. Through employing the optimal thermal setting treatment, the complete heating responsive recovery in SMPU fiber can be achieved because of the counteracting effect of the irreversible strain and thermal shrinkage.
Recurrent Convolutional Neural Network Regression for Continuous Pain Intensity Estimation in Video (2016)

Automatic pain intensity estimation possesses a significant position in healthcare and medical field. Traditional static methods prefer to extract features from frames separately in a video, which would result in unstable changes and peaks among adjacent frames. To overcome this problem, we propose a real-time regression framework based on the recurrent convolutional neural network for automatic frame-level pain intensity estimation. Given vector sequences of AAM-warped facial images, we used a sliding-window strategy to obtain fixed-length input samples for the recurrent network. We then carefully design the architecture of the recurrent network to output continuous-valued pain intensity. The proposed end-to-end pain intensity regression framework can predict the pain intensity of each frame by considering a sufficiently large historical frames while limiting the scale of the parameters within the model. Our method achieves promising results regarding both accuracy and running speed on the published UNBC-McMaster Shoulder Pain Expression Archive Database.
A “Schrödinger Cat” Superposition State of an Atom (1996)

A "Schrodinger cat"-like state of matter was generated at the single atom level. A trapped 9Be+ ion was laser-cooled to the zero-point energy and then prepared in a superposition of spatially separated coherent harmonic oscillator states. This state was created by application of a sequence of laser pulses, which entangles internal (electronic) and external (motional) states of the ion. The Schrodinger cat superposition was verified by detection of the quantum mechanical interference between the localized wave packets. This mesoscopic system may provide insight into the fuzzy boundary between the classical and quantum worlds by allowing controlled studies of quantum measurement and quantum decoherence.