gebhart/patrepeval huggingface dataset:
Associating protein activities with their genes: rapid identification of a gene encoding a methylglyoxal reductase in the yeast Saccharomyces cerevisiae (2003)

Methylglyoxal is associated with a broad spectrum of biological effects, including cytostatic and cytotoxic activities. It is detoxified by the glyoxylase system or by its reduction to lactaldehyde by methylglyoxal reductase. We show that methylglyoxal reductase (NADPH-dependent) is encoded by GRE2 (YOL151w). We associated this activity with its gene by partially purifying the enzyme and identifying by MALDI-TOF the proteins in candidate bands on SDS-PAGE gels whose relative intensities correlated with specific activity through three purification steps. The candidate proteins were then purified using a glutathione-S-transferase tag that was fused to them, and tested for methylglyoxal reductase activity. The advantage of this approach is that only modest protein purification is required. Our approach should be useful for identifying many of the genes that encode the metabolic pathway enzymes that have not been associated with a gene (about 275 in S. cerevisiae, by our estimate).
Nanoengineering of Particle Surfaces (2001)

The creation of core–shell particles is attracting a great deal of interest because of the diverse applicability of these colloidal particles; e.g., as building blocks for photonic crystals, in multi-enzyme biocatalysis, and in drug delivery. This review presents the state-of-the-art in strategies for engineering particle surfaces, such as the layer-by-layer deposition process (see Figure), which allows fine control over shell thickness and composition.
Alanine-scanning Mutations in the ;Primer Grip; of p66 HIV-1 Reverse Transcriptase Result in Selective Loss of RNA Priming Activity (1997)

Alanine-scanning mutants of the primer grip region of human immunodeficiency virus type 1 reverse transcriptase were tested for their ability to extend RNA and DNA versions of the polypurine tract primer, and an oligonucleotide representing the 18-nucleotide sequence at the 3' end of tRNALys3. A majority of the mutant enzymes were either completely or severely deficient in RNA priming activity, but, with only one exception, were able to efficiently extend DNA versions of the same primers. The mutant enzymes were able to bind to RNA primers, indicating that the defect in RNA priming was not simply a loss of binding activity. Mutations at positions 229, 233, and 235 dramatically reduced the amount of specific RNase H cleavage at the 3' terminus of the polypurine tract, which is required for primer removal. An alanine substitution at position 232 led to loss of cleavage specificity, although total activity was close to the wild-type level. Taken together, these results demonstrate for the first time that there are residues in human immunodeficiency virus type 1 reverse transcriptase which are specifically involved in protein-nucleic acid interactions with RNA primers.
Enantioselective synthesis of ibuprofen esters in AOT/isooctane microemulsions by Candida cylindracea lipase (1993)

The enantioselective esterification of racemic ibuprofen, catalyzed by a Candida cylindracea lipase, was studied in a water-in-oil microemulsion (AOT/isooctane). By using n-propanol as the alcohol, an optimal W(0) ([H(2)O]/[AOT] ratio) of 12 was found for the synthesis of n-propyl-ibuprofenate at room temperature. The lipase showed high preference for the S(+)-enantiomer of ibuprofen, which was esterified to the corresponding S(+)-ibuprofen ester. The R(-)-ibuprofen remained unesterified in the microemulsion. The calculated enantioselectivity value (E) for S-ibuprofen ester was greater than 150 (conversion 0.32). The enzyme activities of n-alcohols with different chain lengths (3-12) were compared, and it appeared that short- (propanol and butanol) and long-chained (decanol and dodecanol) alcohols were better substrates than the intermediate ones (pentanol, hexanol, and octanol). However, unlike secondary and tertiary alcohols, all of the tested primary alcohols were substrates for the lipase. The reversible reaction (i.e., the hydrolysis of racemic ibuprofen ester in the microemulsion) was also carried out enantioselectively by the enzyme. Only the S form of the ester was hydrolyzed to the corresponding S-ibuprofen. The reaction yield was, however, only about 4% after 10 days of reaction. The corresponding yield for the esterification of ibuprofen was about 35% (10 days). The high enantioselectivity displayed by the lipase in the microemulsion system was seen neither in a similar esterification reaction in a pure organic solvent system (isooctane) nor in the hydrolysis reaction in an aqueous system (buffer). The E value for S-ibuprofen ester in the isooctane system was 3.0 (conversion 0.41), and only 1.3 for S-ibuprofen in the hydrolysis reaction (conversion 0.32). The differences in enantioselectivity for the lipase in various systems are likely due to interfacial phenomena. In the microemulsion system, the water in which the enzyme is dissolved is separated from the solvent by a layer of surfactant molecules, thus creating an interface with a relatively large area. Such interfaces are not present in the pure organic solvent systems (no surfactant) nor in aqueous systems.
Design of Potent IGF1‐R Inhibitors Related to Bis‐azaindoles (2010)

From an azaindole lead, identified in high throughput screen, a series of potent bis-azaindole inhibitors of IGF1-R have been synthesized using rational drug design and SAR based on a in silico binding mode hypothesis. Although the resulting compounds produced the expected improved potency, the model was not validated by the co-crystallization experiments with IGF1-R.
Solution-Phase Single Quantum Dot Fluorescence Resonance Energy Transfer (2006)

We present a single particle fluorescence resonance energy transfer (spFRET) study of freely diffusing self-assembled quantum dot (QD) bioconjugate sensors, composed of CdSe-ZnS core-shell QD donors surrounded by dye-labeled protein acceptors. We first show that there is direct correlation between single particle and ensemble FRET measurements in terms of derived FRET efficiencies and donor-acceptor separation distances. We also find that, in addition to increased sensitivity, spFRET provides information about FRET efficiency distributions which can be used to resolve distinct sensor subpopulations. We use this capacity to gain information about the distribution in the valence of self-assembled QD-protein conjugates and show that this distribution follows Poisson statistics. We then apply spFRET to characterize heterogeneity in single sensor interactions with the substrate/target and show that such heterogeneity varies with the target concentration. The binding constant derived from spFRET is consistent with ensemble measurements.
Pulse arrival time estimation from the impedance plethysmogram obtained with a handheld device (2011)

This paper describes a novel method to estimate pulse arrival time (PAT) from the electrocardiogram (ECG) and the impedance plethysmogram (TPG) obtained by using a compact and easy-to-use handheld device with only four electrodes. A proof-of-concept has been carried out where PAT values obtained with the proposed device have been compared to PAT values measured between the ECG and the photoplethysmogram (PPG) during three experiments of paced respiration to induce controlled PAT changes. The results show that both methods yield equivalent PAT values in within ± 7 ms (95 % confidence interval), which is less than typical deviations reported for common PAT measurements.
Up-regulation of Frizzled-10 (FZD10) by β-estradiol in MCF-7 cells and by retinoic acid in NT2 cells (2002)

Frizzled (FZD) genes encode receptors for WNTs, which play key roles in carcinogenesis and embryogenesis. We have previously cloned the FZD10 gene, and demonstrated up-regulation of FZD10 mRNA in the cervical cancer cell line HeLa S3, gastric cancer cell lines TMK1 and MKN74, and 4 cases out of 10 cases of primary gastric cancer. Here, effects of beta-estradiol, retinoic acid, and inflammatory cytokines on expression of FZD10 mRNA in human cancer cell lines were investigated. FZD10 mRNA was undetectable in MCF-7 cells derived from breast cancer, and was significantly up-regulated by beta-estradiol in MCF-7 cells with a peak at 24 h after treatment. FZD10 mRNA was expressed in NT2 cells, which are reported to differentiate into neuronal cells after exposure to retinoic acid. Although expression level of FZD10 mRNA was unchanged until 36 h after retinoic-acid treatment, FZD10 mRNA was up-regulated at 48 and 72 h after retinoic-acid treatment in NT2 cells. Effects of inflammatory cytokines on FZD10 mRNA expression in a gastric cancer cell line MKN45 was next investigated. FZD10 mRNA was undetectable in MKN45 cells, and was not up-regulated by IFNgamma and TNFalpha in MKN45 cells. Because we have previously demonstrated up-regulation of WNT2 mRNA by beta-estradiol in MCF-7 cells, FZD10 and WNT2 mRNAs were found to be up-regulated together by beta-estradiol in MCF-7 cells with the same time course. Synchronous up-regulation of FZD10 and WNT2 mRNAs might lead to activation of the WNT signaling pathway in human breast cancer.
Human Induced Pluripotent Stem Cells Differentiation into Oligodendrocyte Progenitors and Transplantation in a Rat Model of Optic Chiasm Demyelination (2011)

These results showed that oligodendrocyte progenitors generated efficiently from hiPSCs can be used in future biomedical studies once safety issues have been overcome.
Small-molecule modulators of the Sonic Hedgehog signaling pathway (2009)

Sonic hedgehog (Shh) is the most widely characterized of the three vertebrate Hedgehog homologs, and is essential for proper embryonic development. Shh binds to its receptor, Patched (Ptch1), resulting in the de-repression of Smoothened (Smo). This leads to the activation of Gli2, which regulates the transcription of target genes that include Gli1 and Ptch1. Several synthetic and naturally occurring small-molecule modulators of Smo have been discovered. Shh-signaling antagonists that bind to Smo include cyclopamine, SANT1, and Cur-61414. Shh signaling agonists that bind to Smo include the synthetic small molecules purmorphamine and SAG. Small molecules that inhibit Shh signaling downstream of Smo, GANT58 and GANT61 have also been reported. Robotnikinin inhibits the Shh pathway by directly targeting Shh. Although progress has been made in understanding and modulating Shh signaling, fundamental aspects of Shh signal transduction remain obscure, including the mechanism(s) whereby Ptch1 regulates Smo activity. Small-molecule modulators of Shh signaling provide a means to regulate the activity of a pathway implicated in medulloblastoma, basal cell carcinoma (BCC), pancreatic cancer, prostate cancer and developmental disorders. Several Shh inhibitors have not succeeded in the clinic for unknown reasons, but clinical trials in BCC and pancreatic cancer with the promising Smo antagonists GDC-0449 and IPI-926 are currently underway.
Positron Emission Tomography in Urologic Oncology (2002)

PET imaging has demonstrated great potential in certain applications, but further investigations are necessary to determine its eventual place as an imaging modality in genitourinary malignancies.
Silk Properties Determined by Gland-Specific Expression of a Spider Fibroin Gene Family (1996)

Spiders produce a variety of silks that range from Lycra-like elastic fibers to Kevlar-like superfibers. A gene family from the spider Araneus diadematus was found to encode silk-forming proteins (fibroins) with different proportions of amorphous glycine-rich domains and crystal domains built from poly(alanine) and poly(glycine-alanine) repeat motifs. Spiders produce silks of different composition by gland-specific expression of this gene family, which allows for a range of mechanical properties according to the crystal-forming potential of the constituent fibroins. These principles of fiber property control may be important in the development of genetically engineered structural proteins.
Dissection of Individual Functions of the Sendai Virus Phosphoprotein in Transcription (1999)

The Sendai virus P protein is an essential component of the viral RNA polymerase (P-L complex) required for RNA synthesis. To identify amino acids important for P-L binding, site-directed mutagenesis of the P gene changed 17 charged amino acids, singly or in groups, and two serines to alanine within the L binding domain from amino acids 408 to 479. Each of the 10 mutants was wild type for P-L and P-P protein interactions and for binding of the P-L complex to the nucleocapsid template, yet six showed a significant inhibition of in vitro mRNA and leader RNA synthesis. To determine if binding was instead hydrophobic in nature, five conserved hydrophobic amino acids in this region were also mutated. Each of these P mutants also retained the ability to bind to L, to itself, and to the template, but two gave a severe decrease in mRNA and leader RNA synthesis. Since all of the mutants still bound L, the data suggest that L binding occurs on a surface of P with a complex tertiary structure. Wild-type biological activity could be restored for defective polymerase complexes containing two P mutants by the addition of wild-type P protein alone, while the activity of two others could not be rescued. Gradient sedimentation analyses showed that rescue was not due to exchange of the wild-type and mutant P proteins within the P-L complex. Mutants which gave a defective RNA synthesis phenotype and could not be rescued by P establish an as-yet-unknown role for P within the polymerase complex, while the mutants which could be rescued define regions required for a P protein function independent of polymerase function.
Overexpression of a rabbit liver carboxylesterase sensitizes human tumor cells to CPT-11. (1998)

CPT-11 [7-ethyl-10-[4-(1-piperidino)-1-piperidino]carbonyloxycamptothecin ] is a prodrug that is converted to the active metabolite SN-38 by carboxylesterases. In its active form, the drug inhibits topoisomerase I, causes DNA damage, and induces apoptosis. Data in this study show metabolism of CPT-11 to SN-38 (7-ethyl-10-hydroxycamptothecin) by a rabbit liver carboxylesterase in vitro and growth-inhibitory activity of the products of the reaction. Additionally, stable expression of the cDNA encoding this protein in Rh30 human rhabdomyosarcoma cells increased the sensitivity of the cells to CPT-11 8.1-fold. We propose that this prodrug/enzyme combination can be exploited therapeutically in a manner analogous to approaches currently under investigation with the combinations of ganciclovir/herpes simplex virus thymidine kinase and 5-fluorocytosine/cytosine deaminase.
Interleukin 2-dependent release of interleukin 3 activity by T4+ human T-cell clones. (1985)

We have isolated and studied two alloreactive, T4+, human lymphocyte clones that release interleukin 2 (IL-2) and interleukin 3 (IL-3) bioactivities upon stimulation with IL-2, alloantigen, or Sepharose-conjugated antibodies directed against the T3 protein. Anti-IL-2 receptor monoclonal antibodies block IL-2-, alloantigen-, or anti-T3-stimulated IL-3 release. Hence, release of IL-3 activity in each circumstance is rigorously dependent upon activation of the IL-2 receptor. Even low, nonmitogenic concentrations of recombinant IL-2 stimulated IL-3 release.
Theoretical calculations of a square multilayer Bragg-Fresnel lens by quantum theory (2000)

Abstract A theoretical method based on the quantum scattering theory is presented to evaluate the performances of a two-dimensional (2-D) focusing square multilayer Bragg–Fresnel lens. The numerical application results of the square multilayer Bragg–Fresnel lens working at 0.7 nm wavelength (W/Si 25 periods with a double layer thickness of 5.38 nm, the size of the diffraction pattern is about 291×291 μm, the size of the center square in the diffraction pattern is 21.4×21.4 μm, and the size of the smallest square in the diffraction pattern is 0.39×0.39 μm) are given. Our theoretical results are compared with the experimental results of the linear Bragg–Fresnel lens reported by other researchers; an analysis and a discussion are carried out regarding the advantages of an optical system based on the 2-D focusing square multilayer Bragg–Fresnel lens, in contrast to a Kirkpatrick–Baez optical system on the basis of a two-linear Bragg–Fresnel lens.
Limited Tissue Penetration of Taxanes: A Mechanism for Resistance in Solid Tumors (2007)

These results indicate that limited distribution is an important mechanism of tumor resistance to taxanes.
Practice patterns in haemophilia A therapy – global progress towards optimal care (2006)

This paper reports the findings of a global survey of practice patterns for the management of patients with haemophilia A. A total of 147 haemophilia treatment centres worldwide responded to the questionnaire, supplying data for 16 115 patients with haemophilia A. From these responses, 38% (range: 25-48%) of patients were under 18 years old. Almost half (47%) of patients were reported to have mild or moderate haemophilia A, 48% had severe haemophilia A (no inhibitor) and 5% were inhibitor patients. Less than half of patients with severe haemophilia A received prophylactic therapy (37%, excluding inhibitor patients) and 54% received on-demand treatment; the remaining 9% were inhibitor patients. Primary prophylaxis rates for severe haemophilia ranged from 73% in Sweden to 17% in the USA. Most respondents (80%) ranked infrequent bleeds as one of the top five reasons for not administering prophylactic treatment, followed by venous access (60%) and cost (45%). Of patients with severe haemophilia (non-inhibitor), 32% on primary prophylaxis and 27% on secondary prophylaxis had indwelling catheters. Risk of infection and the patient's inability to maintain the line were the key concerns cited by nurses relating to venous access. The mean ratio of nurses to patients with haemophilia A was 1:69 and nurses felt that they were either fully (26%) or mostly (45%) autonomous in assessment and treatment decisions. Results from this current survey suggest that worldwide research should be continued so as to improve outcomes through the identification of optimal treatment protocols for the management of haemophilia A.
Autocatalytic decomposition of cobalt complexes as an indicator system for the determination of trace amounts of cobalt and effectors (1996)

From theoretical considerations, the possibility of developing a constant sensitivity detection system for the determination of ultratrace levels of metal ions by the use of an autocatalytic degradation reaction of metal complexes was considered. The idea was realized by the use of the oxidative decomposition of the inert CoIII–2-(5-bromo-2-pyridylazo)-5-(N-propyl-N-sulfopropylamino)phenolate complex with peroxomonosulfate as oxidant and cobalt ion as catalyst. The inflection time of the absorbance–time curve is controlled by effectors such as cobalt(II) ion and ligands present in excess. Based on these properties, the system was successfully applied to the spectrophotometric determination of 10–10 mol dm–3 levels of cobalt ion and 10–5 mol dm–3 levels of effectors. The method does not require measurement of the rate constants.
Laser Patterning of Silver Nanowire (2012)

The use of laser patterning on silver nanowire enables reduced manufacturing costs and increased flexibility for touch‐panel manufacturers.
The hydrophobic moment of the amphipathic helix of salmon calcitonin and biological potency (1986)

The formation of an amphipathic helix in the central portion of calcitonin contributes to the potency of this hormone. We have synthesized a number of analogs of salmon calcitonin, containing deletions in the region of the peptide which is thought to form an amphipathic helix. There is no direct relationship between the hydrophobic moment of the helix and the biological activity of the peptide. For example, salmon des-Leu19-calcitonin and des-Ser13-calcitonin both have lower helical hydrophobic moments but have greater or equal biological potency compared with the native hormone. We suggest that other conformational features, such as flexibility and helix-forming potential, are also important in determining biological potency.
SACE-CSCW: a synchronous asynchronous common environment for computer supported cooperative work to aid concurrent engineering processes (2002)

This paper presents a system prototype that provides computer support for different modes of meetings concerning the decision making process. Besides supporting the two obvious domains of cooperation: space (same or different) and time (synchronous or asynchronous) it also allows to work with other dimensions such as group/subgroup, user roles, public or closed type of meeting, anonymous or nominated method of meeting and three modes of cooperation: full view, partial view and single view. The framework includes the brainstorming, organization/consolidation, voting and action sessions of a typical decision making meeting. The system is actually being implemented in the Java environment using the remote method invocation. The new SACE-CSCW tool is part of a wider structure that aims to construct Concurrent Engineering facilities to aid the cooperation/collaboration of people designing and producing products and services of any kind of industry.
Viscosity‐adjustable block copolymer for DNA separation by capillary electrophoresis (1998)

The viscosity-adjustable property of F127 block copolymer PEO99PPO69PEO99, PEO and PPO being poly(ethylene oxide) and poly(propylene oxide), respectively, was found to be useful for the development of automated capillary electrophoresis (CE). The polymer solution can form a gel-like structure with sieving ability and can also serve as a dynamic coating material, thereby effectively suppressing the electroosmotic flow induced by the ionization of the silanol group on the quartz capillary inner wall. When applied to CE as a separation medium, F127 block copolymer can provide the advantages of high separation resolution, easy injection and replacement of the triblock copolymer solution and convenient capillary column treatment. High reproducibility of DNA electrophoretic migration time in CE by replenishing F127 solution in acid-washed capillary tubings can be achieved. The relative standard deviation of the DNA migration time is less than 2%. In the investigation of F127 concentration and temperature effects on the performance of DNA separation in CE, we have found that the DNA electrophoretic migration behavior in the F127 gel-like solution cannot be described by any one of the existing models.