gebhart/patrepeval huggingface dataset:
Fluorescence ratio measurements of double‐labeled probes for multiple in situ hybridization by digital imaging microscopy (1992)

To expand the multiplicity of the in situ hybridization (ISH) procedure, which is presently limited by the number of fluorochromes spectrally separable in the microscope, a digital fluorescence ratio method is proposed. For this purpose, chromosome-specific repetitive probes were double-labeled with two haptens and hybridized to interphase nuclei of human peripheral blood lymphocytes. The haptens were immunocytochemically detected with specific antibodies conjugated with the fluorochromes FITC or TRITC. The FITC and TRITC fluorescence intensities of spots obtained with different double-haptenized probes were measured, and the fluorescence ratio was calculated for each ISH spot. Combinations of different haptens, such as biotin, digoxigenin, fluorescein, sulfonate, acetyl amino fluorene (AAF), and mercury (Hg) were used. The fluorescence intensity ratio (FITC/TRITC) of the ISH spots was fairly constant for all combinations used, with coefficients of variation between 10 and 30%. To study the feasibility of a probe identification procedure on the basis of probe hapten ratios, one probe was double-labeled with different ratios, by varying the relative concentrations of the modified nucleotides (biotin-11-dUTP and digoxigenin-11-dUTP) in the nick-translation reaction. Measurement of the FITC and TRITC intensities of the ISH spots showed that the concentration of modified nucleotides used in the labeling procedures was reflected in the mean fluorescence intensity of the ISH spots. Furthermore, the ratio distributions showed little overlap due to the relatively small coefficients of variation. The results indicate that a multiple ISH procedure based on fluorescence ratio imaging of double-labeled probes is feasible.
Ultrasensitive silver‐based color staining of polypeptides in polyacrylamide gels (1981)

Abstract A color development system for staining polypeptides in one‐ and two‐dimensional polyacrylamide gel electrophoresis is described. The basis of the Process involves the complexing of silver with polypeptides reactive centers. The reaction is initiated by placing a polypeptide‐containing gel, previously equilibrated with an appropriate concentration of silver nitrate, into a reducing solution that contains sodium hydroxide, sodium borohydride, and formaldehyde. After an appropriate time in the reducing solution, the gel is equilibrated through two changes of an enhancing solution that contains sodium carbonate. The sodium carbonate is necessary for optimal color appear in the polypeptide ‐silver complexes after several hours in the enhancing solution and are best appreciated while viewing over a fluorescent light box that radiates light at 5000°K. The color of each polypeptide‐silver complex is clearly visible above the light background of the stained polyacrylamide gel. Colors of stained polypeptide are blue, green, yellow, and red. Subtle shades of colors also appear and thereby allow easy discrimination of overlapping spots of polypeptides in a two‐dimensional gel. To illustrate the method's relative sensitively, a two‐dimensional pattern of human fibroblast polypeptides is compared with patterns of a duplicate gel that is stained with Coomassie Blue and developed by autoradiography. The sensitivity of the silver stain process is superior to Coomassie Blue and is comparable to autoradiography after in corporation of conventional levels of 35 S‐ methionine. The utility of the procedure for identifying and characterizing human proteins is illustrated by staining human proteins is illustrated by staining human plasma and platelet polypeptides after two‐dimensional gel electrophoresis. The gel electrophoresis color development system consists of steps that are simple, reproducible, and sensitive, and most importantly, which yield colored polypeptide‐silver complexes that are reproducible from gel to gel and tissue to tissue.
The molecular program induced in T cells undergoing homeostatic proliferation (2004)

Naïve T cells proliferate independently of cognate antigen when introduced into lymphopenic hosts. Lymphopenia-induced proliferation depends on low-affinity MHC/self-peptide complexes and on IL-7. To elucidate the intracellular signals mediating this proliferation, we analyzed changes in gene expression in naive CD8+ T cells at different times after their transfer into a lymphopenic environment. The genes induced in response to lymphopenia were largely an attenuated subset of those turned up by full antigenic stimulation, including genes related to cell cycling, whereas excluding genes specifically associated with effector activity. After the initial phase of proliferation in an empty compartment, the naive T cells adopted a stable pattern of gene expression similar to that of antigen-experienced memory cells. Thus, T cells proliferating in lymphopenic hosts do not exhibit a unique gene-expression profile, instead relying on "traditional" signals for this antigen-independent proliferation; this process ultimately results in differentiation to "authentic" memory cells.
A Multifunctional Pasteurella multocida Sialyltransferase:  A Powerful Tool for the Synthesis of Sialoside Libraries (2005)

A multifunctional sialyltransferase has been cloned from Pasteurella multocida strain P-1059 and expressed in E. coli as a truncated C-terminal His6-tagged recombinant protein (tPm0188Ph). Biochemical studies indicate that the obtained protein is (1) an alpha2,3-sialyltransferase (main function), (2) an alpha2,6-sialyltransferase, (3) an alpha2,3-sialidase, and (4) an alpha2,3-trans-sialidase. The recombinant tPm0188Ph is a powerful tool in the synthesis of structurally diverse sialoside libraries due to its relaxed substrate specificity, high solubility, high expression level, and multifunctionality.
Genetic fusion to albumin improves the pharmacokinetic properties of factor IX (2009)

Haemophilia B is a X-chromosome linked disease characterised by a deficiency of functionally active coagulation Factor IX (FIX). Patients with severe haemophilia B at risk of recurrent bleeding are treated approximately twice a week in a prophylactic setting by application of FIX concentrates. To increase convenience and compliance of the therapy it is desirable to reduce the dosing frequency by improving the pharmacokinetic properties of FIX. Here a concept of rFIX (recombinant factor IX) albumin fusion proteins (rIX-FPs) with cleavable linker peptides derived from the FIX activation sequence is presented. Constructs of the genetic fusion of FIX to albumin via cleavable linkers were expressed in mammalian cells and characterised after purification. In vitro activation studies with FXIa demonstrated that cleavage of the linker and the activation peptide proceeded comparably well. In a clotting assay the rIX-FPs with cleavable linker showed a 10- to 30-fold increase in the molar specific clotting activity compared to fusion proteins with non-cleavable linkers. Furthermore, in-vivo recovery, terminal half-life and the AUC of rIX-FPs in rats and rabbits as determined by FIX antigen measurements were significantly increased compared to rFIX (BeneFIX). In FIX deficient (FIX(-/-)) mice the in-vivo recovery and the AUC were also significantly increased. The efficacy in reducing bleeding time was shown in FIX(-/-) mice by a tail tip bleeding model. The results suggest that rIX-FPs with a cleavable linker between FIX and albumin are a promising concept that may support the use of the albumin fusion technology to extend the half-life of FIX.
Regioselective Synthesis of Polysubstituted Pyrazoles and Isoxazoles (2001)

A regioselective synthesis has been developed for the preparation of unsymmetrical 1,3,5-triaryl-4-alkylpyrazolines and -pyrazoles by treatment of alpha-benzotriazolyl-alpha,beta-unsaturated ketones with monosubstituted hydrazines followed by alkylation at the 4-position of the pyrazoline ring. Reaction of alpha-benzotriazolyl-alpha,beta-unsaturated ketones with hydroxylamine gives 3,5-disubstituted isoxazoles regioselectively.
The Mannich Reaction of Malonates with Simple Imines Catalyzed by Bifunctional Cinchona Alkaloids:  Enantioselective Synthesis of β-Amino Acids (2006)

We describe the first efficient, direct asymmetric Mannich reactions with malonates and N-Boc aryl and alkyl imines by cooperative hydrogen-bonding catalysis with a cinchona alkaloid bearing a thiourea functionality. We have also extended the scope of this reaction to beta-ketoesters. The synthetic value of this new reaction is demonstrated in the establishment of a convergent enantioselective route toward the biologically important beta-amino acids under mild and air- and moisture-tolerant conditions.
Repeated quantum error correction on a continuously encoded qubit by real-time feedback (2016)

Reliable quantum information processing in the face of errors is a major fundamental and technological challenge. Quantum error correction protects quantum states by encoding a logical quantum bit (qubit) in multiple physical qubits. To be compatible with universal fault-tolerant computations, it is essential that states remain encoded at all times and that errors are actively corrected. Here we demonstrate such active error correction on a continuously protected logical qubit using a diamond quantum processor. We encode the logical qubit in three long-lived nuclear spins, repeatedly detect phase errors by non-destructive measurements, and apply corrections by real-time feedback. The actively error-corrected qubit is robust against errors and encoded quantum superposition states are preserved beyond the natural dephasing time of the best physical qubit in the encoding. These results establish a powerful platform to investigate error correction under different types of noise and mark an important step towards fault-tolerant quantum information processing.
Automatic spacecraft docking using computer vision-based guidance and control techniques (1993)

Peer Reviewed
N-terminal fatty acylation of the α-subunit of the G-protein Gi1: only the myristoylated protein is a substrate for palmitoylation (1994)

The alpha-subunit of the G-protein Gi1 carries two fatty acyl moieties covalently bound to its N-terminal region: myristic acid is linked to glycine-2 and palmitic acid is linked to cysteine-3. Using site-directed mutagenesis on a cDNA construct of alpha i1 we have generated an alpha i1-G2A mutant, carrying alanine instead of glycine at position 2, and alpha i1-C3S mutant, in which serine replaced cysteine-3 and a double mutant with both substitutions (alpha i1-G2A/C3S). These constructs were individually expressed by transfection in Cos-7 cells, and incorporation of fatty acids into the various mutants was compared with wild-type alpha i1 monitoring metabolic labelling with [3H]palmitate or [3H]myristate. The disruption of the palmitoylation site in alpha i1-C3S did not influence myristoylation, whereas prevention of myristoylation in alpha i1-G2A also abolished palmitoylation. Co-translational myristoylation is thus an absolute requirement for alpha i1 to be post-translationally palmitoylated. The non-palmitoylated alpha i1-C3S showed reduced membrane binding to the same extent as the non-myristoylated/non-palmitoylated alpha i1-G2A and alpha i1-G2A/C3S mutants, indicating that the attachment of palmitic acid is necessary for proper interaction with the membrane.
A Unifying Parameter to Describe the Clinical Mechanics of Hydrogel Contact Lenses (1989)

We studied the relation of postlens squeeze pressure to the clinical fit of hydrogel contact lenses. This relation was statistically significant (p less than 0.01) for a variety of contact lenses currently prescribed over a range of thickness, water content, back central optic radius, diameter, and back vertex power. The squeeze pressure provided a useful parameter to describe and compare the clinical fit of hydrogel contact lenses and a model with which the fit of a lens to an eye could be predicted. There was virtually no movement of the contact lenses across the eye when the squeeze pressure was more than -14 mm H2O (-1370 dynes/cm2). However, the mechanics of the lens motion when the squeeze pressure was less than this critical pressure appeared to be related to a more complicated combination of the squeeze pressure and the other forces in the eye-lens system.
ATP-Dependent Histone Octamer Mobilization and Histone Deacetylation Mediated by the Mi-2 Chromatin Remodeling Complex (2000)

The Mi-2 complex has been implicated in chromatin remodeling and transcriptional repression associated with histone deacetylation. Here, we use a purified Mi-2 complex containing six components, Mi-2, Mta 1-like, p66, RbAp48, RPD3, and MBD3, to investigate the capacity of this complex to destabilize histone-DNA interactions and deacetylate core histones. The Mi-2 complex has ATPase activity that is stimulated by nucleosomes but not by free histones or DNA. This nucleosomal ATPase is relatively inefficient, yet is essential to facilitate both translational movement of histone octamers relative to DNA and the efficient deacetylation of the core histones within a mononucleosome. Surprisingly, ATPase activity had no effect on deacetylation of nucleosomal arrays.
Partial purification of adeno-associated virus Rep78, Rep52, and Rep40 and their biochemical characterization (1992)

We have used differential cell extraction and conventional chromatography to separate and partially purify the four adeno-associated virus (AAV) nonstructural proteins Rep78, Rep68, Rep52, and Rep40. In the cytoplasmic extracts Rep52 and Rep40 were present in greater abundance than Rep68 and Rep78, with Rep78 being the least abundant. In nuclear extracts the four Rep proteins were approximately equal in abundance. Regardless of the subcellular fraction examined, three of the Rep proteins (Rep78, Rep68, and Rep40) consisted of two protein species with slightly different mobilities during polyacrylamide gel electrophoresis. In contrast, Rep52 consisted of only one protein species. Both Rep78 and Rep68 were capable of binding efficiently to AAV terminal hairpin DNA substrates, but we could not detect site-specific DNA binding by Rep52 and Rep40. Like Rep68, Rep78 had both an ATP-dependent trs endonuclease and a DNA helicase activity. Both Rep78 and Rep68 cut the terminal AAV sequence at the same site (nucleotide 124). The binding, trs endonuclease, and DNA helicase activities comigrated during sucrose density gradient centrifugation with a mobility expected for a monomer of the protein, suggesting that the three biochemical activities were intrinsic properties of the larger Rep proteins. The chromatographic behavior and the DNA-binding properties of the four Rep proteins identified at least two domains within the rep coding region, an exposed hydrophobic domain within the C-terminal end (amino acids 578 to 621) and a region within the N terminus (amino acids 1 to 214) which was necessary for binding to the terminal repeat sequence. No site-specific nuclease activity was seen in the presence of nucleotide analogs ATP-gamma-S or AMP-PNP, suggesting that ATP hydrolysis was required for the endonuclease reaction. Furthermore, although ATP was the only cofactor which would support the trs endonuclease activity of Rep78, Rep68 nuclease activity was seen in the presence of several other nucleotide cofactors, including CTP, GTP, and UTP.
Alzheimer‐related neuronal protein A68: Specificity and distribution (1987)

We previously reported that the monoclonal antibody Alz-50 recognizes a protein (A68) with an apparent molecular weight of 68,000 daltons in the brains of patients who died with Alzheimer's disease, but not in brain tissue from individuals free of neurological disease. We now report that substantial quantities of this protein are found in brain tissue only from patients with Alzheimer's disease. Although trace amounts of A68 may be detected in cases of Guam-Parkinson dementia complex and Pick's disease, accumulation of A68 in neuronal perikarya and particularly in neuronal processes appears to be a unique feature of Alzheimer's disease. A68 can readily be detected in cerebrospinal fluid after concentration and partial purification. These data, combined with the quantitation of immunoreactivity in other neurological diseases, suggest the usefulness of detection of A68 in cerebrospinal fluid for diagnosis of Alzheimer's disease.
Intracellular Pools of Thymidine Reduce the Antiviral Action of Acyclovir (1983)

Acyclovir inhibits herpes simplex virus (HSV) infections better in human fibroblasts than in green monkey kidney cells. Thymidine and acyclovir compete for the active site of HSV thymidine kinase. Large intracellular pools of thymidine found by high-performance liquid chromatography (HPLC) seemed to be responsible for the reduced activity of acyclovir. Such intracellular thymidine pools could not be measured previously, and the HPLC technique may help in evaluating the expected efficiency of acyclovir in cells and tissues prior to treatment.
Zinc-finger protein-targeted gene regulation: Genomewide single-gene specificity (2003)

Zinc-finger protein transcription factors (ZFP TFs) can be designed to control the expression of any desired target gene, and thus provide potential therapeutic tools for the study and treatment of disease. Here we report that a ZFP TF can repress target gene expression with single-gene specificity within the human genome. A ZFP TF repressor that binds an 18-bp recognition sequence within the promoter of the endogenous CHK2 gene gives a >10-fold reduction in CHK2 mRNA and protein. This level of repression was sufficient to generate a functional phenotype, as demonstrated by the loss of DNA damage-induced CHK2-dependent p53 phosphorylation. We determined the specificity of repression by using DNA microarrays and found that the ZFP TF repressed a single gene (CHK2) within the monitored genome in two different cell types. These data demonstrate the utility of ZFP TFs as precise tools for target validation, and highlight their potential as clinical therapeutics.
Microchip Capillary Electrophoresis: An Introduction (2006)

Microchip capillary electrophoresis emerged in the early 1990s as an interesting and novel approach to the high-speed separation of biological compounds, including DNA and proteins. Since the early development in this area, growth in the research field has exploded and now includes chemists and engineers focused on developing new and better microchips, as well as biologists and biochemists who have begun to apply this exciting and still relatively new methodology to real-world problems. This chapter seeks to outline the historical development of microchip, the key elements of microchip capillary electrophoresis, and finally some of the important applications being developed that utilize microchip capillary electrophoresis.
Anticachectic Efficacy of Megestrol Acetate at Different Doses and Versus Placebo in Patients With Neoplastic Cachexia (1998)

Anorexia and cachexia are present in the majority of patients with advanced-stage cancer. Several agents have been tested for their ability to reverse weight loss in these patients. Megestrol acetate has been demonstrated to improve appetite and weight, independent of tumor response, when used in the treatment of metastatic breast cancer. Several trials have studied the ability of megestrol acetate to stimulate weight gain in patients with non-hormone-sensitive tumors. One hundred fifty patients with a weight lost of more than 5% in the 3 previous months were randomized between double-blind megestrol acetate 160 mg daily (LMA), megestrol acetate 480 mg daily (HMA), or placebo (P). Weight, mid-arm circumference, triceps skinfold thickness (TST), performance status (Karnofsky index), and a quality-of-life status by seven linear analogic self-assessment scales were assessed before the start of treatment and at 4, 8, and 12 weeks thereafter. One hundred seven patients were assessable at 4 weeks, 79 at 8 weeks, and 64 at 12 weeks. Sixty-eight percent of patients treated with HMA increased their weights during their permanence on study, versus 37% and 38% of patients treated with P or LMA (p < 0.03). The mean weight gain after 12 weeks of treatment with HMA was 5.41 kg. A significant increase on TST was observed in the HMA group versus the LMA and P groups. There was no gain in performance status or quality of life in any group of treatment. The toxicity registered was mild. There were no thromboembolic events. This trial supports the efficacy of megestrol acetate at 480 mg/day in the treatment of cancer-related cachexia and anorexia, with mild toxicity. However, performance status and quality of life were not influenced by this treatment.
The Asymmetric Synthesis of Erythromycin B (1997)

ADVERTISEMENT RETURN TO ISSUEPREVCommunicationNEXTThe Asymmetric Synthesis of Erythromycin BStephen F. Martin, Tsuneaki Hida, Philip R. Kym, Michael Loft, and Anne HodgsonView Author Information Department of Chemistry and Biochemistry The University of Texas, Austin, Texas 78712 Cite this: J. Am. Chem. Soc. 1997, 119, 13, 3193–3194Publication Date (Web):April 2, 1997Publication History Received15 October 1996Published online2 April 1997Published inissue 1 April 1997https://pubs.acs.org/doi/10.1021/ja963575yhttps://doi.org/10.1021/ja963575yrapid-communicationACS PublicationsCopyright © 1997 American Chemical SocietyRequest reuse permissionsArticle Views1903Altmetric-Citations54LEARN 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-AlertscloseSupporting Info (1)»Supporting Information Supporting Information SUBJECTS:Alcohols,Hydroxyls,Protective groups,Reaction products,Reagents Get e-Alerts
A new intracavitary probe for detecting the site of origin of ectopic ventricular beats during one cardiac cycle. (1987)

An olive-shaped probe (25 X 12 mm) with 41 evenly distributed recording electrodes on its surface was introduced into the left ventricles of seven open-chest dogs via the left atrium. In two other dogs a cylindrical probe (40 X 3 mm) was used. Electrical stimuli were delivered at 66 endocardial, midwall, or epicardial sites in the left and right ventricular walls and the septum. Mechanical stimuli were also applied at various epicardial sites. On-line mapping of equipotential contour lines on the surface of the probe invariably revealed a clear-cut potential minimum on the electrode that faced the pacing site. Time of appearance of potential minimum was 3 to 5 msec after endocardial stimuli, 10 to 25 msec for midwall and epicardial pacing, and 30 msec or more for right ventricular stimulation. Simultaneous stimulation at two sites 1.2 cm apart gave rise to two separate minima on the maps. "Pseudoisochrones" derived from electrograms recorded by the new probe were slightly less accurate in indicating the site of origin of extrasystoles. We conclude that equipotential and "isochrone" contour maps recorded from an array of semidirect electrodes, regularly distributed on the surface of an intraventricular probe, provide information on the site of origin (location and intramural depth) of ectopic paced beats in a normal dog heart.