gebhart/patrepeval huggingface dataset:
Phage Display : A Laboratory Manual (2001)

SECTION 1 - PHAGE DISPLAY Chapter 1. Filamentous Phage Biology Chapter 2. Phage-display Vectors Chapter 3. Antibody Libraries Chapter 4. Peptide Libraries Chapter 5. Functional Domains and Scaffolds Chapter 6. Gene Fragment Libraries and Genomic and cDNA Expression Cloning SECTION 2 - ANTIBODY LIBRARIES Chapter 7. Overview: Amplification of Antibody Genes Chapter 8. Generation of Antibody Libraries: Immunization, RNA Preparation, and cDNA Synthesis Chapter 9. Generation of Antibody Libraries: PCR Amplification and Assembly of Light- And Heavy-chain Coding Sequences Chapter 10. Selection from Antibody Libraries Chapter 11. Analysis of Selected Antibodies Chapter 12. Production and Purification of Fab and scFv Chapter 13. Antibody Engineering SECTION 3 - PEPTIDE LIBRARIES Chapter 14. Overview: Peptide Libraries Chapter 15. General Phage Methods Chapter 16. Production of Peptide Libraries Chapter 17. Screening Peptide Libraries Chapter 18. Analysis of Phage-borne Peptides Chapter 19. Construction and Use of pIII-displayed Peptide Libraries SECTION 4 - OTHER LIBRARIES AND OTHER METHODS OF PANNING Chapter 20. Construction and Selection from Gene Fragment Phage-display Expression Libraries Chapter 21. Construction and Selection from cDNA Phage-display Expression Libraries Chapter 22. In Vivo Selection of Phage-display Libraries Chapter 23. Cell-surface Selection and Analysis of Monoclonal Antibodies from Phage Libraries SECTION 5 - APPENDICES Appendix 1. Useful Information Appendix 2. Recipes Appendix 3. General Procedures Appendix 4. Cautions Appendix 5. Suppliers Appendix 6. Trademarks
Two-Dimensional Arrays of Colloidal Gold Particles:  A Flexible Approach to Macroscopic Metal Surfaces (1996)

Covalent attachment of nanometer-scale colloidal Au particles to organosilane-coated substrates is a flexible and general approach to formation of macroscopic Au surfaces that have well-defined nanostructure. Variations in substrate (glass, metal, Al2O3), geometry (planar, cylindrical), functional group (−SH, −P(C6H5)2, −NH2, −CN), and particle diameter (2.5−120 nm) demonstrate that each component of these assemblies can be changed without adverse consequences. Information about particle coverage and interparticle spacing has been obtained using atomic force microscopy, field emission scanning electron microscopy, and quartz crystal microgravimetry. Bulk surface properties have been probed with UV−vis spectroscopy, cyclic voltammetry, and surface enhanced Raman scattering. Successful application of the latter two techniques indicates that these substrates may have value for Raman and electrochemical measurements. The assembly method described herein is compared with previous methods for controlling the nanoscale roughness of metal surfaces, and its potential applicability to the assembly of other colloidal materials is discussed.
Probabilistic location and routing (2003)

We propose probabilistic location to enhance the performance of existing peer-to-peer location mechanisms in the case where a replica for the queried data item exists close to the query source. We introduce the attenuated Bloom filter, a lossy distributed index data structure. We describe how to use these data structures for document location and how to maintain them despite document motion. We include a detailed performance study which indicates that our algorithm performs as desired, both finding closer replicas and finding them faster than deterministic algorithms alone.
The effects of anandamide on memory consolidation in mice involve both D1and D2 dopamine receptors (1997)

Post-training administration of anandamide (1.5, 3, 6 mg/kg) dose-dependently impairs the retention of an inhibitory avoidance response in mice. The effects on retention performance induced by the drug appear to be due to an effect on memory consolidation, as they were observed when drugs were given at short, but not long, periods of time after training, i.e. when the memory trace was susceptible to modulation. Pretreatment with either selective D1 or D2 dopamine (DA) receptor agonists, SKF 38393 and quinpirole, at doses that were ineffective when given alone (5 and 0.25 mg/kg, respectively), antagonized the effects of anandamide on memory consolidation, suggesting that D1 and D2 receptors are similarly involved in the effects of anandamide on memory consolidation. These results are discussed in terms of a possible inverse relationship between the modulation of memory processes by endogenous cannabinoid and DA systems.
Random Signals: Detection Estimation and Data Analysis (1988)

Review of Probability and Random Variables Random Processes and Sequences Response of Systems to Random Inputs Special Classes of Random Processes Signal Detection Linear Minimum MSE Filtering Statistics Estimating Parameters of Random Processes from Data.
Semisynthetic Peptides and Protein (1981)

Semisynthesis provides a flexible approach for using chemical synthesis to produce large, biologically active polypeptides and analogues. Currently developing improvements in the basic methods used, including polypeptide fragmentation, peptide synthesis, and reconstitution of synthetic and native components, make this overall approach applicable to a variety of species. Sequence modification through semisynthesis thus provides a flexible route to explore the code of rules whereby primary structure directs higher order properties of folded conformation and biological function of large peptides and proteins. The fruits of this endeavor, an understanding of how these macromolecules work, and therein, a basis for design of new structures that ultimately may be produced directly or by recombinant DNA methods, have begun to emerge.
Real-time anomaly detection using a nonparametric pattern recognition approach (2002)

Obstacles to achieving anomaly detection in real time include the large volume of data associated with user behavior and the nature of that data. The paper describes preliminary results from a research project which is developing a new approach to handling such data. The approach involves nonparametric statistical methods which permits considerable data compression and which supports pattern recognition techniques for identifying user behavior. This approach applies these methods to a combination of measurements of resource usage and structural information about the behavior of processes. Preliminary results indicate that both accuracy and real time response can be achieved using these methods.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
New evidence in the treatment of overactive bladder (2015)

The treatment of OAB is often complex, and can require trials of multiple different treatment modalities. Although the treatment advances discussed in this review have augmented treatment of OAB, the condition continues to negatively impact quality of life for our ageing female population. Clinical trials and development of novel therapies continue to be paramount.
Positive Effect of an Autologous Platelet Concentrate in Lateral Epicondylitis in a Double-Blind Randomized Controlled Trial (2010)

Treatment of patients with chronic lateral epicondylitis with PRP reduces pain and significantly increases function, exceeding the effect of corticosteroid injection. Future decisions for application of the PRP for lateral epicondylitis should be confirmed by further follow-up from this trial and should take into account possible costs and harms as well as benefits.
Inhibition of Bacterial Adherence by Nasopharyngeal Secretions (1991)

The role of secretory immunoglobulin (Ig) A in nasopharyngeal secretions in the adherence of Streptococcus pneumoniae and Hemophilus influenzae to nasopharyngeal epithelial cells was investigated in vitro. The adherence was remarkably reduced by treating bacteria with nasopharyngeal secretions, and the antiadhesive activity was significantly greater in nasopharyngeal secretions having secretory IgA antibody activity against bacteria than in those having no activity. Noticeable changes were not observed in the antiadhesive activity caused by absorption of IgG from nasopharyngeal secretions. Results suggest that secretory IgA in nasopharyngeal secretions is related to bacterial adherence and adds to the prevention of nasopharyngeal infections.
Ghrelin secretion stimulated by β 1 -adrenergic receptors in cultured ghrelinoma cells and in fasted mice (2010)

Ghrelin, an octanoylated peptide hormone produced in the stomach, rises dramatically in mouse plasma during chronic severe calorie deprivation, an event that is essential to maintain life. The mechanism for this increase is not understood. Here, we study the control of ghrelin secretion in tissue culture cells derived from mice bearing ghrelinomas induced by a tissue-specific SV40 T-antigen transgene. We found that the ghrelin-secreting cells express high levels of mRNA encoding beta(1)-adrenergic receptors. Addition of norepinephrine or epinephrine to the culture medium stimulated ghrelin secretion, and this effect was blocked by atenolol, a selective beta(1)-adrenergic antagonist. When WT mice were treated with reserpine to deplete adrenergic neurotransmitters from sympathetic neurons, the fasting-induced increase in plasma ghrelin was blocked. Inhibition was also seen following atenolol administration. We conclude that ghrelin secretion during fasting is induced by adrenergic agents released by sympathetic neurons and acting directly on beta(1) receptors on the ghrelin-secreting cells of the stomach.
Hyperplasia and Spontaneous Tumor Development in the Gynecologic System in Mice Lacking the BRCA1-Δ11 Isoform (2006)

Alternative splicing in the BRCA1 locus generates multiple protein products including BRCA1-Delta11, which is identical to the BRCA1 full-length isoform (BRCA1-FL) except for the absence of exon 11. Mutation analysis using gene targeting to create null mutations or disrupt BRCA-FL has provided much of our understanding of BRCA1 functions; however, targeted mutation of specific short forms of BRCA1 has not been reported. To understand the physiologic functions of BRCA1-Delta11, we used a knock-in approach that blocks alternative splicing between exons 10 and 12 to prevent the formation of this form of BRCA1. We showed that homozygous mutant mice (Brca1(FL/FL)) were born at a Mendelian ratio without obvious developmental defects. However, the majority of Brca1(FL/FL) female mice showed mammary gland abnormalities and uterine hyperplasia after one year of age with spontaneous tumor formation. Cultured Brca1(FL/FL) cells exhibited abnormal centrosome amplification and reduction of G(1) population that was accompanied by accumulation of cyclin E and cyclin A. Accumulation of cyclin E was also found in epithelial layers of dilated ducts and hyperproliferative lobular regions in the mammary glands of Brca1(FL/FL) mice. These observations provide evidence that BRCA1 splicing variants are involved in BRCA1 functions in modulating G(1)/S transition, centrosome duplication, and repressing tumor formation.
N-acetyl-p-benzoquinone imine: a cytochrome P-450-mediated oxidation product of acetaminophen. (1984)

N-acetyl-p-benzoquinone imine (NAPQI) has been proposed as the toxic metabolite of acetaminophen for the past 10 years, although it has never been detected as an enzymatic oxidation product of acetaminophen. We report (i) direct detection of NAPQI formed as an oxidation product of acetaminophen by cytochrome P-450 and cumene hydroperoxide and (ii) indirect evidence that is compelling for NAPQI formation from acetaminophen by cytochrome P-450, NADPH, and NADPH-cytochrome P-450 reductase. Evidence is provided for the rapid reduction of NAPQI back to acetaminophen by NADPH and NADPH-cytochrome P-450 reductase such that steady-state levels of NAPQI were below our detection limits of 6.7 X 10(-8) M. In mouse liver microsomal incubations, radiolabeled analogs of both NAPQI and acetaminophen bound covalently to microsomal protein with the loss of approximately equal to 20% of the acetyl group as acetamide. The binding in each case was decreased by glutathione with concomitant formation of 3-S-glutathionylacetaminophen. The binding also was decreased by L-ascorbic acid, NADPH, and NADH with reduction of NAPQI to acetaminophen. Results of partitioning experiments indicate that NAPQI is a major metabolite of acetaminophen, a considerable fraction of which is rapidly reduced back to acetaminophen.
DNA-binding domain and recognition sequence of the yeast BAS1 protein, a divergent member of the Myb family of transcription factors (1994)

The yeast BAS1 protein is a transcriptional activator with an amino-terminal domain homologous to the DNA-binding domain of the oncoprotein Myb containing three imperfect tryptophan-rich repeats. In contrast to Myb-related transcription factors from higher eukaryotes, where the second and third repeat constitutes a minimal independent DNA-binding domain, all three repeats of BAS1 were found to be necessary for sequence-specific DNA binding. Moreover, an active DNA-binding subdomain was obtained only if the first repeat was enlarged in the amino-terminal direction to include 3 tryptophans and a 23-amino acid insertion and if 55 amino acids carboxyl-terminal to the third repeat were included. The BAS1 DNA-binding site was analyzed in detail and found to cover 8-9 base pairs with no similarity to the Myb recognition element. The binding site included a conserved hexameric TGACTC motif, the methylation of which abolished BAS1 binding, as well as a 3-base pair extension that seemed to have a modulatory effect on BAS1 affinity and where binding was less affected by methylation.
Birth of Piglets Derived from Porcine Zygotes Cultured in a Chemically Defined Medium1 (2002)

We evaluated the in vitro development of porcine zygotes that were cultured in a novel culture medium, porcine zygote medium (PZM), under different conditions and compared to in vivo development. The viability of these zygotes to full term after culture was also evaluated by embryo transfer to recipients. Porcine single-cell zygotes were collected from gilts on Day 2 after hCG injection. Culture of zygotes in PZM containing 3 mg/ml of BSA (PZM-3) produced better results in terms of proportion of Day 6 blastocysts, Day 8 hatching rate, and numbers of inner cell mass (ICM) cells and total cells in Day 8 embryos than that in North Carolina State University (NCSU)-23 medium. In culture with PZM-3, embryo development was optimized in an atmosphere of 5% CO2:5% O2:90% N2 compared to 5% CO2 in air. The ICM and total cell numbers in Day 6 embryos cultured in PZM-3 or in PZM-3 in which BSA was replaced with 3 mg/ml of polyvinyl alcohol (PZM-4) were also greater than those of NCSU-23 but less than those developed in vivo. However, no difference was found in the ratio of ICM to total cells among embryos developed in PZM-3, PZM-4, or in vivo. When the Day 6 embryos that developed in PZM-4 (99 embryos) or in vivo (100 embryos) were each transferred into six recipients, no difference was found in the farrowing rate (83.3% for both treatments) and in the number of piglets born (33 and 42 piglets, respectively). Our results indicate that porcine zygotes can develop into blastocysts in a chemically defined medium and to full term by transfer to recipients after culture.
Transcription of a Drosophila heat shock gene is heat-induced in Xenopus oocytes. (1982)

Xenopus cells, like many other eukaryotic cells, respond to heat treatments by increasing the rate of synthesis of a few characteristic proteins, the heat shock proteins. Because of the generality of this response, it seemed possible to examine the expression of isolated heat shock genes in a heterologous system. Phage 122 DNA, containing two identical genes coding for the Drosophila 70,000-dalton heat shock protein (hsp70 genes), was microinjected into Xenopus oocyte nuclei. The Drosophila hsp70 genes are transcribed efficiently in heat-treated oocytes (35-37 degrees C) to give RNA of the correct size and sequence content. Transcription is sensitive to low levels of alpha-amanitin and therefore is carried out by RNA polymerase II. At normal temperatures (20-28 degrees C) essentially no Drosophila-specific RNA is formed. The isolated insert fragment of phage 122 also gives RNA of correct length in heat-treated oocytes which hybridizes to the coding segment of Drosophila hsp70 genes only. At normal temperatures, however, its rate of transcription is variable and only RNA heterogeneous in size is formed.
A double-blind randomised controlled investigation into the efficacy of Mirococept (APT070) for preventing ischaemia reperfusion injury in the kidney allograft (EMPIRIKAL): study protocol for a randomised controlled trial (2017)

ISRCTN registry, ISRCTN49958194 . Registered on 3 August 2012.
Candidate Gene Genotypes, Along with Conventional Risk Factor Assessment, Improve Estimation of Coronary Heart Disease Risk in Healthy UK Men (2006)

For a modest panel of selected genotypes, CHD-risk estimates incorporating CRFs and genotype-risk factor interactions were more effective than risk estimates that used CRFs alone.
Sensory and chemical analysis methods for earthy and musty odours in drinking water caused by geosmin and 2-methylisoborneol (2006)

Earthy and musty odours are amongst the most frequently observed objectionable odours in water supplies, and geosmin and 2-methylisoborneol are identified as the chemical compounds most closely associated with these odours. In this paper, the sensory properties, and the water matrix effects on taste and odour panel studies, as well as the chemical analysis methods for earthy and musty odours in drinking water caused by geosmin and 2-methylisoborneol, are reviewed. Insights are developed to enable better evaluation of earthy and musty odours in drinking water. Early detection of geosmin and MIB can prevent off-flavour occurrence by providing information for potential treatment.
Amyloid Fibril Formation by Aβ16-22, a Seven-Residue Fragment of the Alzheimer's β-Amyloid Peptide, and Structural Characterization by Solid State NMR (2000)

The seven-residue peptide N-acetyl-Lys-Leu-Val-Phe-Phe-Ala-Glu-NH(2), called A beta(16-22) and representing residues 16-22 of the full-length beta-amyloid peptide associated with Alzheimer's disease, is shown by electron microscopy to form highly ordered fibrils upon incubation of aqueous solutions. X-ray powder diffraction and optical birefringence measurements confirm that these are amyloid fibrils. The peptide conformation and supramolecular organization in A beta(16-22) fibrils are investigated by solid state (13)C NMR measurements. Two-dimensional magic-angle spinning (2D MAS) exchange and constant-time double-quantum-filtered dipolar recoupling (CTDQFD) measurements indicate a beta-strand conformation of the peptide backbone at the central phenylalanine. One-dimensional and two-dimensional spectra of selectively and uniformly labeled samples exhibit (13)C NMR line widths of <2 ppm, demonstrating that the peptide, including amino acid side chains, has a well-ordered conformation in the fibrils. Two-dimensional (13)C-(13)C chemical shift correlation spectroscopy permits a nearly complete assignment of backbone and side chain (13)C NMR signals and indicates that the beta-strand conformation extends across the entire hydrophobic segment from Leu17 through Ala21. (13)C multiple-quantum (MQ) NMR and (13)C/(15)N rotational echo double-resonance (REDOR) measurements indicate an antiparallel organization of beta-sheets in the A beta(16-22) fibrils. These results suggest that the degree of structural order at the molecular level in amyloid fibrils can approach that in peptide or protein crystals, suggest how the supramolecular organization of beta-sheets in amyloid fibrils can be dependent on the peptide sequence, and illustrate the utility of solid state NMR measurements as probes of the molecular structure of amyloid fibrils. A beta(16-22) is among the shortest fibril-forming fragments of full-length beta-amyloid reported to date, and hence serves as a useful model system for physical studies of amyloid fibril formation.
Macroeconomic Expectations of Households and Professional Forecasters (2003)

Economists have long emphasized the importance of expectations in determining macroeconomic outcomes. Yet there has been almost no recent effort to model actual empirical expectations data; instead, macroeconomists usually simply assume that expectations are "rational." This paper shows that while empirical household expectations are not rational in the usual sense, expectational dynamics are well captured by a model in which households' views derive from news reports of the views of professional forecasters, which in turn may be rational. The model's estimates imply that people only occasionally pay attention to news reports; this inattention generates "stickyness" in aggregate expectations, with important macroeconomic consequences.
Very high-rejection optical fibre filters (1986)

An optical filter has been developed using holmium-doped optical fibre. Transmission in the blocking band is 10-7% while transmission in the passband is 85%. The wavelength separation between maximum blocking and maximum pass is only 40 nm.
SIGNIFICANT STRUCTURES IN THE LIQUID STATE. I (1958)

The mechanical properties of solids can be understood only by taking proper account of the imperfections present in the crystal lattice. Such lattice imperfections are so important in the liquid as to be an essential part of any description of this less ordered state. When a normal liquid such as argon melts, it expands 12 per cent. Such an expansion is typical. The atypical 10 per cent contraction of ice upon melting can be made to disappear if one first applies some 2,500-atm. pressure, at an appropriate temperature, to the hydrogen-bonded tetrahedral ice I and so transforms it into close-packed ice III, which is a fifth more dense. Ice III then melts with a normal 10 per cent expansion. Anhydrous salts such as sodium chloride melt with about the normal 10 per cent expansion. Metals such as sodium melt with about a 3 per cent expansion. This small expansion on melting of metals was long ago interpreted (1) as a consequence of the small size of the ion formed from atoms which no longer localize their conducting electrons. The ion, being only about one-third atomic size, requires only a third the expansion of normal liquids on melting to provide the same number of vacant sites and therefore the same increased disorder, which leads to melting.