gebhart/patrepeval huggingface dataset:
Structure and function of immunoglobulin domains. III. Isolation and characterization of a fragment corresponding to the Cgamma2 homology region of human immunoglobin G1. (1976)

Exposure of Fc fragments derived from human IgG1 myeloma proteins to acid pH rendered the region between the Cgamma2 and Cgamma3 domains transiently susceptible to cleavage by trypsin upon return to neutral pH. Trypsin covalently linked to Sepharose was used and two fragments derived from the Cgamma2 region and one from the Cgamma3 region were purified by column chromatography. On the basis of amino acid analysis, primary sequency data, antigenic properties, and m.w., one of the Cgamma2 fragments was shown to consist of two polypeptide chains of unequal mass joined by the inter-heavy chain disulfide bonds. The larger chain corresponded to a stretch of gamma-chain between Thr 223 and Lys 338 (Eu numbering) and the shorter chain to the section between Thr 223 and Lys 248. The other Cgamma2-fragment was a disulfide-linked dimer of the Thr 223 to Lys 338 sections of the paired gamma-chains. When this latter fragment was reduced under mild conditions it dissociated into monomers indicating that there was little or no noncovalent interactions between the Cgamma2 domains. The Cgamma3-fragment was shown to be a noncovalent dimer composed of the Glu 345 to Lys 349 sections of the two gamma-chains although some heterogeneity was apparent at the amino-terminus. Circular dichroism was used to probe the conformational relationships between the isolated domains and the parent Fc. The spectral properties of Fc could not be fully accounted for on the basis of the spectra observed for the isolated domains which suggested that inter-domain interaction might be significant in Fc.
Approximate Boyer–Moore String Matching (1993)

The Boyer–Moore idea applied in exact string matching is generalized to approximate string matching. Two versions of the problem are considered. The k mismatches problem is to find all approximate occurrences of a pattern string (length m) in a text string (length n) with at most k mismatches. The generalized Boyer–Moore algorithm is shown (under a mild independence assumption) to solve the problem in expected time $O(kn({1 / {(m - k) + ({k / c})}}))$, where c is the size of the alphabet. A related algorithm is developed for the k differences problem, where the task is to find all approximate occurrences of a pattern in a text with $ \leqslant k$ differences (insertions, deletions, changes). Experimental evaluation of the algorithms is reported, showing that the new algorithms are often significantly faster than the old ones. Both algorithms are functionally equivalent with the Horspool version of the Boyer–Moore algorithm when $k = 0$.
Melting temperatures of semiconductor nanocrystals in the mesoscopic size range (2001)

A model, free of any adjustable parameters, is extended to predict the size dependence of the melting temperature of semiconductor nanocrystals. The model predictions are consistent with the experimental results for Si, Bi and CdS semiconductor nanocrystals. In addition, the simplified model with fixed material constants is in agreement with the usual phenomenological relationship that the size dependence of the melting temperature is proportional to the reciprocal of the nanocrystal radius.
An SHIV DNA/MVA Rectal Vaccination in Macaques Provides Systemic and Mucosal Virus-Specific Responses and Protection against AIDS (2004)

We explored the use of a simian-human immunodeficiency virus (SHIV) DNA vaccine as an effective mucosal priming agent to stimulate a protective immune response for AIDS prevention. Rhesus macaques were vaccinated rectally with a DNA construct producing replication-defective SHIV particles, and boosted with either the same DNA construct or recombinant modified vaccinia virus Ankara (MVA) expressing SIV Gag, SIV Pol, and HIV Env (MVA-SHIV). Virus-specific mucosal and systemic humoral and cell-mediated immune responses could be stimulated by this approach but were present inconsistently among the vaccinated animals. Rectal vaccination with either SHIV DNA alone or SHIV DNA followed by MVA-SHIV induced SIV Gag/Pol- or HIV gp120-specific IgA in rectal secretions of four of seven animals. However, the gp120-specific rectal IgA antibody responses were not durable and had become undetectable in all but one animal shortly before rectal challenge with pathogenic SHIV 89.6P. Only the macaques primed with SHIV DNA and boosted with MVA-SHIV demonstrated SHIV-specific IgG in plasma. In addition, these animals developed more consistent antiviral cell-mediated responses and had better preservation of CD4 T cells following challenge with SHIV 89.6P. Our study demonstrates the utility of a rectal DNA/MVA vaccination protocol for the induction of diverse responses in different immunological compartments. In addition, the immunity achieved with this mucosal vaccination regimen is sufficient to delay progression to AIDS.
Multichain immune recognition receptor signaling from spatiotemporal organization to human disease. Preface. (2008)

Foreword William Paul Preface Alexander B. Sigalov Section I. MIRRs: Structure and Physiological Function 1. T-Cell Receptor Jose M. Rojo, Raquel Bello and Pilar Portoles Abstract Introduction Minimal Components and Stoichiometry of the TCR/CD3 Complex TCR Clusters on the Cell Surface Topology of Chain Interactions within TCR/CD3 Complexes Interactions between the TCR and Antigen-Role of CD4 and CD8 Coreceptors Other TCRs Are All TCRs Equal, or Are Some TCRs More Equal Than Others? Future Directions 2. B-Cell Receptor Randall J. Brezski and John G. Monroe Abstract Introduction Structure of the BCR B-Cell Development Molecular Aspects of Ligand-Induced BCR Signal Transduction Membrane Compartmentalization of the BCR Balance between Positive and Negative Regulators of BCR Signaling Ligand-Independent BCR-Induced Tonic Signaling Conclusion 3. Fc Receptors Maree S. Powell and P. Mark Hogarth Abstract Introduction Human receptors for immunoglobulin Interaction between Fc receptor and immunoglobulin Spatial organization of FcRs Physiological function of Fc receptors Concluding comments 4. Natural Killer Cell Receptors Roberto Biassoni Abstract Introduction Inhibitory Receptors Activating Receptors Conclusions 5. Platelet Glycoprotein VI Stephanie M. Jung and Masaaki Moroi Abstract Introduction Structure of GPVI Interaction of GPVI with collagen GPVI-mediated signal transduction Physiological Function of GPVI Summary and perspectives Section II. MIRR Signaling:Possible Mechanisms and the Techniques to Study and Visualize 6. Clustering Models Wolfgang W.A. Schamel and Michael Reth Abstract Introduction Homoclustering Heteroclustering Pseudodimer Model Homo- and Heteroclustering and Lipid Rafts The PreTCR and PreBCR 7. Segregation Models Elaine P. Dopfer, Mahima Swamy, Gabrielle M. Siegers, Eszter Molnar, Jianying Yang and Wolfgang W.A. Schamel Abstract Introduction Lipid Rafts Segregation by Raft Clustering Kinetic-Segregation Model Immune Synapse and Microclusters 8. Kinetic Proofreading Model Byron Goldstein, Daniel Coombs, James R. Faeder and William S. Hlavacek Abstract Introduction Kinetic proofreading illustrated through FceRI signaling The extent of kinetic proofreading in FceRI signaling Some responses may escape kinetic proofreading McKeithan's mathematical formulation T-Cell activation and the competition between kinetic proofreading and serial engagement Concluding remarks 9. Serial Triggering Model Jacob Rachmilewitz Abstract T-Cell Receptor Signaling Cascade Serial Triggering Model Flexible and hierarchical T-Cell Activation Thresholds Temporal Summation as a mechanism for Signal Integration Summary 10. Conformational Model Ruth M. Risueno, Angel R. Ortiz and Balbino Alarcon Abstract Introduction Evidence in Favour of Conformational Changes in MIRRs Consequences for Ligand Recognition Model for Transmission of Conformational Changes Conclusions 11. Permissive Geometry Model Susana Minguet and Wolfgang W.A. Schamel Abstract Introduction The clustering model of
The role of fats in the lifecycle stages: pregnancy and the first year of life. (2002)

Fish oil supplementation during pregnancy has been tested in several trials, with small positive effects on length of gestation; there have been no beneficial or harmful effects on cognitive development or growth of infants as a result of fish oil supplementation in pregnancy. The strongest evidence for good developmental outcomes for infants supports breastfeeding for at least six months. Preterm infants are at the greatest risk of DHA deficiency and there is strong evidence for the positive effects of DHA on visual and cognitive outcomes that has resulted in all Australian preterm formulas being supplemented with DHA. Debate continues about the importance of DHA supplementation for term infants; the current consensus is that the benefits of DHA supplementation in term infants are smaller than for preterm infants.
Inhibition of Yersinia Tyrosine Phosphatase by Furanyl Salicylate Compounds (2004)

To avoid detection and targeting by the immune system, the plague-causing bacterium Yersinia pestis uses a type III secretion system to deliver a set of inhibitory proteins into the cytoplasm of immune cells. One of these proteins is an exceptionally active tyrosine phosphatase termed YopH, which paralyzes lymphocytes and macrophages by dephosphorylating critical tyrosine kinases and signal transduction molecules. Because Y. pestis strains lacking YopH are avirulent, we set out to develop small molecule inhibitors for YopH. We used a novel and cost-effective approach, in which leads from a chemical library screening were analyzed and computationally docked into the crystal structure of YopH. This resulted in the identification of a series of novel YopH inhibitors with nanomolar Ki values, as well as the structural basis for inhibition. Our inhibitors lack the polar phosphate-mimicking moiety of rationally designed tyrosine phosphatase inhibitors, and they readily entered live cells and rescued them from YopH-induced tyrosine dephosphorylation, signaling paralysis, and cell death. These inhibitors may become useful for treating the lethal infection by Y. pestis.
Colloidal ZnSe, ZnSe/ZnS, and ZnSe/ZnSeS Quantum Dots Synthesized from ZnO (2004)

Colloidal ZnSe quantum dots were successfully synthesized from ZnO in a lauric acid/hexadecylamine mixture. X-ray diffraction patterns indicated that the ZnSe quantum dots possess a wurtzite structure. Transmission electron microscope images of the quantum dots showed that the average diameter are in the range of 25∼60 Å. The size-dependent photoluminescence was controlled from 400 to 440 nm with the quantum yields of 6∼10% at room temperature. After passivation with 1.8 monolayer of ZnS overcoat by a traditional two-step method, the quantum yields of ZnSe/ZnS QDs are increased ∼4.5-fold (quantum yield ∼32%). An in-situ method of overcoating was done by directly injecting TOPS into the flask containing ZnSe, ZnO/lauric acid/hexadecylamine, and TOPSe. The photoluminescence quantum yields were improved ∼3.8-fold after introduction of 1.6 monolayer ZnSeS overcoat to the ZnSe QDs.
Using Yeast & Ultraviolet Radiation to Introduce the Scientific Method (1993)

Research Article| January 01 1993 Using Yeast & Ultraviolet Radiation to Introduce the Scientific Method Lois T. Mayo, Lois T. Mayo Search for other works by this author on: This Site PubMed Google Scholar Pat J. Friedrichsen Pat J. Friedrichsen Search for other works by this author on: This Site PubMed Google Scholar The American Biology Teacher (1993) 55 (1): 42–43. https://doi.org/10.2307/4449576 Views Icon Views Article contents Figures & tables Video Audio Supplementary Data Peer Review Share Icon Share Twitter LinkedIn Tools Icon Tools Get Permissions Cite Icon Cite Search Site Citation Lois T. Mayo, Pat J. Friedrichsen; Using Yeast & Ultraviolet Radiation to Introduce the Scientific Method. The American Biology Teacher 1 January 1993; 55 (1): 42–43. doi: https://doi.org/10.2307/4449576 Download citation file: Ris (Zotero) Reference Manager EasyBib Bookends Mendeley Papers EndNote RefWorks BibTex toolbar search Search Dropdown Menu nav search search input Search input auto suggest search filter All ContentThe American Biology Teacher Search This content is only available via PDF. Copyright 1993 National Association of Biology Teachers Article PDF first page preview Close Modal You do not currently have access to this content.
A phase I trial of recombinant human gamma interferon (IFN-gamma 4A) in patients with advanced malignancy. (1988)

We report a Phase I study in 39 cancer patients of the tolerance and biologic activity of 47 intravenous (i.v.), intramuscular (i.m.), and subcutaneous (s.c.) treatments with recombinant methional gamma interferon (IFN-gamma 4A) which most closely resembles the natural material produced by T lymphocytes. Patients were treated with IFN-gamma 4A 5 days a week for 2 weeks. After a 2-week rest period, patients were placed on the same dose of drug three times a week. The most common side effects--fever, chills, malaise, myalgias, and nausea and vomiting--were seen with all routes of administration. Reversible increases in hepatic transaminase and decrease in granulocytes counts were seen. The dose-limiting toxicities observed were malaise and orthostatic hypotension. The maximum tolerated dose was 500-1,000 micrograms/M2/day. The t1/2 of IFN-gamma 4A in the circulation was 20 min after i.v. injection. No blood levels were detected after i.m. or s.c. injection. Antibody against IFN-gamma 4A increased in three patients. A complete response was observed in one patient with pulmonary metastases from renal cell carcinoma.
Readthrough strategies for stop codons in Duchenne muscular dystrophy. (2006)

Duchenne muscular dystrophy is due to mutations of the dystrophin gene. These are large deletions or duplications in 80% of cases, while premature stop codons (nonsense point mutations) account for 7% of cases. This subgroup of patients may take advantage of the properties of the antibiotic gentamicin to suppress stop codons (readthrough). The efficiency of the readthrough varies inversely to the efficiency of a stop codon and is also affected by the different components of the drug. Following gentamicin treatment of mdx mice, dystrophin was re-expressed up to 20% of normal level, albeit with variability among animals. Human trials with gentamicin have so far obtained doubtful results. PTC124 belongs to a new class of small molecules that mimics at lower concentrations the readthrough activity of gentamicin. The administration of PTC124 resulted in the production of full-length and functionally active dystrophin both in vitro and in mdx mice. A Phase II clinical trial is now in course and will be terminated at the end of 2006.
Insulin differentially regulates protein phosphotyrosine phosphatase activity in rat hepatoma cells (1992)

We have studied the effect of insulin stimulation on phosphotyrosine phosphatase (PTPase) activity in the well-differentiated rat hepatoma cell line Fao. PTPase activity was measured using a 32P-labeled peptide corresponding to the major site of insulin receptor autophosphorylation. Of the PTPase activity in Fao cells, 14% was in the cytosolic fraction, whereas 86% was in the particulate fraction; this latter fraction also had a 4-fold higher specific activity. Purification of the particulate fraction by lectin chromatography resulted in a 50% increase in specific activity, although this glycoprotein-rich fraction contained only 1.5% of the total activity. Both the cytosolic and particulate PTPase fractions were active toward the tyrosyl-phosphorylated insulin receptor in vitro. The activity of the particulate fraction but not the cytosolic fraction was inhibited by addition of a micromolar concentration of a phosphorylated peptide corresponding to residues 1142-1153 of the human insulin receptor sequence. By contrast, addition of the nonphosphorylated peptide even at millimolar concentration was without effect. Both PTPase fractions were inhibited by Zn+ at similar concentrations, whereas the cytosolic PTPase activity was 10-fold more sensitive to vanadate inhibition. Treatment of cells with 100 nM insulin increased PTPase activity in the particulate fraction by 40% and decreased activity in the cytosolic fraction by 35%. These effects occurred within 15 min and were half-maximal at 3-4 nM insulin. When assessed as total activity, the magnitude of the changes in PTPase activity in the particulate and cytosolic fractions could not be explained on the basis of a translocation of PTPases between the two pools.(ABSTRACT TRUNCATED AT 250 WORDS)
Bioactive Hydrogels: Maleimide Cross‐Linked Bioactive PEG Hydrogel Exhibits Improved Reaction Kinetics and Cross‐Linking for Cell Encapsulation and In Situ Delivery (Adv. Mater. 1/2012) (2011)

The cover image shows a biofunctionalized hydrogel that is bonded directly onto myocardial tissue, delivering regenerative cells and therapeutics. On page 64, Andrés García and co-workers describe how maleimide-based cross-linking improves polyethylene glycol hydrogel engineering, leading to rapid gelation, high cytocom-patibility, and facile in situ delivery.
General Routes to 4-Oxo-4H-pytano[2,3-b]pyridine-3-carboxylates and Related Compounds: Synthesis of the Oxygen and Sulfur Isosteres of Nalidixic Acid (1993)

Imidazolides of 2-hydroxy- and 2-mercaptonicotinic acids with LiCH 2 CO 2 Bu-t gave ketoesters which were cyclised with MeOCH=NMe 2 + MeOSO 3 − and i-Pr 2 NEt or with (RCO) 2 O-NEt 3 -DMAP to the title 2-H or 2-R bicyclic esters; the corresponding 3-methylsulfonyl and 3-phosphonate analogs were similarly prepared. The 2-unsubstituted 4-oxopyranopyridine-3-carboxylates were unstable at physiological pH, whereas the thio analogs were stable
Contacts between Escherichia coli RNA polymerase and an early promoter of phage T7. (1980)

Specific contacts between the Escherichia coli RNA polymerase (nucleosidetriphosphate:RNA nucleotidyl-transferase, EC2.7.7.6) and the phosphates and purine bases of the A3 promoter of phage T7 cluster into three regions located approximately 10, 16, and 35 base pairs before RNA initiation site. Two of these contain nucleotide sequences that are fairly conserved among many promoters, known as the "Pribnow box" and "-35 region" homologies; the third, just upstream from the Pribnow box, is not conserved. The polymerase binds preferentially to the coding strand and for the most part touches only one face of the DNA helix.
Liver regeneration studies with rat hepatocytes in primary culture. (1982)

Adult rat parenchymal hepatocytes in primary culture can be induced to enter into DNA synthesis and mitosis. The optimal conditions for hepatocyte replication are low plating density (less than 10,000 cells/sq cm) and 50% serum from two-thirds partially hepatectomized rats (48 hr after hepatectomy). Approximately 80% of the hepatocytes enter the cell cycle, and most of these cells go through mitosis. The replicating hepatocytes remain positive for glucose-6-phosphatase and negative for gamma-glutamyl transpeptidase, and they accumulate fat, in analogy to regenerating liver. Most of the replicating hepatocytes enter into multiple consecutive rounds of DNA synthesis. Dose-response studies between control animal serum and hepatocyte labeling index indicate that in unoperated animals the serum contains substances stimulatory as well as inhibitory for hepatic growth, with the inhibitory effect prevailing at high concentrations. After partial hepatectomy, the inhibitory activity disappears whereas the hepatopoietin activity reaches almost 90% of maximal biological effectiveness at 25% serum concentration. Addition of hormones to the system shows that the hepatopoietin activity is not identical to epidermal growth factor, platelet-derived growth factor, thyroxine, glucagon, or hydrocortisone. Norepinephrine abolishes the difference between control and hepatectomized serum but does not restore hepatopoietin activity when added to heat-inactivated serum. The results show that this system of replicating hepatocytes can be used to investigate the trophic factors that control growth of normal and neoplastic hepatocytes.
Incremental Learning for Visual Tracking (2004)

Most existing tracking algorithms construct a representation of a target object prior to the tracking task starts, and utilize invariant features to handle appearance variation of the target caused by lighting, pose, and view angle change. In this paper, we present an efficient and effective online algorithm that incrementally learns and adapts a low dimensional eigenspace representation to reflect appearance changes of the target, thereby facilitating the tracking task. Furthermore, our incremental method correctly updates the sample mean and the eigenbasis, whereas existing incremental subspace update methods ignore the fact the sample mean varies over time, The tracking problem is formulated as a state inference problem within a Markov Chain Monte Carlo framework and a particle filter is incorporated for propagating sample distributions over time. Numerous experiments demonstrate the effectiveness of the proposed tracking algorithm in indoor and outdoor environments where the target objects undergo large pose and lighting changes. 1
Targeting the Hedgehog Pathway to Mitigate Treatment Resistance (2007)

'Hedgehog' (HH) molecules are secretory signaling proteins that were first discovered in Drosophila. Three HH homologs have been identified in humans including Sonic hedgehog (SHH), Indian hedgehog (IHH) and Desert hedgehog (DHH). During embryonic development, the Hedgehog (HH) signaling pathway is critical, and it regulates both proliferation and differentiation of various types of stem cells.1This article provides a brief overview of HH signaling, summarizes the correlation between HH signaling and treatment resistance of cancer cells, and discusses the recent advances in targeting this signaling cascade to overcome treatment resistance with supporting experimental results.
Neuromodulation of intestinal transport in the suckling mouse (1989)

The influence of enteric nerves on intestinal ion and sugar transport was investigated in 3- to 4-wk-old suckling mice. Whole thickness segments of jejunum were mounted as flat sheets in flux chambers equipped to electrically stimulate nerves in the intestinal wall. Tetrodotoxin significantly reduced basal short-circuit current in a subset of tissues containing 3-O-methylglucose in the mucosal bath. Electrical field stimulation of intrinsic nerves evoked an increase in short-circuit current of 86 +/- 15 microA/cm2 that was due to an increase in active chloride secretion with no significant change in the net movement of other ions. The secretory response to neural stimulation was abolished by tetrodotoxin and reduced by the muscarinic antagonist, atropine. Mucosal-to-serosal fluxes of 3-O-methylglucose were not altered by the cholinergic agonist carbachol. These results show that ion transport in the suckling mouse jejunum is regulated by the enteric nervous system. Neural stimulation evokes a chloride secretory response that is mediated by acetylcholine and other noncholinergic transmitters. Sugar transport in the murine small intestine does not appear to be influenced by muscarinic cholinergic agonists.
A critique of SVD-based image coding systems (2003)

During the past couple of decades several proposals for image coders using singular value decomposition (SVD) have been put forward. The results using SVD in this context have never been spectacular. The main problem with the SVD is that the transform itself must be transmitted as side information. We demonstrate through some simple experiments that for a given image reconstruction quality, more scalar parameters must be transmitted using the SVD, than when using the discrete cosine transform (DCT). Also, using an alternative interpretation of the SVD we show that the SVD representation necessitates quantization of individual factors as compared to quantization of the associated product. This is clearly suboptimal.