gebhart/patrepeval huggingface dataset:
Influence of heavy chain constant regions on antigen binding and HIV-1 neutralization by a human monoclonal antibody (1995)

F105, a neutralizing IgG1 kappa human mAb, is reactive with a discontinuous epitope within the gp120 CD4 binding site. Because isotype usage may affect Ab function, we examined the effect of isotype on Ag/Ab interactions and HIV-1 neutralization. An IgG3 kappa Ab was prepared by linking the variable regions of F105 to cloned human kappa and gamma 3 constant regions. Immunoreactivity of F105 IgG1 and IgG3 with IIIB-, MN-, and RF-infected cells was equivalent. Inhibition of binding and fusion of IIIB to uninfected cells and neutralization of IIIB virus was comparable for F105 IgG1 and IgG3, with 14 to 23 micrograms/ml required for 90% neutralization. In contrast, F105 IgG3 was marginally more effective at inhibition of MN binding/fusion and significantly more effective at neutralization of MN virus (62 micrograms/ml for IgG3 and > 100 micrograms/ml for IgG1 to achieve 90% neutralization). Despite high affinity binding to RF-infected cells, F105 IgG1 minimally neutralizes free RF virus. F105 IgG3 is dramatically more effective against the RF isolate, with 2 to 20 micrograms/ml of Ab required for 50% neutralization. Both isotypes were relatively ineffective at inhibition of RF binding/fusion. Thus, whereas affinity with native Ags on the surface of HIV-1-infected cells was unaffected by heavy chain constant regions, Ab isotype can strongly influence virion neutralization. Structural changes in gp120, as a result of increased flexibility conferred by the elongated IgG3 hinge region, are suggested as a possible mechanism to increase neutralization of selected HIV-1 isolates. These results may have significant implications in the design of immunotherapeutic and vaccine agents.
Gene expression in tobacco low-nicotine mutants. (1994)

Two nuclear genes, Nic1 and Nic2, regulate nicotine levels in tobacco. nic1 and nic2 are semidominant mutations in Burley 21 that reduce leaf nicotine levels and the activities of multiple enzymes in the nicotine pathway and simultaneously increase polyamine levels in cultured roots. Cultured roots homozygous for both mutations were used to isolate two cDNAs by subtraction hybridization; the transcript levels of these two cDNAs were much lower in the mutant roots than in the wild-type roots. The A411 gene encodes a 41-kD protein with considerable homology to mammalian spermidine synthase, whereas the A622 gene encodes a 35-kD protein with high homology to isoflavone reductase. When these genes were expressed in Escherichia coli, A411 had no spermidine synthase activity but did show putrescine N-methyltransferase activity, which is the first enzyme committed to the nicotine biosynthetic pathway, and A622 did not show isoflavone reductase activity. Both the methyltransferase and A622 genes are predominantly expressed in the root, and their expression levels in cultured roots are coordinately decreased by the nic mutations in the order of wild type > nic2 > nic1 > nic1 nic2. Removal of tobacco flower heads and young leaves rapidly and coordinately induced both genes in the root. Further, exogenous supply of auxin down-regulated both genes in cultured tobacco roots. These results suggest that Nic1 and Nic2 are regulatory genes for nicotine biosynthesis.
The role of neutrophils in cystic fibrosis (2013)

This article reviews the past 12 months of research that contributes to our understanding of the role of neutrophils and immune dysfunction in CF.
Ectopic expression of neutrophil gelatinase‐associated lipocalin suppresses the invasion and liver metastasis of colon cancer cells (2005)

Neutrophil gelatinase-associated lipocalin (NGAL), also known as lipocalin 2, is a 25-kDa lipocalin initially purified from neutrophil granules. It is thought to play a role in regulating cellular growth since its expression is highly upregulated in a variety of proliferative cells such as cancer cells. However, experimental evidence showing a clear causal relationship between NGAL expression and the proliferation of tumor cells is lacking. Here, we found NGAL expression in highly and poorly metastatic colon cancer cell lines of the same genetic origin correlated inversely with the metastatic potential of these cells, which suggests NGAL participates in the metastatic process. To explore the role NGAL plays in tumor growth and metastasis, the KM12SM human colon cancer cell line, which is highly metastatic while showing decreased NGAL expression, was genetically manipulated to overexpress NGAL. The effects of this on tumor growth and liver metastasis were then analyzed using experimental animal models established by injecting BALB/c nude mice with tumor cells subcutaneously or intrasplenically. Ectopic expression of NGAL in the colon cancer cells had little effect on the growth and viability of the tumor cells both in vitro and in vivo. However, NGAL expression not only suppressed the ability of the colon carcinoma cells to invade Matrigel in vitro, it also substantially inhibited liver metastasis in an experimental animal model. Collectively, these results indicate that NGAL may be a candidate metastasis suppressor in colon cancer cells.
Toll-Like Receptor 4 Deficiency Increases Disease and Mortality after Mouse Hepatitis Virus Type 1 Infection of Susceptible C3H Mice (2009)

Severe acute respiratory syndrome (SARS) is characterized by substantial acute pulmonary inflammation with a high mortality rate. Despite the identification of SARS coronavirus (SARS-CoV) as the etiologic agent of SARS, a thorough understanding of the underlying disease pathogenesis has been hampered by the lack of a suitable animal model that recapitulates the human disease. Intranasal (i.n.) infection of A/J mice with the CoV mouse hepatitis virus strain 1 (MHV-1) induces an acute respiratory disease with a high lethality rate that shares several pathological similarities with SARS-CoV infection in humans. In this study, we examined virus replication and the character of pulmonary inflammation induced by MHV-1 infection in susceptible (A/J, C3H/HeJ, and BALB/c) and resistant (C57BL/6) strains of mice. Virus replication and distribution did not correlate with the relative susceptibilities of A/J, BALB/c, C3H/HeJ, and C57BL/6 mice. In order to further define the role of the host genetic background in influencing susceptibility to MHV-1-induced disease, we examined 14 different inbred mouse strains. BALB.B and BALB/c mice exhibited MHV-1-induced weight loss, whereas all other strains of H-2(b) and H-2(d) mice did not show any signs of disease following MHV-1 infection. H-2(k) mice demonstrated moderate susceptibility, with C3H/HeJ mice exhibiting the most severe disease. C3H/HeJ mice harbor a natural mutation in the gene that encodes Toll-like receptor 4 (TLR4) that disrupts TLR4 signaling. C3H/HeJ mice exhibit enhanced morbidity and mortality following i.n. MHV-1 infection compared to wild-type C3H/HeN mice. Our results indicate that TLR4 plays an important role in respiratory CoV pathogenesis.
Analysis of retrieval performance for selected file organization techniques (1970)

It is noted that file organization techniques of this type are frequently augmented with a pre-store sort. * This is reasonable in view of the fact that we are concerned solely with retrieval. Other performance characteristics such as sequential processing efficiency are, of course, dependent on the organization of the main file. ** Here a record consists of an identifier-address pair. Case II: Calculated index *The E['] notation is used to denote the expectation of the variable enclosed within the brackets. * Ideally the transformation T should evenly distribute the m records over the set of n blocks. ** Obviously this can be accomplished providing m > nb
First superconducting prototype magnets for a compact synchrotron radiation source in operation (1988)

The design and construction of a pair of 180 degrees superconducting bending magnets ar briefly described. Both magnets reached the design flux density of 4.5 T at the electrons' orbit. The maximum flux density of 6.0 T at the winding corresponds to a current of 1.6 kA.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Abstract 4882: Genomic mechanisms of disease progression in pediatric medullary thyroid cancer (MTC) (2017)

Abstract Background: Multiple Endocrine Neoplasia (MEN) 2B is a rare hereditary disorder characterized by medullary thyroid cancer (MTC) in early childhood, pheochromocytoma, and mucosal neuromas. Patients with advanced MTC are treated with rearranged during transfection (RET) targeting tyrosine kinase inhibitors (TKIs) such as vandetanib. Despite initial responses, many patients progress on TKI therapy and mechanisms of resistance are yet to be elucidated. We analyzed tumor samples from seven children with MEN2B and MTC enrolled in a natural history study (NCT01660984). Methods: DNA samples from tumor and adjacent normal tissue from paraffin embedded blocks or unstained slides were analyzed by a custom capture next-generation sequencing panel. Bioinformatics analyses identified point mutations, insertions, deletions and copy number variations. Results: Seven patients (median age at study enrollment 14 years, range 11-17 years) with the RET p.Met918Thr germline mutation were included in analysis. Tumor samples were available for three patients pre-TKI (four samples), two patients at progression on TKI (three samples), and two patients both, pre-TKI and at progression (five samples). Pre-TKI samples exhibited few tumor specific mutations or copy number variations and 4/5 patients had loss of chromosome 1p. Progression for one patient was associated with acquisition of a previously unidentified p.Leu790Phe mutation within the kinase domain of the RET gene. Loss of heterozygosity and increase in copy number variations were noted in 4/5 samples at tumor progression. Two patients had copy number loss of chromosome 14 and three had copy number gain of chromosome 1q. Recurrent, somatic, non-synonymous mutations were not identified in the sample set. Conclusion: In children with MEN2B and MTC, we identified increase in copy number variations and a somatic mutation within the RET gene as potential mechanisms of drug resistance. Our data imply that a common genetic mechanism for progression on TKI may not exist within this small sample set and highlight the need for serial collection of tumor tissue. Further, whole genome aneuploidy may provide rationale for the evaluation of cytotoxic chemotherapy in patients who experience progressive disease on TKI therapy. Analysis of additional samples and whole exome DNA and RNA sequencing are ongoing. Citation Format: Ira L. Kraft, Srivandana Akshintala, Keith J. Killian, Robert B. Hufnagel, John W. Glod, Claudia Derse-Anthony, Yuelin Zhu, Holly S. Stevenson, Diana Bradford, Maria J. Merino, Frank M. Balis, Elizabeth Fox, Brigitte C. Widemann, Jack F. Shern, Paul S. Meltzer. Genomic mechanisms of disease progression in pediatric medullary thyroid cancer (MTC) [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 4882. doi:10.1158/1538-7445.AM2017-4882
Inhibition of acyl-CoA synthetase by triacsins. (1987)

Triacsin A, 1-hydroxy-3-(E,E-2',4'-undecadienylidine) triazene and triacsin C, 1-hydroxy-3-(E,E,E-2',4',7'-undecatrienylidine) triazene are potent inhibitors of acyl-CoA synthetase (EC 6.2.1.3). The concentrations of triacsin A required for 50% inhibition of acyl-CoA synthetase from Pseudomonas aeruginosa and from rat liver are 17 and 18 microM, and those of triacsin C are 3.6 and 8.7 microM, respectively. Kinetic analysis indicates that inhibition of triacsin A is non-competitive with respect to the two substrates ATP and coenzyme A, but is competitive with respect to long-chain fatty acids. The apparent Ki value is 8.97 microM when oleic acid is used as substrate. Acid hydrolysis of triacsins results in corresponding polyenic aldehydes with no activity. This suggests that the N-hydroxytriazene moiety is essential for inhibitory activity against acyl-CoA synthetase.
Neuroprotective activity of N-acetylaspartylglutamate in cultured cortical cells (1998)

The endogenous dipeptide, alpha-N-acetylaspartylglutamate behaves as a partial agonist of N-methyl-D-aspartate receptors, but can also activate metabotropic glutamate receptors, with a high degree of selectivity for the metabotropic glutamate receptor 3 subtype. Knowing that agonists of group-II metabotropic glutamate receptors (i.e. of mGlu2 and -3 receptors) are neuroprotective, we have examined the neuroprotective activity of alpha-N-acetylaspartylglutamate in mixed cultures of mouse cortical cells exposed to a toxic pulse with N-methyl-D-aspartate. Alpha-N-acetylaspartylglutamate co-applied with N-methyl-D-aspartate was neuroprotective, but its action was insensitive to the selective group-II metabotropic glutamate receptor antagonist, ethylglutamate. Protection was instead antagonized by ethylglutamate when alpha-N-acetylaspartylglutamate was applied to the cultures immediately after the N-methyl-D-aspartate pulse, a condition in which there was no direct competition between alpha-N-acetylaspartylglutamate and N-methyl-D-aspartate at the level of N-methyl-D-aspartate receptors. alpha-N-acetylaspartylglutamate was highly neuroprotective when transiently applied to pure cultures of cortical astrocytes and the conditioned medium, collected 20 h later, was transferred to sister mixed cultures challenged with N-methyl-D-aspartate. This particular form of neuroprotection was attenuated or abolished when astrocytes where exposed to alpha-N-acetylaspartylglutamate in the presence of the group-II metabotropic glutamate receptor antagonists ethylglutamate or (2S, 1'S,2'S,3'R)-2-(2'-carboxy-3'-phenylcyclopropyl)glycine, but not in the presence of the N-methyl-D-aspartate receptor antagonist, D-2-amino-5-phosphonopentanoate. These results indicate that alpha-N-acetylaspartylglutamate induces neuroprotective effects in culture, which are mediated, at least in part, by the activation of glial metabotropic glutamate receptor 3 receptors.
Management of Hyperglycemia in Type 2 Diabetes: A Consensus Algorithm for the Initiation and Adjustment of Therapy (2007)

The consensus algorithm for the management of type 2 diabetes was developed on behalf of the American Diabetes Association and the European Association for the Study of Diabetes approximately 1 year ago (1,2). This evidence-based algorithm was developed to help guide health care providers to choose the most appropriate treatment regimens from an ever-expanding list of approved medications. The authors continue to endorse the major features of the algorithm, including the need to achieve and maintain glycemia within or as close to the nondiabetic range as is safely possible, the initiation of lifestyle interventions and treatment with metformin at the time of diagnosis, the rapid addition of medications and transition to new regimens when target glycemia is not achieved, and the early addition of insulin therapy in patients who do not meet target A1C levels.

The availability of newly approved medications and the accrual of new clinical trial and other data should inform the algorithm. In this update, we primarily address one important issue that has received much recent attention: our current understanding of the advantages and disadvantages of the thiazolidinediones. In addition, we have revised the original Table 1 to include the dipeptidylpeptidase-4 inhibitor sitagliptin, which was not approved by the U.S. Food and Drug Administration at the time of our original publication (Table 1).

We are mindful of the importance of not changing this consensus guideline in …
Treatment of aggressive non-Hodgkin's lymphoma. (1999)

Clinically aggressive lymphomas are defined by the Revised European-American Classification for lymphoid neoplasms as diffuse large B-cell lymphoma, peripheral T-cell lymphoma, anaplastic large cell lymphoma, and lymphoblastic lymphoma. Mantle cell lymphoma is atypical due to its indolent presentation and refractoriness to treatments. A review of current therapeutic possibilities for these different lymphomas is presented.
Serum YKL-40 concentrations in patients with rheumatoid arthritis: relation to disease activity (1999)

Serum YKL-40 varies according to disease activity in RA, but provides in some respect information different from conventional markers. Our previous studies are consistent with a local release of YKL-40 in the arthritic joint followed by a secondary increase in serum YKL-40. YKL-40 may prove to be a new tool for the study of disease activity and pathophysiology of RA.
The Human Growth Hormone Antagonist B2036 Does Not Interact with the Prolactin Receptor (1999)

Abstract The human growth hormone (hGH) antagonist B2036 combines a single amino acid substitution impairing receptor binding site 2 (G120K) with eight additional amino acid substitutions that improve binding site 1 affinity. This hGH antagonist is being tested for treating pathologies linked to excess hGH levels. B2036-PEG is a polyethylene glycol (PEG) conjugated form of B2036 that has an increased half-life due to reduced renal clearance. It is currently in phase III trials for acromegaly. Human GH is also able to bind to the receptor of prolactin (PRLR). Since activation of PRLR can promote an array of pathological states (reproduction disorders, breast cancer), the ability of B2036-PEG to interact with the PRLR had to be determined. In this study, we compared four hGH antagonists (G120K, G120K-PEG, B2036 and B2036-PEG) in three bioassays: proliferation of rat Nb2 cells, binding to the human PRLR and activation of human PRLR-mediated signaling in a cell line stably expressing this receptor and a luciferase reporter gene. Agonistic and antagonistic properties were characterized. Our data show that B2036-PEG does not bind, activate or antagonize PRLRs, either from rat or human origin. These observations further demonstrate that the eight amino acid substitutions within binding site 1 provide binding specificity directed towards the human GH receptor.
Applications of Influenza Virosomes as a Delivery System (2006)

The induction of effective cellular and humoral immune responses against antigens is the major goal in vaccination strategies against infectious diseases and cancer. In this review, we will discuss influenza virosomes as a versatile delivery system for molecules of a different nature, such as proteins, peptides and nucleic acids. These molecules can be administered in different ways, such as nasal, muscular or dermal routes, also facilitating the uptake of the antigen by antigen-presenting cells (APC) and inducing a specific humoral and cell-mediated immune response, particularly a CTL response. Influenza virosomes, due to their applicability in different medical fields, are a promising tool in vaccinology and immunotherapy applications.
Serum Tests for Diagnosis and Follow-Up of Hepatocellular Carcinoma after Treatment (1998)

Hepatocellular carcinoma (HCC) is a well-established complication of liver cirrhosis with an annual incidence of 2–7% [1]. Since patients with HCC are prone to develop recurrent and second liver tumors after potentially curative therapy, it is mandatory to screen these patients using several diagnostic methods, including ultrasonographyand appropriate serological tumor markers. In the past years, a variety of new tumor markersother than α-fetoprotein have been proposed for diagnosis and follow-up of HCC.
Time-Wavelength Spectroscopy for Chemical Sensing (2004)

Time-wavelength spectroscopy, using a linearly chirped broad-band pulse, eliminates the need for an optical spectrometer and enables real-time analysis. Utilizing digital filtering and matched detection, we demonstrate identification of gas signatures that are entirely masked by highly nonuniform source spectra.
Singing Mice, Songbirds, and More: Models for FOXP2 Function and Dysfunction in Human Speech and Language (2006)

In 2001, a point mutation in the forkhead box P2 (FOXP2) coding sequence was identified as the basis of an inherited speech and language disorder suffered by members of the family known as "KE." This mini-symposium review focuses on recent findings and research-in-progress, primarily from five laboratories. Each aims at capitalizing on the FOXP2 discovery to build a neurobiological bridge between molecule and phenotype. Below, we describe genetic through behavioral techniques used currently to investigate FoxP2 in birds, rodents, and humans for discovery of the neural bases of vocal learning and language.
Therapeutic opportunities for targeting the ubiquitous cell surface receptor CD47 (2012)

Ongoing studies are revealing a central role of CD47 for conveying signals from the extracellular microenvironment that limit cell and tissue survival upon exposure to various types of stress. Based on this key function, therapeutics targeting CD47 or its ligands thrombospondin-1 and SIRPα could have broad applications spanning reconstructive surgery, engineering of tissues and biocompatible surfaces, vascular diseases, diabetes, organ transplantation, radiation injuries, inflammatory diseases, and cancer.
Fatty Aldehydes in Cyanobacteria Are a Metabolically Flexible Precursor for a Diversity of Biofuel Products (2013)

We describe how pathway engineering can be used to convert a single intermediate derived from lipid biosynthesis, fatty aldehydes, into a variety of biofuel precursors including alkanes, free fatty acids and wax esters. In cyanobacteria, long-chain acyl-ACPs can be reduced to fatty aldehydes, and then decarbonylated to alkanes. We discovered a cyanobacteria class-3 aldehyde-dehydrogenase, AldE, that was necessary and sufficient to instead oxidize fatty aldehyde precursors into fatty acids. Overexpression of enzymes in this pathway resulted in production of 50 to 100 fold more fatty acids than alkanes, and the fatty acids were secreted from the cell. Co-expression of acyl-ACP reductase, an alcohol-dehydrogenase and a wax-ester-synthase resulted in a third fate for fatty aldehydes: conversion to wax esters, which accumulated as intracellular lipid bodies. Conversion of acyl-ACP to fatty acids using endogenous cyanobacterial enzymes may allow biofuel production without transgenesis.
Genetic design for facilitated production and recovery of recombinant proteins in Escherichia coli (2002)

Genetic strategies have been used for more than two decades to improve bacterial bioprocesses and to simplify recovery procedures. Such strategies include the design of efficient expression vectors and the improvement of bacterial production strains in different ways, e.g. by deletion of protease genes or engineering for overexpression of rare-codon tRNAs, foldases or chaperones. Gene multimerization is another such principle that has proved beneficial to improve production yields. Genetic strategies have furthermore been exploited to facilitate recovery processes by adapting the product for a particular purification principle. In this area, affinity fusions have been commonly used, but other principles, such as modified isoelectric point (pI) or hydrophobic properties have also been successfully investigated. A recent drastic step forward in the use of gene technology to improve recovery processes for recombinant proteins is the introduction of combinatorial protein engineering to generate tailor-made product-specific affinity ligands. This strategy, which allows efficient recovery of a recombinant protein in its native form, is likely to be increasingly used also in industrial-scale bioprocesses, since novel protein ligands have been described that can be sanitized using common industrial cleaning-in-place procedures. The examples presented in this review make it evident that genetic strategies will be of utmost importance in the future for facilitating production and recovery of recombinant proteins.