gebhart/patrepeval huggingface dataset:
Acquisition of protease resistance by prion proteins in scrapie-infected cells does not require asparagine-linked glycosylation. (1990)

The scrapie and cellular isoforms of the prion protein (PrPSc and PrPC) differ strikingly in a number of their biochemical and metabolic properties. The structural features underlying these differences are unknown, but they are thought to result from a posttranslational process. Both PrP isoforms contain complex type oligosaccharides, raising the possibility that differences in the asparagine-linked glycosylation account for the properties that distinguish PrPC and PrPSc. ScN2a and ScHaB cells in culture produce several PrP molecules with relative molecular masses of 26-35 kDa and proteinase K-resistant cores of 19-29 kDa. When the cells were treated with tunicamycin, this heterogeneity was eliminated and a single PrP species of 26 kDa was observed. Several hours after its synthesis, a fraction of this protein became insoluble in detergents and acquired a proteinase K-resistant core, thus displaying two of the biochemical hallmarks of PrPSc. Synthesis in the presence of tunicamycin restricted the proteinase K-resistant cores of PrP to a single species of 19 kDa. No proteinase K-resistant PrP was found in uninfected cells. Expression of a mutated PrP gene lacking both asparagine-linked glycosylation sites in ScN2a cells resulted in the synthesis of 19-kDa proteinase K-resistant PrP molecules. We conclude that asparagine-linked glycosylation is not essential for the synthesis of proteinase K-resistant PrP and that structural differences unrelated to asparagine-linked oligosaccharides must exist between PrPC and PrPSc. Whether unglycosylated PrPSc molecules are associated with scrapie prion infectivity remains to be established.
Regioselectivity in the nickel-catalysed coupling of cyclic carbonates of but-3-ene-1,2-diols with organoborates (1995)

The regioselectivity of nickel-catalysed coupling of but-3-ene-1,2-diol cyclic carbonates 1 and organoborates 3 is examined, in which an ester or olefin directs the coupling site to afford conjugated products.
Three contiguous lipoprotein genes in Pasteurella haemolytica A1 which are homologous to a lipoprotein gene in Haemophilus influenzae type b (1993)

An Escherichia coli clone carrying the recombinant plasmid pPH24 has been found to express highly immunoreactive antigens of Pasteurella haemolytica A1. Two or three antigens of approximately 30 kDa were located to both the inner and outer membranes of the E. coli clone and in P. haemolytica A1. From the insert DNA of 8.2 kbp on pPH24, a fragment of 4.6 kbp was found to code for these antigens. Nucleotide sequence analysis of the 4.6-kbp DNA identified three genes (designated plpA, -B, and -C) arranged in tandem which code for three proteins, Plp1, -2, and -3, with predicted molecular masses of 30.1, 30.3, and 29.0 kDa, respectively. Comparison of the nucleic acid sequence of plpA, -B, and -C with GenBank sequences showed extensive homology with a Haemophilus influenzae 28-kDa lipoprotein gene. [14C]palmitate labelling coupled with glybomycin inhibition experiments showed that Plp1, -2, and -3 are also lipoproteins. In addition, plpA, -B, and -C were found to be present only in A biotypes of P. haemolytica by Southern blot analysis. Since Plp1, -2, and -3 were found to be antigenic components in a culture supernatant vaccine, they could be candidates for further investigation as vaccine components.
Acyclic Sugar Analogs of Triciribine: Lack of Antiviral and Antiproliferative Activity Correlate with Low Intracellular Phosphorylation (1999)

Triciribine and triciribine monophosphate have antiviral and antiproliferative activity at low or submicromolar concentrations. In an effort to improve and better understand this activity, we have synthesized a series of acyclic analogs and evaluated them for activity against select viruses and cancer cell lines. We conclude that the rigid ribosyl ring system of triciribine must be intact in order to be phosphorylated and to obtain significant antiviral and antiproliferative activity.
Chromosomal protein HMG1 removes the transcriptional block caused by the cruciform in supercoiled DNA. (1990)

The binding of chromosomal protein HMG1 to a palindromic sequence that can form the cruciform structure in supercoiled DNA and the subsequent effect on the transcription of the sequence were examined with pBR322 and its derivative plasmids. The plasmid DNA under negative supercoiling showed a selective sensitivity to nuclease S1. HMG1 protected against the nuclease S1 digestion. The results of the filter binding assay indicated that the primary binding target of HMG1 is the single-stranded region within the cruciform in supercoiled DNA. In the transcription from pBR322 DNA in the absence of HMG1, intermediate transcripts of RNA-I, which are encoded from a DNA region containing the palindromic sequence that can form a cruciform, were accumulated with the increase in negative superhelical density whereas the full-length RNA-I was synthesized without an accumulation of intermediate transcripts in the presence of HMG1. The intermediates that accumulated in the absence of HMG1 were elongated to the final product by adding HMG1. These results suggest that the cruciform structure formed under negative supercoiling blocks transcription and that HMG1 can remove the block by altering the DNA conformation to allow the stalled RNA polymerase at the block to resume transcription.
Reducing AD-Like Pathology in 3xTg-AD Mouse Model by DNA Epitope Vaccine — A Novel Immunotherapeutic Strategy (2008)

Data from this transitional pre-clinical study suggest that our DNA epitope vaccine could be used as a safe and effective strategy for AD therapy. Future safety and immunology studies in large animals with the goal to achieve effective humoral immunity without adverse effects should help to translate this study to human clinical trials.
Masked polycythemia vera diagnosed according to WHO and BCSH classification (2013)

Polycythemia vera (PV) is currently diagnosed by the World Health Organization (WHO) criteria regarding hemoglobin (HB) levels and JAK2V617F and related mutations or by the British Committee for Standards in Haematology (BCSH) guidelines predominantly based on hematocrit (HCT) values (&gt;52% in men and &gt;48% in women) in JAK2 mutated patients. We examined clinical features at diagnosis and outcome in 397 mutated PV patients showing a bone marrow (BM) morphology conforming with the WHO descriptions but including also cases with a HB level &lt;18.5 g/dL in males (range 16.0–18.4) and &lt;16.5 g/dL in females (range 15.0–16.4). These patients were regarded as masked PV (mPV) comprising 140 (35%) cases of our cohort. A comparison with the BCSH criteria based on HCT levels revealed a decrease of mPV patients to 59 (15%). In both classification systems, mPV patients were more males, presented more frequently with higher platelet counts, and increased BM reticulin fibrosis. A worsening of overall survival was documented in mPV patients in comparison with overt PV following the WHO ( P = 0.011) as well as the BCSH ( P = 0.0019) criteria. Risk factors for inferior survival in mPV were age &gt;65 years and white blood cell count &gt;15 × 10 9 /L. Without these risk factors mPV patients had the same survival as overt PV suggesting that a fraction of patients with HB lower than that required for WHO diagnosis should still be considered as overt PV. This study has established the existence of mPV by two different classification systems based on either HB or HCT threshold values. Am. J. Hematol. 89:199–202, 2014. © 2013 Wiley Periodicals, Inc.
Comparison of Integrases Identifies Bxb1-GA Mutant as the Most Efficient Site-Specific Integrase System in Mammalian Cells (2019)

Phage-derived integrases can catalyze irreversible, site-specific integration of transgenic payloads into a chromosomal locus, resulting in mammalian cells that stably express transgenes or circuits of interest. Previous studies have demonstrated high-efficiency integration by the Bxb1 integrase in mammalian cells. Here, we show that a point mutation (Bxb1-GA) in Bxb1 target sites significantly increases Bxb1-mediated integration efficiency at the Rosa26 locus in Chinese hamster ovary cells, resulting in the highest integration efficiency reported with a site-specific integrase in mammalian cells. Bxb1-GA point mutant sites do not cross-react with Bxb1 wild-type sites, enabling their use in applications that require orthogonal pairs of target sites. In comparison, we test the efficiency and orthogonality of ϕC31 and Wβ integrases, and show that Wβ has an integration efficiency between those of Bxb1-GA and wild-type Bxb1. Our data present a toolbox of integrases for inserting payloads such as gene circuits or therapeutic transgenes into mammalian cell lines.
Infection and Propagation of Human Rhinovirus C in Human Airway Epithelial Cells (2012)

Human rhinovirus species C (HRV-C) was recently discovered using molecular diagnostic techniques and is associated with lower respiratory tract disease, particularly in children. HRV-C cannot be propagated in immortalized cell lines, and currently sinus organ culture is the only system described that is permissive to HRV-C infection ex vivo. However, the utility of organ culture for studying HRV-C biology is limited. Here, we report that a previously described HRV-C derived from an infectious cDNA, HRV-C15, infects and propagates in fully differentiated human airway epithelial cells but not in undifferentiated cells. We demonstrate that this differentiated epithelial cell culture system supports infection and replication of a second virus generated from a cDNA clone, HRV-C11. We show that HRV-C15 virions preferentially bind fully differentiated airway epithelial cells, suggesting that the block to replication in undifferentiated cells is at the step of viral entry. Consistent with previous reports, HRV-C15 utilizes a cellular receptor other than ICAM-1 or LDLR for infection of differentiated epithelial cells. Furthermore, we demonstrate that HRV-C15 replication can be inhibited by an HRV 3C protease inhibitor (rupintrivir) but not an HRV capsid inhibitor previously under clinical development (pleconaril). The HRV-C cell culture system described here provides a powerful tool for studying the biology of HRV-C and the discovery and development of HRV-C inhibitors.
The Site of the Inhibition of the Shikimate Pathway by Glyphosate (1980)

In the presence of the nonselective herbicide glyphosate (N-[phosphonomethyl]glycine), buckwheat (Fagopyrum esculentum Moench) hypocotyls and cultured cells of Galium mollugo L. accumulate an organic acid, which was identified as shikimate by mass-spectroscopy of its methyl ester. After growth in 0.5 millimolar glyphosate for 10 days, G. mollugo cells contained shikimate in amounts of up to 10% of their dry weight. Synthesis of chorismate-derived anthraquinones in G. mollugo was blocked by glyphosate. Chorismate and o-succinylbenzoate (an anthraquinone precursor) alleviated the inhibition. The conclusion drawn from these experiments, that glyphosate inhibits a step in the biosynthetic sequence from shikimate to chorismate, was substantiated by the finding that glyphosate is a powerful inhibitor of the conversion of shikimate to chorismate in cell-free extracts from Aerobacter aerogenes 62-1.
Manipulating Immunological Checkpoints to Maximize Antitumor Immunity (2006)

Initial clinical trials have demonstrated the safety and bioactivity of cancer vaccines, but vaccine-induced immune responses have seldom translated into clinically meaningful tumor regressions, particularly in advanced disease. It is increasingly clear that tumor-specific immune tolerance represents a layered system of controls that keep the immune system turned off. Immunoregulatory checkpoints map locoregionally to the tumor microenvironment and draining lymph nodes, and arise from the dynamic interactions between the tumor and the immune system. It is now apparent that cancer vaccines will have to be combined with other therapeutics that abrogate immune tolerance, further amplify vaccine-induced T-cell responses, or modify the tumor microenvironment to make it more conducive to the concerted action of innate and antigen-specific immune effector mechanisms. Here, we review the host-tumor dynamic from the perspective of immune tolerance and review current data supporting the integration of cancer vaccines with standard and novel therapeutic agents that can maximize their activity.
Receptors for human alpha and beta interferon but not for gamma interferon are specified by human chromosome 21. (1984)

We examined the proposed role of human chromosome 21 in determining the cellular sensitivity to human alpha, beta, and gamma interferons (HuIFN-alpha, -beta, and -gamma) and the expression of the receptors for the HuIFNs with the use of mouse-human hybrid cells containing human chromosome 21. Hybrid cells (WA17) containing three copies of human chromosome 21 showed specific displaceable binding of 125I-labeled HuIFN-alpha 2 (125I-HuIFN-alpha 2), which was not observed with mouse parent (A9) cells. Crosslinking of 125I-HuIFN-alpha 2 bound to WA17 cells with disuccinimidyl suberate yielded a complex of Mr approximately equal to 150,000 similar to the 125I-HuIFN-alpha 2-receptor complex obtained with human cells as described earlier. Such a complex was not obtained with mouse parent (A9) cells or with hybrid cells containing certain other human chromosomes but not chromosome 21. Mice inoculated with mouse-human hybrid cells containing human chromosome 21 produce antibodies that block the antiviral action of HuIFN-alpha and -beta on human cells. Such antibodies could immunoprecipitate the 125I-HuIFN-alpha 2-receptor complex obtained from human cells but not free 125I-HuIFN-alpha 2, indicating that these antibodies were directed against the receptor. WA17 hybrid cells were highly sensitive to the antiviral action of HuIFN-alpha 2, -alpha (Le) and -beta but were completely insensitive to HuIFN-gamma. Furthermore, 125I-HuIFN-gamma showed specific binding to human WISH cells but not to WA17 hybrid cells or A9 mouse cells. The results indicate that the receptors for HuIFN-alpha and -beta but not for HuIFN-gamma are specified by human chromosome 21. Hybrid cells containing one, two, or three copies of human chromosome 21 were found to be increasingly sensitive to HuIFN-alpha 2, indicating that a chromosome 21-specified component (possibly the HuIFN-alpha receptor) may be a limiting factor in the cellular sensitivity to HuIFN-alpha.
Stealth liposomes: an improved sustained release system for 1-beta-D-arabinofuranosylcytosine. (1992)

Newly developed liposomes with prolonged circulation half-lives and dose-independent pharmacokinetics (Stealth liposomes) have been tested for their efficacy as a slow release system for the rapidly degraded, schedule-dependent, antineoplastic drug 1-beta-D-arabinofuranosylcytosine (ara-C) in the treatment of murine L1210/C2 leukemia. Mice were given injections of either 10(5) cells or 10(6) cells by either the i.v. or the i.p. routes. Leukemia-bearing mice were treated with either i.v. or i.p. injections of free drug, i.v. or i.p. injections of liposome-entrapped drug, or 24-h i.v. infusions of free drug. Long-circulating liposomes contained, as the stealth component, either monosialoganglioside or polyethylene glycol-distearoylphosphatidylethanolamine. Liposomes lacking the stealth components (non-stealth liposomes) were also injected for comparison. At lower dose ranges, stealth liposomes were superior to non-stealth liposomes in prolonging mean survival times of the mice, and all liposome preparations were superior to injections of the free drug. Drug entrapped in stealth liposomes, when administered at or near the maximum tolerated dose of 100 mg/kg ara-C were considerably superior to 24-h free drug infusions given at the same total drug dose. Therapeutic effect was related to the half-life of leakage of ara-C from the liposome formulations, as well as to circulation half-life, with maximum therapeutic effect achieved with long circulation half-lives and more rapid leakage rates. The therapeutic efficacy of non-stealth liposomes increased with increasing liposome (and drug) dose as a result of saturation of liposome uptake by the mononuclear phagocyte system, which resulted in longer circulation half-lives for these liposomes at higher doses (Michaelis-Menten pharmacokinetics). Liposome entrapment can protect rapidly degraded drugs from breakdown in vivo, with release of the drugs in a therapeutically active form over periods of up to several days. The dose-independent pharmacokinetics and reduced mononuclear phagocyte system uptake of stealth liposomes gives them distinct advantages over non-stealth liposomes.
Repair of bone defects with marrow cells and porous ceramic: Experiments in rats (1989)

We studied the role of bone-marrow reconstituted porous ceramics in enhancing healing of a 5-mm femoral diaphyseal defect fixed with a rigid polyethylene plate in rats. Osseous repair was evaluated by histologic scoring. When blocks of porous calcium phosphate ceramics alone were introduced into the defects, most cases showed fibrous tissue interposition at the host bone-ceramic junction 1 month after implantation, and only four of 12 defects developed osseous or osteochondral union at both the proximal and distal junctions 2 months after surgery. However, when the ceramic was combined with syngeneic viable marrow cells, new bone formation occurred in isolated pore regions of the ceramic at 1 month, and extensive bone formation was seen in most pore regions 2 months after implantation. Out of 12 implants, complete bone union was seen in eight, and one showed osseous or osteochondral union at both junctions 2 months after surgery. Our results indicated that composite grafts of porous calcium phosphate ceramics and marrow cells may be clinically applicable to enhance osteogenesis and osteoconduction.
Regional localization of the human c-ros-1 on 6q22 and flt on 13q12. (1987)

We have regionally localized the two human tyrosine kinase proto-oncogenes, c-ros-1 and flt, by in situ hybridization. The c-ros-1 has been mapped to 6q22 and the flt to 13q12.
In Vitro Selection of Clinically Relevant Bevirimat Resistance Mutations Revealed by “Deep” Sequencing of Serially Passaged, Quasispecies-Containing Recombinant HIV-1 (2010)

Initial in vitro studies of bevirimat resistance failed to observe mutations in the clinically significant QVT motif in SP1 of HIV-1 gag. This study presents a novel screening method involving mixed, clinically derived gag-protease recombinant HIV-1 samples to more accurately mimic the selection of resistance seen in vivo. Bevirimat resistance was investigated via population-based sequencing performed with a large, initially antiretroviral-naïve cohort before (n = 805) and after (n = 355) standard HIV therapy (without bevirimat). The prevalence of any polymorphism in the motif comprising Q, V, and T was ∼ 6%, 29%, and 12%, respectively, and did not change appreciably over the course of therapy. From these samples, three groups of 10 samples whose bulk sequences were wild type at the QVT motif were used to generate gag-protease recombinant viruses that captured the existing diversity. Groups were mixed and passaged with various bevirimat concentrations for 9 weeks. gag variations were assessed by amplicon-based "deep" sequencing using a GS FLX sequencer (Roche). Unscreened mutations were present in all groups, and a V370A minority not originally detected by bulk sequencing was present in one group. V370A, occurring together with another preexisting, unscreened resistance mutation, was selected in all groups in the presence of a bevirimat concentration above 0.1 μM. For the two groups with V370A levels below consistent detectability by deep sequencing, the initial selection of V370A required 3 to 4 weeks of exposure to a narrow range of bevirimat concentrations, whereas for the group with the V370A minority, selection occurred immediately. This approach provides quasispecies diversity that facilitates the selection of mutations observed in clinical trials and, coupled with deep sequencing, could represent an efficient in vitro screening method for detecting resistance mutations.
Formation of three‐dimensional cell/polymer constructs for bone tissue engineering in a spinner flask and a rotating wall vessel bioreactor (2002)

The aim of this study is to investigate the effect of the cell culture conditions of three-dimensional polymer scaffolds seeded with rat marrow stromal cells (MSCs) cultured in different bioreactors concerning the ability of these cells to proliferate, differentiate towards the osteoblastic lineage, and generate mineralized extracellular matrix. MSCs harvested from male Sprague-Dawley rats were culture expanded, seeded on three-dimensional porous 75:25 poly(D,L-lactic-co-glycolic acid) biodegradable scaffolds, and cultured for 21 days under static conditions or in two model bioreactors (a spinner flask and a rotating wall vessel) that enhance mixing of the media and provide better nutrient transport to the seeded cells. The spinner flask culture demonstrated a 60% enhanced proliferation at the end of the first week when compared to static culture. On day 14, all cell/polymer constructs exhibited their maximum alkaline phosphatase activity (AP). Cell/polymer constructs cultured in the spinner flask had 2.4 times higher AP activity than constructs cultured under static conditions on day 14. The total osteocalcin (OC) secretion in the spinner flask culture was 3.5 times higher than the static culture, with a peak OC secretion occurring on day 18. No considerable AP activity and OC secretion were detected in the rotating wall vessel culture throughout the 21-day culture period. The spinner flask culture had the highest calcium content at day 14. On day 21, the calcium deposition in the spinner flask culture was 6.6 times higher than the static cultured constructs and over 30 times higher than the rotating wall vessel culture. Histological sections showed concentration of cells and mineralization at the exterior of the foams at day 21. This phenomenon may arise from the potential existence of nutrient concentration gradients at the interior of the scaffolds. The better mixing provided in the spinner flask, external to the outer surface of the scaffolds, may explain the accelerated proliferation and differentiation of marrow stromal osteoblasts, and the localization of the enhanced mineralization on the external surface of the scaffolds.
Synthesis of metal colloids in inverse microemulsions (1990)

Abstract Colloidal silver and gold particles have been prepared by reduction of aqueous metal salt solutions in inverse microemulsions. The sols are characterized by absorption spectroscopy and electron microscopy. Ultrasound treatment during reduction results in a narrower size distribution of the colloidal particles, as evidenced by a narrower absorption band. Photochemical silver and gold sol formation, without the addition of a reducing agent, has been observed for inverse microemulsions of metal salt solutions in a medium consisting of dodecyl-heptaethyleneglycol-ether and hexane. The particle sizes determined from electron microscopy have been used as input parameters for the simulation of absorption spectra, based on the electromagnetic theory of localized surface plasmon excitation. For the gold sols a quantitative agreement between experimental and simulated spectra is obtained. With the silver colloids, the observed red-shift of the absorption maximum points to the presence of an ionic layer on the surface of the particles. When this layer is included in the theoretical model, good agreement with the experiment is achieved.