gebhart/patrepeval huggingface dataset:
Suppression of murine neuroblastoma growth in vivo by mevinolin, a competitive inhibitor of 3-hydroxy-3-methylglutaryl-coenzyme A reductase. (1985)

3-Hydroxy-3-methylglutaryl-coenzyme A (HMG-CoA) reductase catalyzes the formation of mevalonate, an essential precursor for isoprenoid compounds in mammalian cells. Recent studies have shown that mevinolin, a competitive inhibitor of the reductase, inhibits cell proliferation and induces differentiation in cultured C1300 (Neuro-2A) murine neuroblastoma cells. We now report that mevinolin can inhibit neuroblastoma growth in vivo. The specific activity of HMG-CoA reductase in subcutaneous neuroblastomas increased more than 20-fold between the fifth and eighth days after tumor inoculation, and remained elevated for the remainder of the tumor lifetime in mice. The increase in reductase activity was correlated with a marked increase in tumor DNA content and exponential increase in tumor weight. Using an in vitro assay to monitor the ability of mouse serum to suppress sterol synthesis, we determined that mevinolin was inactivated or cleared from the circulation within 3-6 h after a single subcutaneous injection. However, by using subcutaneous osmotic pumps to deliver a constant infusion of mevinolin, we were able to maintain adequate blood levels of the drug for 7 d. Mevinolin (5 mg/kg per h) suppressed tumor growth (wet weight) significantly when treatment was carried out between day 1 and day 8 or between day 5 and day 12 after tumor inoculation. Histopathological examination of tumors from mevinolin-treated mice revealed few or no mitotic figures and marked cellular degeneration. Measurements of incorporation of (3H)acetate into neuroblastoma sterols and ubiquinones 24 h after implantation of osmotic pumps showed that mevinolin produced a marked inhibition of isoprenoid synthesis in the tumors in vivo. The data suggest that, in addition to their demonstrated utility as cholesterol-lowering drugs, competitive inhibitors of HMG-CoA reductase may have considerable potential as novel antineoplastic agents.
Identification of a Common Sphingolipid-binding Domain in Alzheimer, Prion, and HIV-1 Proteins (2002)

The V3 loop of the human immunodeficiency virus (HIV)-1 surface envelope glycoprotein gp120 is a sphingolipid-binding domain mediating the attachment of HIV-1 to plasma membrane microdomains (rafts). Sphingolipid-induced conformational changes in gp120 are required for HIV-1 fusion. Galactosylceramide and sphingomyelin have been detected in highly purified preparations of prion rods, suggesting that the prion protein (PrP) may interact with selected sphingolipids. Moreover, a major conformational transition of the Alzheimer beta-amyloid peptide has been observed upon interaction with sphingolipid-containing membranes. Structure similarity searches with the combinatorial extension method revealed the presence of a V3-like domain in the human prion protein PrP and in the Alzheimer beta-amyloid peptide. In each case, synthetic peptides derived from the predicted V3-like domain were found to interact with monomolecular films of galactosylceramide and sphingomyelin at the air-water interface. The V3-like domain of PrP is a disulfide-linked loop (Cys(179)-Cys(214)) that includes the E200K mutation site associated with familial Creutzfeldt-Jakob disease. This mutation abrogated sphingomyelin recognition. The identification of a common sphingolipid-binding motif in gp120, PrP, and beta-amyloid peptide underscores the role of lipid rafts in the pathogenesis of HIV-1, Alzheimer, and prion diseases and may provide new therapeutic strategies.
Site-specific recombination of a transgene in fertilized eggs by transient expression of Cre recombinase. (1995)

An efficient method of transgene modulation in fertilized eggs has been developed that uses the Cre/loxP recombination system. Twelve transgenic mouse lines carrying a chicken beta-actin promoter-loxP-chloramphenicol acetyltransferase (CAT) gene-loxP-beta-galactosidase gene construct were produced. After selection of the line showing the highest expression of the CAT gene in a variety of tissues, eggs of this line were injected in the male or female pronucleus with a Cre expression vector placed under the control of the chicken beta-actin promoter and kept in a circular form to avoid genomic integration. This resulted in a transient expression of Cre in the eggs, leading to recombination of the transgene as detected by galactosidase expression and DNA analysis. Recombination was completed before the morula stage with both types of pronuclear injections and occurred with a very high frequency; no mosaicism, no incomplete recombination, and no integration of the Cre sequence were observed in 18 mice born with this modified transgene. The beta-galactosidase gene was expressed in various tissues at levels comparable to those found for the CAT gene in the founder line. This Cre transient expression system should be useful for breeding transgenic lines in which transgene expression leads to sterility or lethality--in particular, for selecting transgenic lines with high expression of a potentially lethal transgene whose full activity is difficult to explore in a conventional transgenic system because of the risk of selecting for transgenic lines carrying only poorly expressed transgenes.
Mechanisms of Integrin–Vascular Endothelial Growth Factor Receptor Cross-Activation in Angiogenesis (2007)

The functional responses of endothelial cells are dependent on signaling from peptide growth factors and the cellular adhesion receptors, integrins. These include cell adhesion, migration, and proliferation, which, in turn, are essential for more complex processes such as formation of the endothelial tube network during angiogenesis. This study identifies the molecular requirements for the cross-activation between beta3 integrin and tyrosine kinase receptor 2 for vascular endothelial growth factor (VEGF) receptor (VEGFR-2) on endothelium. The relationship between VEGFR-2 and beta3 integrin appears to be synergistic, because VEGFR-2 activation induces beta3 integrin tyrosine phosphorylation, which, in turn, is crucial for VEGF-induced tyrosine phosphorylation of VEGFR-2. We demonstrate here that adhesion- and growth factor-induced beta3 integrin tyrosine phosphorylation are directly mediated by c-Src. VEGF-stimulated recruitment and activation of c-Src and subsequent beta3 integrin tyrosine phosphorylation are critical for interaction between VEGFR-2 and beta3 integrin. Moreover, c-Src mediates growth factor-induced beta3 integrin activation, ligand binding, beta3 integrin-dependent cell adhesion, directional migration of endothelial cells, and initiation of angiogenic programming in endothelial cells. Thus, the present study determines the molecular mechanisms and consequences of the synergism between 2 cell surface receptor systems, growth factor receptor and integrins, and opens new avenues for the development of pro- and antiangiogenic strategies.
Cytotoxic T cell recognition of an endogenous class I HLA peptide presented by a class II HLA molecule. (1990)

Human leukocytes were stimulated in vitro with peptides corresponding in sequence to the highly variable helix of the alpha 1 domain of various HLA-B and -C molecules. A CD4+ CD8- cytotoxic T cell line, CTL-AV, that is specific for the HLA-B7 peptide presented by HLA-DR11.1 was obtained. The HLA-DR11.2 molecule, which only differs at three residues from HLA-DR11.1, did not present the HLA-B7 peptide to CTL-AV. Peptides from the alpha 1 domain helix of other HLA-A and HLA-B molecules, but not HLA-C molecules, competed with the HLA-B7 peptide for binding to HLA-DR11.1. A cell line (WT50) that coexpresses HLA-B7 and HLA-DR11.1 was killed by CTL-AV in the absence of any added HLA-B7 peptide. The processing and presentation of HLA-B7 in these cells appears to be through the endogenous, and not the exogenous, pathway of antigen presentation. Thus, Brefeldin A inhibits presentation and chloroquine does not. Furthermore, introduction of purified HLA-B7 molecules into HLA-DR11.1+, HLA-B7- cells by cytoplasmic loading via osmotic lysis of pinosomes, but not by simple incubation, rendered them susceptible to CTL-AV killing. These results provide an example of class II major histocompatibility complex (MHC) presentation of a constitutively synthesized self protein that uses the endogenous pathway of antigen presentation. They also emphasize the capacity for presentation of MHC peptides by MHC molecules.
Achieving long-term stability of lipid nanoparticles: examining the effect of pH, temperature, and lyophilization (2016)

The broadest clinical application of siRNA therapeutics will be facilitated by drug-loaded delivery systems that maintain stability and potency for long times under ambient conditions. In the present study, we seek to better understand the stability and effect of storage conditions on lipidoid nanoparticles (LNPs), which have been previously shown by our group and others to potently deliver RNA to various cell and organ targets both in vitro and in vivo. Specifically, this study evaluates the influence of pH, temperature, and lyophilization on LNP efficacy in HeLa cells. When stored under aqueous conditions, we found that refrigeration (2°C) kept LNPs the most stable over 150 days compared to storage in the -20°C freezer or at room temperature. Because the pH of the storage buffer was not found to influence stability, it is suggested that the LNPs be stored under physiologically appropriate conditions (pH 7) for ease of use. Although aggregation and loss of efficacy were observed when LNPs were subjected to freeze-thaw cycles, their stability was retained with the use of the cryoprotectants, trehalose, and sucrose. Initially, lyophilization of the LNPs followed by reconstitution in aqueous buffer also led to reductions in efficacy, most likely due to aggregation upon reconstitution. Although the addition of ethanol to the reconstitution buffer restored efficacy, this approach is not ideal, as LNP solutions would require dialysis prior to use. Fortunately, we found that the addition of trehalose or sucrose to LNP solutions prior to lyophilization facilitated room temperature storage and reconstitution in aqueous buffer without diminishing delivery potency.
Group B Arbovirus Structural and Nonstructural Antigens III. Serological Specificity of Solubilized Intracellular Viral Proteins (1973)

Solubilized nonstructural antigen III from Saint Louis encephalitis (SLE)-Japanese B encephalitis (JBE)-West Nile (WN) and dengue-2 arbovirus-infected pig kidney cells was purified by employing Brij-58 solubilization, organic solvent extraction, and column chromatography. Diethylaminoethyl-cellulose column peak C eluate contained only intracellular viral envelope protein designated antigen I. Antigen I of SLE virus absorbed homologous neutralizing antibody; however, the intracellular nonstructural protein designated antigen III did not. The antigenic relationships of solubilized antigens I and III prepared from SLE, JBE, and WN virus-infected cells were determined by complement-fixation (CF) and immunodiffusion analyses. Solubilized antigen I of each virus cross-reacted broadly with both homologous and heterologous antibody at high antigen concentrations in the CF test. Antigen III of each virus reacted with only homologous antibody by both CF and immunoprecipitation. This study demonstrates that during SLE, JBE, WN, and dengue-2 infections, virus-specific proteins containing both type-specific and group-reactive determinants are synthesized. Antigen III, a nonstructural protein, is serologically virus type specific and may be useful as a type-specific diagnostic reagent.
Thermal coagulation of serum proteins; deficient coagulation in cancer and the iodoacetate index. (1949)

Summary In most cases of human cancer there is a qualitative defect in the proteins of serum which may be identified by the thermal coagulation tests. The defect is not specific and reactions similar to that in cancer are obtained in the presence of pulmonary tuberculosis and some acute massive inflammatory processes as well. The defect was not observed in normal pregnancy, in new-born infants, or in non-pulmonary tuberculosis. By determining the iodoacetate index as related to the total protein content of serum, it was found that all of 85 consecutive clinically active cancers fell in a group with a low index (less than 9). However, 16 of 95 patients with non-malignant pathology fell in this same range.
Molecular Cloning and Characterization of a Putative Mouse Hyaluronan Synthase (1996)

We report the isolation of a novel mouse gene which encodes a putative hyaluronan synthase. The cDNA was identified using degenerate reverse transcriptase-polymerase chain reaction. Degenerate primers were designed based upon an alignment of the amino acid sequences of Streptococcus pyogenes HasA, Xenopus laevis DG42, and Rhizobium meliloti NodC. A mouse embryo cDNA library was screened with the resultant polymerase chain reaction product, and multiple cDNA clones spanning 3 kilobase pairs (kb) were isolated. The open reading frame predicted a 63-kDa protein with several transmembrane sequences, multiple consensus phosphorylation sites, and four putative hyaluronan binding motifs. The amino acid sequence displayed 55% identity to mouse HAS, 56% identity to Xenopus DG42, and 21% identity to Streptococcus HasA. Northern analysis identified transcripts of 4.8 kb and 3.2 kb, which were expressed highly in the developing mouse embryo and at lower levels in adult mouse heart, brain, spleen, lung, and skeletal muscle. Transfection experiments demonstrated that mouse Has2 could direct hyaluronan coat biosynthesis in transfected COS cells, as evidenced by a classical particle exclusion assay. These results suggest that mammalian HA synthase activity is regulated by at least two related genes. Accordingly, we propose the name Has2 for this gene.
Potential Markers of Tongue Tumor Progression Selected by cDNA Micro Array (2005)

Squamous cell carcinoma (SCC), the most frequent malignant tumor of the oral cavity, generally exhibits a poor prognosis and metastases are the main cause of death. This tumor often arises from pre-malignant lesions. To date, it is difficult to predict if and which pre-malignant lesions may progress into oral SCC using traditional methods. For these reasons, several studies are trying to identify markers useful in the progression of pre-malignant lesions and tumors. To define the genetic expression profile of tongue tumor progression we compared 9 dysplasias (DS), 8 tumors without metastasis (TWM), 11 metastasizing SCCs (MT) of the tongue, and a baseline of 11 normal tissues by using cDNA microarray containing 19.2 K clones. We initially applied hierarchical agglomerative clustering based on information from all 6026 clones. Results were obtained by performing a two steps analysis: a Significance Analysis of Microarray (SAM) and a Gene Ontology search. One hundred and five clones have statistically significant different expression levels (FDR < 0.01) between DS and TWM, whereas 570 genes have statistically significant difference expression levels between TWM and MT (FDR < 0.01) as detected by SAM. By filtering with FatiGo only 33 genes were differentially expressed in TWN, respect to DS, whereas 155 genes were differentially expressed in MT respect to TWM. We detected some genes which encode for oncogenes, transcription factors and cell cycle regulators as potential markers of DS progression. Examples are BAG4, PAX3 and CCNI, respectively. Among potential markers of metastases are some genes related to cell mobility (TSPAN-2 and SNTA1), intercellular adhesion (integrin alpha 7) or extracellular matrix components (ADAMTS2 and cathepsin O). Additionally, under-expressed genes encoded apoptosis-related proteins (PDCD4 and CASP4). In conclusion, we identified several genes differentially expressed in tumor progression which can potentially help in better classifying pre-malignant lesions and tongue SCCs.
Solution conformation of salmon calcitonin in sodium dodecyl sulfate micelles as determined by two-dimensional NMR and distance geometry calculations (1991)

The 32 amino acid hormone salmon calcitonin was studied at pH 3.7 and 7.4 by two-dimensional NMR in sodium dodecyl sulfate (SDS) micelles at 310 K. The spectrum was fully assigned, and the secondary structure was obtained from nuclear Overhauser enhancement spectroscopy (NOESY), 3JHN alpha coupling constants, and slowly exchanging amide data. Three-dimensional structures consistent with NMR data were generated by using distance geometry calculations. A set of 260 interproton distances, derived from NOESY, and hydrogen-bond constraints, obtained from analysis of the amide exchange, were used. From the initial random conformations, 13 distance geometry structures with minimal violations were selected for further refinement with restrained energy minimization. In SDS, at both pHs, the main conformational feature of the hormone is an alpha-helix from Thr6 through Tyr22, thus including the amphipathic 8-22 segment and two residues of the Cys1-Cys7 N-terminal loop. The C-terminal decapeptide forms a loop folded back toward the helix. The biological significance of this conformation is discussed.
Scanning probe microscopes go video rate and beyond (2005)

In this article we introduce a, video-rate, control system that can be used with any type of scanning probe microscope, and that allows frame rates up to 200images∕s. These electronics are capable of measuring in a fast, completely analog mode as well as in the more conventional digital mode. The latter allows measurements at low speeds and options, such as, e.g., atom manipulation, current–voltage spectroscopy, or force–distance curves. For scanning tunneling microscope (STM) application we implemented a hybrid mode between the well-known constant-height and constant-current modes. This hybrid mode not only increases the maximum speed at which the surface can be imaged, but also improves the resolution at lower speeds. Acceptable image quality at high speeds could only be obtained by pushing the performance of each individual part of the electronics to its limit: we developed a preamplifier with a bandwidth of 600kHz, a feedback electronics with a bandwidth of 1MHz, a home-built bus structure for the fast data transfer, fast analog to digital converters, and low-noise drivers. Future improvements and extensions to the control electronics can be realized easily and quickly, because of its open architecture with its modular plug-in units. In the second part of this article we show our high-speed results. The ultrahigh vacuum application of these control electronics on our (UHV)-STM enabled imaging speeds up to 0.3mm∕s, while still obtaining atomic step resolution. At high frame rates, the images suffered from noticeable distortions, which we have been able to analyze by virtue of the unique access to the error (dZ) signal. The distortions have all been associated with mechanical resonances in the scan head of the UHV-STM. In order to reduce such resonance effects, we have designed and built a scan head with high resonance frequencies (⩾64kHz), especially for the purpose of testing the fast electronics. Using this scanner we have reached video-rate imaging speeds up to 200frames∕s (5ms∕image), while still obtaining atomically resolved structures.
Microwave-Accelerated Solvent-Free Synthesis of Thioketones, Thiolactones, Thioamides, Thionoesters, and Thioflavonoids (1999)

[reactions: see text] An expeditious, solvent-free, and high yield conversion of ketones, flavones, isoflavones, lactones, amides, and esters to the corresponding thio analogues is described utilizing Lawesson's reagent in a process that circumvents the use of dry solvents and excess of the reagent.
The Impact of Opening Trade and Direct Shipping across Taiwan Strait to the Growth of Taiwan's Global Container Throughput (2014)

There are significant structural shifts in container flows across the Taiwan Strait since the launch of direct shipping between Taiwan and Mainland China in the end of 2008. The purpose of this paper is aiming to identify the main driving forces for the growth of Taiwan's international container throughput via (1) the impact analysis of relaxing trade regulations between Taiwan and China since 1990 up to now, and (2) applying general theories to examine the impact of the establishment of cross-strait direct shipping link on the growth of Taiwan's container throughput from December 2008 up to now. This paper creates two time-related dummy variables to explore the impacts of ＂unilateral＂ import trade constraint and the relaxing ＂bilateral＂ cross-strait shipping regulations on the growth of Taiwan's container throughput in the past two decades. The result shows that (i) relaxing cross-strait trade regulations resulting in gradual rising import-export trade volume which has a positive impact on the growth of Taiwan's international container throughput, and (ii) the demand elasticity and constant return to scale of cross-strait trade (including export and import) to container throughput growth are found to be statistically significant only during 1990-2001, but no significant impact is found in the period of 2002-2012. We conclude that gradually relaxing cross-strait import regulations was a correct and fair policy for both Taiwan and China between 1990 and 2001. However, the impact of direct shipping link and cross-strait economic cooperation negotiations after 2002 should be further examined in the future. Finally, the growth of industrial GDP has positive impact and the fluctuating oil price has a negative impact on the growth of Taiwan's container throughput during 2004 to 2012.
Major histocompatibility complex class II expression deficiency caused by a RFXANK founder mutation: a survey of 35 patients (2011)

Inherited deficiency of major histocompatibility complex (MHC) class II molecules impairs antigen presentation to CD4(+) T cells and results in combined immunodeficiency (CID). Autosomal-recessive mutations in the RFXANK gene account for two-thirds of all cases of MHC class II deficiency. We describe here the genetic, clinical, and immunologic features of 35 patients from 30 unrelated kindreds from North Africa sharing the same RFXANK founder mutation, a 26-bp deletion called I5E6-25_I5E6 + 1), and date the founder event responsible for this mutation in this population to approximately 2250 years ago (95% confidence interval [CI]: 1750-3025 years). Ten of the 23 patients who underwent hematopoietic stem cell transplantation (HSCT) were cured, with the recovery of almost normal immune functions. Five of the patients from this cohort who did not undergo HSCT had a poor prognosis and eventually died (at ages of 1-17 years). However, 7 patients who did not undergo HSCT (at ages of 6-32 years) are still alive on Ig treatment and antibiotic prophylaxis. RFXANK deficiency is a severe, often fatal CID for which HSCT is the only curative treatment. However, some patients may survive for relatively long periods if multiple prophylactic measures are implemented.
Prooxidant iron and copper, with ferroxidase and xanthine oxidase activities in human atherosclerotic material (1995)

Low density lipoproteins are highly sensitive to oxidation by copper salts, and such peroxidation is accompanied by macrophage scavenger receptor recognition. This study shows that fresh human atherosclerotic material (aneurysms and endarterectomies) can contain detectable amounts of redox active iron and copper that is chelatable from tissue homogenates. Such material is often prooxidant towards lipid peroxidation and deoxyribose degradation. Aneuryems and endarterectomies contain ferroxidase 1 activities, whereas only in aneurysms could caeruloplasmin be immunologically detected. Ferroxidase 2 activity, characteristic of a copper‐oxidised lipoprotein complex, could not, however, be detected in any of the atherosclerotic samples. A third ferroxidase activity, attributable to xanthine oxidase, was present in several aneurysms and endarterectomies.