gebhart/patrepeval huggingface dataset:
Bioengineering of Surface GD3 Ganglioside for Immunotargeting Human Melanoma Cells (2004)

N-Propionyl, N-butyryl (N-Bu), and N-benzoyl mannosamine, as precursors of sialic acid biosynthesis, were incubated with human melanoma SK-MEL-28 cells and resulted in the replacement of N-acetyl groups on the cell surface sialic acid residues, including those associated with GD3. Meanwhile, vaccines containing GD3 and modified GD3 tetrasaccharide-keyhole limpet hemocyanin conjugates were synthesized, and BALB/c mice were immunized with them together with monophosphoryl lipid A adjuvant. The GD3Bu-keyhole limpet hemocyanin conjugate raised the highest IgG titers without any cross-reactivity to unmodified GD3. Expression of GD3Bu epitopes on the surface of SK-MEL-28 cells was confirmed in vitro and in vivo by the binding of a polyclonal antiserum and monoclonal antibody (mAb) 2A, both of which specifically recognize GD3Bu, and by mass spectroscopic analysis of glycolipids extracted from cells. Following expression of GD3Bu on the surface of SK-MEL-28 cells, the cells could be lysed by mAb 2A and GD3Bu antiserum in the presence of complement. Although less effective in the control of existing large size tumors (∼10 mm inner diameter) on BALB/c nu/nu mice, mAb 2A in combination with ManNBu effectively protected mice from SK-MEL-28 tumor grafting. This approach may provide a method to augment the immunogenicity of sialylated human antigens and to avoid generating an autoimmune response to them at same time. N-Propionyl, N-butyryl (N-Bu), and N-benzoyl mannosamine, as precursors of sialic acid biosynthesis, were incubated with human melanoma SK-MEL-28 cells and resulted in the replacement of N-acetyl groups on the cell surface sialic acid residues, including those associated with GD3. Meanwhile, vaccines containing GD3 and modified GD3 tetrasaccharide-keyhole limpet hemocyanin conjugates were synthesized, and BALB/c mice were immunized with them together with monophosphoryl lipid A adjuvant. The GD3Bu-keyhole limpet hemocyanin conjugate raised the highest IgG titers without any cross-reactivity to unmodified GD3. Expression of GD3Bu epitopes on the surface of SK-MEL-28 cells was confirmed in vitro and in vivo by the binding of a polyclonal antiserum and monoclonal antibody (mAb) 2A, both of which specifically recognize GD3Bu, and by mass spectroscopic analysis of glycolipids extracted from cells. Following expression of GD3Bu on the surface of SK-MEL-28 cells, the cells could be lysed by mAb 2A and GD3Bu antiserum in the presence of complement. Although less effective in the control of existing large size tumors (∼10 mm inner diameter) on BALB/c nu/nu mice, mAb 2A in combination with ManNBu effectively protected mice from SK-MEL-28 tumor grafting. This approach may provide a method to augment the immunogenicity of sialylated human antigens and to avoid generating an autoimmune response to them at same time.
Development of fluorescent probes based on protection–deprotection of the key functional groups for biological imaging (2015)

Recently, the strategy of protection-deprotection of functional groups has been widely employed to design fluorescent probes, as the protection-deprotection of functional groups often induces a marked change in electronic properties. Significant advances have been made in the development of analyte-responsive fluorescent probes based on the protection-deprotection strategy. In this tutorial review, we highlight the representative examples of small-molecule based fluorescent probes for bioimaging, which are operated via the protection-deprotection of key functional groups such as aldehyde, hydroxyl, and amino functional groups reported from 2010 to 2014. The discussion includes the general protection-deprotection methods for aldehyde, hydroxyl, or amino groups, as well as the design strategies, sensing mechanisms, and deprotection modes of the representative fluorescent imaging probes applied to bio-imaging.
A view through a different lens ... strategies for increasing the number of African American nurses. (2001)

These strategies emphasize nursing as a viable career option comparable to other careers often selected by African American students. Psychosocial issues as well as academic issues related to recruitment and retention were addressed by concentrating efforts on individuals interested in nursing, and academically prepared for the rigors of a university program. These strategies offer short-term and long-term remedies to the problem of shortage of African American professional nurses. A new paradigm for increasing the number of African American nurses is needed. To be effective, it is time for colleges of nursing to view recruitment and retention of African American individuals into the profession of nursing through a different lens.
Peptide-Based Intracellular Shuttle Able To Facilitate Gene Transfer in Mammalian Cells (1999)

Loligomers are peptide-based intracellular vehicles able to penetrate cells and self-localize into distinct cellular compartments. Loligomers can be rapidly assembled by automated solid-phase approaches and were designed to act as nonviral, nonlipophilic intracellular shuttles. One nucleus-directed loligomer, termed loligomer 4, was evaluated for its ability to function as a transfection agent. Loligomer 4 readily associates with plasmids to form noncovalent complexes. The migration of loligomer 4-plasmid complexes into cells was monitored by flow cytometry and fluorescence microscopy. Populations of plasmids labeled with 7-AAD exist either free or in association with loligomer 4 inside cells and are visible throughout the cytosol and nucleus of chinese hamster ovary (CHO) cells. Loligomer 4-plasmid complexes were not cytotoxic to cells and were readily imported by most cells (>70%). CHO cells were transfected with complexes of loligomer 4 and plasmids harboring luciferase, green fluorescent protein or beta-galactosidase reporter genes. The transfection efficiency of loligomer 4-plasmid DNA complexes was greater when cells were maintained as suspensions instead of monolayers. Transfections could be performed with cells suspended in serum-containing medium. The observed levels of transfection, however, were modest with 5-10% of CHO cells expressing either a green fluorescent protein or the enzyme beta-galactosidase. Loligomers have recently been observed in vesicular compartments [Singh, D., Kiarash, R., Kawamura, K, LaCasse, E. C., and Gariépy, J. (1998) Biochemistry 37, 5798-5809] and differences between levels of cellular import and transfection efficiency may well reflect the need to optimize the release of loligomers and their complexes from these compartments in future designs. In summary, loligomer 4 behaves as a stable, soluble and effective transfection agent. These results demonstrate the feasibility of designing loligomers able to act as intracellular guided agents aimed at gene transfer applications.
Rearrangement of morphinandienes in methanesulfonic acid (1993)

Besides 2-fluoroapocodeine 7, the methanesulfonic acid-induced rearrangement of 6-fluoro-6-demethoxythebaine 2 gave the C-2 substituted apocodeines 8,11 and 20. Analogous rearrangement of thebaine 1 in the presence of alcohols offers a convenient and high-yielding route to the 2-alkoxymorphothebaine 6, 11, 12 and 13. Formation of the products has been explained in terms of nucleophilic substitution of the cationic intermediates 21 and 22 from the acid-catalysed reaction.
Mechanisms by which lipoprotein lipase alters cellular metabolism of lipoprotein(a), low density lipoprotein, and nascent lipoproteins. Roles for low density lipoprotein receptors and heparan sulfate proteoglycans. (1992)

We sought to investigate effects of lipoprotein lipase (LpL) on cellular catabolism of lipoproteins rich in apolipoprotein B-100. LpL increased cellular degradation of lipoprotein(a) (Lp(a)) and low density lipoprotein (LDL) by 277% +/- 3.8% and 32.5% +/- 4.1%, respectively, and cell association by 509% +/- 8.7% and 83.9% +/- 4.0%. The enhanced degradation was entirely lysosomal. Enhanced degradation of Lp(a) had at least two components, one LDL receptor-dependent and unaffected by heparitinase digestion of the cells, and the other LDL receptor-independent and heparitinase-sensitive. The effect of LpL on LDL degradation was entirely LDL receptor-independent, heparitinase-sensitive, and essentially absent from mutant Chinese hamster ovary cells that lack cell surface heparan sulfate proteoglycans. Enhanced cell association of Lp(a) and LDL was largely LDL receptor-independent and heparitinase-sensitive. The ability of LpL to reduce net secretion of apolipoprotein B-100 by HepG2 cells by enhancing cellular reuptake of nascent lipoproteins was also LDL receptor-independent and heparitinase-sensitive. None of these effects on Lp(a), LDL, or nascent lipoproteins required LpL enzymatic activity. We conclude that LpL promotes binding of apolipoprotein B-100-rich lipoproteins to cell surface heparan sulfate proteoglycans. LpL also enhanced the otherwise weak binding of Lp(a) to LDL receptors. The heparan sulfate proteoglycan pathway represents a novel catabolic mechanism that may allow substantial cellular and interstitial accumulation of cholesteryl ester-rich lipoproteins, independent of feedback inhibition by cellular sterol content.
No Signaling and Quantum Key Distribution (2005)

Standard quantum key distribution protocols are provably secure against eavesdropping attacks, if quantum theory is correct. It is theoretically interesting to know if we need to assume the validity of quantum theory to prove the security of quantum key distribution, or whether its security can be based on other physical principles. The question would also be of practical interest if quantum mechanics were ever to fail in some regime, because a scientifically and technologically advanced eavesdropper could perhaps use postquantum physics to extract information from quantum communications without necessarily causing the quantum state disturbances on which existing security proofs rely. Here we describe a key distribution scheme provably secure against general attacks by a postquantum eavesdropper limited only by the impossibility of superluminal signaling. Its security stems from violation of a Bell inequality.
Retrotransposon-mediated restoration of Chlorella telomeres: accumulation of Zepp retrotransposons at termini of newly formed minichromosomes (2003)

To elucidate the contribution of LINE-like retrotransposon Zepp elements to the formation and maintenance of chromosomal telomeres, newly formed minichromosomes in irradiated Chlorella vulgaris cells were isolated and structurally characterized. A minichromosome (miniV4) of approximately 700 kb in size contained a Zepp cluster taking the place of the telomeric repeats on one terminus, whereas the other end of this chromosome consisted of canonical telomeric repeats. The Zepp copies in this cluster were in a tandem array with their poly(A) tails towards the centromere. Another minichromosome Y32 ( approximately 400 kb in size) was shown to have several copies of Zepp elements on both termini. On the right arm terminus, two copies of Zepp were found in a tandem array with poly(A) tracts facing towards the chromosomal end. The poly(A) tail and the 3'-end of approximately 400 bp of the distal copy were replaced by the telomeric repeats. On the 5'-side of the proximal copy was another Zepp element in the reverse orientation. These newly formed telomeric structures are very similar to those previously found in the left arm of chromosome I and the terminus of an unidentified chromosome and support the model of Zepp-mediated restoration and maintenance of Chlorella telomeres.
Construction of a software development environment based on a high‐level language architecture (1987)

Abstract In software development it is becoming more important to offer an environment which helps decrease software cost and increase productivity and reliability. On the other hand, for program coding, different programming languages are used depending on the application fields of newly developed software systems. Thus, we must prepare a dedicated development environment for each programming language. Moreover, when we realize a language processing system for a programming language which has high descriptive capability such as Ada, a problem arises on how to achieve appropriate load distribution between software and hardware. From such a viewpoint, we have developed a high‐level language architecture SPRING for language classes such as Ada and Pascal. SPRING performs run‐time checks at the architecture level, for example, checks indices of arrays, the value range of subtype variables, etc. Further, we constructed a software development environment EDMAS on a computer based on this architecture as a concrete example of a software development environment. EDMAS aids in developing in a top‐down fashion, a software system in case Ada is used. This paper describes the high‐level language architecture SPRING and the software development environment EDMAS.
House dust mites and human dander (1987)

The occurrence of house dust mites was measured in the homes of 12 patients with the scaly skin disease, psoriasis. The median number of mites in the mattress dust and floor dust was 27 (range 10-153)/0.1 g and 56 (range 12-114)/0.1 g respectively, which is significantly higher than the background pollution of house dust mites in normal Danish homes. The results support the idea that the amount of mites in our homes not only depend on relative air humidity but also on the production of dandruff.
Sulforaphane Enhances the Therapeutic Potential of TRAIL in Prostate Cancer Orthotopic Model through Regulation of Apoptosis, Metastasis, and Angiogenesis (2008)

The ability of sulforaphane to inhibit tumor growth, metastasis, and angiogenesis and to enhance the therapeutic potential of TRAIL suggests that sulforaphane alone or in combination with TRAIL can be used for the management of prostate cancer.
Extracellular Vesicles Isolated from the Leaf Apoplast Carry Stress-Response Proteins (2016)

Exosomes are extracellular vesicles (EVs) that play a central role in intercellular signaling in mammals by transporting proteins and small RNAs. Plants are also known to produce EVs, particularly in response to pathogen infection. The contents of plant EVs have not been analyzed, however, and their function is unknown. Here, we describe a method for purifying EVs from the apoplastic fluids of Arabidopsis (Arabidopsis thaliana) leaves. Proteomic analyses of these EVs revealed that they are highly enriched in proteins involved in biotic and abiotic stress responses. Consistent with this finding, EV secretion was enhanced in plants infected with Pseudomonas syringae and in response to treatment with salicylic acid. These findings suggest that EVs may represent an important component of plant immune responses.
Use of multiple-wavelength and/or TE/TM effective-refractive-index measurements to reconstruct refractive-index profiles (1997)

A method is presented whereby the refractive-index profile of a planar, surface-dielectric optical waveguide may be reconstructed from sets of effective refractive indices, measured at different wavelengths and/or with sets of effective refractive indices measured with TE and TM polarisation. The index change and the substrate index may be wavelength dispersive and birefringent. The method is compared, both theoretically and experimentally, with a conventional single-wavelength method for a number of index profiles. This technique provides more information about the profile than can be obtained from one measured set and is used to analyse the index profiles of potassium ion exchange guides formed in soda-lime glass. The limitations of the technique are also discussed.
Effect of Cardiolipin Oxidation on Solid-Phase Immunoassay for Antiphospholipid Antibodies (2001)

Diagnostic assays for antiphospholipid antibodies are routinely performed on microtitre plates coated with cardiolipin. Here we show that contact between cardiolipin and NUNC-Immuno plates leads to extensive oxidation, generating a series of peroxy-cardiolipins which were identified by electrospray ionization mass spectrometry. To investigate the impact of oxidation on the antibody assay. cardiolipin was resolved into 12 molecular species, including oxidized species and non-oxidized species with different degrees of unsaturation. All 12 species reacted under anaerobic conditions with serum from patients with primary antiphospholipid syndrome. Immune reactivity was similar for tetralinoleoyl-cardiolipin, trilinoleoyl-oleoyl-cardiolipin, and peroxycardiolipins, but somewhat lower for tristearoyl-oleoyl-cardiolipin. Oxidative treatment of cardiolipin with air, cytochrome c, or Cu2+/tert-butylhydroperoxide, either before or during the assay, did not enhance immune reactivity. Similar results were obtained with a monoclonal IgM from lupus-prone mice, that binds cardiolipin in the absence of protein cofactors. We conclude that the solid-phase assay for antiphospholipid antibodies can be supported by various oxidized and non-oxididized molecular species of cardiolipin.
Correlation of aPKC-iota and E-cadherin expression with invasion and prognosis of cholangiocarcinoma. (2008)

The expressions of aPKC-iota and E-cadherin may reflect the differentiation and invasive potential of cholangiocarcinoma. aPKC-iota and E-cadherin may be independent prognostic factors and, when used in combination with clinicopathological characteristics, may increase the accuracy in predicting the prognosis of patients with cholangiocarcinoma. As a polar regulative associated protein, aPKC-iota may play an important role in the invasion and metastasis of cholangiocarcinoma.
Hibernator (2005)

Energy consumption has become an important issue in high-end data centers, and disk arrays are one of the largest energy consumers within them. Although several attempts have been made to improve disk array energy management, the existing solutions either provide little energy savings or significantly degrade performance for data center workloads.Our solution, Hibernator, is a disk array energy management system that provides improved energy savings while meeting performance goals. Hibernator combines a number of techniques to achieve this: the use of disks that can spin at different speeds, a coarse-grained approach for dynamically deciding which disks should spin at which speeds, efficient ways to migrate the right data to an appropriate-speed disk automatically, and automatic performance boosts if there is a risk that performance goals might not be met due to disk energy management.In this paper, we describe the Hibernator design, and present evaluations of it using both trace-driven simulations and a hybrid system comprised of a real database server (IBM DB2) and an emulated storage server with multi-speed disks. Our file-system and on-line transaction processing (OLTP) simulation results show that Hibernator can provide up to 65% energy savings while continuing to satisfy performance goals (6.5--26 times better than previous solutions). Our OLTP emulated system results show that Hibernator can save more energy (29%) than previous solutions, while still providing an OLTP transaction rate comparable to a RAID5 array with no energy management.
Divergent evolution of fucosyltransferase genes from vertebrates, invertebrates, and bacteria (1999)

On the basis of function and sequence similarities, the vertebrate fucosyltransferases can be classified into three groups: alpha-2-, alpha-3-, and alpha-6-fucosyltransferases. Thirty new putative fucosyltransferase genes from invertebrates and bacteria and six conserved peptide motifs have been identified in DNA and protein databanks. Two of these motifs are specific of alpha-3-fucosyltransferases, one is specific of alpha-2-fucosyltransferases, another is specific of alpha-6-fucosyltransferases, and two are shared by both alpha-2- and alpha-6-fucosyltranserases. Based on these data, literature data, and the phylogenetic analysis of the conserved peptide motifs, a model for the evolution offucosyltransferase genes by successive duplications, followed by divergent evolution is proposed, with either two different ancestors, one for the alpha-2/6-fucosyltransferases and one for the alpha-3-fucosyltransferases or a single common ancestor for the two families. The expected properties of such an hypothetical ancestor suggest that the plant or insect alpha-3-fucosyltransferases using chitobiose as acceptor might be the present forms of this ancestor, since fucosyltransferases using chitobiose as acceptor are expected to be of earlier appearance in evolution than enzymes using N -acetyllactosamine. However, an example of convergent evolution of fucosyltransferase genes is suggested for the appearance of the Leaepitopes found in plants and primates.
Effects of Altering the Transcription Termination Signals of Respiratory Syncytial Virus on Viral Gene Expression and Growth In Vitro and In Vivo (2003)

Nonsegmented negative-sense RNA viruses (mononegaviruses) control viral gene expression largely through a transcription gradient such that promoter-proximal genes are transcribed more abundantly than downstream genes. For some paramyxoviruses, naturally occurring differences in the levels of efficiency of transcription termination by various gene end (GE) signals provide an additional level of regulation of gene expression. The first two genes (NS1 and NS2) of respiratory syncytial virus (RSV) are particularly inefficient in termination. We investigated whether altering the termination efficiency (TE) of these two genes in infectious recombinant virus would affect transcription of promoter-proximal and promoter-distal genes, production of viral proteins, and viral replication in cell culture and in the respiratory tract of mice. Recombinant RSVs were constructed with mutations that increased or decreased the TE of the NS1 GE signal, increased that of the NS2 GE signal, or increased that of both signals. Increasing the TE of either or both GE signals resulted in decreased production of the related polycistronic readthrough mRNAs, which normally arise due to the failure of the viral polymerase to recognize the GE signal. This was accompanied by a small increase in the levels of monocistronic NS1 and NS2 mRNAs. Conversely, decreasing the TE of the NS1 GE increased the production of readthrough mRNAs concomitant with a decrease of monocistronic NS1 and NS2 mRNA levels. These changes were reflected in the levels of NS1 and NS2 protein. All of the mutant viruses displayed growth kinetics and virus yields similar to wild-type recombinant RSV (rA2) in both HEp-2 and Vero cells. In addition, all mutants grew similarly to rA2 in the upper- and lower-respiratory tract of BALB/c mice, though some of the mutants displayed slightly decreased replication. These data suggest that the natural inefficiencies of transcription termination by the NS1 and NS2 GE signals do not play important roles in controlling the magnitude of RSV gene expression or the efficiency of virus replication. Furthermore, while changes in the TE of a GE signal clearly can affect the transcription of its gene as well as that of the one immediately downstream, these changes did not have a significant effect on the overall transcriptional gradient.