gebhart/patrepeval huggingface dataset:
The SJL/J T cell response to both spontaneous and transplantable syngeneic reticulum cell sarcoma is mediated predominantly by the V beta 17a+ T cell clonotype. (1988)

Previous studies have revealed that the reticulum cell sarcoma (RCS) of SJL/J (H-2s, IE-) mice express an "IE-like" stimulatory tumor-associated antigen, the expression of which is requisite for stimulating host T cells necessary for tumor growth. Herein, we present evidence that the predominant T cells raised in the syngeneic response to both spontaneous and transplantable RCS tumors are of the V beta 17a TCR clonotype. The V beta 17a+ clonotype of T cells has been shown to interact with IE allogeneic specificities. We demonstrate that all four characterized RCS-specific T cell hybridomas stained positively for the anti-V beta 17a mAb, KJ23a. Additionally, KJ23a, when added to cocultures of the T cell hybridomas and RCS tumors, inhibited the release of IL-2 by the hybridomas. Further, KJ23a was shown to markedly inhibit the proliferation of SJL/J T cells when cocultured with either spontaneous or transplantable RCS tumor cells. When analyzed by flow cytometry, the T cell blast population raised in response to both spontaneous and transplantable RCS were greater than 80% KJ23a+. These T cells were brightly stained by the anti-CD4 mAb, Gk1.5, and, therefore, represent class II-responsive T cells. In corroboration of the in vitro data, T cells derived from mesenteric lymph nodes of RCS tumor-bearing mice had likewise undergone a similar expansion of V beta 17a+, CD4+ T cells. Together, these results indicate that KJ23a+ T cells play an important and predominant role in the response of SJL/J mice to spontaneous RCS tumors and provide further suggestive evidence that the stimulatory antigen(s) on the RCS tumor is IE or an "IE-like" molecule. Significantly, the important role V beta 17a+ T cells play in the response to RCS suggests a potential therapeutic role for KJ23a mAb in the intervention and prevention of RCS tumors in SJL/J mice.
Cross‐antigenicity of horse serum albumin with dog and cat albumins: study of three short peptides with significant inhibitory activity towards specific human IgE and IgG antibodies (1996)

Horse serum albumin is present in the near vicinity of the animal, while dog and cat serum albumins are very common allergens present in house dust. Human patients clinically defined as allergic to horse could react with horse serum albumin by means of IgE or IgG antibodies. Studies regarding the specificities of these antibodies by inhibition enzyme-linked immunosorbent assay (ELISA) and depletion experiments have demonstrated that they are directed against dog serum albumin and cross-react not only with horse serum albumin but with other serum albumins from different origins. To investigate these observations further, we isolated and characterized three tryptic peptides (P1, P2 and P3) from horse serum albumin. The peptide P1 contains loops 1 and 2 of the first domain, P2 is derived from loop 4 of the second domain, and P3 contains the disulphide loop 9 of the third domain. These were able to inhibit the binding of the patients' IgE and IgG antibodies to horse albumin as well as to dog and cat serum albumins. This indicates that these peptides are involved in the observed cross-reactions. They also shared common epitopes, as revealed by human IgE antibodies. After reduction and alkylation, they totally lost their inhibitory capacity, suggesting that the intra-chain disulphide bridges, essential for the preservation of the loop structure, probably maintain their allergenic/antigenic reactivity.
The Facts About Fictions And Vice Versa: Public Understanding of Human Genetics (2001)

How does one draw the boundary between scientific fact and science fiction? As is well-known, this seemingly innocent question belies the complex inter-weavings—and the co-constitution—of the ‘factual’ and the ‘fictional’. For example, over recent years there has been a growth in popular dramas that use developments in the biomedical
sciences as central features of their narratives. In many of these dramas the actual content of biomedical knowledge is often little more than a theatrical prop to the psychology of the main protagonist—who has the potential to use knowledge in the furtherance of either good (e.g. The Citadel, 1938, Dr. Finlays Case Book, 1962) or harm (e.g. Frankenstein, 1931). More recently, fictional products, while still using the personality
of the medical scientist as a narrative device, have attempted to depict some of the content of the biomedical sciences and associated technologies. For example, the film Gattaca (1997) portrayed a future world obsessed with genetic screening and pre-implantation genetic diagnosis—technologies that have been available for the last 10 years. Indeed, the producers of the film made use of genetics consultants to ‘make sure the science wasn’t absurd’. Originally the film contained a final segment, cut from most versions on general release, that returned the viewer from a ‘fictional’ future to a ‘factual’ past. Stills of modern heroes such as John F. Kennedy and Albert
Einstein were shown to emphasis that these individuals might never have been born into a world keen to eliminate all inherited ills. The final on-screen message was to be ‘of course, the other birth that may never have taken place is your own’. After test screenings and focus
groups with lay people, this segment of the film was cut because audiences were left feeling ‘personally attacked’ as genetic defectives (Science, 1997).
Zeolite catalyzed acylation of alcohols and amines with acetic acid under microwave irradiation (2006)

Zeolite Hβ is found to be an efficient catalyst for the acylation of alcohols and amines with acetic acid under microwave irradiation. The process is environmentally safe and heterogeneous with excellent yields.
Transport of PEGylated liposomes from the splenic marginal zone to the follicle in the induction phase of the accelerated blood clearance phenomenon (2012)

The accelerated blood clearance (ABC) phenomenon has been reported to enhance the clearance of PEGylated liposomes from the blood circulation when the liposomes are injected into the same animal repeatedly. We have shown that anti-PEG IgM production from splenic B cells is crucial in the ABC phenomenon. In this study, we describe the crucial role of marginal zone (MZ) B cells in the anti-PEG IgM production and recognition of PEGylated liposomes in the induction phase of ABC phenomenon. Suppression of the anti-PEG IgM production was correlated with the disappearance of IgM(high) cells in the MZ, particularly MZ-B cells, following cyclophosphamide (CPA)-treatment, confirming that splenic MZ-B cells are responsible for anti-PEG IgM production. The MZ-B cells stimulated by a first dose of PEGylated liposomes internalized the second dose of PEGylated liposomes in a PEG modification-dependent manner and transported the liposomes into the follicle (FO) region. To the best of our knowledge, this is the first report showing that PEGylated liposome is recognized by MZ-B cells and transported to the FO region like blood-borne antigens or immune complexes. It is likely that PEGylated liposomes are recognized as a TI-2 antigen by the first line of defense against life-threatening infections by blood-borne organisms. Our study may have implications for immunogenicity of synthesized polymer-grafted therapeutics including nanocarriers, nucleic acids and proteins.
Recombination and Spontaneous Mutation at the Major Cluster of Resistance Genes in Lettuce (Lactuca sativa) (2001)

Two sets of overlapping experiments were conducted to examine recombination and spontaneous mutation events within clusters of resistance genes in lettuce. Multiple generations were screened for recombinants using PCR-based markers flanking Dm3. The Dm3 region is not highly recombinagenic, exhibiting a recombination frequency 18-fold lower than the genome average. Recombinants were identified only rarely within the cluster of Dm3 homologs and no crossovers within genes were detected. Three populations were screened for spontaneous mutations in downy mildew resistance. Sixteen Dm mutants were identified corresponding to spontaneous mutation rates of 10(-3) to 10(-4) per generation for Dm1, Dm3, and Dm7. All mutants carried single locus, recessive mutations at the corresponding Dm locus. Eleven of the 12 Dm3 mutations were associated with large chromosome deletions. When recombination could be analyzed, deletion events were associated with exchange of flanking markers, consistent with unequal crossing over; however, although the number of Dm3 paralogs was changed, no novel chimeric genes were detected. One mutant was the result of a gene conversion event between Dm3 and a closely related homolog, generating a novel chimeric gene. In two families, spontaneous deletions were correlated with elevated levels of recombination. Therefore, the short-term evolution of the major cluster of resistance genes in lettuce involves several genetic mechanisms including unequal crossing over and gene conversion.
5-Bromodeoxyuridine-Induced Differentiation of a Neuroblastoma (1970)

5-Bromodeoxyuridine induces the differentiation of mouse neuroblastoma C1300 to cells that morphologically resemble mature neurons. The induced differentiation can take place in the absence of DNA synthesis. This suggests that the halogenated pyrimidine need not be incorporated into DNA to alter the phenotype of the cell.
Cholesterol metabolism in hypothyroidism and hyperthyroidism in man. (1981)

Studies were carried out on cholesterol metabolism in 11 nonobese patients and 16 obese patients with hypothyroidism and 13 with hyperthyroidism. The patients underwent several investigations under metabolic ward conditions. Hypothyroid patients usually had an increase in low density lipoprotein (LDL)-cholesterol. Several mechanisms may have combined to cause a high LDL. For instance, the obese hypothyroid patients had an increase in cholesterol synthesis. Absorption of cholesterol also was increased frequently. However, other mechanisms not explored in this study probably contributed to most of the fall in LDL-cholesterol. Treatment of hypothyroid patients produced the expected fall in LDL. One possible mechanism could be that thyroid hormones enhance the conversion of cholesterol into bile acids; this mechanism has been suggested by other workers from animal studies. However, no evidence was obtained in either hypothyroid or hyperthyroid patients that thyroid hormones alter synthesis of bile acids. On the other hand, the hormones appeared to increase the synthesis of cholesterol. Patients with hypothyroidism frequently had supersaturated bile. The cause was mostly an enhanced secretion of biliary cholesterol associated with a tendency to obesity and increased synthesis of cholesterol. In contrast, the usually thin hyperthyroid patients did not have supersaturated bile. The studies show that thyroid hormones a) influence LDL-cholesterol by an action on the catabolism of LDL-independent of alterations in synthesis, catabolism, absorption, or excretion: b) stimulate synthesis of cholesterol; and c) affect biliary lipid metabolism in large part by influencing energy balance and cholesterol synthesis.
Rapid In Situ Detection of PCR-Amplified HIV-1 DNA (1992)

The low copy number of human immunodeficiency virus 1 (HIV-1) DNA infected cells precludes routine detection by in situ hybridization. The inability to detect cells latently infected by HIV-1 makes difficult the study of factors that induce viral transcription, an essential factor in the development of the acquired immune deficiency syndrome (AIDS). A sensitive and rapid technique to detect HIV-1 DNA could be used as a diagnostic test for AIDS and to differentiate latent versus active viral infection. We describe a 3-h technique whereby HIV-1 DNA is amplified by hot start polymerase chain reaction (PCR) and detected directly in infected cells. The specificity of the assay was demonstrated by double labeling the positive cells with CD4. Using a CR10 HIV-1-infected cell line, the 90% of cells that were HIV-1 DNA positive could be distinguished from the 10% that were actively expressing HIV-1 RNA. The PCR in situ technique should allow for the direct localization of DNA sequences in cells that would otherwise be undetectable by conventional in situ analysis.
Interstrain Variation of the Polysaccharide B Biosynthesis Locus of Bacteroides fragilis : Characterization of the Region from Strain 638R (1999)

The sequence and analysis of the capsular polysaccharide biosynthesis locus, PS B2, of Bacteroides fragilis 638R are described, and the sequence is compared with that of the PS B1 biosynthesis locus of B. fragilis NCTC 9343. Two genes of the region, wcgD and wcgC, are shown by complementation to encode a UDP-N-acetylglucosamine 2-epimerase and a UDP-N-acetylmannosamine dehydrogenase, respectively.
The theory of thermally activated delayed fluorescence for organic light emitting diodes (2018)

The interest in organic molecules exhibiting thermally activated delayed fluorescence (TADF) has been reinvigorated in recent years owing to their potential to be exploited as emitters in highly efficient purely organic light emitting diodes (OLEDs). However, designing new molecules that exhibit efficient TADF is a non-trivial task because they would appear to require the optimisation of a number of contrasting properties. For example these molecules must exhibit rapid conversion between the singlet and triplet manifolds without the use of heavy elements to enhance spin-orbit coupling. They should also display a large fluorescence rate, but simultaneously a small energy gap between low lying singlet and triplet states. Consequently to achieve systematic material design, a detailed understanding of the fundamental factors influencing the photophysical behaviour of TADF emitters is essential. Towards achieving this goal, theory and computation is playing a crucial role. In this feature article the recent progress in the theory of organic TADF molecules in the context of OLEDs is presented, with a view of achieving a deeper understanding of these molecules and driving systematic material design.
Evaluation of bone‐grafting materials in a new canine segmental spinal fusion model (1993)

This paper describes a new canine segmental spinal fusion model for the comparison of bone-grafting materials. The test sites in the model are three separate posterior interfacet-interlaminar fusion sites in the lumbar spine (L1-2, L3-4, and L5-6). The outcome was assessed by scoring of the fusion sites for union and by mechanical testing of fused segments. The results from two experiments are presented. Autogenous cancellous bone was the most effective material tested and had a statistically superior score for union compared with all other materials (p = 0.01). The results with an osteoconductive matrix of collagen and ceramic alone were no better than those with the controls (no graft). However, addition of an extract of matrix-derived proteins (15-30 kDa) to the collagen-ceramic carrier appeared to improve the score for union. The inclusion of nonresorbed ceramic granules had no evident effect on the mechanical properties of fusions, with a comparable score for union. This model appears to be a sensitive and efficient method for the comparison of graft materials. Advantages over previously described models are discussed.
The DNA Methylome As A Biomarker for Epigenetic Instability and Human Aging (2013)

Methylation of DNA is intimately involved in control of mammalian/vertebrate gene expression as part of a complex epigenetic regulatory system. We hypothesize that DNA methylation at cytosine-phosphate-guanine sites (CpGs), the "DNA methylome," evolved to increase stability of the differentiated state in somatic vertebrate cells, especially post-mitotic cells, which may have helped to increase longevity. Therefore, the DNA methylome may play a key role in human aging and be an ideal source of biomarkers aging. A new model that links the methylome to chronological age has been reported by Hannum et al.( 1 ) that accurately predicts age and rate of aging from the DNA methylation state of 71 markers in human blood samples. This model may make possible the development of new anti-aging therapeutics as well as more accurately assess the impact of anti-aging regimens, such as caloric restriction and drugs such as rapamycin. Furthermore, the model reveals information loss with increased age consistent with noise/unstable diffentiation-based models of aging. The model may eventually lead to experiments to differentiate the contributions of biomolecular damage and noise/incomplete structural replication during aging.
New linearization method using interstage second harmonic enhancement (1998)

Efficient use of the frequency spectrum necessitates the use of modulation formats such as /spl pi//4-DQPSK, which requires linear amplification to minimize spectral regrowth. A new linearization technique is presented that allows a more efficient operation of these linear amplifiers by combining both the advantage of the transparent nature of feed-forward linearization with the efficiency of feedback linearization. The method of convolution is used to analyze the amplifier characteristics and to determine how linearization can be achieved. This method is verified experimentally and proves that by careful use of the second harmonic component, a new method of linearization has been realized.
Amino Acid Sequence Studies of Horseradish Peroxidase (1979)

Horseradish peroxidase C dominates quantitatively among the isoperoxidases of horseradish root and has an isoelectric point close to 9. It consists of a hemin prosthetic group, 2 Ca 2+ and 308 amino acid residues, including 4 disulfide bridges, in a single polypeptide chain that carries 8 neutral carbohydrate side‐chains. The molecular weight of the polypeptide chain is 33890. Assuming an average carbohydrate composition of (GlcNAc) 2 , Man 3 , Fuc, Xyl for each carbohydrate chain, the molecular weight of native horseradish peroxidase C is close to 44000. Cyanogen bromide fragments of reduced and carboxymethylated apo‐peroxidase were purified by a combination of gel filtration and isoelectric focusing in urea, and cystine‐containing tryptic fragments of apo‐peroxidase were purified by gel filtration followed by disulfide cleavage and rechromatography at the initial conditions. The present paper discusses (a) isoelectric points and charge distribution within the native protein, the apoprotein and the cyanogen bromide fragments, (b) a buried pyrrolidonecarboxylyl amino terminus, (c) heterogeneity at the carboxyl terminus, and (d) a possible domain structure, likely from partial tryptic digestion.
Infinite-Acting Physically Representative Networks for Capillarity-Controlled Displacements (2007)

Abstract Drainage/imbibition simulations are traditionally performed on finite regular lattices. If physically representative networks are used instead, the spatial correlation of pore space features inherent in granular materials is automatically accounted for. However, even these networks are obtained from finite samples, and conditions must be specified on the boundaries. Making the conditions correspond to physically realistic situations is difficult, especially for simulations of phase trapping. This paper presents a method of constructing infinite-acting model rocks, in which a well-defined criterion for phase trapping is possible that is independent of boundary conditions. The foundation of the model is computer generated dense random periodic packings of spheres. We illustrate the method with simulations of drainage and irreducible wetting phase saturations. To eliminate possible confounding effects from grains being arranged differently, we compare simulations in infinite-acting networks with simulations in the finite network taken from the unit cell of the periodic packing. Wetting phase connectivity is assessed globally and accounts for all phase morphologies, including pendular rings. This enables a physically rigorous method of identifying clusters of trapped pores: A "wrap-around" cluster of wetting phase is effectively infinite, and drainage of one or more pores in the cluster is deemed possible. All other clusters of wetting phase cannot undergo further drainage. Qualitatively different behavior is observed than when local connectivity criteria are used for trapping. The nonwetting phase percolation threshold and the drainage endpoint are not sensitive to the choice of inlet pores in infinite-acting networks. For a finite network the percolation threshold was similarly insensitive, but the drainage endpoint was highly sensitive to the number and location of the exit pores. Comparison with experiments showed that a strict criterion of wetting phase connectivity (pores connected only by throats filled with wetting phase) cannot account for typical values of Sw,irr and that connectivity must persist via pendular rings. Typical laboratory experiments and simulations in finite networks yield drainage curves that approach irreducible wetting phase saturation Sw,irr gradually, with large changes in capillary pressure inducing only small changes in saturation. Simulations in infinite-acting networks do not exhibit this behavior. We argue that these simulations are more representative of behavior in the field, and that typical laboratory measurements underestimate the value of Sw,irr.
Towards on-line analytical mining in large databases (1998)

Great efforts have been paid in the Intelligent Database Systems Research Lab for the research and development of efficient data mining methods and construction of on-line analytical data mining systems.Our work has been focused on the integration of data mining and OLAP technologies and the development of scalable, integrated, and multiple data mining functions. A data mining system, DBMiner, has been developed for interactive mining of multiple-level knowledge in large relational databases and data warehouses. The system implements a wide spectrum of data mining functions, including characterization, comparison, association, classification, prediction, and clustering. It also builds up a user-friendly, interactive data mining environment and a set of knowledge visualization tools. In-depth research has been performed on the efficiency and scalability of data mining methods. Moreover, the research has been extended to spatial data mining, multimedia data mining, text mining, and Web mining with several new data mining system prototypes constructed or under construction, including GeoMiner, MultiMediaMiner, and WebLogMiner.This article summarizes our research and development activities in the last several years and shares our experiences and lessons with the readers.
A programmable router architecture supporting control plane extensibility (2000)

The Internet is evolving from an infrastructure that provides basic communication services into a more sophisticated infrastructure that supports a wide range of electronic services such as virtual reality games and rich multimedia retrieval services. However, this evolution is happening only slowly, in part because the communication infrastructure is too rigid. In this article we present a programmable router architecture in which the control plane functionality of the router can be extended dynamically through the use of delegates. Delegates can control the behavior of the router through a well-defined control interface, allowing service providers and third-party software vendors to implement customized traffic control policies or protocols. We describe Darwin, a system that implements such an architecture. We emphasize the runtime environment the system provides for delegate execution and the programming interface the system exports to support delegates. We demonstrate the advantages of using this system with two delegate examples.