gebhart/patrepeval huggingface dataset:
Low-Dimensional Semiconductor Structures (2001)

Low-Dimensional Semiconductor Structures provides a seamless, atoms-to-devices introduction to the latest quantum heterostructures. It covers their fabrication, their electronic, optical and transport properties, their role in exploring physical phenomena, and their utilization in devices. The authors begin with a detailed description of the epitaxial growth of semiconductors. They then deal with the physical behaviour of electrons and phonons in low-dimensional structures. A discussion of localization effects and quantum transport phenomena is followed by coverage of the optical properties of quantum wells. They then go on to discuss non-linear optics in quantum heterostructures. The final chapters deal with semiconductor lasers, mesoscopic devices, and high-speed heterostructure devices. The book contains many exercises and comprehensive references. It is suitable as a textbook for graduate-level courses in electrical engineering and applied physics. It will also be of interest to engineers involved in the development of semiconductor devices.
Object-oriented retrieval mechanism for semistructured image collections (1998)

~ls paper presents the object-oriented image retrieval mechanism ~vhlchprovides the content model, the indexing scheme, and tie query processing techniques m a whole. Three types of image content i.e., visual features, semantic features, and keywords, are define~and they are represented using the object-oriented data model. Three types of index structures corresponding to the identied features are elaborated to facilitate the semch. The query processing techniques to process complex queries which use multiple types of indexes are also descriied Experiments have been carried out on large image collections to demonstrate the effectiveness of the proposed retrieval mechanism.
Biochemical Characterization, Cloning, and Sequencing of ADP-Dependent (AMP-Forming) Glucokinase from Two Hyperthermophilic Archaea, Pyrococcus furiosus and Thermococcus litoralis (2000)

The ADP-dependent (AMP-forming) glucokinases from the hyperthermophilic archaea Pyrococcus furiosus and Thermococcus litoralis catalyze the phosphorylation of glucose using ADP as the essential phosphoryl group donor. Both enzymes were purified to homogeneity and characterized with regard to each other. The enzymes had similar enzymological properties as to substrate specificity, coenzyme specificity, optimum pH, and thermostability. However, a difference was observed in the subunit composition; while the T. litoralis enzyme is a monomer with a molecular mass of 52 kDa, the P. furiosus enzyme has a molecular mass of about 100 kDa and consists of two subunits with identical molecular masses of 47 kDa. The genes encoding these enzymes were cloned and sequenced. The gene for the P. furiosus enzyme contains an open reading frame for 455 amino acids with a molecular weight of 51,265, and that for the T. litoralis enzyme contains an open reading frame for 467 amino acids with a molecular weight of 53,621. About 59% similarity in amino acid sequence was observed between these two enzymes, whereas they did not show similarity with any ATP-dependent kinases that have been reported so far. In addition, two phosphate binding domains, and adenosine and glucose binding motifs commonly conserved in the eukaryotic hexokinase family were not observed.
Split T Cell Tolerance against a Self/Tumor Antigen: Spontaneous CD4+ but Not CD8+ T Cell Responses against p53 in Cancer Patients and Healthy Donors (2011)

Analyses of NY-ESO-1-specific spontaneous immune responses in cancer patients revealed that antibody and both CD4(+) and CD8(+) T cell responses were induced together in cancer patients. To explore whether such integrated immune responses are also spontaneously induced for other tumor antigens, we have evaluated antibody and T cell responses against self/tumor antigen p53 in ovarian cancer patients and healthy individuals. We found that 21% (64/298) of ovarian cancer patients but no healthy donors showed specific IgG responses against wild-type p53 protein. While none of 12 patients with high titer p53 antibody showed spontaneous p53-specific CD8(+) T cell responses following a single in vitro sensitization, significant p53-specific IFN-γ producing CD4(+) T cells were detected in 6 patients. Surprisingly, similar levels of p53-specific CD4(+) T cells but not CD8(+) T cells were also detected in 5/10 seronegative cancer patients and 9/12 healthy donors. Importantly, p53-specific CD4(+) T cells in healthy donors originated from a CD45RA(-) antigen-experienced T cell population and recognized naturally processed wild-type p53 protein. These results raise the possibility that p53-specific CD4(+) T cells reflect abnormalities in p53 occurring in normal individuals and that they may play a role in processes of immunosurveillance or immunoregulation of p53-related neoplastic events.
Selection of representative protein data sets (1992)

The Protein Data Bank currently contains about 600 data sets of three-dimensional protein coordinates determined by X-ray crystallography or NMR. There is considerable redundancy in the data base, as many protein pairs are identical or very similar in sequence. However, statistical analyses of protein sequence-structure relations require nonredundant data. We have developed two algorithms to extract from the data base representative sets of protein chains with maximum coverage and minimum redundancy. The first algorithm focuses on optimizing a particular property of the selected proteins and works by successive selection of proteins from an ordered list and exclusion of all neighbors of each selected protein. The other algorithm aims at maximizing the size of the selected set and works by successive thinning out of clusters of similar proteins. Both algorithms are generally applicable to other data bases in which criteria of similarity can be defined and relate to problems in graph theory. The largest nonredundant set extracted from the current release of the Protein Data Bank has 155 protein chains. In this set, no two proteins have sequence similarity higher than a certain cutoff (30% identical residues for aligned subsequences longer than 80 residues), yet all structurally unique protein families are represented. Periodically updated lists of representative data sets are available by electronic mail from the file server "netserv@embl-heidelberg.de." The selection may be useful in statistical approaches to protein folding as well as in the analysis and documentation of the known spectrum of three-dimensional protein structures.
Distinct Roles for MAX Protein Isoforms in Proliferation and Apoptosis (1997)

MAX is a basic helix-loop-helix-leucine zipper protein that plays a central role in the transcriptional control of Myc oncoproteins. MYC-MAX heterodimers stimulate transcription, whereas MAX homodimers, or heterodimers between MAX and members of the MAD family of basic helix-loop-helix-leucine zipper proteins, repress transcription. Max exists in two major isomeric forms, MAX(L) and MAX(S), which differ from one another only by a 9-amino acid insertion/deletion. We show here that MAX(L) is much more effective at homodimeric DNA binding than MAX(S). In NIH3T3 cells, MAX(L) was able to repress a c-Myc-responsive reporter gene whereas MAX(S) either stimulated the reporter gene or had little effect on its expression. In comparison to control cell lines or those stably over-expressing MAX(S), MAX(L)-over-expressing cell lines showed reduced expression of transiently expressed or endogenous c-Myc responsive genes, grew more slowly, possessed a higher growth factor requirement, and showed accelerated apoptosis following growth factor deprivation. Differential effects on growth and apoptosis represent two previously unrecognized properties of MAX proteins. These can at least partly be explained by the differences in their DNA binding abilities and their effects on target gene expression.
Interference between non‐a, non‐b and hepatitis b virus infection in chimpanzees (1983)

Pre-existing chronic or concurrent acute non-A, non-B (NANB) virus infection has been found to interfere with hepatitis B virus (HBV) replication and to delay and moderate markedly the appearance of disease related to HBV infection in chimpanzees. The mechanism for this phenomenon remains unclear. These findings are of practical significance for vaccine safety testing and evaluation of methods for virus inactivation in chimpanzees. The possible occurrence of dual NANB and HBV infection requires that prolonged follow-up be carried out. Attempts to carry out inactivation studies on materials containing both types of virus may also provide misleading observations.
达尔马提亚（克罗地亚）中部始新统—中新统复理石底部的巨厚层状沉积（ … (1998)

砂尔马提亚（Ｄａｌｍａｔｉａｎ）地区始新世一中新世复理石盆地底部（东亚得里亚海）中的一些巨厚状碳酸盐岩的下伏地层和上覆地层均为扇形三角液砾岩。而薄层浊积岩与扇形天角洲砾岩呈指状穿插关系。扇形三角洲和指状穿插的浊积岩被解释为低水位期或海平面上升早期的产物，认为巨厚层状沉积是海平面加速上升时期形成的发育不全的扇形三角洲。这基于以下观察：（１）它们是一些扇形三角洲砾岩的上覆地层；（２）巨厚层状沉积中的骨
Switching of Exchange-Coupled Perpendicularly Magnetized Layers Under Spin–Orbit Torque (2018)

We proposed a multilayer structure to reduce the critical spin current density of perpendicularly magnetized layers switched by spin-orbit torque (SOT) from the spin Hall effect. In the structure, we introduced exchange-coupled perpendicularly magnetized layers composed of soft and hard magnetic layers in lieu of a single magnetic layer. The switching loops and dynamic processes under periodic spin currents have been studied by micromagnetic simulation. We have found that the critical spin current density can be substantially reduced when the saturation magnetization of the soft layer is sufficiently low. Moreover, the critical spin current density is quite insensitive to the change of exchange interaction between the two magnetic layers, which enables the multilayer structure to tolerate the variation of material composition or structure imperfections during fabrication. The introduction of exchange-coupled layers provides a way to design and optimize the SOT-driven devices and paves the path for their applications.
Cancer Pharmacogenomics: SNPs, Chips, and the Individual Patient (2003)

There is great heterogeneity in a patient's response to medications, often requiring empirical strategies to define the appropriate drug therapy for each patient. Pharmacogenomics aims to elucidate further the inherited nature of interindividual differences in drug disposition and effects, with the ultimate goal of providing a stronger scientific basis for selecting the optimal drug therapy and dosage for each patient. These genetic insights should also lead to mechanism-based approaches to the discovery and development of new medications. Genetic polymorphisms in drug metabolizing enzymes, transporters, receptors, and other drug targets have been linked to interindividual differences in the efficacy and toxicity of many medications. For example, polymorphism in thiopurine methyltransferase (TPMT) results in altered degradation of the commonly prescribed agent 6-mercaptopurine. This genetic variant has significant clinical implications because patients with functionally relevant homozygous mutations in the TPMT gene experience extreme or fatal toxicity after administration of normal doses of 6-MP. In addition, patients heterozygous for mutations in TPMT require slight dosage reduction of 6-MP and experience a greater degree of systemic toxicity from the agent. This and other examples of genetic polymorphism relevant to the treatment of cancer are highlighted to illustrate the promise and pitfalls of the exciting area of cancer therapeutics, with the potential of providing a stronger scientific basis to optimize drug therapy on the basis of each patient's genetic constitution.
Analysis of Tat function in human immunodeficiency virus type 1-infected low-level-expression cell lines U1 and ACH-2 (1994)

The U1 and ACH-2 cell lines are subclones of human monocytic and T-lymphoid cells, respectively, persistently infected with human immunodeficiency virus type 1. These cell lines harbor the viral genome but produce only very low levels of viral progeny, which can be increased by stimulation with agents such as phorbol ester and cytokines. As such, they provide an in vitro model for human immunodeficiency virus type 1 latency. In order to examine the basis for their latent state, we have analyzed the activity of endogenous Tat protein in these cells and investigated the effect on viral replication of the addition of exogenous Tat protein. We find that U1 cells seem to have levels of Tat protein that are suboptimal for long terminal repeat (LTR) transcription, because transcription from a transfected LTR-chloramphenicol acetyltransferase plasmid can be enhanced by cotransfection of a Tat expression plasmid. Furthermore, viral replication can be stimulated in this cell line by incubation with purified Tat protein. In contrast, ACH-2 cells are not limited for LTR-chloramphenicol acetyltransferase transcription by endogenous levels of Tat, and virus production is not increased by the addition of exogenous Tat protein. By semiquantitative PCR analysis of viral RNA, we have demonstrated that Tat protein caused an increase in human immunodeficiency virus RNA expression in U1 cells but had no effect in ACH-2 cells. This suggests that a different mechanism underlies the latent state in U1 and ACH-2 cells.
A Simple Computational Market for Network Information Services (1995)

Visionary projections of a wide-area network teeming with intelligent agents describe an environment where end-users and their agents can pick and choose among a great variety of potentially valuable information services. However, neither network capabilities nor users&amp;apos; time and money are infinite. Computational markets provide one type of mechanism for allocating limited resources in such an environment in a distributed, dynamic way. Moreover, the underlying economic theory provides an analytical framework for predicting aggregate behavior and designing individual agents. In this paper, we describe a prototypical computational market model for information services distributed over a network. Our initial focus is on the economic problem of when and where to establish mirror sites for the more popular information services. Competitive agents choose to set up mirrors based on going prices for network bandwidth, computational resources, and the information service. Depending on the experi...
The digital library integrated task environment (DLITE) (1997)

We descriie a case study in the &sign of a user interface to a digital library. Our &sign stems fr0m a vision of a li%rary as a channel to the vast array of digital information and a00ument services that are becoming available. Based on published studies of library use and on scenarios, we developed a metaphor called workcenters, which are customized for users' tasks. Due to our scenarios and to prior work in the CHI community, we chose a direct-manipulation realization of the metaphor. Our system, called DLITE, is &signed to make it easy for users to interact with many different services while focusing on a task. Users have reacted favorably to the interface design in pilot testing. We conclude by descriiing our approaches to this problem.
Expression of the human OX40 (hOX40) antigen in normal and neoplastic tissues (1995)

The Ber-ACT35 mAb was raised against the human T-cell lymphotrophic virus (HTLV) 1-transformed, CD4+ HUT 102 cell line and recognizes the human homologue of the OX40 (hOX40) antigen. The analysis of the expression of hOX40 by immunohistochemical techniques in malignant lymphomas, carcinomas and non-malignant tissues of different organs shows that hOX40 expression was almost completely restricted to T lymphocytes. Besides T cells only a small subpopulation of macrophages in Langerhans' cell histiocytosis and a few blasts in B-cell non-Hodgkin's lymphoma (B-NHL) revealed a faint immunostaining with the Ber-ACT35 mAb. Furthermore, most of the hOX40+ T-cells are CD4+.
Antiphospholipid antibodies are directed against epitopes of oxidized phospholipids. Recognition of cardiolipin by monoclonal antibodies to epitopes of oxidized low density lipoprotein. (1996)

The optimal clinical management of patients with antiphospholipid antibody syndrome (APS) is uncertain because of a lack of an underlying hypothesis to explain why antiphospholipid autoantibodies (aPL) form to such ubiquitous compounds as phospholipids (PL). In this paper, we demonstrate that many, if not most, aPL are actually directed at neoepitopes of oxidized PL, or neoepitopes generated by adduct formation between breakdown products of oxidized PL and associated proteins. Each cardiolipin (CL) molecule contains four unsaturated fatty acids and is highly susceptible to oxidation, particularly upon exposure to air. Yet, standard anticardiolipin antibodies (aCL) immunoassays routinely bind CL to microtiter wells by evaporation of the ethanol solvent overnight at 4 degrees C. Using a variety of techniques, we demonstrated that rapid oxidation occurs when CL is plated and exposed to air. Sera from apo E-deficient mice, which have high autoantibody titers to oxidized low density lipoprotein, showed a striking time-dependent increase in binding to CL that was exposed to air for increasing periods of time. Monoclonal antibodies to oxidized LDL, cloned from the apo E-deficient mice, also bound to oxidized CL. Both sera and affinity-purified aCL-IgG from APS patients bound to CL progressively as it was oxidized. However, the monoclonal antibodies from apo E-deficient mice, or sera or aCL-IgG from APS patients did not bind to a reduced CL analog that was unable to undergo peroxidation. These data demonstrate that many aPL are directed at neoepitopes of oxidized phospholipids, and suggest that oxidative events may be important in the pathophysiology of APS. In turn, this suggests new therapeutic strategies, possibly including intensive antioxidant therapy.
Determination of DNA adducts of malonaldehyde in humans: effects of dietary fatty acid composition (1996)

The effects of dietary fatty acid composition on the endogenous formation of DNA adducts of malonaldehyde (MA), the major product of lipid peroxidation, were investigated in humans. A group of 59 healthy individuals of both sexes and different ages was initially fed a milk fat-based diet rich in saturated fatty acids for 14 days. Following this initial period, after which the group was considered homogeneous with respect to diet, 30 randomly chosen subjects were given a sunflower oil-based (rich in polyunsaturated fatty acids) (SO) diet and the remaining 29 individuals a low erucic acid rapeseed oil-based (rich in monounsaturated fatty acids) (RO) diet for 25 days. The fatty acid composition of plasma lipid fractions and the level of DNA adducts of MA in total white blood cells were then determined at the end of the SO and RO dietary periods. DNA adduct levels were measured by 32p-postlabelling using reversed-phase HPLC with on-line detection of radioactivity. Higher concentrations of polyunsaturated fatty acids in plasma triglycerides and higher levels of DNA adducts of MA were found in the subjects on the SO diet when compared with those in the RO dietary group. A large inter-individual variation in adduct levels was observed. The average adduct level in the SO diet group was 7.4 +/- 8.7 adducts/10(7) nucleotides (n = 23). This level was 3.6-fold higher than that found in individuals in the RO diet group (P < 0.001). Our results, in conjunction with the mutagenic and carcinogenic properties of MA, thus suggest the interaction of lipid peroxidation products such as MA with DNA as one plausible mechanism explaining the involvement of dietary fat in carcinogenesis.
Structure and expression of murine germ-line immunoglobulin epsilon heavy chain transcripts induced by interleukin 4. (1990)

The murine lymphokine, interleukin 4 (IL-4) is able to specifically promote isotype switching to IgG1 and IgE in cultures of mitogen-stimulated B cells. Emerging evidence suggests that germ-line immunoglobulin heavy chain gene transcription may direct switching by modulating switch-region accessibility to a recombinase. In this study, cloned cDNA copies of the germ-line epsilon heavy chain transcript have been used to determine the genomic organization of this transcription unit. The 5' end of these transcripts are derived from an exon, denoted I epsilon, located 2 kilobases 5' of the C epsilon switch region [C epsilon = epsilon heavy chain constant (C) region gene]. Nucleotide sequence analysis reveals that this RNA does not encode a protein, as the I epsilon exon contains termination codons in all reading frames. Germ-line epsilon chain transcripts can be detected in cultures of normal splenic B cells treated with IL-4 within 24 hr, and this expression correlates with subsequent switching to C epsilon. Consistent with the IL-4 inducibility of this RNA is the identification of a motif upstream from the site of transcription initiation that closely resembles a transcription element implicated in the IL-4 regulation of the gene encoding the murine class II histocompatibility antigen, A alpha k. These data lend support to the accessibility model of isotype switching and implicate IL-4 in the transcriptional activation of the C epsilon locus.
A bioluminescence resonance energy transfer (BRET) system: Application to interacting circadian clock proteins (1999)

We describe a method for assaying protein interactions that offers some attractive advantages over previous assays. This method, called bioluminescence resonance energy transfer (BRET), uses a bioluminescent luciferase that is genetically fused to one candidate protein, and a green fluorescent protein mutant fused to another protein of interest. Interactions between the two fusion proteins can bring the luciferase and green fluorescent protein close enough for resonance energy transfer to occur, thus changing the color of the bioluminescent emission. By using proteins encoded by circadian (daily) clock genes from cyanobacteria, we use the BRET technique to demonstrate that the clock protein KaiB interacts to form homodimers. BRET should be particularly useful for testing protein interactions within native cells, especially with integral membrane proteins or proteins targeted to specific organelles.
Targeting of the Arabidopsis Homomeric Acetyl-Coenzyme A Carboxylase to Plastids of Rapeseeds (1997)

Acetyl-coenzyme A carboxylase (ACCase) occurs in at least two forms in rapeseed (Brassica napus): a homomeric (HO) and presumably cytosolic isozyme and a heteromeric, plastidial isozyme. We investigated whether the HO-ACCase of Arabidopsis can be targeted to plastids of B. napus seeds. A chloroplast transit peptide and the napin promoter were fused to the Arabidopsis ACC1 gene and transformed into B. napus, with the following results. (a) The small subunit transit peptide was sufficient to provide import of this very large protein into developing seed plastids. (b) HO-ACCase in isolated plastids was found to be biotinylated at a level comparable to extraplastidial HO-ACCase. (c) In vitro assays of HO-ACCase in isolated plastids from developing seeds indicate that it occurs as an enzymatically active form in the plastidial compartment. (d) ACCase activity in mature B. napus seeds is normally very low; however, plants expressing the SSU/ACC1 gene had 10- to 20-fold higher ACCase activity in mature seeds, suggesting that plastid localization prevents the turnover of HO-ACCase. (e) ACCase over-expression altered seed fatty acid composition, with the largest effect being an increase approximately 5% by the expression of HO-ACCase in plastids.