gebhart/patrepeval huggingface dataset:
Characterization of the Interaction between the Herpes Simplex Virus Type I Fc Receptor and Immunoglobulin G (1999)

Herpes simplex virus type I (HSV-1) virions and HSV-1-infected cells bind to human immunoglobulin G (hIgG) via its Fc region. A complex of two surface glycoproteins encoded by HSV-1, gE and gI, is responsible for Fc binding. We have co-expressed soluble truncated forms of gE and gI in Chinese hamster ovary cells. Soluble gE-gI complexes can be purified from transfected cell supernatants using a purification scheme that is based upon the Fc receptor function of gE-gI. Using gel filtration and analytical ultracentrifugation, we determined that soluble gE-gI is a heterodimer composed of one molecule of gE and one molecule of gI and that gE-gI heterodimers bind hIgG with a 1:1 stoichiometry. Biosensor-based studies of the binding of wild type or mutant IgG proteins to soluble gE-gI indicate that histidine 435 at the CH2-CH3 domain interface of IgG is a critical residue for IgG binding to gE-gI. We observe many similarities between the characteristics of IgG binding by gE-gI and by rheumatoid factors and bacterial Fc receptors such as Staphylococcus aureus protein A. These observations support a model for the origin of some rheumatoid factors, in which they represent anti-idiotypic antibodies directed against antibodies to bacterial and viral Fc receptors.
Functional characterization of the T4 DNA ligase: a new insight into the mechanism of action (1997)

ATP-dependent DNA ligases are essential enzymes in both DNA replication and DNA repair processes. Here we report a functional characterization of the T4 DNA ligase. One N-terminal and two C-terminal deletion mutants were expressed in Escherichia coli as histidine- tagged proteins. An additional mutant bore a substitution of Lys159 in the active site that abolished ATP binding. All the proteins were tested in biochemical assays for ATP-dependent self-adenylation, DNA binding, nick joining, blunt-end ligation and AMP- dependent DNA relaxation. From this analysis we conclude that binding to DNA is mediated by sequences at both protein ends and plays a key role in the reaction. The enzyme establishes two different complexes with DNA: (i) a transient complex (T.complex) involving the adenylated enzyme; (ii) a stable complex (S.complex) requiring the deadenylated T4 DNA ligase. The formation of an S. complex seems to be relevant during both blunt-end ligation and DNA relaxation. Moreover the inactive His-K159L substitution mutant, although unable to self-adenylate, still possesses AMP-dependent DNA nicking activity.
Evidence for a prevalent dimorphism in the activation peptide of human coagulation factor IX. (1985)

We have independently isolated and characterized cDNA and genomic clones for the human coagulation factor IX. Sequence analysis in both cases indicates that threonine is encoded by the triplet ACT as the third residue of the activation peptide. This is in agreement with some earlier reports but in disagreement with others that show the alanine triplet GCT at this position. The discrepancy can thus be accounted for by natural variation of a single nucleotide in the normal population. Amino acid sequence analyses of activated factor IX from plasma samples of four individuals yielded two cases of alanine and two cases of threonine at the third position of the activation peptide. In factor IX from pooled plasma and in factor IX from a heterozygous individual, however, both alanine and threonine were found. Taken together, the findings show that a prevalent nondeleterious dimorphism exists in the activation peptide of human coagulation factor IX.
Testing patterns for software transactional memory engines (2007)

The emergence of multi-core processors is promoting the use of concurrency and multithreading. To raise the abstraction level of synchronization constructs is fundamental to ease the development of concurrent software, and Software Transactional Memory (STM) is a good approach towards such goal. However, execution environment issues such as the processor instruction set, caching policy, and memory model, may have strong influence upon the reliability of STM engines. This paper addresses the testing of STM engines aiming at improving their reliability and independence from execution environment. From our experience with porting and extending a specific STM engine, we report on some of the bugs found and synthesize some testing patterns that proved to be useful at testing STM engines.
Analysis and Optimization of Current-Driven Passive Mixers in Narrowband Direct-Conversion Receivers (2009)

Properties of the current-driven passive mixer are explored to maximize its performance in a zero-IF receiver. Since there is no reverse isolation between the RF and baseband sides of the mixer, the mixer reflects the baseband impedance to the RF and <i xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">vice versa</i> through simple frequency shifting. It is also shown that in an IQ down-conversion system the lack of reverse isolation causes a mutual interaction between the two quadrature mixers, which results in different high- and low-side conversion gains, and unexpected IIP2 and IIP3 values. With a thorough and accurate mathematical analysis it is shown how to design this mixer and its current buffer, and how to size components to get the best linearity, conversion gain and noise figure while alleviating the IQ cross-talk problem.
Designing Immunogens to Elicit Broadly Neutralizing Antibodies to the HIV-1 Envelope Glycoprotein (2007)

To date HIV-1 vaccines have not been able to elicit potent, long lasting, and broadly neutralizing antibodies to the virus. Our knowledge of HIV envelope glycoprotein (Env) structure/function and the existence of a handful of broadly neutralizing antibodies is guiding rational immunogen design. We review here the potential targets on the HIV Env (the glycan shield, the CD4 binding site, the coreceptor binding site, Env fusion intermediates, and the membrane proximal region) and their associated rational immunogen design strategies. Moreover, we discuss immune dampening and immune refocusing strategies designed to counter immunodominant, decoy responses generated by the virus. In this regard, an immunogen design strategy of "in vitro de-evolution" is presented, which begins to distill the HIV Env to its most critical, core functional domains. While we are beginning to have some understanding as to where we would like out immune system to go, we find that our immune repertoire may actually have limits that preclude successful completion of the task at hand. The repertoire limits appear to be a byproduct of autoantibody tolerance mechanisms and the complex structural requirements for effective, potent broadly neutralizing antibodies. Nevertheless, the hope is that through novel insights and creative solutions that we will be able to design immunogens capable of eliciting broadly neutralizing antibodies to the HIV envelope glycoprotein.
Microfabricated Devices for Capillary Electrophoresis−Electrospray Mass Spectrometry (1999)

Two fundamental approaches for the coupling of microfabricated devices to electrospray mass spectrometry (ESI-MS) have been developed and evaluated. The microdevices, designed for electrophoretic separation, were constructed from glass by standard photolithographic/wet chemical etching techniques. Both approaches integrated sample inlet ports, preconcentration sample loops, the separation channel, and a port for ESI coupling. In one design, a modular, reusable microdevice was coupled to an external subatmospheric electrospray interface using a liquid junction and a fused silica transfer capillary. The transfer capillary allowed the use of an independent electrospray interface as well as fiber optic UV detection. In the second design, a miniaturized pneumatic nebulizer was fabricated as an integral part of the chip, resulting in a very simple device. The on-chip pneumatic nebulizer provided control of the flow of the electrosprayed liquid and minimized the dead volume associated with droplet formation at the electrospray exit port. Thus, the microdevice substituted for a capillary electrophoresis instrument and an electrospray interface--traditionally two independent components. This type of microdevice is simple to fabricate and may thus be developed either as a part of a reusable system or as a disposable cartridge. Both devices were tested on CE separations of angiotensin peptides and a cytochrome c tryptic digest. Several electrolyte systems including a transient isotachophoretic preconcentration step were tested for separation and analysis by an ion trap mass spectrometer.
THE ANTINEOPLASTIC DRUG PACLITAXEL HAS IMMUNOSUPPRESSIVE PROPERTIES THAT CAN EFFECTIVELY PROMOTE ALLOGRAFT SURVIVAL IN A RAT HEART TRANSPLANT MODEL1 (2002)

Paclitaxel, a clinically proven antineoplastic agent, also has potent immunosuppressive properties in rodent organ transplantation. This drug could be extremely valuable in transplant situations where de novo cancer develops, or when organ transplantation is performed to treat isolated, but typically recurrent, neoplasms.
Crystal Structure of Tl 2 Ba 2 Ca 2 Cu 3 O 10 , a 125 K Superconductor (1988)

There is now a new series of high-temperature superconductors that may be represented as (A(III)O)(2)A(2)(II)Can-1CunO2+2n where A(III) is Bi or Tl, A(II) is Ba or Sr, and n is the number of Cu-O sheets stacked consecutively. There is a general trend toward higher transition temperatures as n increases. The highest n value for a bulk phase is three and is found when A(III) is Tl. This compound, Tl(2)Ba(2)Ca(2)Cu(3)O(10), has the highest transition temperature( approximately 125 K) of any presently known bulk superconductor. The structure of Tl(2)Ba(2)Ca(2)Cu(3)O(10) has been determined from single-crystal x-ray diffraction data and is tetragonal, with a = 3.85 A and c = 35.9 A. No superstructure is observed, and the material is essentially twin-free. Electron microscopy in the Tl/Ba/Ca/Cu/O system has revealed intergrowths where n = 5; such regions may well be responsible for the superconducting onset behavior observed in this system at about 140 K.
Structural requirements for interleukin-8 function identified by design of analogs and CXC chemokine hybrids. (1994)

Structure-activity relationships of human interleukin-8 (IL-8) were probed using chemically synthesized analogs with single or double amino acid substitutions, as well as hybrids derived by substituting IL-8 regions into IP10, a related protein that lacks IL-8 activity. The analogs were tested for functional activity by measuring induction of elastase release from human neutrophils and competition for binding of radiolabeled IL-8. The hybrid studies indicated that Gly31 and Pro32, as well as the NH2-terminal region from IL-8 are required to convert IP10 into a fully functional protein, suggesting that these elements are critical for IL-8 activity. Both disulfide bridges, linking residue 7 to 34 and residue 9 to 50, were critical for function, as shown by substituting the cysteine pairs with alpha-aminobutyric acid. Single conservative substitutions were generally accepted into the 10-22 region of IL-8, which contrasts with the ELR motif (residues 4-6), previously shown to be essential for activity. The importance of residues within the 10-15 region and the 17-22 region was demonstrated with hybrids. In addition, some of the 4-22 residues have structural roles that may be important; for example, Tyr13, Phe17, and Phe21 are involved in aromatic interactions in the IL-8 structure, and are also moderately sensitive to modification. Except for Cys50, the results argue against a role for the 36-72 region, including the COOH-terminal alpha-helix, in receptor binding. We conclude that the disulfide bridges and 30-35 turn provide a structural scaffold for the NH2-terminal region which includes the primary receptor-binding site (the ELR motif) and secondary binding and conformational determinants between residues 10 and 22.
Lasting Remissions in Hairy-Cell Leukemia Induced by a Single Infusion of 2-Chlorodeoxyadenosine (1990)

2-Chlorodeoxyadenosine is a simple purine nucleoside that has previously been shown to be effective in the treatment of low-grade malignant disorders of lymphoid tissue, including chronic lymphocytic leukemia and non-Hodgkin's lymphoma. Because of these encouraging results, we treated 12 patients with another low-grade B-cell neoplasm, hairy-cell leukemia. The patients received 2-chlorodeoxyadenosine (0.1 mg per kilogram of body weight per day) by continuous infusion for seven days. All the patients responded to treatment. Eleven had complete remissions characterized by the normalization of peripheral blood and bone marrow and disappearance of tumor masses. The longest remission has been 3.8 years. None of the patients have relapsed, and the median duration of remission has been 15.5 months. No serious toxic reactions occurred as a result of 2-chlorodeoxyadenosine therapy. These results suggest that 2-chlorodeoxyadenosine may be the most effective therapy available for hairy-cell leukemia. The administration of 2-chlorodeoxyadenosine resulted in a higher rate of complete remission than is observed with interferon alfa, and it required no maintenance therapy. Its toxicity may be lower than that of deoxycoformycin, and the responses were achieved with single courses of treatment.
Enzymatic polyesterification in organic media. II. Enzyme‐catalyzed synthesis of lateral‐substituted aliphatic polyesters and copolyesters (1993)

Abstract Enzymatic polymerization of hydroxyesters in organic media has been the subject of a previous and ongoing research in our laboratory. As part of that study, four ϵ‐substituted‐ϵ‐hydroxyesters were synthesized, and then polymerized using crude porcine pancreatic lipase (PPL) in n ‐hexane. These lateral‐substituted hydroxyesters polymerized enantioselectively to produce optically active oligomers and a resolved optically active unreacted monomer. It was found that with increasing bulkiness of the lateral substituent, in the order Me &gt;Et &gt;Ph, the enzymatic reaction becomes slower, yet the enantioselectivity is higher. The lateral‐substituted hydroxyesters were also copolymerized enzymatically with the more reactive linear methyl ϵ‐hydroxyhexanoate. Optically active copolymers were obtained, higher in molecular weight than the analogous homopolymers. © 1993 John Wiley &amp; Sons, Inc.
Editorial: The New Politics of Sex and the State (1994)

This issue of Feminist Review focuses on the new politics of sex and the state.The emphasis is on Britain, but we begin with an important overview from the Caribbean.Jacqui Alexander's account of recent legislation on sexual practices and sexuality considers ways in which postcolonial states attempt the public arbitration of private morality as a means of resolving crises of political legitimation.Powerful feelings about sexuality, femininity and masculinity are mobilized in the form of a claim by the state to embody and represent 'the nation'.One of the preconditions for this is the construction that the nation itself is in a process of disintegration-a notion reflected in popular discourses about moral decay.This disintegration manifests itself in part in a crisis of authority relations between men and women: state and civil society.M. Jacqui Alexander's frame for reading recent changes in legislation in the Caribbean governing sexualities foregrounds the relationship between sexuality, legitimation and individual and national identity.Many aspects of contemporary British debates about sex and the state can be read using a similar frame, although there is an additional emphasis on ideological contestations about the family.In the eighteen months since we planned this issue of Feminist Review, Britain has seen an explosion of entanglements involving the sexual morality of politicians within the Tory government.Many of these cases graphically illustrate the changing nature of contemporary familial relations and sexual morality.These changes are at the same time being ignored and refused in a whole range of Tory policies and campaigning •rhetoric which adversely affect women and young girls.Nowhere is this more apparent than in the workings of the Child Support Agency.In the UK, this agency is attempting a major redistribution of resources in the form of reprivatizing income support for single mothers.Although this process is proving administratively and politically problematic, there is no doubt that the goal ofthese new sexual politics is to divest the state of other than minimal public and collective support for the families of single mothers.This policy of
Timing, self‐control and a sense of direction are the secrets of multicopy plasmid stability (1998)

Multicopy plasmids of Escherichia coli are distributed randomly at cell division and, as long as copy number remains high, plasmid-free cells arise only rarely. Copy number variation is minimized by plasmid-encoded control circuits, and the limited data available suggest that deviations are corrected efficiently under most circumstances. However, plasmid multimers confuse control circuits, leading to copy number depression. To make matters worse, multimers out-replicate monomers and accumulate clonally within the culture, creating a subpopulation of cells with a significantly increased rate of plasmid loss. Multimers of natural multicopy plasmids, such as ColE1, are resolved to monomers by a site-specific recombination system (Xer-cer) whose activity is limited to intramolecular recombination. Recombination requires the heterodimeric XerCD recombinase plus two accessory proteins (ArgR and PepA), which activate recombination and prevent intermolecular events. Evidence is accumulating that Xer-cer recombination is relatively slow, and there is a risk that cells might divide before multimer resolution is complete. The Rcd transcript encoded within cer may solve this problem by preventing the division of multimer-containing cells. Working in concert, the triumvirate of copy number control, multimer resolution and cell division control achieve an extremely high fidelity of plasmid maintenance.
Analysis of the diphtheria tox promoter by site-directed mutagenesis (1988)

By oligonucleotide-directed mutagenesis, we introduced alterations in the two putative -10 regions of the diphtheria tox promoter which are positioned at -50 and -56 from the GUG tox initiation signal. The -10 region positioned at -50 is favored in the expression of ADP-ribosyltransferase activity from the wild-type tox promoter in recombinant Escherichia coli; however, the promoter down mutation at position -50 is compensated for by increased activity of the -10 region positioned at -56.
A Temporal Foundation for Continuous Queries over Data Streams (2005)

Despite the surge of research in continuous stream processing, there is still a semantic gap. In many cases, continuous queries are formulated in an enriched SQL-like query language without specifying the semantics of such a query precisely enough. To overcome this problem, we present a sound and well-defined temporal operator algebra over data streams ensuring deterministic query results of continuous queries. In analogy to traditional database systems, we distinguish between a logical and physical operator algebra. While our logical operator algebra specifies the semantics of each operation in a descriptive way over temporal multisets, the physical operator algebra provides adequate implementations in form of stream-to-stream operators. We show that query plans built with either the logical or the physical algebra produce snapshot-equivalent results. Moreover, we introduce a rich set of transformation rules that forms a solid foundation for query optimization, one of the major research topics in the stream community. Examples throughout the paper motivate the applicability of our approach and illustrate the steps from query formulation to query execution.
Specific expression of an extensin-like gene in the style of Nicotiana alata. (1992)

cDNAs and corresponding genomic clones encoding a putative proline-rich protein (NaPRP3) were isolated from libraries prepared from Nicotiana alata style mRNA and genomic DNA. The predicted NaPRP3 protein is structurally similar to extensin in containing six copies of the characteristic extensin sequence Ser-Pro4, but differs in being smaller (151 residues compared with greater than 300 residues) and lacking Tyr residues. In contrast to most extensin genes, the NaPRP3 gene is not induced by mechanical wounding, and its expression is restricted to cells of the transmitting tract of the style.
Regularized Evolution for Image Classifier Architecture Search (2019)

The effort devoted to hand-crafting neural network image classifiers has motivated the use of architecture search to discover them automatically. Although evolutionary algorithms have been repeatedly applied to neural network topologies, the image classifiers thus discovered have remained inferior to human-crafted ones. Here, we evolve an image classifier— AmoebaNet-A—that surpasses hand-designs for the first time. To do this, we modify the tournament selection evolutionary algorithm by introducing an age property to favor the younger genotypes. Matching size, AmoebaNet-A has comparable accuracy to current state-of-the-art ImageNet models discovered with more complex architecture-search methods. Scaled to larger size, AmoebaNet-A sets a new state-of-theart 83.9% top-1 / 96.6% top-5 ImageNet accuracy. In a controlled comparison against a well known reinforcement learning algorithm, we give evidence that evolution can obtain results faster with the same hardware, especially at the earlier stages of the search. This is relevant when fewer compute resources are available. Evolution is, thus, a simple method to effectively discover high-quality architectures.
Maternal Effect for DNA Mismatch Repair in the Mouse (2002)

DNA mismatch repair (DMR) functions to maintain genome stability. Prokaryotic and eukaryotic cells deficient in DMR show a microsatellite instability (MSI) phenotype characterized by repeat length alterations at microsatellite sequences. Mice deficient in Pms2, a mammalian homolog of bacterial mutL, develop cancer and display MSI in all tissues examined, including the male germ line where a frequency of approximately 10% was observed. To determine the consequences of maternal DMR deficiency on genetic stability, we analyzed F(1) progeny from Pms2(-/-) female mice mated with wild-type males. Our analysis indicates that MSI in the female germ line was approximately 9%. MSI was also observed in paternal alleles, a surprising result since the alleles were obtained from wild-type males and the embryos were therefore DMR proficient. We propose that mosaicism for paternal alleles is a maternal effect that results from Pms2 deficiency during the early cleavage divisions. The absence of DMR in one-cell embryos leads to the formation of unrepaired replication errors in early cell divisions of the zygote. The occurrence of postzygotic mutation in the early mouse embryo suggests that Pms2 deficiency is a maternal effect, one of a limited number identified in the mouse and the first to involve a DNA repair gene.