gebhart/patrepeval huggingface dataset:
Regulation of Bacterial RecA Protein Function (2007)

The RecA protein is a recombinase functioning in recombinational DNA repair in bacteria. RecA is regulated at many levels. The expression of the recA gene is regulated within the SOS response. The activity of the RecA protein itself is autoregulated by its own C-terminus. RecA is also regulated by the action of other proteins. To date, these include the RecF, RecO, RecR, DinI, RecX, RdgC, PsiB, and UvrD proteins. The SSB protein also indirectly affects RecA function by competing for ssDNA binding sites. The RecO and RecR, and possibly the RecF proteins, all facilitate RecA loading onto SSB-coated ssDNA. The RecX protein blocks RecA filament extension, and may have other effects on RecA activity. The DinI protein stabilizes RecA filaments. The RdgC protein binds to dsDNA and blocks RecA access to dsDNA. The PsiB protein, encoded by F plasmids, is uncharacterized, but may inhibit RecA in some manner. The UvrD helicase removes RecA filaments from RecA. All of these proteins function in a network that determines where and how RecA functions. Additional regulatory proteins may remain to be discovered. The elaborate regulatory pattern is likely to be reprised for RecA homologues in archaeans and eukaryotes.
A Methylaspartate Cycle in Haloarchaea (2011)

Access to novel ecological niches often requires adaptation of metabolic pathways to cope with new environments. For conversion to cellular building blocks, many substrates enter central carbon metabolism via acetyl-coenzyme A (acetyl-CoA). Until now, only two such pathways have been identified: the glyoxylate cycle and the ethylmalonyl-CoA pathway. Prokaryotes in the haloarchaea use a third pathway by which acetyl-CoA is oxidized to glyoxylate via the key intermediate methylaspartate. Glyoxylate condensation with another acetyl-CoA molecule yields malate, the final assimilation product. This cycle combines reactions that originally belonged to different metabolic processes in different groups of prokaryotes, which suggests lateral gene transfer and evolutionary tinkering of acetate assimilation. Moreover, it requires elevated intracellular glutamate concentrations, as well as coupling carbon assimilation with nitrogen metabolism.
Edge subdivision for fast diffraction calculations (2006)

A continuous-time edge-diffraction impulse response (IR) can be expressed as a line-integral along the diffracting edge. With such a formulation, the discrete-time IR is found by subdividing the edge into segments, and for each segment integrating over its length and distributing the result among the appropriate time samples. Two basic subdivision strategies have been considered previously: one in which the segments are aligned with samples of the impulse response (i.e. each segment contributes to exactly one sample), and a second in which the segments are of a fixed length, and thus may contribute to one or multiple samples. In this paper, a hybrid subdivision strategy is proposed in which a sample-aligned segment is used only for the first sample of the IR, and evenly sized segments which span many samples are used to process the remainder of the edge. It has been found that the use of this hybrid method can result in a significant decrease in processing time with a minimal reduction in the accuracy of the IR calculation, and thus may allow for rapid diffraction calculations in complex, multi-edge simulation environments.
Alternatives to Copyright Law Protection of Graphic Characters: The Lanham Act and Antidilution Statutes (1990)

In an "information age" dominated by mass media entertainment, graphic characters have become increasingly valuable commodities. Federal trademark law and state antidilution statutes provide alternatives to copyright law protection of such hot properties as the "Teenage Mutant Ninja Turtles." This Essay explores how courts determine the existence of secondary meaning in characters, as well as which aspects of a character, such as a costume or nickname, may receive protection. The Essay concludes with an examination of new trends introduced by the entertainment industry and the law of unfair competition.
Implications of Amyloid Precursor Protein and Subsequent β‐Amyloid Production to the Pharmacotherapy of Alzheimer's Disease (2002)

Alzheimer's disease is the most common type of dementia in older people. It is highly prevalent, affecting 35-45% of those aged 85 years or older. This disease has devastating consequences to patients, their families, caregivers, and the health care system. Much has been learned about its pathobiology, which has led to the beta-amyloid (Abeta) hypothesis. This hypothesis continues to be the predominant postulate of the pathobiology of Alzheimer's disease. Under this hypothesis, abnormal accumulation of Abeta is followed by a cascade of neurotoxic effects, which eventually result in neurodegeneration and development of Alzheimer's disease. This is thought to be the result of altered processing of the amyloid precursor protein (APP), preferentially by beta- and gamma-secretase enzymes rather than nonamyloidogenic processing by alpha-secretase. The growing body of knowledge regarding the processing of APP to various forms of Abeta has resulted in new approaches to the investigation of putative anti-Alzheimer's disease compounds, including immune-based therapies and various agents that can positively affect APP processing.
Melamine Deaminase and Atrazine Chlorohydrolase: 98 Percent Identical but Functionally Different (2001)

The gene encoding melamine deaminase (TriA) from Pseudomonas sp. strain NRRL B-12227 was identified, cloned into Escherichia coli, sequenced, and expressed for in vitro study of enzyme activity. Melamine deaminase displaced two of the three amino groups from melamine, producing ammeline and ammelide as sequential products. The first deamination reaction occurred more than 10 times faster than the second. Ammelide did not inhibit the first or second deamination reaction, suggesting that the lower rate of ammeline hydrolysis was due to differential substrate turnover rather than product inhibition. Remarkably, melamine deaminase is 98% identical to the enzyme atrazine chlorohydrolase (AtzA) from Pseudomonas sp. strain ADP. Each enzyme consists of 475 amino acids and differs by only 9 amino acids. AtzA was shown to exclusively catalyze dehalogenation of halo-substituted triazine ring compounds and had no activity with melamine and ammeline. Similarly, melamine deaminase had no detectable activity with the halo-triazine substrates. Melamine deaminase was active in deamination of a substrate that was structurally identical to atrazine, except for the substitution of an amino group for the chlorine atom. Moreover, melamine deaminase and AtzA are found in bacteria that grow on melamine and atrazine compounds, respectively. These data strongly suggest that the 9 amino acid differences between melamine deaminase and AtzA represent a short evolutionary pathway connecting enzymes catalyzing physiologically relevant deamination and dehalogenation reactions, respectively.
Efficient evaluation of XML middle-ware queries (2001)

We address the problem of efficiently constructing materialized XML views of relational databases. In our setting, the XML view is specified by a query in the declarative query language of a middle-ware system, called SilkRoute. The middle-ware system evaluates a query by sending one or more SQL queries to the target relational database, integrating the resulting tuple streams, and adding the XML tags. We focus on how to best choose the SQL queries, without having control over the target RDBMS.
Human RNase III Is a 160-kDa Protein Involved in Preribosomal RNA Processing (2000)

A human RNase III gene encodes a protein of 160 kDa with multiple domains, a proline-rich, a serine- and arginine-rich, and an RNase III domain. The expressed purified RNase III domain cleaves double-strand RNA and does not cleave single-strand RNA. The gene is ubiquitously expressed in human tissues and cell lines, and the protein is localized in the nucleus of the cell. The levels of transcription and translation of the protein do not change during different phases of the cell cycle. However, a significant fraction of the protein in the nucleus is translocated to the nucleolus during the S phase of the cell cycle. That this human RNase III is involved in processing of pre-rRNA, but might cleave at sites different from those described for yeast RNase III, is shown by antisense inhibition of RNase III expression. Inhibition of human RNase III expression causes cell death, suggesting an essential role for human RNase III in the cell. The antisense inhibition technique used in this study provides an effective method for functional analysis of newly identified human genes.
The role of the PI3K-PKB signaling module in regulation of hematopoiesis (2009)

AbstractBone marrow homeostasis is controlled by a series of complex cell fate decisions that determine whether hematopoietic stem and progenitor cells divide, differentiate or die. Exquisite control of the stem cell niche is crucial for the correct maintenance of blood cell production, allowing inductive external signals to modulate stem cell self-renewal or increased production of specific blood cell lineages. Since the first bone marrow transplantation more than 40 years ago, research has been focused on understanding the molecular processes regulating hematopoietic stem cell function. While our appreciation of the transcriptional regulators of hematopoiesis has developed considerably, the role of specific intracellular signal transduction modules remains surprisingly undefined. One such module includes phosphatidylinostiol 3-kinase (PI3K) and protein kinase B (PKB/c-akt). The identification and cloning of PI3K and PKB in the early 1990s has resulted in the publication of a large body of literature providing evidence for a crucial role of these molecules in the regulation of proliferation, apoptosis and differentiation. This review will focus on recent studies that have extended our understanding of how PI3K-PKB can regulate the complex process of hematopoiesis.
Cross-linked envelope-related markers for squamous differentiation in human lung cancer cell lines. (1990)

Lung carcinoma cell lines were analyzed in culture and in nude mouse xenograft for both morphological appearance and expression of specific proteins that participate in cross-linked envelope formation during normal squamous cell terminal differentiation. Cross-linked envelope formation, induced by artificial influx of millimolar Ca2+ into the cultured cells, was an exclusive trait of squamous, adenosquamous, and mucoepidermoid carcinomas. Small cell lung carcinoma and non-squamous non-small cell lung carcinoma lines, such as adenocarcinoma and large cell carcinoma, were uniformly negative for cross-linked envelope formation. Involucrin, which is incorporated into the cross-linked envelope by the enzyme transglutaminase, was expressed at highest levels in squamous tumors, but several of the non-squamous non-small cell lung carcinoma lines also expressed comparable amounts. On the other hand, transglutaminase activity was consistently higher in squamous as opposed to non-squamous lines, so that in cell culture, a clear contrast between the groups could be observed. A Mr 195,000 protein that is incorporated into cultured human epidermal cell cross-linked envelopes was also observed in some but not all of the squamous lines. Two forms of transglutaminase are expressed in cultured keratinocytes. One of them, tissue transglutaminase, was expressed in the majority of squamous cell lines even though it is not a normal product of squamous differentiation in vivo. Keratinocyte transglutaminase, which is distinct from the tissue form and is normally expressed during terminal differentiation in squamous epithelia. was measurably present in only one of the six squamous cell lines tested. In nude mouse xenografts, keratinocyte transglutaminase, localized immunohistochemically with a biotinylated mouse monoclonal antibody, was again present only in a minority of the squamous lines whereas involucrin was expressed in all. In contrast to involucrin, keratinocyte transglutaminase is not an obligatory component of squamous differentiation in the pulmonary carcinoma cell lines tested. Its expression may be of value in further refining their classification.
Efficient detection of point mutations on color-codedstrands of target DNA. (1994)

Presently available methods for screening large genetic regions for unknown point mutations are neither flawless nor particularly efficient. We describe an approach, especially well suited to identifying mutations present in the heterozygous state, that combines several improvements in a protocol called fluorescence-assisted mismatch analysis (FAMA). Appropriate gene regions of the wild-type and the putative mutant allele are simultaneously amplified from genomic DNA by using the polymerase chain reaction, and large DNA fragments, so far up to 800 bp, are end labeled with strand-specific fluorophores. Aliquots are denatured and reannealed to form heteroduplexes and subjected to conventional cytosine- and thymine-specific modifications. Cleavages occurring on opposite strands are detected by denaturing gel electrophoresis using an automated DNA sequencer. Since the DNA fragments derived from the mutant allele are also end labeled, the number of informative mispaired bases is doubled compared to conventional searches using wild-type probes. The sensitivity of detection is also increased, because differential fluorescent end labelling allows the identification and measurement of strand-specific background cleavages at matched cytosine or thymine residues. Automatic superimposition of tracings from different subjects allows mismatch detection at sites that, because of the nature of the bases involved and of the neighboring sequence, are known to be less susceptible to cleavage. The effects of the latter parameters have been studied quantitatively on a series of point mutations found in the human C1-inhibitor gene in patients affected by hereditary angioedema. Dilution experiments have demonstrated that most mutations are detected even when the mutant chromosome is diluted 10-fold or more compared with the normal one.
In vivo promoter activity and transgene expression in mammalian somatic tissues evaluated by using particle bombardment. (1993)

The particle bombardment method of gene transfer provides an alternative approach for analysis of in vivo promoter activity and transgene expression. Transient expression of the firefly luciferase gene from five viral and five cellular promoters was assessed after in vivo gene transfer using this method. The relative strengths of these promoters were quantitatively determined in five different rat tissues: skin epidermis, dermis, muscle, liver, and pancreas. Cytomegalovirus immediate early enhancer/promoter activity was consistently the highest in each tissue, whereas other promoters displayed tissue-specific preferences. In liver, the mouse phosphoenolpyruvate carboxykinase and metallothionein promoters were stimulated in vivo by inducing agents at 1 and 5 days posttransfection. In dermis, sustained luciferase activity was observed for over 1.5 years after gene delivery. In vivo transgene expression was also detected in bombarded mouse, rabbit, and rhesus monkey tissues. These results suggest that particle bombardment provides an effective system for studies of in vivo gene transfer and gene therapy.
Molecular cloning of seprase: a serine integral membrane protease from human melanoma (1997)

Seprase is a homodimeric 170 kDa integral membrane gelatinase whose expression correlates with the invasiveness of the human melanoma cell line LOX. Here, we report the molecular cloning of a cDNA that encodes the 97 kDa subunit of seprase. Its deduced amino acid sequence predicts a type II integral membrane protein with a cytoplasmic tail of 6 amino acids, followed by a transmembrane domain of 20 amino acids and an extracellular domain of 734 amino acids. The carboxyl terminus contains a putative catalytic region (approximately 200 amino acids) which is homologous (68% identity) to that of the nonclassical serine protease dipeptidyl peptidase IV (DPPIV). The conserved serine protease motif G-X-S-X-G is present as G-W-S-Y-G. However, sequence analysis of seprase cDNA from LOX and other cell lines strongly suggests that seprase and human fibroblast activation protein alpha (FAP alpha) are products of the same gene. We propose that seprase/FAP alpha and DPPIV represent a new subfamily of serine integral membrane proteases (SIMP).
Inhibiting signal transducer and activator of transcription 3: rationality and rationale design of inhibitors (2011)

STAT3 is an important target in tumor biology based on its frequent activation in various tumors and its pleiotropic effects on different cell types. Screening large libraries of logically synthesized small molecule inhibitors is one way to rapidly generate many potential molecules, which can then be tested in different biologically relevant models. The stage is, therefore, set for the identification and development of novel STAT3 inhibitors that will, in the very near future, enter the clinical realm.
The Mitochondrial Protein hFis1 Regulates Mitochondrial Fission in Mammalian Cells through an Interaction with the Dynamin-Like Protein DLP1 (2003)

The yeast protein Fis1p has been shown to participate in mitochondrial fission mediated by the dynamin-related protein Dnm1p. In mammalian cells, the dynamin-like protein DLP1/Drp1 functions as a mitochondrial fission protein, but the mechanisms by which DLP1/Drp1 and the mitochondrial membrane interact during the fission process are undefined. In this study, we have tested the role of a mammalian homologue of Fis1p, hFis1, and provided new and mechanistic information about the control of mitochondrial fission in mammalian cells. Through differential tagging and deletion experiments, we demonstrate that the intact C-terminal structure of hFis1 is essential for mitochondrial localization, whereas the N-terminal region of hFis1 is necessary for mitochondrial fission. Remarkably, an increased level of cellular hFis1 strongly promotes mitochondrial fission, resulting in an accumulation of fragmented mitochondria. Conversely, cell microinjection of hFis1 antibodies or treatment with hFis1 antisense oligonucleotides induces an elongated and collapsed mitochondrial morphology. Further, fluorescence resonance energy transfer and coimmunoprecipitation studies demonstrate that hFis1 interacts with DLP1. These results suggest that hFis1 participates in mitochondrial fission through an interaction that recruits DLP1 from the cytosol. We propose that hFis1 is a limiting factor in mitochondrial fission and that the number of hFis1 molecules on the mitochondrial surface determines fission frequency.
Water-Deficit Tolerance and Field Performance of Transgenic Alfalfa Overexpressing Superoxide Dismutase (1996)

Abstract Transgenic alfalfa (Medicago sativa) expressing Mn-superoxide dismutase cDNA tended to have reduced injury from water-deficit stress as determined by chlorophyll fluorescence, electrolyte leakage, and regrowth from crowns. A 3-year field trial indicated that yield and survival of transgenic plants were significantly improved, supporting the hypothesis that tolerance of oxidative stress is important in adaptation to field environments.
Enzymes for biosynthesis de novo and elongation of fatty acids in mycobacteria grown in host cells: is Mycobacterium leprae competent in fatty acid biosynthesis? (1990)

Fatty acid synthetase activity in extracts of Mycobacterium leprae was equivalent to 1.7 pmol malonyl-CoA incorporated into fatty acid min-1 (mg protein)-1. This activity--if representative of living M. leprae organisms--is insufficient to enable them to synthesize their lipid requirements rapidly enough to support growth. The major activity for scavenging fatty acids in extracts of Mycobacterium microti and Mycobacterium avium, as well as in extracts of M. leprae, was acetyl-CoA-dependent fatty acyl-CoA 'elongase'. This activity was about four times higher in M. avium and M. microti grown in a medium which contained lipids, or when grown in mice, than in medium without added lipids. In contrast, the de novo fatty acid synthetase activity was repressed in M. avium and M. microti when grown in medium that contained lipids, or when grown in mice. These results are consistent with the hypothesis that mycobacteria grown in vivo preferentially scavenge lipids from the host cells, and suggest that a source of lipid should be included in media for attempted axenic isolation of M. leprae.
Accumulation of Ultrasmall Superparamagnetic Particles of Iron Oxide in Human Atherosclerotic Plaques Can Be Detected by In Vivo Magnetic Resonance Imaging (2003)

Accumulation of USPIOs in macrophages in predominantly ruptured and rupture-prone human atherosclerotic lesions caused signal decreases in the in vivo MR images.
CB 2 cannabinoid receptor activation produces antinociception by stimulating peripheral release of endogenous opioids (2005)

CB(2) cannabinoid receptor-selective agonists are promising candidates for the treatment of pain. CB(2) receptor activation inhibits acute, inflammatory, and neuropathic pain responses but does not cause central nervous system (CNS) effects, consistent with the lack of CB(2) receptors in the normal CNS. To date, there has been virtually no information regarding the mechanism of CB(2) receptor-mediated inhibition of pain responses. Here, we test the hypothesis that CB(2) receptor activation stimulates release from keratinocytes of the endogenous opioid beta-endorphin, which then acts at opioid receptors on primary afferent neurons to inhibit nociception. The antinociceptive effects of the CB(2) receptor-selective agonist AM1241 were prevented in rats when naloxone or antiserum to beta-endorphin was injected in the hindpaw where the noxious thermal stimulus was applied, suggesting that beta-endorphin is necessary for CB(2) receptor-mediated antinociception. Further, AM1241 did not inhibit nociception in mu-opioid receptor-deficient mice. Hindpaw injection of beta-endorphin was sufficient to produce antinociception. AM1241 stimulated beta-endorphin release from rat skin tissue and from cultured human keratinocytes. This stimulation was prevented by AM630, a CB(2) cannabinoid receptor-selective antagonist and was not observed in skin from CB(2) cannabinoid receptor-deficient mice. These data suggest that CB(2) receptor activation stimulates release from keratinocytes of beta-endorphin, which acts at local neuronal mu-opioid receptors to inhibit nociception. Supporting this possibility, CB(2) immunolabeling was detected on beta-endorphin-containing keratinocytes in stratum granulosum throughout the epidermis of the hindpaw. This mechanism allows for the local release of beta-endorphin, where CB(2) receptors are present, leading to anatomical specificity of opioid effects.
Use of monoclonal antibodies to sialylated Lewisx and sialylated Lewisa for serological tests of cancer. (1985)

A new monoclonal antibody, CSLEX1, directed against sialylated Lewisx was tested in parallel with a monoclonal antibody, CSLEA1, directed against sialylated Lewisa antigen. In tests with a solid-phase radioimmune sandwich assay, the sialylated Lewisx monoclonal antibody detected sera from certain cancer patients that were negative with the sialylated Lewisa monoclonal antibody. Some sera from cancer patients showed the reverse reaction. We conclude that the combined use of these two monoclonal antibodies detects a wider range of sera from cancer patients than the use of a single antibody alone. It should be possible in the future to use multiple monoclonal antibodies to increase detection.