gebhart/patrepeval huggingface dataset:
X-ray diffraction analyses of crystals of rat liver NAD(P)H:(quinone-acceptor) oxidoreductase containing cibacron blue (1989)

NAD(P)H:(quinone-acceptor) oxidoreductase (EC 1.6.99.2) is a widely distributed dicoumarol-inhibitable FAD-containing protein that catalyzes the obligatory two-electron reduction of quinones. The enzyme plays an important role in protecting animal cells against quinone toxicity and may be involved in the vitamin K-dependent blood coagulation cascade. Cocrystallization of rat liver quinone reductase with Cibacron blue, a potent inhibitor with respect to NAD(P)H, was achieved by the method of vapor diffusion in the presence of ammonium sulfate and low concentrations of polyethylene glycol. X-ray diffraction analysis showed these blue crystalline platelets to be monoclinic and to belong to the space group P2(1) (a = 71.6 A, b = 107.1 A, c = 87.8 A and beta = 92.60 degrees) with two dimers in the asymmetric unit. The crystals diffract to a resolution of at least 2.8 A.
Human homolog of the mouse sperm receptor. (1990)

The human zona pellucida, composed of three glycoproteins (ZP1, ZP2, and ZP3), forms an extracellular matrix that surrounds ovulated eggs and mediates species-specific fertilization. The genes that code for at least two of the zona proteins (ZP2 and ZP3) cross-hybridize with other mammalian DNA. The recently characterized mouse sperm receptor gene (Zp-3) was used to isolate its human homolog. The human homolog spans approximately 18.3 kilobase pairs (kbp) (compared to 8.6 kbp for the mouse gene) and contains eight exons, the sizes of which are strictly conserved between the two species. Four short (8-15 bp) sequences within the first 250 bp of the 5' flanking region in the human Zp-3 homolog are also present upstream of mouse Zp-3. These elements may modulate oocyte-specific gene expression. By using the polymerase chain reaction, a full-length cDNA of human ZP3 was isolated from human ovarian poly(A)+ RNA and used to deduce the structure of human ZP3 mRNA. Certain features of the human and mouse ZP3 transcripts are conserved. Both have unusually short 5' and 3' untranslated regions, both contain a single open reading frame that is 74% identical, and both code for 424 amino acid polypeptides that are 67% the same. The similarity between the two proteins may define domains that are important in maintaining the structural integrity of the zona pellucida, while the differences may play a role in mediating the species-specific events of mammalian fertilization.
Ponericins, New Antibacterial and Insecticidal Peptides from the Venom of the Ant Pachycondyla goeldii (2001)

The antimicrobial, insecticidal, and hemolytic properties of peptides isolated from the venom of the predatory ant Pachycondyla goeldii, a member of the subfamily Ponerinae, were investigated. Fifteen novel peptides, named ponericins, exhibiting antibacterial and insecticidal properties were purified, and their amino acid sequences were characterized. According to their primary structure similarities, they can be classified into three families: ponericin G, W, and L. Ponericins share high sequence similarities with known peptides: ponericins G with cecropin-like peptides, ponericins W with gaegurins and melittin, and ponericins L with dermaseptins. Ten peptides were synthesized for further analysis. Their antimicrobial activities against Gram-positive and Gram-negative bacteria strains were analyzed together with their insecticidal activities against cricket larvae and their hemolytic activities. Interestingly, within each of the three families, several peptides present differences in their biological activities. The comparison of the structural features of ponericins with those of well-studied peptides suggests that the ponericins may adopt an amphipathic alpha-helical structure in polar environments, such as cell membranes. In the venom, the estimated peptide concentrations appear to be compatible with an antibacterial activity in vivo. This suggests that in the ant colony, the peptides exhibit a defensive role against microbial pathogens arising from prey introduction and/or ingestion.
A Clinical Trial of Antioxidant Vitamins to Prevent Colorectal Adenoma (1994)

The lack of efficacy of these vitamins argues against the use of supplemental beta carotene and vitamins C and E to prevent colorectal cancer. Although our data do not prove definitively that these antioxidants have no anticancer effect, other dietary factors may make more important contributions to the reduction in the risk of cancer associated with a diet high in vegetables and fruits.
A Double Mutation in Glycoprotein gB Compensates for Ineffective gD-Dependent Initiation of Herpes Simplex Virus Type 1 Infection (2010)

Herpes simplex virus (HSV) entry into cells is triggered by the binding of envelope glycoprotein D (gD) to a specific receptor, such as nectin-1 or herpesvirus entry mediator (HVEM), resulting in activation of the fusion effectors gB and gH and virus penetration. Here we report the identification of a hyperactive gB allele, D285N/A549T, selected by repeat passage of a gD mutant virus defective for nectin-1 binding through cells that express a gD-binding-impaired mutant nectin-1. The gB allele in a wild-type virus background enabled the use of other nectins as virus entry receptors. In addition, combination of the mutant allele with an epidermal growth factor receptor (EGFR)-retargeted gD gene yielded dramatically increased EGFR-specific virus entry compared to retargeted virus carrying wild-type gB. Entry of the gB mutant virus into nectin-1-bearing cells was markedly accelerated compared to that of wild-type virus, suggesting that the gB mutations affect a rate-limiting step in entry. Our observations indicate that ineffective gD activation can be complemented by hypersensitization of a downstream component of the entry cascade to gD signaling.
The Genomic Sequence of the Accidental Pathogen Legionella pneumophila (2004)

We present the genomic sequence of Legionella pneumophila, the bacterial agent of Legionnaires' disease, a potentially fatal pneumonia acquired from aerosolized contaminated fresh water. The genome includes a 45-kilobase pair element that can exist in chromosomal and episomal forms, selective expansions of important gene families, genes for unexpected metabolic pathways, and previously unknown candidate virulence determinants. We highlight the genes that may account for Legionella's ability to survive in protozoa, mammalian macrophages, and inhospitable environmental niches and that may define new therapeutic targets.
A New Approach to the Prediction of Slug Frequency (1990)

ABSTRACT The design of crude oil production systems involving the pipelining of unseparated reservoir fluids requires a detailed understanding of multiphase flow phenomena. Slug flow in particular may cause undesirable process upsets if the separation and processing facilities are not designed to handle the resultant gas and liquid flowrate variations. Slug characteristics, primarily length, holdup and frequency, cannot be adequately predicted by existing empirical correlations. Mechanistic models are more satisfactory if the measured slug frequency is used as an input. However, existing methods for predicting slug frequencies are also unsatisfactory. BP have collected a large database on slug flow characteristics in both low pressure test rigs and field production flowlines. From this database BP have developed an improved method for the prediction of slug frequency. This method correlates slug frequency against the two parameters which appear from test rig observations to be the most important in the initial formation of slugs from a stratified flow. These parameters are the liquid holdup in the stratified film at the start of the line, and the gas-liquid slip velocity. The results indicate a much improved comparison with the data. The phenomenological approach to the correlation development gives increased confidence of its applicability to conditions outside the range of data from which it was developed.
Capillary blood sampling: How much pain is necessary?. Part 2: Relation between penetration depth and puncture pain (1995)

Abstract The relation between penetration depth and puncture pain was studied in 30 healthy subjects with a lancing device which allowed adjustment of depth (0.3–1.1mm). Pain was linearly related to depth as was the blood volume obtained. In about half of the individuals tested, an actual penetration depth of less than 1.0 mm provided sufficient blood for a glucose test.
Keratinocyte intercellular adhesion molecule-1 (ICAM-1) expression precedes dermal T lymphocytic infiltration in allergic contact dermatitis (Rhus dermatitis). (1989)

The ability of small molecules such as urushiol, present as a wax on the poison ivy leaf surface, to cause allergic contact dermatitis (rhus dermatitis) has fascinated immunologists for decades. Current dogma suggests that these epicutaneously applied catechol-containing molecules serve as haptens to conjugate with larger proteins via reactive o-quinone intermediates. These complexes are then recognized as foreign antigens by the immune system and elicit a hypersensitivity reaction. Phorbol ester can directly induce cultured keratinocyte (KC) intercellular adhesion molecule-1 (ICAM-1) expression via a protein kinase C (PK-C)-dependent mechanism. As urushiol is also a known PK-C agonist, we asked if topical application of a poison ivy/oak mixture could directly induce epidermal KC ICAM-1 expression. During the pre-erythematous phase of this reaction (4 to 20 hours), epidermal KCs expressed ICAM-1; this "initiation phase" preceded the appearance of activated memory T lymphocytes in the papillary dermis, and thus appeared to be nonlymphokine mediated. A near-contiguous cellular-adhesion molecular network was identified by ICAM-1 staining of basal KCs, dermal dendrocytes, and endothelial cells. During the second 24-hour period with the onset of erythema and edema, there was an "amplification phase" of more intense KC ICAM-1 expression coupled with relatively weak KC HLA-DR expression that coincided with dermal and epidermal T-cell infiltration. This suggests the presence of lymphokines, such as gamma interferon, during the amplification phase because of KC HLA-DR expression. On cultured KCs, urushiol directly induced ICAM-1 expression but not HLA-DR. Thus, in addition to functioning as an antigenic hapten, urushiol directly induces KC ICAM-1 expression. The KC ICAM-1 expression may then alter the dynamic trafficking of memory T cells in the epidermis, so as to initiate cutaneous inflammation in a nonantigen specific manner. This initiation phase is followed by T-cell infiltration and consequent lymphokine production that significantly amplifies the original stimulus. Thus much can still be learned about the molecular pathophysiology of this common type of cutaneous inflammation.
Antibody inhibits defined stages in the pathogenesis of reovirus serotype 3 infection of the central nervous system. (1989)

The mammalian reoviruses provide a model for studying specific aspects of the immunopathogenesis of viral infection. We have used two serotype 3 reoviruses to define stages in the pathogenesis of central nervous system (CNS) infection at which a mAb specific for the reoviral cell attachment protein sigma 1 (sigma 1mAbG5) acts to protect mice against lethal disease. sigma 1mAbG5 administered either before or at the time of footpad inoculation with reovirus T3D prevented entry of T3D into the CNS. sigma 1mAbG5 also inhibited the spread of reovirus T3C9 from the gastrointestinal tract to the CNS after peroral inoculation with T3C9. These effects occurred in the absence of a significant effect of sigma 1mAbG5 on primary replication in skeletal muscle (T3D) or the gastrointestinal tract (T3C9). sigma 1mAbG5 administered after T3D had reached the spinal cord inhibited subsequent spread of infectious virus from spinal cord to brain. Even after direct intracerebral inoculation of T3D, sigma 1mAbG5 prevented both growth in the brain and spread of infectious virus from brain to eye, spinal cord, and muscle. Treatment with sigma 1mAbG5 after intracerebral inoculation with T3D prevented neuronal necrosis and resulted in a delayed and topographically restricted inflammatory response. We detected no antibody-resistant T3D variants in vivo after treatment with sigma 1mAbG5. We conclude that systemic IgG does not play a significant role at the primary site of infection with reoviruses, while it clearly acts to prevent infection of the CNS and extension of infection with the CNS. Further study will be directed to defining what components of the immune system do act at primary sites of infection, and to defining the mechanisms by which antibody acts at defined stages in pathogenesis.
Sketching shadows and highlights to position lights (2002)

In inverse shading, a user provides information about the desired shading as she/he would like it to appear in the final image. The computer then interprets this information to identify the best values for the various shading parameters that would lead to the desired visual effect. The authors introduce an approach based on sketching in order to position light sources. Point light sources are positioned by sketches of shadows or highlights. Extended light sources are positioned by sketches of umbra or penumbra. The resulting system allows one to quickly position light sources and to refine their positions interactively and more intuitively.
Reactions of modulated molecular beams with pyrolytic graphite. III. Hydrogen (1975)

The reaction of hydrogen and pyrolytic graphite was studied by modulated molecular beam–mass spectrometric methods. Because molecular hydrogen does not react with graphite (within the detection limits of the technique), an atomic hydrogen reactant beam was generated by thermal dissociation of H2 in an effusion oven. For surface temperatures up to 800 °K, methane was the sole product. Acetylene was observed at temperatures above 1000 °K. Between 800 and 1000 °K, no carbon gasification occured; the surface acted only to recombine H atoms to form H2. The data were analyzed in terms of a model in which methane is formed by sequential addition of H atoms to CHn (n=0,1,2,3) and acetylene is formed by surface combination of two CH groups. The agreement between the model and the molecular beam data is very good. The model also predicts previous high pressure (1 atm H2) carbon gasification rates determined in conventional kinetic experiments.
Role of the glutathione/glutaredoxin and thioredoxin systems in yeast growth and response to stress conditions (2001)

Sulphydryl groups (-SH) play a remarkably broad range of roles in the cell, and the redox status of cysteine residues can affect both the structure and the function of numerous enzymes, receptors and transcription factors. The intracellular milieu is usually a reducing environment as a result of high concentrations of the low-molecular-weight thiol glutathione (GSH). However, reactive oxygen species (ROS), which are the products of normal aerobic metabolism, as well as naturally occurring free radical-generating compounds, can alter this redox balance. A number of cellular factors have been implicated in the regulation of redox homeostasis, including the glutathione/glutaredoxin and thioredoxin systems. Glutaredoxins and thioredoxins are ubiquitous small heat-stable oxidoreductases that have proposed functions in many cellular processes, including deoxyribonucleotide synthesis, repair of oxidatively damaged proteins, protein folding and sulphur metabolism. This review describes recent findings in the lower eukaryote Saccharomyces cerevisiae that are leading to a better understanding of their role in redox homeostasis in eukaryotic cell metabolism.
Intracerebroventricular passive immunization with anti‐Aβ antibody in Tg2576 (2003)

Current Alzheimer's disease (AD) research has established the fact that excessive genesis of Abeta derived from amyloidogenic processing of beta-amyloid (Abeta) precursor protein is fundamental to AD pathogenesis. There has been considerable interest in using immunization strategies for clearing excessive Abeta. Studies in animal models of AD have shown that active immunizations or systemic passive immunizations reduced cerebral plaque load and improved behavioral deficits. However, clinical translation of an active immunization strategy was interrupted because of evidence for meningoencephalitis produced in some patients who received Abeta vaccine. Studies in animal models have shown perimicrovascular hemorrhages and inflammation after sustained systemic immunizations in animals with vascular amyloid. In this light, our data showing the effects of a single intracerebroventricular (ICV) injection of anti-Abeta in the Alzheimer's Swedish mutant model Tg2576 are intriguing. We have previously demonstrated that a single ICV injection of anti-Abeta into the third ventricle of 10-month-old Tg2576 mice reduced cerebral plaques, reversed Abeta-induced depletion of presynaptic SNAP-25, and abolished astroglial activation as seen 1 month post-injection (Chauhan and Siegel [2002] J. Neurosci. Res. 69:10-23). The present report demonstrates that a single ICV injection of 10 microg anti-Abeta in 10-month-old Tg2576 mice reduced cerebral plaques, with decreased inflammation at this stage as evidenced by a reduced number of interleukin-1beta-positive microglia surrounding Congophilic plaques. Moreover, at this particular age, no microhemorrhage was discernible, as evidenced by the absence of hemosiderin deposition after a single ICV injection of anti-Abeta. This is the first report demonstrating absence of microhemorrhage and reduced inflammation after the ICV introduction of anti-Abeta in Tg2576 mice at 10 months of age. These facts indicate that, although invasive, ICV injection of anti-Abeta may be a safer method of vaccination in AD, possibly through reducing the vascular exposure to antibody. Further studies are warranted to determine the lasting effects of a single ICV anti-Abeta injection in animals with and without abundant plaque burden and at older ages.
Thermal Environment During Endosperm Cell Division in Maize: Effects on Number of Endosperm Cells and Starch Granules1 (1985)

Reductions in kernel mass are observed when corn ( Zea mays L.) kernels are grown in vitro or when unfavorable temperature occurs during endosperm cell division. We investigated the possibility that a decreased number of endosperm cells or a decreased number of starch granules is responsible for the reduced kernel mass in such environments. Three‐day‐old kernels of the single cross hybrid A619 ✕ W64A were placed in culture on a denned medium at 15, 30, and 35 °C, and their growth was compared with kernels from ears developed in the field or greenhouse. Kernels cultured at 30°C attained a final mass of 164 mg compared with 274 mg for field‐grown controls. At 30°C, endosperm cell division ceased approximately 10 days earlier, and the final number of cells was reduced by 34%. Final kernel mass was reduced by 49 and 78% when kernels were cultured at 15 and 35°C, respectively, compared with those grown at 30°C. At 35°C, the rate and duration of cell division in the endosperm, and the number of endosperm cells were severely reduced. In contrast, the rate of cell division decreased in kernels cultured at 15°C, but the duration was prolonged, and the number of endosperm cells formed was not affected. However, the number of starch granules initiated at 15 and 35°C was reduced by 70 and 97%, respectively. Final kernel mass was highly correlated with the number of endosperm cells ( r =0.85, p ≤0.01) and starch granules formed ( r =0.76, p ≤0.01). These data suggest that thermal regulation of the number of endosperm cells, starch granules, or both are mechanisms by which final kernel mass may be mediated. The reduction in mass of in vitro compared with field‐ or greenhouse‐grown kernels appears to be due mainly to a decline in the number of endosperm cells formed.
L‐428 reed‐sternberg cells and mononuclear hodgkin's cells arise from a single cloned mononuclear cell (1988)

The L-428 cell line derived from nodular sclerosing Hodgkin's disease was verified to be a human female cell line with surface marker and morphologic characteristics similar to native Hodgkin's cells. Single cells were cloned and subcloned twice to determine the characteristics of the clonogenic L-428 Hodgkin's cell (resulting in a 10% cloning efficiency). Both mononuclear L-428 cells and classical Reed-Sternberg cells arose from solitary cells. The clonogenic cell was the mononuclear Hodgkin's cell, although small abortive colonies sometimes arose from classical binucleate Reed-Sternberg cells. Cytogenetic and phenotypic analysis supported the clonality of three subclones and indicated, among many findings, consistent abnormalities of the long arm of chromosome 7 (beta-chain of the T cell receptor) and 14q32 (Ig heavy chain). Distinctive abnormalities of cytogenetics, phenotyping and transforming growth factor-beta production were exhibited for each clone as well. These observations demonstrate the relationship of the continuum of malignant mononuclear and multinuclear Reed-Sternberg cells in this cell culture from nodular sclerosing Hodgkin's disease and suggest that a similar relationship exists in native Hodgkin's disease tissue. These observations also support the theory of clonality in Hodgkin's disease and suggest that in vivo contiguous metastasis in the L-428 Hodgkin's disease patient was most likely accomplished by a Ki-1 positive small mononuclear cell.
Function and clinical significance of circRNAs in solid tumors (2018)

Circular RNA (circRNA) is a new type of endogenous non-coding RNAs (ncRNAs). circRNA regulates gene expression in many biological processes, and it also participates in the initiation and development of various diseases, including tumors, which are the focus of present research. With the development of high-throughput sequencing technique, an increasing number of circRNAs closely related to tumors have been discovered. According to numerous studies, there is a significant difference in the expressions of circRNAs among a variety of tumor tissues and para-carcinoma normal tissues. Some specifically expressed circRNAs may potentially serve as new biomarkers for tumor diagnosis and prognosis. This systemic review briefly introduces the characteristics, biogenesis, and functions of circRNAs, as well as discusses their relationship with cancer in detail. In addition, this article also describes several research strategies for circRNAs.
Conserved C-Termini of Spidroins Are Secreted by the Major Ampullate Glands and Retained in the Silk Thread (2004)

The C-termini of Spidroins produced in the major and minor ampullate glands of spiders are highly conserved. Despite this conservation, no corresponding peptides have been identified in the spinning dopes or the silk filaments so far. To prove their presence or absence, polyclonal antibodies derived against fusion proteins containing the conserved C-terminal regions of both Spidroin 1 and 2 from the spider Nephila clavipes were generated. The antibodies reacted with high molecular weight polypeptides of the corresponding gland extracts and solubilized major ampullate filament and in addition to filament cross-sections. This demonstrates the existence of C-terminal specific peptides in the spinning dope and the mature Spidroins. Both the fusion proteins as well as the proteins contained within the gland lumen showed a reduction in their size under reducing conditions indicating the presence of disulfide bonds. Their high conservation and the biochemical data suggest crucial roles the C-termini play in the formation and/or structure of the corresponding silk filaments.