gebhart/patrepeval huggingface dataset:
Complete cDNA and derived amino acid sequence of human factor V. (1987)

cDNA clones encoding human factor V have been isolated from an oligo(dT)-primed human fetal liver cDNA library prepared with vector Charon 21A. The cDNA sequence of factor V from three overlapping clones includes a 6672-base-pair (bp) coding region, a 90-bp 5' untranslated region, and a 163-bp 3' untranslated region within which is a poly(A) tail. The deduced amino acid sequence consists of 2224 amino acids inclusive of a 28-amino acid leader peptide. Direct comparison with human factor VIII reveals considerable homology between proteins in amino acid sequence and domain structure: a triplicated A domain and duplicated C domain show approximately equal to 40% identity with the corresponding domains in factor VIII. As in factor VIII, the A domains of factor V share approximately 40% amino acid-sequence homology with the three highly conserved domains in ceruloplasmin. The B domain of factor V contains 35 tandem and approximately 9 additional semiconserved repeats of nine amino acids of the form Asp-Leu-Ser-Gln-Thr-Thr/Asn-Leu-Ser-Pro and 2 additional semiconserved repeats of 17 amino acids. Factor V contains 37 potential N-linked glycosylation sites, 25 of which are in the B domain, and a total of 19 cysteine residues.
Fibronectin Immobilized by a Novel Surface Treatment Regulates Fibroblast Attachment and Spreading (2000)

In order to understand the influence of cell-adhesive molecules on anchorage-dependent cell behavior on biomaterial surfaces, a model system is required where these molecules can be applied to surfaces with controlled surface ligand density and resistance to the adsorption of additional proteins present in the medium. This study asked whether fibronectin could be immobilized in a controlled manner to a hydrophobic surface with a chemically modified triblock surfactant. ELISA studies indicated that variation of the soluble fibronectin concentration used for immobilization could be used to control the amount of fibronectin immobilized to the surface. Furthermore, fibroblasts seeded on these surfaces in 10% serum-containing medium attached and spread as a function of the amount of immobilized fibronectin. Surfaces treated with unmodified surfactant did not support cell attachment, suggesting that cell attachment and spreading were primarily regulated by the immobilized fibronectin with minimal interference from adsorption of serum proteins. Together, these results suggest that covalent immobilization to Pluronic F108 provides a method for studying cellular responses to cell adhesive proteins with little interference from competing adsorbates, even in the presence of complex biological fluids such as serum. This technique may be applicable to a variety of existing hydrophobic biomedical polymers as a basic science tool as well as for influencing cell behavior at implant interfaces.
An IFE development strategy (1991)

The development of inertial fusion as a power source will require achieving four principal milestones: ignition and propagating burn; high gain at low drive energy for the reactor driver; pulse repetition rates of a few Hz; and long-term reliability and economics of a reactor. To keep development time and costs to a minimum, these should be accomplished with as few major facilities as possible. A viable scenario for the Inertial Fusion Energy (IFE) Program would include establishing the first milestone in a Nova Upgrade for ignition and gain and the latter three in an upgradable, low-power Engineering Test Facility (ETF)/Demonstration Power Plant (DPP), i.e. two major facilities. To be successful in as short a time as possible operations at the major facilities would have to be supported by off-line reactor driver and other reactor technology development efforts. These efforts would evaluate and prioritize the myriad of options available at present for power plant and subsystem concepts. This paper describes the elements of such a program that could make the first commercial power available in the decade of the 2020s and estimates the resources needed. This program would be carried out in phases with major go/no-go decision points before each large funding change. It is estimated that an IFE evaluation phase in the early 1990s would cost $100--150 M, a concept development phase in the latter 1990s would cost $500--850 M, and an engineering test and demonstration phase after the year 2000 would cost $6--8 over 20 years.
Stability of Producer Hybridoma Cell Lines after Cell Sorting: A Case Study (1994)

Flow cytometry was used in combination with immunofluorescent staining for intracellular and surface-associated antibody contents to identify a significant non-producer cell fraction in a murine hybridoma cell line that had shown a decline in monoclonal antibody productivity with passaging. Viable producer cells stained for surface-associated antibody content were isolated by cell sorting on the basis of surface fluorescence intensity. The fraction of nonproducers was initially reduced from 85% to 20%. Sorting a second time, after these cells were cultivated for 2 weeks, further reduced the fraction of nonproducers to less than 4%. The stability of this purified producer hybridoma cell line during passaging and after a freeze-thaw cycle was investigated. This cell line was found to be highly unstable. A simple batch-growth model simulation was used as follows: (i) to demonstrate that nonproducers appear in hybridoma cell lines after a rare, random mutation event that results in the loss of the heavy-chain gene and/or light-chain gene expression; (ii) to show that a high rate of conversion of producer hybridomas to nonproducer hybridomas cannot entirely explain the population dynamics; (iii) to estimate the rate of conversion of producers to nonproducers to be 8.7 x 10(-5) h-1; (iv) to show that, for this conversion rate, the nonproducer cells' specific growth rates need only be 9% higher than those of the producer cells to dominate the hybridoma culture after only 25 passages; and (v) to predict that producer cells are preferentially lost during cell freezing and thawing procedures. The data suggest that particularly unstable cell lines should be analyzed and purified frequently to prevent overgrowth by nonproducers.
The ArabidopsisREF8 gene encodes the 3‐hydroxylase of phenylpropanoid metabolism (2002)

The activity of p-coumarate 3-hydroxylase (C3H) is thought to be essential for the biosynthesis of lignin and many other phenylpropanoid pathway products in plants; however, no conditions suitable for the unambiguous assay of the enzyme are known. As a result, all attempts to purify the protein and clone its corresponding gene have failed. By screening for plants that accumulate reduced levels of soluble fluorescent phenylpropanoid secondary metabolites, we have identified a number of Arabidopsis mutants that display a reduced epidermal fluorescence (ref) phenotype. Using radiotracer-feeding experiments, we have determined that the ref8 mutant is unable to synthesize caffeic acid, suggesting that the mutant is defective in a gene required for the activity or expression of C3H. We have isolated the REF8 gene using positional cloning methods, and have verified that it encodes C3H by expression of the wild-type gene in yeast. Although many previous reports in the literature have suggested that C3H is a phenolase, the isolation of the REF8 gene demonstrates that the enzyme is actually a cytochrome P450-dependent monooxygenase. Although the enzyme accepts p-coumarate as a substrate, it also exhibits significant activity towards other p-hydroxylated substrates. These data may explain the previous difficulties in identifying C3H activity in plant extracts and they indicate that the currently accepted version of the lignin biosynthetic pathway is likely to be incorrect.
electronic Ligand Builder and Optimization Workbench(eLBOW): a tool for ligand coordinate and restraint generation (2009)

The electronic Ligand Builder and Optimization Workbench (eLBOW) is a program module of the PHENIX suite of computational crystallographic software. It is designed to be a flexible procedure that uses simple and fast quantum-chemical techniques to provide chemically accurate information for novel and known ligands alike. A variety of input formats and options allow the attainment of a number of diverse goals including geometry optimization and generation of restraints.
The Mouth Parts, Alimentary Tract, and Salivary Apparatus of the Female inPhlebotomus Papatasii (1926)

(1926). The Mouth Parts, Alimentary Tract, and Salivary Apparatus of the Female in Phlebotomus Papatasii. Annals of Tropical Medicine & Parasitology: Vol. 20, No. 1, pp. 109-142.
[Efficacy of antioxidant therapy in patients with acute and chronic purulent otitis media]. (1997)

The examination of 90 patients referred to hospital for otitis media purulenta (OMP) and 25 healthy subjects included assessment of lipid peroxidation by content of malonic dialdehyde and intensity of chemoluminescence. Enzymes of antioxidant system were also measured (superoxide dismutase and catalase in blood plasma and wash-offs from the acoustic meatus and postoperative cavities). The measurements gave different values for the above parameters for healthy and OMP subjects. Conventional treatment reduced levels of LPO products and raised the activity of antioxidant enzymes, but control values were reached only in adjuvant parenteral administration of lipostabil and local administration of alpha-tocopherol. Also, earlier relief of clinical symptoms shortened the hospital stay.
Motor design slip performance on cyclic loads (1990)

Cyclic loads such as eccentric pumping units cause a varying torque on the driver. Determination of the most efficient induction motor for the load is discussed. Ultrahigh-slip motors as well as NEMA (National Electric Manufacturers Association) design motors are evaluated. Comparisons of operating costs and investments are presented. The following is concluded: (1) any motor design will work on a pumping unit; (2) the motor must be carefully sized to provide minimum operating cost; (3) the lowest operating cost and the least investment come from the motors with the least slip; (4) the lower-slip motors cause an increase in peak torque on the unit; and (5) an accurate computer model with an easy-to-use program that allows what-if options is highly desirable.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Inhibitory effect of ribbon-type NF-κB decoy oligodeoxynucleotides on osteoclast induction and activity in vitro and in vivo (2006)

In this study we examined the effect of ribbon-type (circular-type) NF-kappaB decoy oligodeoxynucleotides (RNODN) on osteoclast induction and activity. We extracted bone marrow cells from the femurs of rats and incubated non-adherent cells with receptor activator of nuclear factor kappaB ligand (RANKL) and macrophage colony-stimulating factor (M-CSF). First, transfer efficiency into osteoclasts and their precursors, resistance to exonuclease, and binding activity of decoy to NF-kappaB were examined. Next, to examine the effect of RNODN on osteoclast induction and activity, osteoclast differentiation and pit formation assays were performed. RNODN were injected into the ankle joints of rats with collagen-induced arthritis. Joint destruction and osteoclast activity were examined by histological study. The resistance of RNODN to exonuclease and their binding activity on NF-kappaB were both greater than those of phosphorothionated NF-kappaB decoy oligodeoxynucleotides. The absolute number of multinucleate cells scoring positive for tartrate-resistant acid phosphatase was significantly decreased in the RNODN-treated group. The average calcified matrix resorbed area was significantly decreased in the RNODN-treated group. Histological study showed marked suppression of joint destruction and osteoclast activity by intra-articular injection of RNODN. These results suggest the inhibitory effect of RNODN on the induction and activity of osteoclasts. Direct intra-articular injection of RNODN into the joints may be an effective strategy for the treatment of arthritis.
Generation of Human Monoclonal Antibodies against HIV-1 Proteins; Electrofusion and Epstein-Barr Virus Transformation for Peripheral Blood Lymphocyte Immortalization (1994)

Electrofusion and EBV transformation were studied by immortalizing human PBLs from blood of HIV-1-positive volunteers. A panel of 33 cell lines producing human monoclonal antibodies (Hu-MAbs) against HIV-1 was established by cell fusion or EBV transformation. For the first fusion experiments the source of B lymphocytes was peripheral blood of HIV-1-infected donors in CDC stages II or III with CD4 cell counts higher than 500/mm3. Later on, from these patients only, those with high anti-HIV titers were chosen as blood donors. By that means the yield of stable specific hybridomas was increased twofold. In our experiments electrofusion turned out to be a more efficient immortalization method than EBV transformation, due to a high and constant immortalization rate. The hybridomas were stable after intensive subcloning and could be cultivated over a period of 8 months without loss in monoclonal antibody production. Immunoglobulin class, subtype, reactivity against HIV-1 proteins, Western blot patterns, immunofluorescence, and epitopes were characterized. The subtype of all antibodies was IgG1 or IgG3. The light chain was predominantly kappa. All antibodies showed reactivity against HIV-1 envelope or core protein. All hybridomas were stable and suited for mass production. Several Hu-MAbs are becoming an important tool in the field of diagnosis, research, and immunotherapy.
The Role of Klotho Protein in Chronic Kidney Disease: Studies in Animals and Humans (2016)

The identification of Klotho gene was a major discovery as the gene encodes a protein regulating multiple functions. A defect in Klotho gene expression in mice results in a phenotype of premature aging including shortened life span, growth retardation, hypogonadism, skin and muscle atrophies, vascular calcification, cognition impairment, motor neuron degeneration and others. This phenotype is associated with phosphate balance disorders and underlines the major function of Klotho in mineral metabolism. As another 2 related paralogs were discovered (beta-Klotho, which is involved in bile acid and energy metabolism, and gamma-Klotho, with a yet to be defined function), this led to the revised naming of Klotho as alpha-Klotho. Two forms of alpha-Klotho protein have been reported: a membrane-bound and a soluble one. Membrane Klotho forms a complex with fibroblast growth factor (FGF) receptors and functions as an obligate co-receptor for the FGF-23 phosphatonin in distal tubules. The soluble form of Klotho seems to function as a humoral factor and regulates glycoproteins on the cell surface including ion channels and growth factors. There is data suggesting that soluble Klotho exerts phosphaturic effects independently of FGF-23. Circulating soluble Klotho is produced either by proteolytic cleavage of the extracellular domain of the transmembrane form by two membrane-anchored proteases (ADAM10 and ADAM17) or by alternative mRNA splicing. In animal models Klotho has been shown to exert pleiotropic actions, including cytoprotection, anti-oxidation, anti-apoptosis, protection of vasculature, promotion of angiogenesis and vascularization, inhibition of fibrogenesis and preservation of stem cells. The exact diagnostic and therapeutic role of Klotho in humans is not fully known yet. The article presents the role of Klotho in physiology and different stages of chronic kidney disease (CKD).
Can Prosody Aid the Automatic Classification of Dialog Acts in Conversational Speech? (1998)

Identifying whether an utterance is a statement, question, greeting, and so forth is integral to effective automatic understanding of natural dialog. Little is known, however, about how such dialog acts (DAs) can be automatically classified in truly natural conversation. This study asks whether current approaches, which use mainly word information, could be improved by adding prosodic information. The study is based on more than 1000 conversations from the Switchboard corpus. DAs were hand-annotated, and prosodic features (duration, pause, F0, energy, and speaking rate) were automatically extracted for each DA. In training, decision trees based on these features were inferred; trees were then applied to unseen test data to evaluate performance. Performance was evaluated for prosody models alone, and after combining the prosody models with word information--either from true words or from the output of an automatic speech recognizer. For an overall classification task, as well as three subtasks, prosody made significant contributions to classification. Feature-specific analyses further revealed that although canonical features (such as F0 for questions) were important, less obvious features could compensate if canonical features were removed. Finally, in each task, integrating the prosodic model with a DA-specific statistical language model improved performance over that of the language model alone, especially for the case of recognized words. Results suggest that DAs are redundantly marked in natural conversation, and that a variety of automatically extractable prosodic features could aid dialog processing in speech applications.
Systematic yeast synthetic lethal and synthetic dosage lethal screens identify genes required for chromosome segregation (2005)

Accurate chromosome segregation requires the execution and coordination of many processes during mitosis, including DNA replication, sister chromatid cohesion, and attachment of chromosomes to spindle microtubules via the kinetochore complex. Additional pathways are likely involved because faithful chromosome segregation also requires proteins that are not physically associated with the chromosome. Using kinetochore mutants as a starting point, we have identified genes with roles in chromosome stability by performing genome-wide screens employing synthetic genetic array methodology. Two genetic approaches (a series of synthetic lethal and synthetic dosage lethal screens) isolated 211 nonessential deletion mutants that were unable to tolerate defects in kinetochore function. Although synthetic lethality and synthetic dosage lethality are thought to be based upon similar genetic principles, we found that the majority of interactions associated with these two screens were nonoverlapping. To functionally characterize genes isolated in our screens, a secondary screen was performed to assess defects in chromosome segregation. Genes identified in the secondary screen were enriched for genes with known roles in chromosome segregation. We also uncovered genes with diverse functions, such as RCS1, which encodes an iron transcription factor. RCS1 was one of a small group of genes identified in all three screens, and we used genetic and cell biological assays to confirm that it is required for chromosome stability. Our study shows that systematic genetic screens are a powerful means to discover roles for uncharacterized genes and genes with alternative functions in chromosome maintenance that may not be discovered by using proteomics approaches.
Data from 11 Years of Molecular Typing Infectious Bronchitis Virus Field Isolates (2005)

In 1993, a new molecular typing method for infectious bronchitis virus (IBV) was introduced. This method uses reverse transcriptase-polymerase chain reaction (RT-PCR) and restriction fragment length polymorphism (RFLP) analysis of the spike gene to obtain RFLP patterns that correlate with serotype. Using that test at the Poultry Diagnostic and Research Center (PDRC, University of Georgia, Athens, GA), we have identified a total of 1523 IBV isolates in the past 11 yr. The data were obtained from clinical samples submitted to our laboratory from birds with clinical signs characteristic of IBV infection. The samples are primarily from the southeastern United States but are also from many other states as well as from outside the United States. Most of the isolations occurred during July, followed by May, April, November, October, and January. The fewest number of isolates identified on an annual basis was 20 in 2003. An unusually high number of isolations occurred in 1997 (318 isolations) and 1999 (246 isolations), which coincided with the GAV variant virus and GA98 variant virus outbreaks respectively. By far, the Ark-DPI strain was the most frequently identified type of IBV and ranged from 23% to 65% of total isolations per year. Ark-like isolates, defined as having a similar but unique RFLP pattern from the Ark-DPI vaccine strain were identified every year of the study except in 1996. In addition, new Ark-like isolates continued to emerge each year (except in the year 2000) beginning in 1997, reflecting the ability of that IBV type to undergo genetic drift. Eighty-two different variant viruses were identified although only two (GAV and GA98) became persistent and caused widespread disease. Some viruses tended to be geographically restricted to a given area (CAV in California and MX97-8147 in Mexico), whereas others were widespread (Ark-DPI, Conn, DE072, and Mass). The Florida, Gray, Holte, Iowa, and JMK types were not detected during the 11-yr period, and no foreign virus types were detected in the United States. These data show that IBV variant viruses are consistently circulating in commercial poultry and are capable of causing disease outbreaks. Our observations highlight the importance of constantly monitoring IBV as well as other coronaviruses like severe acute respiratory syndrome-coronavirus that have the ability to change and emerge to cause disease in a susceptible host.
Enhancement and Modulation of Enzymatic Activity through Higher‐Order Structural Changes of Giant DNA–Protein Multibranch Conjugates (2012)

A giant DNA leap for enzyme-kind: Giant DNA–protein multibranch conjugates were shown to be composed of a single β-lactamase enzyme (green, see scheme) conjugated to up to four 48.5 kbp lambda phage DNA branches (blue lines). The conjugation of giant DNA induces a two- to fourfold enhancement of the enzymatic activity, which is modulated by changes in the higher-order DNA structure. Detailed facts of importance to specialist readers are published as ”Supporting Information”. Such documents are peer-reviewed, but not copy-edited or typeset. They are made available as submitted by the authors. Please note: The publisher is not responsible for the content or functionality of any supporting information supplied by the authors. Any queries (other than missing content) should be directed to the corresponding author for the article.
LEAP‐1, a novel highly disulfide‐bonded human peptide, exhibits antimicrobial activity (2000)

We report the isolation and characterization of a novel human peptide with antimicrobial activity, termed LEAP-1 (liver-expressed antimicrobial peptide). Using a mass spectrometric assay detecting cysteine-rich peptides, a 25-residue peptide containing four disulfide bonds was identified in human blood ultrafiltrate. LEAP-1 expression was predominantly detected in the liver, and, to a much lower extent, in the heart. In radial diffusion assays, Gram-positive Bacillus megaterium, Bacillus subtilis, Micrococcus luteus, Staphylococcus carnosus, and Gram-negative Neisseria cinerea as well as the yeast Saccharomyces cerevisiae dose-dependently exhibited sensitivity upon treatment with synthetic LEAP-1. The discovery of LEAP-1 extends the known families of mammalian peptides with antimicrobial activity by its novel disulfide motif and distinct expression pattern.