gebhart/patrepeval huggingface dataset:
VirB12 Is a Serological Marker ofBrucellaInfection in Experimental and Natural Hosts (2007)

The Brucella species type IV secretion system, encoded by the virB1-12 locus, is required for intracellular replication and persistent infection in vivo. The requirement of VirB proteins for infection suggests that they are expressed in vivo and may therefore represent serological markers of infection. To test this idea, we purified recombinant VirB1, VirB5, VirB11, and VirB12 and tested for their recognition by antibodies in sera from experimentally infected mice and goats by using an indirect enzyme-linked immunosorbent assay. Antibody responses to VirB12 but not to VirB1, VirB5, or VirB11 were detected in 20/20 mice experimentally inoculated with Brucella abortus and 12/12 goats experimentally infected with Brucella melitensis. The potential use of VirB12 as a serological tool for the diagnosis of brucellosis was evaluated in the natural bovine host. Serum samples from 145 cattle of known serology (29% negative and 71% positive) were analyzed for the production of antibody responses to VirB12. One hundred two cattle samples (70.3%) were positive for antibodies to VirB12, while 43 samples were negative (29.7%). A positive serological response to VirB12 correlated with positive serology to whole B. abortus antigen in 99% of samples tested. These results show that VirB12 is expressed during infection of both experimental and natural hosts of Brucella species, and they suggest that VirB12 may be a useful serodiagnostic marker for brucellosis.
Identification and characterization of microRNAs from the bovine adipose tissue and mammary gland (2007)

We report the identification of bovine miRNAs by cloning small RNAs from adipose tissue and the mammary gland. Fifty-nine distinct miRNAs were identified, five of them were not homologous to known mammalian miRNAs, and many of them had 3' and/or 5' end variants. Ribonuclease protection assays indicated that miR-23a and miR-24, whose genes are closely located on the same chromosome, were co-expressed in different tissues. The assays also suggested a role for several miRNAs in the mammary gland and a role for miR-133, a previously known skeletal and cardiac muscle-specific miRNA, in the rumen, an organ unique to the ruminant.
SERUM PLANT STEROLS AND CHOLESTEROL PRECURSORS REFLECT CHOLESTEROL ABSORPTION AND SYNTHESIS IN VOLUNTEERS OF A RANDOMLY SELECTED MALE POPULATION (1990)

To investigate the regulation of serum levels of cholesterol precursor sterols and plant sterols, these noncholesterol sterols, fatty acids, and various parameters of cholesterol metabolism were analyzed in 63 volunteers from a randomly selected Finnish male population sample of 100 subjects, aged 50 years, who had normal dietary habits. Serum levels of cholesterol precursors, desmosterol and lathosterol (in terms of micrograms/mg cholesterol), were negatively related to both the fractional and absolute absorption of dietary cholesterol and serum high density lipoprotein (HDL) cholesterol, and positively related to overall cholesterol synthesis and serum very low density lipoprotein (VLDL) cholesterol. Serum levels of the plant sterols, campesterol and sitosterol, exhibited positive correlations with the polyunsaturated/saturated fatty acid ratio of dietary fat, the linoleic acid contents of plasma and dietary lipids, the amount of dietary plant sterols (as indicated by fecal output), fractional and absolute absorption of dietary cholesterol, and HDL cholesterol, but were inversely related to the overall cholesterol synthesis and VLDL cholesterol. Stepwise multiple regression analysis revealed that the serum level of campesterol was associated with fractional cholesterol absorption, dietary plant sterols, and biliary cholesterol secretion, and that of sitosterol with dietary plant sterols, cholesterol synthesis, fractional cholesterol absorption, and biliary cholesterol secretion. Thus, the serum non-cholesterol sterols are significant indicators of cholesterol absorption and synthesis even under basal conditions and, since gas liquid chromatographic determination of these sterols is quite simple, their measurement may be valuable for monitoring cholesterol metabolism in large-scale epidemiologic studies.
Up‐regulated expression of cytoplasmic clusterin in human ovarian carcinoma (2004)

The current results suggested that the overexpression of cytoplasmic clusterin may represent an acquired malignant phenotypic feature of ovarian carcinoma and may be one of the important factors in determining the aggressive nature of ovarian carcinoma.
Systematic Review of the Biology and Medical Management of Respiratory Syncytial Virus Infection (2003)

Respiratory syncytial virus, the leading cause of serious upper and lower respiratory tract infection in infants and children, accounts for 125,000 hospitalizations and 450 deaths annually in the United States. It also may predispose to development of asthma later in life. Annual epidemics occur from November to April, and virtually all infants are infected by age 2. Immunity is not durable; hence, reinfection occurs throughout life, although subsequent infections are nearly always mild. Certain populations (eg, premature infants, infants with chronic lung disease, and immunocompromised individuals) are at risk for severe morbidity and have higher risk of mortality. Infection is spread to the nose and eyes by large droplets and direct contact with secretions, and fomites may remain infectious for up to 12 hours. Nosocomial infection is common. The virus infects airway ciliated epithelial cells, spreading by the formation of syncytia. Cellular debris and inflammation cause airway obstruction, hyperinflation, localized atelectasis, wheezing, and impaired gas exchange. Both humoral and cellular immune response are critical to ending the acute infection, but wheezing and reactive airways may persist for as long as 5-10 years after acute infection. No cure exists for respiratory syncytial virus infection, but commonly employed palliative treatments include oxygen, inhaled beta(2) agonists, racemic epinephrine, dornase alfa, systemic and inhaled corticosteroids, inhaled ribavirin, and nasopharyngeal suctioning. Infants suffering severe lower airways disease may require mechanical ventilation. Prophylactic measures include rigorous infection control and administration of polyclonal (RSV-IGIV [respiratory syncytial virus - immunoglobulin intravenous]) and monoclonal (palivizumab) antibodies. The cost of the prophylactic antibody treatment is high; it is cost-effective for only the highest risk patients. Development of a vaccine remains far in the future. Application of evidence-based clinical practice guidelines is making both out-patient and in-patient therapy as effective and economical as possible.
Genes encoding homologues of three consecutive enzymes in the butyrate/butanol-producing pathway ofClostridium acetobutylicumare clustered on theClostridium difficilechromosome (1994)

Screening of a Clostridium difficile lambda EMBL3 gene library with antisera raised against C. difficile culture supernatant identified several clones expressing a 31-kDa protein. A 1.8-kb HindIII fragment subcloned from one of the clones was sufficient for expression of the 31-kDa polypeptide. Southern blot analysis showed a region homologous to this fragment to be present in all of 13 different C. difficile strains tested. Sequence analysis of the 1.8-kb fragment revealed three adjacent open reading frames. A database search showed that these three open reading frames appeared to encode homologues of three consecutive enzymes in the butanol/butyrate-producing pathway of Clostridium acetobutylicum (crotonase, beta-hydroxybutyryl coenzyme A dehydrogenase and thiolase).
An Efficient RNA-Cleaving DNA Enzyme that Synchronizes Catalysis with Fluorescence Signaling (2002)

DNA enzymes are single-stranded DNA molecules with catalytic capabilities that are isolated from random-sequence DNA libraries by "in vitro selection". This new class of catalytic biomolecules has the potential of being used as unique molecular tools in a variety of innovative applications. Here we describe the creation and characterization of an RNA-cleaving autocatalytic DNA, DEC22-18, that uniquely links chemical catalysis with real-time fluorescence signaling capability in the same molecule. A trans-acting DNA molecule, DET22-18, was also developed from DEC22-18 that behaves as a true enzyme with a k(cat) of approximately 7 min(-1)-a rate constant that is the second largest ever reported for a DNA enzyme. It cleaves a chimeric RNA/DNA substrate at the lone RNA linkage surrounded by a closely spaced fluorophore-quencher pair-a unique structure that permits the synchronization of the chemical cleavage with fluorescence signaling. DET22-18 has a stem-loop structure and can be conjugated with DNA aptamers to form allosteric deoxyribozyme biosensors.
Protein Kinase Inhibitors Drug Discovery (2005)

This chapter contains sections titled: Phosphorylation in Signal Transduction Pathways Classification of Protein Kinases General Mechanistic Features of Protein Phosphorylation by Protein Kinases General Structural Features of Protein Kinases Activation of Protein Kinases Protein Kinases in Human Diseases Important Protein Kinases as Therapeutic Targets Protein Kinases as Targets for Inhibitor Design Selected Inhibitors of Protein Kinases on Market or in Clinical Trials Prospects and Future Directions References
Boron Trifluoride Catalyzed Rearrangements of Novel Epoxide Derivatives of Manool and Manoyl Oxide (1993)

The preparation of four epoxides (1)-(4) derived from manool [labda-8(17),14-dien-13-ol] and manoyl oxide (8,13-epoxylabdane) via diosphenols is reported. Lewis acid promoted intramolecular rearrangements of these were investigated. Reaction of epoxide (1) with boron trifluoride etherate resulted in the isolation of a novel dimer (44), the structure being elucidated by X-ray crystallography. However, epoxides (2)-(4) yielded monomeric rearrangement products.
Thermal Stability of Self-Assembled Monolayers from Alkylchlorosilanes (1996)

Contact angle measurements and scanning force microscopy (SFM) have been used to study the morphology of self-assembled monolayers of octadecyltrichlorosilane (OTS) and undecyltrichlorosilane (UTS) on silicon oxide surfaces as a function of annealing temperature. Characterization of the monolayers before annealing indicates that the as-formed monolayers cover the substrate fully and have thicknesses of 2.9 and 1.5 nm, respectively, with the average surface having a roughness of approximately 0.3 nm. Water contact angle results and SFM roughness analysis showed that UTS monolayers annealed for 2 h at temperatures over 125 °C exhibited permanent changes in monolayer structure. Experimental data indicated a higher transition temperature for permanent structural changes for the OTS monolayers. Water contact angle measurements indicated a transition centered at 125 °C, hexadecane contact angle measurements indicated a transition around 130 °C, and SFM indicated a transition centered at 155 °C for OTS monolayers. We have observed that contact angle measurements can be sensitive to surface structure on an angstrom length scale. These results observed after 2 h are not equilibrium results, as evidenced by the further development in the monolayer after an anneal for 5 h. Thermodynamic considerations support the earlier (lower temperature) changes observed for UTS than for OTS monolayers. The observed transition is likely the result of hydrolysis of the organic molecules by water molecules existing at the monolayer−substrate interface.
Metabolic activation of 2-substituted derivatives of myristic acid to form potent inhibitors of myristoyl CoA:protein N-myristoyltransferase (1990)

The importance of myristoylation for the proper biological functioning of many acylated proteins has generated interest in the enzymes of the myristoylation pathway and their interactions with substrates and inhibitors. Previous observations that S-(2-oxopentadecyl)-CoA, a nonhydrolyzable methylene-bridged analogue of myristoyl-CoA, was a potent inhibitor of myristoyl-CoA:protein N-myristoyltransferase (NMT) [Paige, L. A., Zheng, G.-q., DeFrees, S. A., Cassady, J. M., & Geahlen, R. L. (1989) J. Med. Chem. 32, 1665] prompted a closer examination of the effect of substituents at the 2-position on the interactions of myristic acid and myristoyl-CoA analogues with NMT. As an initial approach, three myristic acid derivatives bearing different substituents at the 2-position, 2-fluoromyristic acid, 2-bromomyristic acid, and 2-hydroxymyristic acid, were selected for study. Both 2-bromomyristic acid and 2-hydroxymyristic acid were available commercially; 2-fluoromyristic acid was prepared synthetically. All three compounds were found to be only weak inhibitors of NMT in vitro. Of the three, 2-bromomyristic acid was the most potent (Ki = 100 microM). In cultured cells, however, 2-hydroxymyristic acid was by far the more effective inhibitor of protein myristoylation. Neither 2-hydroxymyristic acid nor 2-bromomyristic acid significantly inhibited protein palmitoylation in cultured cells, indicating that inhibition was not occurring at the level of acyl-CoA synthetase. Activation of the 2-substituted myristic acid derivatives to their corresponding acyl-CoA thioesters by acyl-CoA synthetase resulted in inhibitors of greatly increased potency. The 2-substituted acyl-CoA analogues, 2-hydroxymyristoyl-CoA, 2-bromomyristoyl-CoA, and 2-fluoromyristoyl-CoA, were synthesized and shown to be competitive inhibitors of NMT in vitro (Ki's = 45, 450, and 200 nM, respectively). These data suggested that the enhanced inhibitory potency of 2-hydroxymyristic acid seen in cells was most probably a result of its metabolic activation to the CoA thioester. The presence of substituents at the 2-position also affected the ability of the acyl group to be transferred by NMT to a peptide substrate. Of the three acyl-CoA analogues, only 2-fluoromyristoyl-CoA served as a substrate for NMT.
Evaluation of CHROMagar Staph. aureus, a New Chromogenic Medium, for Isolation and Presumptive Identification of Staphylococcus aureus from Human Clinical Specimens (2000)

CHROMagar Staph. aureus (CSA) is a new chromogenic medium for presumptive identification of Staphylococcus aureus as mauve colonies after 24 h of incubation. We conducted a preliminary study with 100 S. aureus and 45 coagulase-negative Staphylococcus (CoNS) stock isolates plated on CSA. All S. aureus isolates yielded mauve colonies after 24 h of incubation at 37 degrees C, while CoNS isolates grew as blue, white, or beige colonies. Culture on CSA was then prospectively compared to a conventional laboratory method, i.e. , culture on 5% horse blood agar (HBA), catalase test, and latex agglutination test (HBA-catalase-latex), for isolation and presumptive identification of S. aureus from 2,000 consecutive clinical samples. Among the 310 S. aureus isolates recovered by at least one of the two methods, 296 grew as typical mauve colonies on CSA, while only 254 yielded catalase-positive, latex-positive colonies on HBA. The sensitivity of CSA was significantly higher than that of the conventional method (95.5 and 81.9%, respectively; P < 0.001) and allowed the recovery of important clinical isolates that were undetected on blood agar. The specificities of the two methods were not significantly different, although that of CSA was slightly higher (99.4% versus 98.9% for HBA-catalase-latex; P = 0. 08). On the basis of its excellent sensitivity and specificity, ease of identification of positive colonies, and absence of complementary testing, CSA can be recommended as a routine plating medium for presumptive identification of S. aureus in clinical specimens.
The role of third-generation beta-blocking agents in chronic heart failure (1998)

Third-generation beta-blocking agents developed for the hypertension market are proving useful in the treatment of chronic heart failure (HF). These compounds share the ancillary property of vasodilation, which improves acute tolerability by unloading the failing left ventricle at a time when beta-adrenergic withdrawal produces myocardial depression. In the case of carvedilol and bucindolol, this allows for the administration of nonselective beta blockade. Because of blockade of both beta 1 and beta 2 adrenergic receptors as well as other properties, these compounds possess a more comprehensive antiadrenergic profile than second-generation, beta 1-selective compounds. For this and potentially other reasons, third-generation beta-blocking agents have theoretical efficacy advantages that have yet to be demonstrated in large-scale trials. Ongoing trials with either second- or third-generation compounds and one trial directly comparing a compound from each class will provide the answer as to whether third-generation compounds have an advantage in the treatment of chronic HF.
Molecular Mechanics of Cardiac Myosin-Binding Protein C in Native Thick Filaments (2012)

The heart's pumping capacity results from highly regulated interactions of actomyosin molecular motors. Mutations in the gene for a potential regulator of these motors, cardiac myosin-binding protein C (cMyBP-C), cause hypertrophic cardiomyopathy. However, cMyBP-C's ability to modulate cardiac contractility is not well understood. Using single-particle fluorescence imaging techniques, transgenic protein expression, proteomics, and modeling, we found that cMyBP-C slowed actomyosin motion generation in native cardiac thick filaments. This mechanical effect was localized to where cMyBP-C resides within the thick filament (i.e., the C-zones) and was modulated by phosphorylation and site-specific proteolytic degradation. These results provide molecular insight into why cMyBP-C should be considered a member of a tripartite complex with actin and myosin that allows fine tuning of cardiac muscle contraction.
Immunotherapy of Head and Neck Cancer: Current and Future Considerations (2009)

Patients with head and neck squamous cell carcinoma (HNSCC) are at considerable risk for death, with 5-year relative survival rates of approximately 60%. The profound multifaceted deficiencies in cell-mediated immunity that persist in most patients after treatment may be related to the high rates of treatment failure and second primary malignancies. Radiotherapy and chemoradiotherapy commonly have severe acute and long-term side effects on immune responses. The development of immunotherapies reflects growing awareness that certain immune system deficiencies specific to HNSCC and some other cancers may contribute to the poor long-term outcomes. Systemic cell-mediated immunotherapy is intended to activate the entire immune system and mount a systemic and/or locoregional antitumor response. The delivery of cytokines, either by single cytokines, for example, interleukin-2, interleukin-12, interferon-gamma, interferon-alpha, or by a biologic mix of multiple cytokines, such as IRX-2, may result in tumor rejection and durable immune responses. Targeted immunotherapy makes use of monoclonal antibodies or vaccines. All immunotherapies for HNSCC except cetuximab remain investigational, but a number of agents whose efficacy and tolerability are promising have entered phase 2 or phase 3 development.
Identification of two distinct microtubule binding domains on recombinant rat MAP 1B. (1992)

A set of partially overlapping cDNA clones covering 9 kb of continuous sequence encoding the high molecular weight microtubule-associated protein (MAP) 1B, was isolated from a rat brain library in lambda gt11. The protein encoded was immunoreactive with monoclonal antibodies raised against calf MAP 1B, rat MAP 1X, and rat MAP 5, as shown by immunoblotting. Using Northern blot analysis, it was shown that the level of MAP 1B mRNA increased dramatically upon nerve growth factor-induced PC12 cell differentiation. The expression of polypeptides encoded by cDNA constructs, in conjunction with microtubule binding assays, revealed two separate microtubule binding domains, corresponding to sequences at the 5' and 3' end of the mRNA. As shown by DNA sequencing, the binding domain encoded by 5' terminal sequences consisted of the basic repeat motif KKEE(I/V), previously identified in mouse MAP 1B (Noble, M., S. A. Lewis, N. J. Cowan, J. Cell Biol. 109, 3367-3376 (1989)). The second binding domain, too, was found to be basic, but without any apparent repeat structure. It is concluded that single proteolytically unprocessed MAP 1B molecules would have the potential to function as microtubule cross-linkers.
Strong Polarization in the Optical Transmission through Elliptical Nanohole Arrays (2004)

Strong polarization dependence is observed in the optical transmission through nanohole arrays in metals. It is shown that the degree of polarization is determined by the ellipticity and orientation of the holes; the polarization axis lies perpendicular to the broad edge of the ellipse. Furthermore, the depolarization ratio shows a squared dependence on the aspect ratio of the holes, which is discussed in terms of coupling into and out of the surface plasmon modes. The observed results will be useful for tailoring the polarization behavior of metallic nanophotonic elements in many applications, including surface plasmon enhanced optical sensing and ultrafast optical switching.
Klebsiellaspp. as Nosocomial Pathogens: Epidemiology, Taxonomy, Typing Methods, and Pathogenicity Factors (1998)

Bacteria belonging to the genus Klebsiella frequently cause human nosocomial infections. In particular, the medically most important Klebsiella species, Klebsiella pneumoniae, accounts for a significant proportion of hospital-acquired urinary tract infections, pneumonia, septicemias, and soft tissue infections. The principal pathogenic reservoirs for transmission of Klebsiella are the gastrointestinal tract and the hands of hospital personnel. Because of their ability to spread rapidly in the hospital environment, these bacteria tend to cause nosocomial outbreaks. Hospital outbreaks of multidrug-resistant Klebsiella spp., especially those in neonatal wards, are often caused by new types of strains, the so-called extended-spectrum-beta-lactamase (ESBL) producers. The incidence of ESBL-producing strains among clinical Klebsiella isolates has been steadily increasing over the past years. The resulting limitations on the therapeutic options demand new measures for the management of Klebsiella hospital infections. While the different typing methods are useful epidemiological tools for infection control, recent findings about Klebsiella virulence factors have provided new insights into the pathogenic strategies of these bacteria. Klebsiella pathogenicity factors such as capsules or lipopolysaccharides are presently considered to be promising candidates for vaccination efforts that may serve as immunological infection control measures.