gebhart/patrepeval huggingface dataset:
The sex pheromone system of Enterococcus faecalis (1994)

The sex pheromone system of Enterococcus faecalis was discovered by observing a clumping reaction of E. faecalis strains during conjugative transfer of plasmids. It was found that only a special type of E. faecalis plasmids, the so-called sex pheromone plasmids, are transferred via this mechanism. Various experiments, especially by the group of D. B. Clewell, led to the formulation of a model describing how the sex pheromone system works. Small linear peptides, the so-called sex pheromones, are excreted by strains not possessing the corresponding sex pheromone plasmid. Donor strains harboring the plasmid do not produce the corresponding sex pheromone; they react to the presence of the peptide by production of a plasmid-encoded adhesin, the so-called aggregation substance. This adhesin allows contact between the non-motile mating partners; after conjugative transfer of the plasmid, the former recipient possesses and replicates the new plasmid. Thereby the population of E. faecalis strains is shifted to a high percentage of donor strains. This is especially true because a donor strain will still excrete sex pheromones corresponding to plasmids it does not harbor; therefore, such a strain can also function as recipient for other sex pheromone plasmids it does not possess. Various aspects of this unique plasmid collection mechanism have been studied during the last few years. The data indicate that, with the exception of pAM373, all sex pheromone plasmids possess one DNA region which is highly similar to and codes for the adhesin. It is also becoming more and more clear that regulatory functions/proteins are not conserved between different sex pheromone plasmids. Induction of adhesin synthesis needs the action of a regulatory cascade composed of unique features; at the moment we are just beginning to understand this cascade. By sequencing the first structural gene for one of those adhesins, we realized that the aggregation substance might act also as an adhesin for eucaryotic cells, probably by interaction with integrins. At least in the case of the in vitro cultured pig kidney tubulus cell line LLC-PK1 this idea could be verified. An interesting aspect of the sex pheromone system of E. faecalis is its evolution. I will discuss the idea that two different components, both of which well might contribute to virulence of the opportunistic pathogenic bacterium, were combined in the species E. faecalis to result in this unique plasmid collection system.
Synthesis of Polymerized Melanin byCryptococcus neoformansin Infected Rodents (2000)

The ability of Cryptococcus neoformans to synthesize polymerized melanin in vitro has been associated with virulence, but it is unclear whether this fungus synthesizes polymerized melanin during infection. To study this question, we used two approaches: one involved the generation of monoclonal antibodies (MAbs) to melanin for use in immunohistochemical studies of C. neoformans-infected rodents, and the other sought to isolate fungal melanin from infected tissues. Digestion of in vitro-melanized C. neoformans cells with proteases, denaturant, and hot concentrated acid yields melanin particles that retain the shape of fungal cells and are therefore called melanin ghosts. BALB/c mice were immunized with melanin ghosts, and two immunoglobulin M MAbs to melanin were generated from the spleen of one mouse. Immunofluorescence analyses of lung and brain tissues of rodents infected with wild-type melanin-producing (Mel(+)) C. neoformans strains demonstrated binding of the MAbs to the fungal cell wall. No binding was observed when infections were performed with mutant albino (Mel(-)) C. neoformans strains. Particles with striking similarity to melanin ghosts were recovered after digestion of lung and brain tissues from Mel(+) C. neoformans-infected rodents and were reactive with the MAbs to melanin. No particles were recovered from tissues infected with Mel(-) C. neoformans. A Mel(+) C. neoformans strain grown on lung or brain homogenate agar became lightly pigmented and also yielded particles similar to melanin ghosts upon digestion, providing additional evidence that lung and brain tissues contain substrate for C. neoformans melanization. These results demonstrate that C. neoformans synthesizes polymerized melanin during infection, which has important implications for pathogenesis and antifungal drug development.
A novel ADP‐dependent DNA ligase from Aeropyrum pernix K1 (2003)

A gene encoding a putative ATP-dependent DNA ligase from the aerobic hyperthermophilic archaeon Aeropyrum pernix K1 was cloned and the biochemical characteristics of the resulting recombinant protein were examined. The gene (accession no. APE1094) from A. pernix encoding a 69-kDa protein showed a 39-61% identity with other ATP-dependent DNA ligases from the archaea. Normally DNA ligase is activated by NAD(+) or ATP. There has been no report about the other activators for DNA ligase. The recombinant ligase was a monomeric protein and catalyzed strand joining on a singly nicked DNA substrate in the presence of ADP and a divalent cation (Mg(2+), Mn(2+), Ca(2+) and Co(2+)) at high temperature. The optimum temperature and pH for nick-closing activity were above 70 degrees C and 7.5 degrees C, respectively. The ligase remained stable for 60 min of treatment at 100 degrees C, and the half-life was about 25 min at 110 degrees C. This is the first report of a novel hyperthermostable DNA ligase that can utilize ADP to activate the enzyme.
A synthetic, bioactive PDGF mimetic with binding to both α-PDGF and β-PDGF receptors (2007)

A multi-domain peptide, PAB2-1c, was designed and synthesized as a bioactive mimic of PDGF. PBA2-1c bound to both alpha- and beta-PDGF receptors as determined by surface plasmon resonance (SPR). The equilibrium dissociation constant (Kd) of binding to alpha-PDGF receptors by PAB2-1c (1.7 x 10(-8) M) compared favorably rhPDGF-AA (1.34 x 10(-8) M). Binding to -PDGF receptor by PAB2-1c (2.2 x 10(-8) M) was less favorable than, that of recombinant human PDGFBB (1.59 x 10(-9) M). Interestingly, PBA2-1c bound to these two receptors with similar affinity suggesting that, PBA2-1c was not PDGF receptor selective. In a murine myoblast cell line C2C12, PBA2-1c increased the tyrosine phosphorylation on PDGF receptors and the phosphorylation of AKT and ERK1/2 in a concentration-related manner. PBA2-1c also stimulated an increase in cell proliferation, cell migration, and collagen gel contraction. In these cell-based assays, PAB2-1c was effective at 1 microg/ml or lesser. The results support the hypothesis that PBA2-1c is a mimetic of PDGF, although it has a more promiscuous receptor interaction.
Electrospray Ionization for Mass Spectrometry of Large Biomolecules (1989)

Electrospray ionization has recently emerged as a powerful technique for producing intact ions in vacuo from large and complex species in solution. To an extent greater than has previously been possible with the more familiar "soft" ionization methods, this technique makes the power and elegance of mass spectrometric analysis applicable to the large and fragile polar molecules that play such vital roles in biological systems. The distinguishing features of electrospray spectra for large molecules are coherent sequences of peaks whose component ions are multiply charged, the ions of each peak differing by one charge from those of adjacent neighbors in the sequence. Spectra have been obtained for biopolymers including oligonucleotides and proteins, the latter having molecular weights up to 130,000, with as yet no evidence of an upper limit.
R632W mutation in PLA2G6 segregates with dystonia‐parkinsonism in a consanguineous Iranian family (2008)

We conclude that different and even identical PLA2G6 mutations may cause neurodegenerative diseases with heterogeneous clinical manifestations, including INAD, NBIA and dystonia-parkinsonism.
MicroRNAs in biological processes and carcinogenesis (2006)

MicroRNAs (miRNAs) encoding small non-coding RNAs have been recognized as a very large gene family present in most organisms. The precise biological effects of miRNAs are yet to be elucidated in detail, partly because each miRNA is believed to negatively regulate the expression of hundreds of target genes. Nevertheless, recent findings indicate that carcinogenic processes are associated with alterations in the expression of several miRNAs, suggesting that some function as oncogenes or tumor suppressor genes. The present review focuses on recent findings in this exciting new area of research, with special emphasis on the involvement of miRNAs in cancer development and progression. Further studies are clearly warranted to elucidate the molecular and biological roles of miRNAs, which may ultimately provide both a better understanding of disease development, as well as a foundation for novel strategies for cancer diagnosis and therapy.
Determination of the Carbon Kinetic Isotope Effects on Propane Hydroxylation Mediated by the Methane Monooxygenases from Methylococcus capsulatus (Bath) by Using Stable Carbon Isotopic Analysis (2002)

Authentic propane with known position-specific carbon isotope composition at each carbon atom was subjected to hydroxylation by the particulate and soluble methane monooxygenase (pMMO and sMMO) from Methylococcus capsulatus (Bath), and the corresponding position-specific carbon isotope content was redetermined for the product 2-propanol. Neither the reaction mediated by pMMO nor that with sMMO showed an intermolecular (12)C/(13)C kinetic isotope effect effect on the propane hydroxylation at the secondary carbon; this indicates that there is little structural change at the carbon center attacked during formation of the transition state in the rate-determining step. This finding is in line with the concerted mechanism proposed for pMMO (Bath), and suggested for sMMO (Bath), namely, direct side-on insertion of an active "O" species across the C-H bond, as has been previously reported for singlet carbene insertion.
BRAF mutations in non-Hodgkin's lymphoma (2003)

Ras proteins control signalling pathways that are key regulators of several aspects of normal cell growth and malignant transformation. BRAF, which encodes an RAF family member in the downstream pathway of RAS, is somatically mutated in a number of human cancers. The activating mutation of BRAF is known to play a role in tumour development. As there have been no data on the BRAF mutation in non-Hodgkin's lymphoma (NHL), we analysed the genomic DNAs from 164 NHLs by polymerase chain reaction (PCR)-based single-strand conformation polymorphism (SSCP) for the detection of somatic mutations of BRAF (exons 11 and 15). Overall, we detected BRAF mutations in four NHLs (2.4%). Whereas most BRAF mutations in human cancers involved V599 of BRAF, all of the four BRAF mutations in the NHLs involved other amino acids (one G468A, two G468R and one D593G). To our knowledge, this is the first report on BRAF mutation in NHL, and the data indicate that BRAF is occasionally mutated in NHL, and suggest that BRAF mutation may contribute to the tumour development in some NHLs.
Effects of partial substitution of Ni by Pd on the thermoelectric properties of ZrNiSn-based half-Heusler compounds (2001)

We report on the effects of partial substitution of nickel by palladium on the thermoelectric properties of ZrNiSn-based half-Heusler compounds. It is shown that the substitution of palladium for nickel results in a significant, beneficial reduction of the thermal conductivity. The Seebeck coefficient also decreases, but only by a small amount. In the Hf0.5Zr0.5Ni0.8Pd0.2Sn0.99Sb0.01 compound, a power factor of 22.1 μW K−2 cm−1 and a thermal conductivity as low as 4.5 W/m K are measured at room temperature. The dimensionless figure of merit ZT increases with increasing temperature and reaches a maximum value of 0.7 at about 800 K.
Luminescence in the thermal decomposition of 3,3,4-trimethyl-1,2-dioxetane (1969)

Luminescence is observed during the thermal decomposition of 3,3,4-trimethyl-1,2-dioxetane to acetone and acetaldehyde. The wavelength maximum of the luminescence is at 430–440 mμ when the decomposition is carried out at 60° in benzene solution. This shows that the decomposition of the dioxetane is a concerted electrocyclic reaction which forms a carbonyl compound in the excited singlet state, and confirms the suggestion that bioluminescence is due to the decomposition of 1,2-dioxetanes.
Use of the DAF Assay to Assess theFunctional Properties of Polyclonaland Monoclonal Rh D Antibodies (1996)

The mechanism whereby passive Rh (D) immunoglobulins suppress the fetomatemal alloimmunization is still unclear. New in vitro tests are needed to better characterize the functional properties of polyclonal anti-Ds. The DAF assay was developped to monitor the antibody-dependent cell-mediated cytotoxicity (ADCC) and the phagocytosis of anti-Rh (D)-sensitized RBCs by effector cells. The principle of this test is based on the oxydization of the 2,7-diaminofluorene (DAF) by the pseudoperoxidase activity of free hemoglobin. The reaction is proportional to the hemoglobin concentration. This test was performed to determine and emphasize the efficacy of different polyclonal anti-D immunoglobulin preparations to mediate lysis and phagocytosis of sensitized RBCs by human peripheral mononuclear cells. The functional properties of different human RhD monoclonal antibodies were also analyzed and compared. The test was found to be convenient to perform and allowed the avoidance of radioactive labelling of RBCs for ADCC studies. It is mainly useful for the direct quantitation of phagocytosis.
Highly Li-Stuffed Garnet-Type Li7+xLa3Zr2-xYxO12 (2013)

We report the synthesis, microstructure and Li ion conductivity of Li-stuffed garnet-type metal oxides, with nominal chemical formulae Li7.06La3Zr1.94Y0.06O12 and Li7.16La3Zr1.84Y0.16O12. Powder X-ray diffraction (PXRD) shows the formation of cubic garnet-type structure at 950°C (12 h in air) with cell constant of 12.974(3) Å and 12.995(2) Å for Li7.06La3Zr1.94Y0.06O12 and Li7.16La3Zr1.84Y0.16O12, respectively. The slight increase in cubic cell constant is consistent with Y-substitution for Zr in Li7La3Zr2O12. For samples sintered at 1100–1150°C, PXRD displays multi-phase mixtures, but the garnet-type structure remained the major phase. Scanning electron microscopy (SEM) studies show an average crystallite size in the range of 2–5 μm, and particle size increases with increasing sintering temperature, as anticipated. Energy dispersive spectroscopy (EDS) elemental mapping show single homogenous distribution of elements, for samples prepared at 950°C. Electrochemical AC impedance spectra exhibit mainly bulk contribution at temperatures higher than 150°C, and at low temperature, we see contributions from bulk and grain-boundary resistance. The bulk electrical conductivity of the sample was found to be comparable to those of the high temperature tetragonal Li7La3Zr2O12 phase. The electrical conductivity of Y-doped samples investigated in the present work was ∼10−6 Scm−1 at 23°C with an activation energy of 0.47 eV. The lower conductivity of this Y-doped garnet was explained based on Raman spectroscopy and SEM analysis.
GloMoSim: a library for parallel simulation of large-scale wireless networks (1998)

A number of library based parallel and sequential network simulators have been designed. The paper describes a library, called GloMoSim (Global Mobile system Simulator), for parallel simulation of wireless networks. GloMoSim has been designed to be extensible and composable: the communication protocol stack for wireless networks is divided into a set of layers, each with its own API. Models of protocols at one layer interact with those at a lower (or higher) layer only via these APIs. The modular implementation enables consistent comparison of multiple protocols at a given layer. The parallel implementation of GloMoSim can be executed using a variety of conservative synchronization protocols, which include the null message and conditional event algorithms. The paper describes the GloMoSim library, addresses a number of issues relevant to its parallelization, and presents a set of experimental results on the IBM 9076 SP, a distributed memory multicomputer. These experiments use models constructed from the library modules.
Inhibition of Epstein-Barr virus-mediated capping of CD21/CR2 by alpha interferon (IFN-alpha): immediate antiviral activity of IFN-alpha during the early phase of infection (1993)

Early events of human B-lymphocyte infection by Epstein-Barr virus involve the virus binding to CD21, capping, and subsequent internalization of the virus-receptor complex. We show here that alpha interferon (IFN-alpha) inhibits the capping of Epstein-Barr virus-CD21 complexes. Synthetic peptides with the CD21 binding motif of IFN-alpha mimic IFN-alpha activity, suggesting that this effect may be mediated by IFN-alpha-CD21 interaction. Our findings demonstrate a novel and immediate mechanism of IFN-alpha action.
Fast and high resolution analysis of human serum transferrin by high performance isoelectric focusing in capillaries (1989)

Human serum transferrin is a mixture of isoforms (isoproteins) having different amounts of carbohydrates. Each isoform may exist in iron-free and iron-complexed molecular form. The genetic variations in different populations increase the number of combinations of the different forms of transferrin. To resolve the many components in transferrin preparations, the new high performance capillary technique was employed for isoelectric focusing. Iron-free transferrin and transferrin samples of known iron content were examined. The above method gives an exceptionally rapid analysis (within 15-25 min) of small amounts of samples (less than 1 microgram protein) and as good as or better resolution than other isoelectric focusing techniques previously used for transferrin analysis. By monitoring the focused protein zones at both 280 and 460 nm the molecular forms of transferrin (iron-free, monoferric and differic complexes) can easily be identified. Both steps of isoelectric focusing in capillaries (i.e., prefocusing and mobilization) can be used for analysis. We observed that chelating agents (e.g., carrier ampholytes, nitrilotriacetate) may release iron from microsyringes having metal pistons causing the formation of iron-transferrin complexes.
Identification of immunogenic human melanoma antigens in a polyvalent melanoma vaccine. (1992)

An essential element in the development of effective vaccines against human malignant melanoma is the identification of antigens which are relevant for vaccine construction as evidenced by their ability to stimulate antimelanoma immune responses in humans. In this study, we identified immunogenic melanoma antigens using as probes antibodies induced in patients immunized with a vaccine which contains a broad range of potential immunogens. By immunoprecipitation/sodium dodecyl sulfate-polyacrylamide gel electrophoresis analysis of detergent lysates of radioiodinated melanoma cells, we found that 17 (65%) of 26 patients sequentially immunized with a polyvalent melanoma antigen vaccine developed antibodies to one or more melanoma cell surface antigens with approximate molecular weights of 38,000-43,000, 75,000, 110,000, 150,000, and 210,000. The immunodominant antigens which most frequently stimulated antibody responses were the M(r) 110,000 antigen followed by the M(r) 210,000 and 38,000-43,000 antigens, which induced antibody responses in 62%, 27%, and 19% of patients, respectively. These three antigens were commonly expressed on different melanomas but rarely on nonmelanoma cells and are unrelated to class I or II human leukocyte antigens or to the previously described p97 or M(r) 240,000 proteoglycan melanoma-associated antigens. Thus, these three antigens are attractive candidates for the construction of melanoma vaccines, because they are immunogenic in humans and are preferentially expressed on melanomas.
Expression pattern and activity of six glutelin gene promoters in transgenic rice (2008)

The shortage of strong endosperm-specific expression promoters for driving the expression of recombinant protein genes in cereal endosperm is a major limitation in obtaining the required level and pattern of expression. Six promoters of seed storage glutelin genes (GluA-1, GluA-2, GluA-3, GluB-3, GluB-5, and GluC) were isolated from rice (Oryza sativa L.) genomic DNA by PCR. Their spatial and temporal expression patterns and expression potential in stable transgenic rice plants were examined with beta-glucuronidase (GUS) used as a reporter gene. All the promoters showed the expected spatial expression within the endosperm. The GluA-1, GluA-2, and GluA-3 promoters directed GUS expression mainly in the outer portion (peripheral region) of the endosperm. The GluB-5 and GluC promoters directed GUS expression in the whole endosperm, with the latter expressed almost evenly throughout the whole endosperm, a feature different from that of other rice glutelin gene promoters. The GluB-3 promoter directed GUS expression solely in aleurone and subaleurone layers. Promoter activities examined during seed maturation showed that the GluC promoter had much higher activity than the other promoters. These promoters are ideal candidates for achieving gene expression for multiple purposes in monocot endosperm but avoid promoter homology-based gene silencing. The GluC promoter did not contain the endosperm specificity-determining motifs GCN4, AACA, and the prolamin-box, which suggests the existence of additional regulatory mechanism in determining endosperm specificity.
Glaucoma Monitoring in a Clinical Setting (2009)

Nonparametric progression analysis had fairly good agreement with GPA. Especially in cases of more advanced disease, NPA labeled more eyes as having progression than GPA.
Vacuum-assisted closure in the treatment of complex gynecologic wound failures (2002)

We conclude that vacuum-assisted closure therapy should be included in the armamentarium of the gynecologist addressing complex wound failures.
Viral Vectors for Gene Therapy (2007)

Abstract Viruses can be engineered to deliver genetic material to cells without causing disease. Viral gene therapy vectors have therapeutic use in the treatment of hereditary disease, infectious diseases and cancer as well as for vaccine development.
Accelerating Evolutionary Algorithms With Gaussian Process Fitness Function Models (2005)

We present an overview of evolutionary algorithms that use empirical models of the fitness function to accelerate convergence, distinguishing between evolution control and the surrogate approach. We describe the Gaussian process model and propose using it as an inexpensive fitness function surrogate. Implementation issues such as efficient and numerically stable computation, exploration versus exploitation, local modeling, multiple objectives and constraints, and failed evaluations are addressed. Our resulting Gaussian process optimization procedure clearly outperforms other evolutionary strategies on standard test functions as well as on a real-world problem: the optimization of stationary gas turbine compressor profiles.