gebhart/patrepeval huggingface dataset:
MutS-Mediated Detection of DNA Mismatches Using Atomic Force Microscopy (2000)

We have developed an atomic force microscopy-based method for detecting DNA base-pair mismatches using MutS protein isolated from E. coli. MutS is a biological sensor and a locator of DNA base-pair mismatches. It binds specifically to a mismatched DNA base pair and initiates a process of DNA repair. To test the possibility of visually detecting mismatched base pairs by atomic force microscopy, we prepared DNA templates approximately 500 bp in length consisting of a single or multiple base-pair mismatches. We demonstrate that MutS binding sites on individual DNA molecules were readily detectable by atomic force microscopy and that the observed positions were in good agreement with the predicted sites of base-pair mismatches at a few-nanometer resolution. The technique described here is rapid and sensitive and is expected to be useful in screening mutations and DNA polymorphisms.
Letrozole once a week normalizes serum testosterone in obesity-related male hypogonadism (2008)

Letrozole 2.5 mg once a week produced a sustained normalization of serum total testosterone in obese men with IHH. However, free testosterone frequently rose to supraphysiological levels. Therefore, a starting dose <2.5 mg once a week is recommended.
Evaluation of Mycoplasma hyopneumoniae Inactivated Vaccine in Pigs under Field Conditions. (1999)

An inactivated vaccine prepared from broth culture supernatant of Mycoplasma hyopneumoniae with an aluminum adjuvant was evaluated in three herds (herd A: specific pathogen-free herd, herd B: high health status herd with no clinical signs of respiratory infection, herd C: low health status herd with serious epidemiological and economical problems). A total of 212 pigs from the three herds were divided into two groups. One group was injected twice with the vaccine at 4-week intervals and the other was a control group. No adverse reactions were noted following the vaccinations either systematically or locally in any of the vaccinated pigs from any of the herds. In herd A, the vaccination provided antibody response within 4 weeks after the second vaccination and antibody responses continued for more than 12 weeks. In herds B and C, the number of pigs with lung lesions, mean percentage of lung lesions, and the numbers of M. hyopneumoniae recovered from pigs at slaughter in the vaccinated group were significantly (P < 0.05) reduced compared to the control group. Furthermore, vaccination resulted in improved average daily weight gain (ADG), improved feed conversion ratio (FCR), and improved days to market weight in herd C, whereas no difference in growth performance was shown in herd B. It is suggested that the inactivated vaccine prepared from broth culture supernatant of M. hyopneumoniae is effective in reducing clinical signs and lung lesions. Also, vaccination resulted in improved growth performance in herds where clinical signs and economic losses were significant.
Expression of specific high-affinity binding sites for erythropoietin on rat and mouse megakaryocytes. (1989)

Considerable experimental and clinical evidence suggests a relationship between erythropoiesis and thrombopoiesis. This is supported by observations that erythropoietin (Epo), the primary regulator of erythropoiesis, can affect platelet production when injected into animals. In this study we provide experimental evidence for a direct effect of Epo on thrombopoiesis by demonstrating that 125I-labeled recombinant human Epo binds to rat and mouse bone marrow megakaryocytes. Thus, autoradiographic analysis using cold competition to measure specific binding has been used to demonstrate that Epo binding to megakaryocytes increases with megakaryocyte maturation. When corrected for cell size, Epo binding sites per unit surface area increase from Stage I megakaryoblasts to Stage II megakaryocytes, and then remain approximately constant throughout further megakaryocyte maturation. Receptor density on megakaryocytes is similar to that on pronormoblasts in the rat, and in mice is 60% that on pronormoblasts. No binding of Epo to platelets or to naked megakaryocyte nuclei was detected. Equilibrium binding studies with partially purified rat megakaryocytes (20%-40% pure), where megakaryocytes are the only significant Epo binding cell population, showed a single class of saturable, high-affinity binding sites present on average at 6500 binding sites per megakaryocyte with a KD of 287 pM. Binding of [125I]Epo to rat megakaryocytes was inhibited with an antiserum against murine erythroblasts. These results suggest that the effects of Epo on thrombopoiesis may be directly mediated through specific, high-affinity binding sites for Epo on the surface of maturing megakaryocytes.
Inhibition of Ovarian Cancer Growth by a Tumor-Targeting Peptide That Binds Eukaryotic Translation Initiation Factor 4E (2009)

Because ovarian cancer is rarely cured by conventional chemotherapies, GnRH-4EBP fusion peptide may be of therapeutic potential for treatment of this disease.
Secretion of Human Interferons by Yeast (1983)

Plasmids were constructed to direct synthesis of the human interferons IFN-alpha 1, IFN-alpha 2, and IFN-gamma in the yeast Saccharomyces cerevisiae. Expression of IFN genes containing coding sequences for secretion signals resulted in the secretion of IFN activity. A large proportion of the IFN-alpha 1 and IFN-alpha 2 isolated from the yeast cell growth media had the same amino termini as the natural mature interferons, suggesting a removal of the signal sequences identical to that of human cells. These results show that a lower eukaryote, such as yeast, can utilize and process a human signal sequence.
Reversal of the immunosuppressive properties of mesenchymal stem cells by tumor necrosis factor α in collagen‐induced arthritis (2005)

Our data suggest that environmental parameters, in particular those related to inflammation, may influence the immunosuppressive properties of MSCs.
Detection of glutamate release from neurons by genetically encoded surface-displayed FRET nanosensors (2005)

Glutamate is the predominant excitatory neurotransmitter in the mammalian brain. Once released, its rapid removal from the synaptic cleft is critical for preventing excitotoxicity and spillover to neighboring synapses. Despite consensus on the role of glutamate in normal and disease physiology, technical issues limit our understanding of its metabolism in intact cells. To monitor glutamate levels inside and at the surface of living cells, genetically encoded nanosensors were developed. The fluorescent indicator protein for glutamate (FLIPE) consists of the glutamate/aspartate binding protein ybeJ from Escherichia coli fused to two variants of the green fluorescent protein. Three sensors with lower affinities for glutamate were created by mutation of residues peristeric to the ybeJ binding pocket. In the presence of ligands, FLIPEs show a concentration-dependent decrease in FRET efficiency. When expressed on the surface of rat hippocampal neurons or PC12 cells, the sensors respond to extracellular glutamate with a reversible concentration-dependent decrease in FRET efficiency. Depolarization of neurons leads to a reduction in FRET efficiency corresponding to 300 nM glutamate at the cell surface. No change in FRET was observed when cells expressing sensors in the cytosol were superfused with up to 20 mM glutamate, consistent with a minimal contribution of glutamate uptake to cytosolic glutamate levels. The results demonstrate that FLIPE sensors can be used for real-time monitoring of glutamate metabolism in living cells, in tissues, or in intact organisms, providing tools for studying metabolism or for drug discovery.
Utilization of Escherichia coli Outer-Membrane Endoprotease OmpT Variants as Processing Enzymes for Production of Peptides from Designer Fusion Proteins (2004)

Escherichia coli outer-membrane endoprotease OmpT has suitable properties for processing fusion proteins to produce peptides and proteins. However, utilization of this protease for such production has been restricted due to its generally low cleavage efficiency at Arg (or Lys)-Xaa, where Xaa is a nonbasic N-terminal amino acid of a target polypeptide. The objective of this study was to generate a specific and efficient OmpT protease and to utilize it as a processing enzyme for producing various peptides and proteins by converting its substrate specificity. Since OmpT Asp(97) is proposed to interact with the P1' amino acid of its substrates, OmpT variants with variations at Asp(97) were constructed by replacing this amino acid with 19 natural amino acids to alter the cleavage specificity at Arg (P1)-Xaa (P1'). The variant OmpT that had a methionine at this position, but not the wild-type OmpT, efficiently cleaved a fusion protein containing the amino acid sequence -Arg-Arg-Arg-Ala-Arg downward arrow motilin, in which motilin is a model peptide with a phenylalanine at the N terminus. The OmpT variants with leucine and histidine at position 97 were useful in releasing human adrenocorticotropic hormone (1-24) (serine at the N terminus) and human calcitonin precursor (cysteine at the N terminus), respectively, from fusion proteins. Motilin was produced by this method and was purified up to 99.0% by two chromatographic steps; the yield was 160 mg/liter of culture. Our novel method in which the OmpT variants are used could be employed for production of various peptides and proteins.
Rapid genotyping of blood group antigens by multiplex polymerase chain reaction and DNA microarray hybridization (2005)

This study shows that the HPA microarray provides a reliable and fast genotyping procedure. With further development an automated throughput for complete typing of large donor cohorts can be obtained.
Où l'auteur propose un plan de travail pour une histoire dite sociale de l'aménagement urbain (1995)

L'histoire de l'aménagement urbain, plus connue sous le nom "d'histoire de l'urbanisme" et développée sous les normes croisées d'une certaine histoire de l'art, de la critique architecturale et de l'histoire des idées, est-elle capable d'aider à l'intelligibilité des formes de l'urbain et de leur évolution dans le temps ? Les biographies, les monographies d'écoles, de bâtiments, de styles, sont-elles les outils les plus adaptés ? Sur la base des travaux menés par Rémi Baudouï, Viviane Claude, Jean-Pierre Gaudin, Christian Topalov ou Danièle Voldman, on tente de dégager ici un programme de travail pour inaugurer une histoire qui soit celle des groupes, des réseaux, des savoirs et des pouvoirs qui ont présidé à l'élaboration des formes urbaines pour la période contemporaine.
The characteristics of biomass production, lipid accumulation and chlorophyll biosynthesis of Chlorella vulgaris under mixotrophic cultivation (2011)

The main objective of this study was to investigate the behaviors of Chlorella vulgaris for biomass production, lipid accumulation and chlorophyll biosynthesis under mixotrophic cultivation. The obtained results show that mixotrophism might be a competitive pattern for the culture of C. vulgaris on a large scale based on the achieved maximum biomass and volumetric productivities of lipid and chlorophyll. Glucose was the optimal carbon source for mixotrophic cultivation of C. vulgaris and the effects of glucose content on the alga growth under mixotrophic conditions were considerable because lower glucose content (1 g/l) promoted the production of biomass and photosynthetic pigments; higher glucose contents ( > 5 g/l) increased the biomass and lipid accumulation but inhibited the chlorophyll biosynthesis. The microalga could not grow well without pH control when ammonium and organic nitrogen were the sole nitrogen sources in the mixotrophic cultures because of the remarkable drop in pH value, while the critical urea concentration was observed at 0.50 g/l. It was concluded that mixotrophic cultivation of C. vulgaris is a feasible approach for lipid accumulation and chlorophyll biosynthesis that are dependent on the enhancement of biomass content and volumetric  productivity. Key words: Chlorella vulgaris, mixotrophic cultivation, biomass production, lipid accumulation, chlorophyll biosynthesis.
The Exploratory (2005)

An exploratory is an introduction activity to engage the student’s interest in the material that is to be studied. It is a blending of the “explore” and “engage” phases of the learning cycle, where the students are allowed to explore some of the phenomena that will be examined. They are introduced to a series of, hopefully novel, experiences with which they interact as a method to engage their interest.
The I-V characteristics of double-barrier resonant tunneling diodes: Observation and calculation on their temperature dependence and asymmetry (1991)

We report a calculation on the current-voltage characteristics of double-barrier resonant tunneling diodes. The results can well-explain experimental observations, in particular, the temperature dependence of both the absolute current amplitude and the resonant voltage positions. Our calculation takes into account the self-consistent Poisson equation, quantum mechanical tunneling, and band-gap offset at the heterojunctions. In addition, the calculation includes a realistic scattering-induced broadening effect, with which a quantitative fit throughout the entire negative differential resistance (NDR) region is demonstrated. Finally, we show that the differential resistance in the NDR region can be tuned, when asymmetrical tunneling barriers are used.
Solid‐Phase polymerase chain reaction (1994)

The polymerase chain reaction (PCR) has facilitated the diagnosis of infectious diseases and genetic disorders, because of its ability to amplify minute amounts of nucleic acids. To distinguish genes of interest from nonspecifically amplified DNA, PCR products commonly are fractionated by electrophoresis, transferred to membranes, and then probed with a labeled internal sequence-specific oligonucleotide. Alternatively, the PCR products have been labeled directly, and hybridized to immobilized oligonucleotide probes. These methods require the tedious physical transfer of the PCR products. In order to amplify and immobilize genes simultaneously, we have developed a simple solid-phase PCR method. The technique enabled us to detect the HIV envelope gene readily without any transfer of amplified DNA.
One-Pot Processing of Swabs for Organic Explosives and Firearms Residue Traces (1990)

Abstract By the procedure described, swabs may be extracted and the cleanup of the extracts continued, by solid phase extraction, in the containers issued for the return of the used swabs to the laboratory. Thus, problems associated with techniques that involve transfer between containers of the swabs or their extracts are avoided. The procedure is designed for work with explosives and firearm traces and residues but is in principle applicable to any trace material that can be taken into solution.
Modulation of protein release from biodegradable core–shell structured fibers prepared by coaxial electrospinning (2006)

Biodegradable core-shell structured fibers with poly(epsilon-caprolactone) as shell and bovine serum albumin (BSA)-containing dextran as core were prepared by coaxial electrospinning for incorporation and controlled release of proteins. BSA loading percent in the fibers and its release rate could be conveniently varied by the feed rate of the inner dope during electrospinning. With the increase in the feed rate of the inner dope, there was an associated increase in the loading percent and accelerated release of BSA. Poly(ethylene glycol) (PEG) was added to the shell section of the fibers to further finely modulate the release behavior of BSA. It was revealed that the release rate of BSA increased with the PEG percent in the shell section. By varying the feed rate of the inner dope and PEG content, most of BSA could be released from the core-shell structured fibers within the period of time ranging from 1 week to more than 1 month. The effect of the feed rate of the inner dope and addition of PEG into the shell section on the fiber morphology was also examined by scanning electron microscope.
Chemical and carbon-13 nuclear magnetic resonance studies of the blood group M and N active sialoglycopeptides from human glycophorin A. (1981)

The NH2-terminal sialoglycopeptides from human erythrocyte glycophorin A have been obtained by specific proteolytic cleavage and gel filtration chromatography. By cyanogen bromide cleavage, a glycosylated octapeptide was obtained from blood group M donors having an amino acid composition and 13C NMR spectrum consistent with the structure (formula: see text) was demonstrated. By Staphylococcus aureus protease cleavage, a glycosylated pentapeptide was obtained from N donors having the same structure as II, without the carboxyl-terminal sequence Val . Ala . Hse. Methanolysis/gas chromatographic analysis and 13C NMR spectroscopy of I and II and their asialo derivatives reveal that the M- and N-active sialoglyco-octapeptides both have identical oligosaccharide structures, each containing three O-linked tetrasaccharides with the structure NeuNAc alpha 2-3Gal beta 1-3(NeuNAc alpha 2-6)GalNAc alpha 1-O-Ser(Thr). The demonstration of the anomeric form of GalNAc-peptide linkages revealed by 13C NMR has previously been inaccessible by chemical analysis. Conformationally, I and II appear identical and both manifest several unusual resonance shifts suggestive of a glycopeptide secondary structure involving four specific hydrogen bonds. Calcium ion titration was also found to induce shifts in the NeuNAc 13C resonances that may be of functional significance. Serological studies reveal that both the M and N glyco-octapeptides and the N glyco-pentapeptide retain all of the M and N activity of the parent structure. Deamination and/or desialylation completely destroys this activity. These data are consistent with a model in which the M or N determinant is the NH2-terminal amino acid and a NeuNAc residue(s). From these data it is concluded that there is no chemical basis for assertions in the literature that M and N antigens differ in their oligosaccharide structure or that the N antigen is biosynthetically transformed to the M antigen by sialylation.
Nucleotide sequence and expression of the capsid protein gene of feline calicivirus (1991)

The sequence of the 3'-terminal 2,486 bases of the feline calicivirus (FCV) genome was determined. This region of the FCV genome, from which the 2.4-kb subgenomic RNA is derived, contained two open reading frames. The larger open reading frame, found in the 5' end of the subgenomic mRNA, contained 2,004 bases encoding a polypeptide of 73,467 Da. The smaller open reading frame, encoded in the 3' end of the mRNA, was composed of 318 bases, encoding a polypeptide of 12,185 Da. The AUG initiation codon of the second open reading frame overlapped the UGA termination codon of the first, with the sequence AUGA. The nucleotide sequence of the region containing this overlap resembles the -1 frameshift sequences of the retroviruses. The 5' end of the 2.4-kb subgenomic RNA was mapped by primer extension analysis. There were two apparent transcription initiation points, both of which were 5' to the AUG initiation codon of the large open reading frame. Transcription from these sites yielded RNA transcripts with 5' nontranslated leader regions of 17 and 18 bases. The total length of the 2.4-kb subgenomic RNA was 2,375 bases (from the 5'-most start site) excluding the poly(A) tail. Edman degradation of the purified capsid protein of FCV showed that the capsid protein was encoded by the large open reading frame. Western immunoblot analysis of FCV-infected cells using a feline anti-FCV antiserum demonstrated that translation of the capsid protein was detectable at 3 h postinfection and continued to accumulate until 8 h postinfection, the last time examined.
Comparative assessment of clinical response in patients with rheumatoid arthritis between PF‐05280586, a proposed rituximab biosimilar, and rituximab (2016)

NCT01526057.
Th1 T Cell Responses to HIV-1 Gag Protein Delivered by a Listeria monocytogenes Vaccine Are Similar to Those Induced by Endogenous Listerial Antigens (1999)

Listeria monocytogenes is a facultative intracellular bacterium that lives and grows in the cytoplasm of the host cell. The hallmark of a listerial infection is a cell-mediated immune response to its own secreted virulence factors. Thus, L. monocytogenes vaccines engineered to secrete HIV proteins may be ideal vectors for boosting cellular immune responses against HIV. Using strains of L. monocytogenes that stably express and secrete HIV Gag (Lm-Gag) to deliver this Ag to the immune system, we have previously shown strong MHC class I-restricted cytotoxic T cell responses to this protein. In this study, we examine MHC class II-restricted T cell responses to HIV-Gag delivered by Lm-Gag. We demonstrate the induction of CD4+ T cells that are HIV-Gag specific and identify three epitopes in two strains of mice, BALB/c (H-2d) and C57BL/6 (H-2b), two of which are both H-2d and H-2b restricted, but are not immunodominant for both haplotypes. In addition, we show that the CD4+ T cells induced are of the Th1 phenotype that produce IFN-gamma at levels similar to CD4+ T cells induced to endogenous listerial Ags. These studies suggest that chromosomally modified strains of L. monocytogenes may be useful as vaccine vectors for the induction of Th1 T cell responses against HIV.
A novel method of photonic band-gap lithography of porous silicon heterostructures (2007)

A method to modulate the local optical properties of porous silicon photonic crystals is reported. The porous silicon photonic crystals are fabricated by electrochemical etching in a hydrofluoric acid-based electrolyte. Local oxidation was performed using either a UV lamp or 532 nm laser to irradiate selective regions of the photonic crystal. The sample was then soaked in an alcohol solution. Unmasked regions of the porous silicon photonic crystal exhibited significant spectral degradation and loss of the microcavity resonance. The region of the porous silicon photonic crystal protected by the oxide exhibited no significant changes in the reflectance spectrum. This simple photolithographic technique can be used to fabricate a variety of spatially localized silicon-based structures such as photonic bandgap mirrors, optical filters, waveguides and optical switches.
In Vivo Drug Interactions of the Teratogen Thalidomide with Midazolam: Heterotropic Cooperativity of Human Cytochrome P450 in Humanized TK-NOG Mice (2013)

In vivo drug interactions of the teratogen thalidomide with the model cytochrome P450 (P450) 3A substrate midazolam were investigated in mice with humanized livers. The clearance of midazolam (administered intravenously, 10 mg kg(-1)) in chimeric mice was enhanced by orally co-administered thalidomide (100 mg kg(-1)). A larger area under the curve of the major metabolite 1'-hydroxymidazolam (1.7-fold) was obtained with thalidomide because of the heterotropic cooperativity of human P450 3A enzymes. A larger area under the curve of the minor metabolite 4-hydroxymidazolam (3.5-fold) was seen with daily pretreatment with thalidomide for 3 days, presumably because of human P450 3A induction. These results demonstrate that livers of humanized mice mediate drug interactions of thalidomide and suggest interactions of therapeutic agents during therapies with thalidomide.