gebhart/patrepeval huggingface dataset:
Enhanced acetone‐butanol fermentation using repeated fed‐batch operation coupled with cell recycle by membrane and simultaneous removal of inhibitory products by adsorption (1995)

A novel acetone-butanol production process was developed which integrates a repeated fed-batch fermentation with continuous product removal and cell recycle. The inhibitory product concentrations of the fermentation by Clostridium acetobutylicum were reduced by the simultaneous extraction process using polyvinylpyridine (PVP) as an adsorbent. Because of the reduced inhibition effect, a higher specific cell growth rate and thus a higher product formation rate was achieved. The cell recycle using membrane separation increased the total cell mass density and, therefore, enhanced the reactor productivity. The repeated fed-batchoperation overcame the drawbacks typically associated with a batch operation such as down times, long lag period, and the limitation on the maximum initial substrate concentration allowed due to the substrate inhibition. Unlike a continuous operation, the repeated fed-batch operation could beoperated for a long time at a relatively higher substrate concentration without sacrificing the substrate loss in the effluent. As a result, the integrated process reached 47.2 g/L in the equivalent solvent concentration (including acetone, butanol, and ethanol) and 1.69 g/L . h in the fermentor productivity, on average, over a 239.5-h period. Compared with a controlled traditional batch acetone-butanol fermentation, the equivalent solvent concentration and the tormentor productivity were increased by 140% and 320%, respectively. (c) 1995 John Wiley & Sons Inc.
Lipase catalyzed alcoholysis of sunflower oil (1990)

Abstract Lipase‐catalyzed alcoholysis of sunflower oil under anhydrous conditions was examined. Lipases from Pseudomonas fluorescens and 2 immobilized enzymes from Mucor miehei and a Candida sp. gave sufficient conversion with petroleum ether as the solvent, even when methanol and ethanol were used. The overall content of tri‐, di‐ and monoglycerides, as well as the corresponding alkyl esters, was measured. Because Pseudomonas lipase led to almost quantitative esterification, further studies were carried out with that enzyme varying the amounts of enzyme or the alcohols. Acceptable conversions were achieved even without solvent. Reaction rates of alcoholysis with 5 homologous alcohols, with or without the addition of water, were measured, and in all cases the reaction rates increased with higher chain length of the alcohol. In the case of methanol the highest rate was obtained without any addition of water, but a significantly higher rate was observed with 96% ethanol as opposed to absolute ethanol. The main advantages of lipasecatalyzed, nonaqueous alcoholysis as compared to classical procedures are the mild reaction conditions, the isolation of glycerin without further purification and without the formation of chemical waste, and the ability of lipases to catalyze the esterification of free fatty acids.
The physical and mechanical properties of polyurethanes from oleic acid polyols (2009)

Abstract Three different polyester polyols, with various oleic acid content, were used in the preparation of polyurethane (PUR) coatings. The polyols were designated as Alk28, Alk40, and Alk65, in which 28, 40, and 65 represent the percentage of oleic acid of the polyol formulations. These polyester polyols were reacted with aromatic diisocyanate [toluene diisocyanate (TDI)] to form PUR coatings. The acid value, hydroxyl value, molecular weight, and viscosity of the polyols have been determined. The reaction between the polyols and TDI was studied by Fourier Transform Infrared spectroscopy and X‐ray diffraction (XRD). The effects of varying NCO/OH ratio and oleic acid content of polyols on physical and mechanical properties of PUR films were studied. XRD results indicate that the samples are amorphous. PURs, made with Alk28, have the best mechanical properties followed by Alk40 and Alk65. The mechanical properties of the samples have increased as the NCO/OH ratio was increased from 1.2 to 1.6. © 2009 Wiley Periodicals, Inc. J Appl Polym Sci, 2009
Enzymatic replication of viral and complementary strands of duplex DNA of phage phiX174 proceeds by seprate mechanisms. (1976)

Multiplication of the duplex, circular, phage phiX174DNA (replicative form, RF) in stage II of the replicative life cycle has been observed with a crude enzyme preparation [Eisenberg et al. (1976) Proc, Natl. Acad, Sci. USA 73, 1594-1597]. This stage has now been partially reconstituted with purified proteins and subdivided into two stages: II(+) and II(-). In stage II(+), viral (+) strand synthesis is carried out by four proteins: the phage-induced, cistron A-dependent protein, rep-dependent protein, DNA unwinding protein, and DNA polymerase III holenzyme. In stage II(-), complementary (-) strand synthesis utilizes the product of stage II(+) as template and the multiprotein system previously identified in the stage I synthesis of a complementary strand on the viral DNA template to produce RF. The multiprotein system includes DNA unwinding protein, proteins i and n, dnaB protein, dnaC protein, dnaG protein, and DNA polymerase III holoenzyme. A discussion of these two separate mechanism for synthesis of (+) and (-) strands suggests that they may account for essentially all the replicative stages in the life cycle of phiX174.
Human Thyroid Peroxidase Activity in Benign and Malign Thyroid Disorders (1977)

Peroxidase activity in various human benign and malignant pathological conditions has been investigated. The activity was measured in vitro by oxidation of iodide and by iodination of bovine serum albumin (BSA). The deficiency of hormone synthesis observed in various diffuse benign thyroid disorders was certainly not due to a lack of peroxidase activity. In hyperthyroid patients treated with carbimazole and in a euthyroid state at surgery, iodide-peroxidase activity (24 patients) and DNA content (12 patients), both expressed per g of wet weight, were enhanced (288% and 122% increases over control, respectively) and the cellular enzyme activity was almost double than that of normal tissue. An increase in peroxidase activity when measured by iodination of BSA (11 patients) was also observed (350% increase over control). It is suggested that high cellular peroxidase activity might be due not to the treatment but to the disease. In euthyroid patients with diffuse sporadic goiter, the peroxidase activity measured by oxidation of iodide (29 patients) and by iodination of BSA (13 patients) was almost twice that of normal tissue while the DNA content (17 patients) was the same. In these two diffuse pathological benign conditions and in normal gland an inverse relationship has been found between cellular enzymatic activity and iodine content. In the group of sporadic goiter itself, this correlation was also observed. In contrast, no correlation was found between peroxidase activity and iodine content in localized benign lesions. In “hot” nodules (15 cases) a statistical increase in iodide peroxidase activity was observed and the DNA content was also enhanced (7 patients). However, in “cold” nodules the DNA content was not statistically different from normal (12 patients), and the cellular iodide-peroxidase activity was higher in this disease than in any other benign thyroid disorders. On the other hand, when measured by iodination of BSA, no statistical increase in peroxidase activity was found. In the 16 cases of differentiated carcinomas studied, the results were variable but in most cases, the peroxidase activity, measured by oxidation of iodide as well as by iodination of BSA, was below that of normal tissue. In more than 50% of the cases, no detectable activity was found and no relationship was observed between the iodine content of the malignant tissue and the peroxidase activity. In contrast with the benign pathological conditions, the peroxidase was lower than normal only in cancerous tissues.
Exploiting Ligand-Protein Conjugates to Monitor Ligand-Receptor Interactions (2012)

We introduce three assays for analyzing ligand-receptor interactions based on the specific conjugation of ligands to SNAP-tag fusion proteins. Conjugation of ligands to different SNAP-tag fusions permits the validation of suspected interactions in cell extracts and fixed cells as well as the establishment of high-throughput assays. The different assays allow the analysis of strong and weak interactions. Conversion of ligands into SNAP-tag substrates thus provides access to a powerful toolbox for the analysis of their interactions with proteins.
Indole-3-propionic acid, a melatonin-related molecule, protects hepatic microsomal membranes from iron-induced oxidative damage: Relevance to cancer reduction (2001)

Excessive free iron and the associated oxidative damage are commonly related to carcinogenesis. Among the antioxidants known to protect against iron-induced oxidative abuse and carcinogenesis, melatonin and other indole compounds recently have received considerable attention. Indole-3-propionic acid (IPA), a deamination product of tryptophan, with a structure similar to that of melatonin, is present in biological fluids and is an effective free radical scavenger. The aim of the study was to examine the effect of IPA on experimentally induced oxidative changes in rat hepatic microsomal membranes. Microsomes were preincubated in presence of IPA (10, 3, 2, 1, 0.3, 0.1, 0.01 or 0.001 mM) and, then, incubated with FeCl(3) (0.2 mM), ADP (1.7 mM) and NADPH (0.2 mM) to induce oxidative damage. Alterations in membrane fluidity (the inverse of membrane rigidity) were estimated by fluorescence spectroscopy and lipid peroxidation by measuring concentrations of malondialdehyde+4-hydroxyalkenals (MDA+4-HDA). IPA, when used in concentrations of 10, 3 or 2 mM, increased membrane fluidity, although at these concentrations it did not influence lipid peroxidation significantly. The decrease in membrane fluidity due to Fe(3+) was completely prevented by preincubation in the presence of IPA at concentrations of 10, 3, 2 or 1 mM. The enhanced lipid peroxidation due to Fe(3+) was prevented by IPA only at the highest concentration (10 mM). It is concluded that Fe(3+)-induced rigidity and, to a lesser extent, lipid peroxidation in microsomal membranes may be reduced by IPA. However, IPA in high concentrations increase membrane fluidity. Besides melatonin, IPA may be used as a pharmacological agent to protect against iron-induced oxidative damage to membranes and, potentially, against carcinogenesis.
Plasma concentrations of triazolam are increased by concomitant ingestion of grapefruit juice (1995)

Grapefruit juice can increase the plasma concentrations and effects of oral triazolam.
Decreased Platelet Derived Growth Factor Expression During Fracture Healing in Diabetic Animals (2003)

Animal model experiments have suggested that diabetes inhibits cell proliferation during fracture healing. Immunohistochemical analysis of proliferating cell nuclear antigen revealed significant reductions in cellular proliferation rates in the fracture callus of spontaneously diabetic BB Wistar rats as compared with healthy BB Wistar rats. Because platelet derived growth factor is associated with the early stage of fracture healing, it was hypothesized that diabetes causes decreased platelet derived growth factor expression during the early phase of fracture healing with a concomitant decrease in cell proliferation. Midshaft femur fractures were created in healthy and spontaneously diabetic BB Wistar rats and analyzed at Days 2, 4, and 7 after fracture for expression of platelet derived growth factor. Immunohistochemistry showed decreased localization of platelet derived growth factor in early diabetic fracture callus compared with healthy controls. Platelet derived growth factor messenger ribonucleic acid levels, as determined by reverse transcription and polymerase chain reaction, also were decreased in early diabetic fractures compared with healthy controls. Therefore the decreased cell proliferation rates associated with diabetic fracture healing are consistent with decreased platelet derived growth factor levels and suggest a causal relationship. These results suggest that diabetes is affecting the early phase of fracture healing by inhibiting cell proliferation through decreasing expression of platelet derived growth factor.
Cluster Headache: Conventional Pharmacological Management (2013)

Cluster headache pain is very intense, usually increases in intensity very rapidly from onset, and attacks are often frequent. These clinical features result in significant therapeutic challenges. The most effective pharmacological treatment options for acute cluster attack include subcutaneous sumatriptan, 100% oxygen, and intranasal zolmitriptan. Subcutaneous or intramuscular dihydroergotamine and intranasal sumatriptan are additional options. Transitional therapy is applicable mainly for patients with high-frequency (>2 attacks per day) episodic cluster headache, and options include short courses of high-dose oral corticosteroids, dihydroergotamine, and occipital nerve blocks with local anesthetic and steroids. Prophylactic therapy is important both for episodic and chronic cluster headache, and the main options are verapamil and lithium. Verapamil is drug of first choice but may cause cardiac arrhythmias, and periodic electrocardiograms (EKGs) during dose escalation are important. Many other drugs are also in current use, but there is an insufficient evidence base to recommend them.
Treatment of high‐risk acute myelogenous leukaemia by myeloablative chemoradiotherapy followed by co‐infusion of T cell‐depleted haematopoietic stem cells and culture‐expanded marrow mesenchymal stem cells from a related donor with one fully mismatched human leucocyte antigen haplotype (2002)

A 20-year-old woman with high-risk acute myelogenous leukaemia was transplanted with granulocyte colony stimulating factor (G-CSF)-mobilized peripheral blood CD34+ haematopoietic stem cells and bone-marrow-derived mesenchymal stem cells (MSC) from her human leucocyte antigen haplotype-mismatched father after myeloablative conditioning therapy. The patient engrafted rapidly and had no acute or chronic graft-versus-host disease. Since transplantation, the patient has shown an enduring trilineage haematological complete response without any evidence of leukaemia relapse at 31 months. We suggest that MSC can be used effectively for genetically haploidentical haematopoietic stem cell transplantation for acute leukaemia.
Parasin I, an antimicrobial peptide derived from histone H2A in the catfish, Parasilurus asotus (1998)

In response to epidermal injury, Parasilurus asotus, a catfish, secreted a strong antimicrobial peptide into the epithelial mucosal layer. The molecular mass of the antimicrobial peptide, named parasin I, was 2000.4 Da, as determined by matrix-associated laser desorption ionization mass spectrometry. The complete amino acid sequence of parasin I, which was determined by automated Edman degradation, was Lys-Gly-Arg-Gly-Lys-Gln-Gly-Gly-Lys-Val-Arg-Ala-Lys-Ala-Lys-Thr-Arg-Ser- Ser. Eighteen of the 19 residues in parasin I were identical to the N-terminal of buforin I, a 39-residue antimicrobial peptide derived from the N-terminal of toad histone H2A [Kim et al. (1996) Biochem. Biophys. Res. Commun. 229, 381-387], which implies that parasin I was cleaved off from the N-terminal of catfish histone H2A. Parasin I showed strong antimicrobial activity, about 12-100 times more potent than magainin 2, against a wide spectrum of microorganisms, without any hemolytic activity. Circular dichroism spectra of parasin I indicated a structural content of 11% alpha-helix, 33% beta-sheet, and 56% random coils. The beta-sheet axial projection diagram of parasin I showed an amphipathic structure. Our results indicate that the catfish may produce parasin I from its histone H2A by a specific protease upon injury to protect against invasion by microorganisms.
A symptom-driven expert system for isolating and correcting network faults (1988)

A description is given of Troubleshooter, a system for diagnosing problems in the Datakit Virtual Circuit Switch networking environment. This system is representative of applications using expert systems as diagnostic tools. Troubleshooter uses software tools from the academic laboratories, most notably OP24 from Carnegie-Mellon University and Franz LISP from the University of California at Berkeley. Extensive laboratory tests has confirmed Troubleshooter's ability to detect faults.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Post‐translational modifications of the linker histone variants and their association with cell mechanisms (2009)

In recent years, a considerable amount of research has been focused on establishing the epigenetic mechanisms associated with DNA and the core histones. This effort is driven by the fact that epigenetics is intimately involved with genomics in a whole range of molecular processes. However, there is now a consensus that the epigenetics of the linker histones are just as important. The result of that consensus is that the post-translational modifications (PTMs) for most of the linker histone variants in human and mouse have now been established by a number of experimental techniques, foremost of which is mass spectrometry (MS). MS was also used by our group to establish the PTMs of the linker histone variants in chicken erythrocytes. Although it is now known which types of PTM occur at particular locations on the linker histone variants, there is still a large gap in the knowledge of how this data relates to function. The focus of this review is an analysis of the PTM data for the linker histones from several species, but with an emphasis on human, mouse, and chicken. Our analysis reveals that certain PTMs can be clearly correlated with specific functions of the linker histones in particular cell types, and that unique PTM patterns exist for different cell types.
Reverse genetics with a full-length infectious cDNA of severe acute respiratory syndrome coronavirus (2003)

A previously undescribed coronavirus (CoV) is the etiologic agent responsible for severe acute respiratory syndrome (SARS). Using a panel of contiguous cDNAs that span the entire genome, we have assembled a full-length cDNA of the SARS-CoV Urbani strain, and have rescued molecularly cloned SARS viruses (infectious clone SARS-CoV) that contained the expected marker mutations inserted into the component clones. Recombinant viruses replicated as efficiently as WT virus and both were inhibited by treatment with the cysteine proteinase inhibitor (2S,3S)-transepoxysuccinyl-L-leucylamido-3-methylbutane ethyl ester. In addition, subgenomic transcripts were initiated from the consensus sequence ACGAAC in both the WT and infectious clone SARS-CoV. Availability of a SARS-CoV full-length cDNA provides a template for manipulation of the viral genome, allowing for the rapid and rational development and testing of candidate vaccines and therapeutics against this important human pathogen.
Recombinant herpes vector-mediated analgesia in a primate model of hyperalgesia (2005)

Some chronic pain syndromes are characterized by episodes of intense burning and hyperalgesia in localized areas of skin. These sensations are thought to be mediated, at least in part, by the activity of damaged, unmyelinated C nociceptors. These phenomena were modeled by assaying responses of macaques to thermal and chemical stimuli that produced periodic activation and sensitization of C nociceptors. Upon validation of this method, a recombinant herpes simplex vector encoding human preproenkephalin was topically applied to the dorsal surface of the feet of the monkeys. Immunohistochemistry and radioimmunoassay revealed that enkephalin peptides were being produced in releasable pools in sensory neurons innervating the treated skin area. Behavioral responses evoked by periodic sensitization and activation of C nociceptors innervating the vector-treated skin area revealed a substantial and long-lasting (at least 20 weeks) antihyperalgesic and analgesic effect limited to the areas to which the virus was applied. This approach may be a viable means of treating localized cutaneous burning pain and hyperalgesia.
Cellular Uptakes, Biostabilities and Anti‐miR‐210 Activities of Chiral Arginine‐PNAs in Leukaemic K562 Cells (2012)

A series of 18-mer peptide nucleic acids (PNAs) targeted against micro-RNA miR-210 was synthesised and tested in a cellular system. Unmodified PNAs, R(8) -conjugated PNAs and modified PNAs containing eight arginine residues on the backbone, either as C2-modified (R) or C5-modified (S) monomers, all with the same sequence, were compared. Two different models were used for the modified PNAs: one with alternated chiral and achiral monomers and one with a stretch of chiral monomers at the N terminus. The melting temperatures of these derivatives were found to be extremely high and 5 M urea was used to assess differences between the different structures. FACS analysis and qRT-PCR on K562 chronic myelogenous leukaemic cells indicated that arginine-conjugated and backbone-modified PNAs display good cellular uptake, with best performances for the C2-modified series. Resistance to enzymatic degradation was found to be higher for the backbone-modified PNAs, thus enhancing the advantage of using these derivatives rather than conjugated PNAs in the cells in serum, and this effect is magnified in the presence of peptidases such as trypsin. Inhibition of miR-210 activity led to changes in the erythroid differentiation pathway, which were more evident in mithramycin-treated cells. Interestingly, the anti-miR activities differed with use of different PNAs, thus suggesting a role of the substituents not only in the cellular uptake, but also in the mechanism of miR recognition and inactivation. This is the first report relating to the use of backbone-modified PNAs as anti-miR agents. The results clearly indicate that backbone-modified PNAs are good candidates for the development of very efficient drugs based on anti-miR activity, due to their enhanced bioavailabilities, and that overall anti-miR performance is a combination of cellular uptake and RNA binding.
Silicon-based molecular nanotechnology (2000)

One potential application of molecular nanotechnology is the integration of molecular electronic function with advanced silicon technology. One step in this process is the tethering of individual molecules at specific locations on silicon surfaces. This paper reports the fabrication of arrays of individual organic molecules on H-passivated Si(100) surfaces patterned with an ultrahigh vacuum scanning tunnelling microscope (STM). Feedback controlled lithography (FCL) is used to create templates of individual silicon dangling bonds. Molecules introduced in the gas phase then spontaneously assemble onto these atomic templates. Norbornadiene (NBE), copper phthalocyanine (CuPc), and C60 molecular arrays have been made by this technique and studied by STM imaging and spectroscopy. Both NBE and CuPc molecules appear as depressions in empty states images, whereas in filled states images they are nearly indistinguishable from Si dangling bonds. Furthermore, the fourfold symmetry and central copper atom of CuPc are clearly observed at positive sample bias. Spatial tunnelling conductance maps of CuPc illustrate charge transfer from the surrounding substrate when the molecule is bound to the surface via its central copper atom. On the other hand, when the CuPc molecule interacts with the substrate via an outer benzene ring, molecular rotation is observed. C60 molecules display intramolecular structure in topographic images and spectroscopic data. The local density of states of C60 clearly shows the location of the lowest unoccupied molecular orbital, which suggests that the highest occupied molecular orbital is located within 0.3 eV of the fermi level.