gebhart/patrepeval huggingface dataset:
Characterization of a pH‐inducible promoter system for high‐level expression of recombinant proteins in Escherichia coli (1995)

A pH-inducible promoter system was characterized and its potential applicability in recombinant protein production was evaluated using a plasmid construct, pSM552-545C(-), in which the promoter and activator coding sequences of the cad operon were inserted into the upstream region of a lacZ' reporter gene. Graded gene expression levels with respect to culture pH between 8.0 and 5.5 were observed and the induction range can be as high as 200-fold. The effects of several cultivation parameters, including pH, temperature, induction cell density, and inoculum size, were systematically examined. The practical application of this expression system to high level production of recombinant proteins was successfully demonstrated using a rich medium, superbroth. An extremely high recombinant protein productivity at a value of approximately 1.4 g/L with a specific expression level as high as 35% of total cellular protein can be obtained in a simple batch cultivation. The behavior of this expression system was further investigated using chemostat cultures. An uncommon relationship between the volumetric or specific recombinant protein activity and the dilution rate, with a maximal activity at a dilution rate of approximately 0.4 h(-1)was observed. (c) 1995 John Wiley & Sons, Inc.
The role of synchronization in digital communications using chaos. II. Chaotic modulation and chaotic synchronization (1998)

For pt. I see ibid., vol. 44, p. 927-36 (1997). In a digital communications system, data are transmitted from one location to another by mapping bit sequences to symbols, and symbols to sample functions of analog waveforms. The analog waveform passes through a bandlimited (possibly time-varying) analog channel, where the signal is distorted and noise is added. In a conventional system the analog sample functions sent through the channel are weighted sums of one or more sinusoids; in a chaotic communications system the sample functions are segments of chaotic waveforms. At the receiver, the symbol may be recovered by means of coherent detection, where all possible sample functions are known, or by noncoherent detection, where one or more characteristics of the sample functions are estimated. In a coherent receiver, synchronization is the most commonly used technique for recovering the sample functions from the received waveform. These sample functions are then used as reference signals for a correlator. Synchronization-based coherent receivers have advantages over noncoherent receivers in terms of noise performance, bandwidth efficiency (in narrow-band systems) and/or data rate (in chaotic systems). These advantages are lost if synchronization cannot be maintained, for example, under poor propagation conditions. In these circumstances, communication without synchronization may be preferable. The theory of conventional telecommunications is extended to chaotic communications, chaotic modulation techniques and receiver configurations are surveyed, and chaotic synchronization schemes are described.
Topical diltiazem ointment in the treatment of chronic anal fissure (2001)

Topical 2 per cent diltiazem ointment used as an agent for chemical sphincterotomy for chronic anal fissure offers significant healing rates but does not have a significant side-effect profile, which may aid compliance to treatment. Early recurrences are common but usually amenable to further chemical sphincterotomy.
Mandibular Distraction Lengthening in the Severely Hypoplastic Mandible (1994)

Distraction lengthening is a technique that was initially developed for correction of lower limb length discrepancies. It has recently been adapted to maxillofacial problems and has gained increasing popularity in this application. This report illustrates the principles involved in mandibular distraction lengthening and offers possible solutions to potentially limiting clinical problems. First, conventional technique dictates that a distinct periosteal sleeve is necessary for distraction osteogenesis to occur. However, in this case, distraction was performed through an area of scar tissue in which the native periosteum was destroyed. The ability to extend the use of the technique of distraction successfully to suboptimal clinical situations may broaden the indications for its use. Second, fixator instability is a potentially common problem in these cases because of the forces involved in distraction osteogenesis and the duration of the process. However, mechanical rigidity is essential consolidation (typically requiring twice as long as the distraction phase). Fixator instability can be successfully salvaged during the mineralization phase of bony healing through the use of an onlay corticocancellous bone "plate," which resorbs as the distraction gap gains strength. This report highlights one of the main advantages of the distraction process: the expansion of the soft-tissue matrix of the face.
c-myc antisense transcripts accelerate differentiation and inhibit G1 progression in murine erythroleukemia cells. (1988)

Friend murine erythroleukemia (F-MEL) cells were transfected with a plasmid bearing tandemly arranged mouse c-myc antisense and dihydrofolate reductase transcription units. Sixteen clones were isolated, each containing unrearranged c-myc sequences and expressing high levels of antisense transcripts. All antisense clones examined contained reduced amounts of cytoplasmic endogenous c-myc transcripts. The kinetics of reaccumulation of endogenous c-myc mRNA during a 24-h exposure to dimethyl sulfoxide (DMSO) were also retarded and the ultimate transcript levels attained were less than in control cells. Antisense clones grew as well as control F-MEL cells in medium containing 10% fetal calf serum but at only a half and a quarter of the control rates in media containing 5 and 2% serum, respectively. Antisense clones differentiated faster and to a greater degree than control cells following DMSO exposure. myc antisense transcript expression was increased by growing cells in methotrexate, which resulted in an enhanced response to DMSO. Fluorescence-activated cell sorter (FACS) analysis of cellular DNA content indicated that a greater fraction of antisense nuclei contained a G0/G1 2n DNA content following a 24-h exposure to DMSO. When density-arrested antisense clones were diluted into fresh medium to allow reentry into the cell cycle, they incorporated less [3H]thymidine than control cells. FACS analysis showed that this was because only a portion of the cell population was entering S phase. Whereas control cells did not increase in size following release from density arrested antisense cells contained a subpopulation which were initially smaller and which eventually attained the same size as control cells. Quiescent antisense cells thus comprise two populations, each arrested at a different point in G1. Dilutional replating allowed both populations to reenter the cell cycle. We propose a model which postulates that certain minimal myc levels are necessary for cells to traverse G1. Those with insufficient levels, due, for example, to antisense inhibition, are unable to completely traverse G1 during density arrest and synchronize at an earlier point than do control cells. This earlier point may be along the differentiation pathway and may account for the greater responsiveness of antisense cells to DMSO induction. This model postulates that F-MEL cells overexpressing myc fail to differentiate because myc levels are never sufficiently low enough to allow cells to enter the differentiation pathway.
Effect of fourth ventricular neuropeptide Y and peptide YY on ingestive and other behaviors (1990)

We studied the effect of fourth intracerebroventricular administration of neuropeptide Y (NPY) and peptide YY (PYY) on ingestive and other behaviors in awake nondeprived rats. Injection of NPY or PYY into the fourth ventricle produced a significant dose-related increase in food intake and reduction in the latency to eat. PYY was more potent than NPY in increasing food intake and decreasing latency to eat, suggesting that PYY-preferring receptors sensitive to the orexigenic effects of NPY and PYY exist in the hindbrain. In addition, both peptides increased water intake when food was present but not when food was absent, suggesting that a neural substrate supporting a direct action of NPY and PYY on water intake is not present in the hindbrain. In time sampling of behaviors occurring during a 90-min feeding test, we found that both peptides increased the time spent eating and reduced grooming. In addition PYY, but not NPY, reduced apparent sleep and increased exploratory activity. This suggests that PYY, but not NPY, influences a hindbrain neural substrate involved in sleep and activity.
Addressing, bridging, and source routing (LAN interconnection) (1988)

The concept of source routing for the interconnection of local networks is described. An architectural framework is provided to emphasize the principal advantages inherent with such a bridging mechanism. Motivation for this form of routing is shown to be a consequence of the address structure within the local network standards that have been adopted by IEEE, the European Computer Manufacturers Association (ECMA), and the International Organization for Standardization (ISO). As with many internetworking protocols, the use of a qualified address structure allows a more efficient routing mechanism. The physical address of a station, although not explicitly present in each transmitted frame, is implied by its attachment to a specific segment of the local network. This subtle point relative to local network addressing provides the foundation for the incorporation of source routing protocols.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Potent Reduction of Apolipoprotein B and Low-Density Lipoprotein Cholesterol by Short-Term Administration of an Antisense Inhibitor of Apolipoprotein B (2006)

Administration of an antisense oligonucleotide to human apoB resulted in a significant, prolonged, and dose-dependent reduction in apoB and LDL-C. Although injection-site reactions were common, adherence to protocol was unaffected.
Self‐Organization of Oriented Calcium Carbonate/Polymer Composites: Effects of a Matrix Peptide Isolated from the Exoskeleton of a Crayfish (2006)

Gone fishing: Unidirectionally oriented CaCO3 crystalline films have been prepared on chitin matrices in the presence of calcification-associated peptide (CAP-1), which was isolated from the exoskeleton of the red swamp crayfish. The interactions of CAP-1 with the matrix and the acidic nature of the peptide lead to a filmlike assembly of CaCO3 nanocrystals through transformation of amorphous calcium carbonate (see picture).
Identification, cloning, and characterization of rcsF, a new regulator gene for exopolysaccharide synthesis that suppresses the division mutation ftsZ84 in Escherichia coli K-12 (1992)

A new gene, designated rcsF, was located adjacent to drpA at the 5.2-min position of the genetic map of Escherichia coli. The deduced amino acid sequence encoded by the rcsF gene indicates a small protein of 133 amino acid residues with a calculated pI of 10.8 that is rich in proline, serine, alanine, and cysteine residues. When overexpressed as a result of its presence on a multicopy plasmid, rcsF confers a mucoid phenotype and restores colony formation to ftsZ84 mutant cells on L agar medium containing no added NaCl. These two phenotypes are not observed in rcsB mutant cells. Ion mutant cells harboring an rcsF mutation accumulate considerably lower levels of exopolysaccharides, whereas the presence of a multicopy rcsF plasmid not only increases capsule synthesis but also confers a mucoid phenotype at 37 degrees C, a temperature at which ion mutant cells are known not to form mucoid colonies. RcsF does not stimulate the expression of rcsB, indicating that it exerts its action through the RcsB protein, possibly by phosphorylation. It is also shown that RcsF stimulation of capsule synthesis is RcsA-dependent, whereas colony formation of ftsZ84 mutant cells can be restored by RcsF in the absence of RcsA.
A new flow reactor for the treatment of polluted water with microwave and ultrasound (2007)

Abstract Microwave (MW) and high‐intensity ultrasound (US) provide innovative techniques for the degradation of persistent organic pollutants (POPs). When Fenton's reagent is used to treat industrial wastes, organic pollutants are degraded by highly reactive hydroxyl radicals (HO·) that can oxidize almost any organic compound to carbon dioxide and water. These reactions, when carried out under US or MW, are faster and much more efficient. The present work assesses the combined effect of US and MW using a new flow reactor developed in our laboratory. In this 5 L pilot reactor the liquid was pumped in parallel through a modified domestic MW oven and through a cell where it was irradiated with two US generators working at 20 and 300 kHz, while MW irradiation took place in a modified domestic oven. We studied the degradation of 2,4‐dibromophenol (0.1 g L −1 in water) by Fenton's reagent, assessing the contribution of each energy source to the overall effect, and found that MW and US‐300 kHz played the main role. A modest amount of oxidant (6 mL 30% H 2 O 2 per 1 L of polluted water) sufficed to achieve complete degradation within 6 h, at which time organic compounds were no longer detectable. Even if no Fenton's reagent was added, about one half of the pollutant was degraded after 3 h irradiation. Copyright © 2007 Society of Chemical Industry
Improved Surgical Approach to Left Atrial Appendage Aneurysm (1992)

Left atrial appendage aneurysm is a rare anomaly, which usually presents with arrhythmia or cerebral embolism. Diagnostic evaluation traditionally required cardiac catheterization, and surgical resection required cardiopulmonary bypass. Utilizing intraoperative transesophageal echocardiography and surgical stapling devices, we have streamlined our operative technique, allowing resection of a left atrial appendage aneurysm without cardiopulmonary bypass. This report of two cases treated over the past decade demonstrates the evolution of our surgical technique.
KEGG for integration and interpretation of large-scale molecular data sets (2011)

Kyoto Encyclopedia of Genes and Genomes (KEGG, http://www.genome.jp/kegg/ or http://www.kegg.jp/) is a database resource that integrates genomic, chemical and systemic functional information. In particular, gene catalogs from completely sequenced genomes are linked to higher-level systemic functions of the cell, the organism and the ecosystem. Major efforts have been undertaken to manually create a knowledge base for such systemic functions by capturing and organizing experimental knowledge in computable forms; namely, in the forms of KEGG pathway maps, BRITE functional hierarchies and KEGG modules. Continuous efforts have also been made to develop and improve the cross-species annotation procedure for linking genomes to the molecular networks through the KEGG Orthology system. Here we report KEGG Mapper, a collection of tools for KEGG PATHWAY, BRITE and MODULE mapping, enabling integration and interpretation of large-scale data sets. We also report a variant of the KEGG mapping procedure to extend the knowledge base, where different types of data and knowledge, such as disease genes and drug targets, are integrated as part of the KEGG molecular networks. Finally, we describe recent enhancements to the KEGG content, especially the incorporation of disease and drug information used in practice and in society, to support translational bioinformatics.
Query expansion for intelligent information retrieval on Internet (2002)

Most systems that manage distributed information on Internet have difficulties in retrieving relevant information for they are not able to include the exact semantics of retrieval queries that users request. In this paper, we propose an automatic query expansion method based on term distribution, which naturally reflects semantics of retrieval terms in order to enhance the performance of information retrieval. The SVD technique in the LSI is utilized in the proposed method to measure the term distribution which appears similar to a query. Terms appearing most similar to the query in consideration of the distribution are appended to the query. Thereby, the query can hit documents without having common terms but with common concepts. An automatic term reduction technique is also proposed which does not choose to append all the terms in the same distribution area. The experimental results show our method maintains comparable retrieval effectiveness as the other LSI methods without having to append many unnecessary terms.
Effects of Recombinant Human Granulocyte–Macrophage Colony-Stimulating Factor in Patients with Myelodysplastic Syndromes (1987)

The myelodysplastic syndromes are characterized by ineffective hematopoiesis and refractory cytopenias. In an attempt to improve hematopoiesis, we administered recombinant human granulocyte--macrophage colony-stimulating factor (GM-CSF) to eight patients with myelodysplastic syndrome, as part of a Phase I trial. The GM-CSF was given by continuous intravenous infusion daily for two weeks and then again after a two-week rest period. Over the entire dose range tested (30 to 500 micrograms per square meter of body-surface area), treatment was associated with marked increases in peripheral-blood leukocytes (5- to 70-fold), including granulocytes (5- to 373-fold), in all eight patients. The absolute number of monocytes, eosinophils, and lymphocytes increased in all patients. Three of eight patients also had 2- to 10-fold increases in platelet counts and improvement in erythropoiesis, with the result that two of three patients who had required red-cell and platelet transfusions no longer needed them (at 20 to 27 weeks of follow-up). Treatment was also associated with increased marrow cellularity and a decreased percentage of blasts in the bone marrow of patients with excess blasts, resulting in an increase in the ratio of differentiated myeloid cells to immature myeloid cells. We observed relatively few side effects, but bone pain was dose-limiting when it was associated with high white-cell counts. Our results showed that GM-CSF is a potent stimulator of hematopoiesis in vivo and may produce hematologic improvement in the short term (8 to 32 weeks of observation) in patients with myelodysplastic syndrome. More experience, with longer follow-up periods, will be necessary to assess the long-term safety and efficacy of this new treatment.
Synthesis of Antisense Oligonucleotides Conjugated to a Multivalent Carbohydrate Cluster for Cellular Targeting (2002)

Carrier-mediated delivery holds great promise for significantly improving the cellular uptake and therefore the therapeutic efficacy of antisense oligonucleotides in vivo. A multivalent carbohydrate recognition motif for the asialoglycoprotein receptor has been designed for tissue- and cell-specific delivery of antisense drugs to parenchymal liver cells. To combine low molecular weight with high receptor affinity, the synthetic ligand contains three galactosyl residues attached to a cholane scaffold via epsilon-aminocapramide linkers. Three-dimensional structural calculations indicate that this unique design provides proper spacing and orientation of the three galactosyl residues to accomplish high affinity binding to the receptor. Covalent conjugation of the bulky carbohydrate cluster to oligonucleotides has been achieved by solid-phase synthesis using low-loaded macroporous resins and optimized synthesis protocols.
Assessment of nootropic and amnestic activity of centrally acting agents (1997)

Cognitive deficits have long been recognized as severe and consistent neurological disorders associated with numerous psychiatric and neurodegenerative states such as Alzheimer's disease. Many experimental models are currently available for the evaluation of agents that affect learning and memory processes. Mazes are the traditional tool in assessing cognitive performance in animals. Apart from passive-avoidance task for short-term memory and Morris water maze task for spatial learning, other paradigms such as radial arm maze and Y-maze consistently measure the working/reference memory and agents that affect these processes. The transfer latency on elevated plus-maze is another simple paradigm to reveal the nootropic and amnestic activity of centrally acting agents. The complex-mazes such as Stone T-maze are built by combining several simple maze segments to assess mixed spatial, working/reference and taxon learning skills in animals. The active-avoidance behaviour induced by a sequence of conditioned and unconditional stimuli is a classic model for the assessment of cognitive performance after brain lesions or pharmacological disruption of cognition. Drug-induced acquisition/re-tention deficits, brain lesion-induced task specific cognitive dysfunction and electroshock-induced general amnesia may provide a consistent battery of screening models for the development of agents that ameliorates the memory deficits in rodents. Several human psychometric and verbal learning skill tests are also available for the clinical assessment and confirmation of nootropic activity. These rapid developments in the field of animal models of learning and memory processes may hopefully lead to an improved understanding of the pathophysiology of cognitive disorders, and finally permit a rational designing of novel therapeutic strategies. for distinct cognitive dysfunctions.
Ectopic Overexpression of Wild-Type and Mutant hipA Genes in Escherichia coli : Effects on Macromolecular Synthesis and Persister Formation (2006)

Persistence is an epigenetic trait that allows a small fraction of bacteria, approximately one in a million, to survive prolonged exposure to antibiotics. In Escherichia coli an increased frequency of persisters, called "high persistence," is conferred by mutations in the hipA gene, which encodes the toxin entity of the toxin-antitoxin module hipBA. The high-persistence allele hipA7 was originally identified because of its ability to confer high persistence, but little is known about the physiological role of the wild-type hipA gene. We report here that the expression of wild-type hipA in excess of hipB inhibits protein, RNA, and DNA synthesis in vivo. However, unlike the RelE and MazF toxins, HipA had no effect on protein synthesis in an in vitro translation system. Moreover, the expression of wild-type hipA conferred a transient dormant state (persistence) to a sizable fraction of cells, whereas the rest of the cells remained in a prolonged dormant state that, under appropriate conditions, could be fully reversed by expression of the cognate antitoxin gene hipB. In contrast, expression of the mutant hipA7 gene in excess of hipB did not markedly inhibit protein synthesis as did wild-type hipA and yet still conferred persistence to ca. 10% of cells. We propose that wild-type HipA, upon release from HipB, is able to inhibit macromolecular synthesis and induces a bacteriostatic state that can be reversed by expression of the hipB gene. However, the ability of the wild-type hipA gene to generate a high frequency of persisters, equal to that conferred by the hipA7 allele, may be distinct from the ability to block macromolecular synthesis.