gebhart/patrepeval huggingface dataset:
Structure−Activity Relationship of 4(5)-Aryl-2-amino-1H-imidazoles, N1-Substituted 2-Aminoimidazoles and Imidazo[1,2-a]pyrimidinium Salts as Inhibitors of Biofilm Formation by Salmonella Typhimurium and Pseudomonas aeruginosa (2010)

A library of 112 4(5)-aryl-2-amino-1H-imidazoles, 4,5-diphenyl-2-amino-1H-imidazoles, and N1-substituted 4(5)-phenyl-2-aminoimidazoles was synthesized and tested for the antagonistic effect against biofilm formation by Salmonella Typhimurium and Pseudomonas aeruginosa. The substitution pattern of the 4(5)-phenyl group and the nature of the N1-substituent were found to have a major effect on the biofilm inhibitory activity. The most active compounds of this series were shown to inhibit the biofilm formation at low micromolar concentrations. Furthermore, the influence of 6 imidazo[1,2-a]pyrimidines and 18 imidazo[1,2-a]pyrimidinium salts on the biofilm formation was tested. These compounds are the chemical precursors of the 2-aminoimidazoles in our synthesis pathway. A good correlation was found between the activity of the imidazo[1,2-a]pyrimidinium salts and their corresponding 2-aminoimidazoles, supporting the hypothesis that the imidazo[1,2-a]pyrimidinium salts are possibly cleaved by cellular nucleophiles to form the active 2-aminoimidazoles. However, the imidazo[1,2-a]pyrimidines did not show any biofilm inhibitory activity, indicating that these molecules are not susceptible to in situ degradation to 2-aminoimidazoles. Finally, we demonstrated the lack of biofilm inhibitory activity of an array of 37 2N-substituted 2-aminopyrimidines, which are the chemical precursors of the imidazo[1,2-a]pyrimidinium salts in our synthesis pathway.
Protease II from Escherichia coli: Sequencing and Expression of the Enzyme Gene and Characterization of the Expressed Enzyme1 (1991)

Protease II gene of Escherichia coli HB101 was cloned and expressed in E. coli JM83. The transformant harboring a hybrid plasmid, pPROII-12, with a 2.4 kbp fragment showed 90-fold higher enzyme activity than the host. The whole nucleotide sequence of the inserted fragment of plasmid pPROII-12 was clarified by the dideoxy chain-terminating method. The sequence that encoded the mature enzyme protein was found to start at an ATG codon, as judged by comparison with amino terminal protein sequencing. The molecular weight of the enzyme was estimated to be 81,858 from the nucleotide sequence. The reactive serine residue of protease II was identified as Ser-532 with tritium DFP. The sequence around the serine residue is coincident with the common sequence of Gly-X-Ser-X-Gly, which has been found in the active site of serine proteases. Except for this region, protease II showed no significant sequence homology with E. coli serine proteases, protease IV and protease La (lon gene), or other known families of serine proteases. However, 25.3% homology was observed between protease II and prolyl endopeptidase from porcine brain. Although the substrate specificities of these two enzymes are quite different, it seems possible to classify protease II as a member of the prolyl endopeptidase family from the structural point of view.
Performance anomaly detection in microservice architectures under continuous change (2017)

The idea of DevOps and agile approaches like Continuous Integration (CI) and microservice architectures are bocoming more and more popular as the demand for flexible and scalable solutions is increasing. By raising the degree of automation and distribution new challenges in terms of application performance monitoring arise because microservices are possibly short-lived and may be replaced within seconds. The fact that microservices are added and removed on a regular basis brings new requirements in the way anomaly detection is conducted as these changes could also be the cause for anomalies. This work proposes to take information about such events into account to improve the anomaly detection quality. Additionally, a meta model for microservice environments and supplemental tooling was developed that can be used to generate actual microservice environments from an instance of such a meta model. The generation tool also comprises the means to instrument the generated microservices with Kieker to collect monitoring data and generate supplemental files to be able to create Docker images and Kubernetes configuration files which allow to run the microservices on a Kubernetes cluster. In the evaluation such a generated microservice environment is run in a lab experiment with delay injections. The obtained data were then used to evaluate a customized version of the RanCorr approach which was modified to fit in the microservice context and a newly developed basic approach named Event-aware Anomaly Revisor (EAR) that takes event information into account when conducting anomaly detection. The evaluation results showed, that the customized RanCorr approach could not satisfy the expectations in terms of improvement of the anomaly detection results while the EAR approach could slightly improve the anomaly detection quality.
A GLYCOPROTEIN NONCOVALENTLY ASSOCIATED WITH CELL‐WALL POLYSACCHARIDE OF THE RED MICROALGAPORPHYRIDIUMSP. (RHODOPHYTA)1 (2004)

The cells of the red microalga Porphyridium sp. (UTEX 637) are encapsulated in a cell wall of a negatively charged mucilaginous polysaccharide complex composed of 10 different sugars, sulfate, and proteins. In this work, we studied the proteins associated with the cell‐wall polysaccharide. A number of noncovalently associated proteins were resolved by SDS‐PAGE, but no covalently bound proteins were detected. The most prominent protein detected was a 66‐kDa glycoprotein consisting of a polypeptide of approximately 58 kDa and a glycan moiety of approximately 8 kDa containing N‐ linked terminal mannose. In size‐exclusion chromatography, the 66‐kDa protein was coeluted with the polysaccharide and could be separated from the polysaccharide only after denaturation of the protein, indicating that the 66‐kDa protein was tightly bound to the polysaccharide. Western blot analysis revealed that the 66‐kDa protein was specific to Porphyridium sp. and P. cruentum , because it was not detected in the other species of red microalgae examined. Indirect immunofluorescence assay confirmed the location of the protein in the algal cell wall. The sequence of cDNA clone encoding the 66‐kDa glycoprotein, detected in our in‐house expressed sequence tag database of Porphyridium sp., revealed that this is a novel protein with no similarity to any protein in the public domain databases and our in‐house expressed sequence tag database of the red microalga Rhodella reticulata . The 66‐kDa protein bound polysaccharides from red algae but not from those of other origins tested. Possible roles of the 66‐kDa protein in the biosynthesis of the polysaccharide are discussed.
Recent advancements in surface-enhanced laser desorption/ionization-time of flight-mass spectrometry (2000)

The overall history and recent advances in surface enhanced laser desorption/ionization-time of flight-mass spectrometry (SELDI-TOF-MS) technology is reviewed herein. Fundamentals of SELDI-TOF analysis are presented while drawing comparisons with other laser-based mass spectrometry techniques. The application of SELDI-TOF-MS to functional genomics and biomarker discovery is discussed and exemplified by elucidating a biomarker candidate for prostatic carcinoma. Finally, a short discussion regarding future SELDI requirements and developments is supplied.
Malaria Pathogenesis (1994)

Malaria is a disease caused by repeated cycles of growth of the parasite Plasmodium in the erythrocyte. Various cellular and molecular strategies allow the parasite to evade the human immune response for many cycles of parasite multiplication. Under certain circumstances Plasmodium infection causes severe anemia or cerebral malaria; the expression of disease is influenced by both parasite and host factors, as exemplified by the exacerbation of disease during pregnancy. This article provides an overview of malaria pathogenesis, synthesizing the recent field, laboratory, and epidemiological data that will lead to the development of strategies to reduce mortality and morbidity.
NITRIC OXIDE INHIBITS TYROSINE PHOSPHORYLATION OF THE IGF-I RECEPTOR (2000)

Gmonomethyl-L-arginine (L-NMA) was used to inhibit NO synthesis by iNOS. NO production was estimated by measuring nitrite in conditioned media using a spectrophotometric assay based on the Griess reaction. Proteoglycan synthesis was measured as the incorporation of 35 SO4 2into macromolecular material [8 hr pulse labeling with 35 SO4 -2 from 24 to 32 hr after stimulation with IGF-I as previously described (4)]. Western analysis of IGF-I receptor phosphorylation was done using published procedures (5) using antibody to
Integer Ambiguity Resolution on Undifferenced GPS Phase Measurements and its Application to PPP (2007)

Integer ambiguity resolution has been traditionally applied on double differenced phase measurements to achieve precise positioning of receivers antennas. This methodology is interesting because it removes most of the common errors between the different signal paths. It also minimizes the size of the problem to be solved by removing directly the clock contributions. However, double differencing creates a large number of short passes where there are only a few undifferenced passes. If common errors are known, it becomes attractive to solve directly integer ambiguities on the undifferenced measurements. In this case, the unambiguous phase measurement becomes a code-like measurement with a noise level lower than 1 cm. In this paper we present a new method for solving dual frequency GPS ambiguities on undifferenced measurements on a local or global network. Applications on precise point positioning (PPP) of a user receiver are also detailed. The problem is solved in two independent steps. -First, to eliminate unknown ionospheric propagation delays, undifferenced wide-lanes are estimated by a new approach. Validation using the differences with the obtained solutions is presented on various baselines, including space borne receivers, like the two formation-flying Grace satellites. -Second, we show how to estimate undifferenced ambiguities on L1 on a network of ground stations, once wide-lane ambiguities are known. The important point is to have a good initial modeling of the geometry in order to identify the integer ambiguities with a good confidence level. This initial modeling is given by a floating solution of the problem, in particular to obtain correct estimates of tropospheric delays. This complete process directly estimates around 90% of L1 elementary ambiguities on the entire network. Single or double differenced residuals show that the overall solution is correct. Finally, we show how to use the preceding results for an integer Precise Point Positioning of a moving ground receiver, relative to the reference network. The achieved performance is at the centimeter level. All the results presented in this paper are obtained through real data processing.
Low-operation voltage of InGaN-GaN light-emitting diodes with Si-doped In/sub 0.3/Ga/sub 0.7/N/GaN short-period superlattice tunneling contact layer (2001)

InGaN/GaN multiple-quantum-well light-emitting diode (LED) structures including a Si-doped In/sub 0.23/Ga/sub 0.77/N/GaN short-period superlattice (SPS) tunneling contact were grown by metalorganic vapor phase epitaxy. In/sub 0.23/Ga/sub 0.77/N/GaN(n/sup +/)-GaN(p) tunneling junction, the low-resistivity n/sup +/-In/sub 0.3/Ga/sub 0.77/N/GaN SPS instead of high-resistivity p-type GaN as a top contact layer, allows the reverse-biased tunnel junction to form an "ohmic" contact. In this structure, the sheet electron concentration of Si-doped In/sub 0.23/Ga/sub 0.77/N/GaN SPS is around 1/spl times/10/sup 14//cm/sup 2/, leading to an averaged electron concentration of around 1/spl times/10/sup 20//cm/sup 3/. This high-conductivity SPS would lead to a low-resistivity ohmic contact (Au/Ni/SPS) of LED. Experimental results indicate that the LEDs can achieve a lower operation voltage of around 2.95 V, i.e., smaller than conventional devices which have an operation voltage of about 3.8 V.
Ventricular asystole during vagus nerve stimulation for epilepsy in humans (1999)

Electrical stimulation of the vagus nerve, a recently available option for patients with refractory epilepsy, has demonstrated safety and efficacy. We report four patients with refractory epilepsy who experienced ventricular asystole intraoperatively during initial testing for implantation of the vagus nerve stimulator. Acute intraoperative vagus nerve stimulation may create ventricular asystole in humans. Extracorporeal cervical vagus nerve stimulation testing with continuous EKG monitoring intraoperatively before generator implantation is warranted.
Gut dysfunction in Parkinson's disease (2016)

Early involvement of gut is observed in Parkinson's disease (PD) and symptoms such as constipation may precede motor symptoms. α-Synuclein pathology is extensively evident in the gut and appears to follow a rostrocaudal gradient. The gut may act as the starting point of PD pathology with spread toward the central nervous system. This spread of the synuclein pathology raises the possibility of prion-like propagation in PD pathogenesis. Recently, the role of gut microbiota in PD pathogenesis has received attention and some phenotypic correlation has also been shown. The extensive involvement of the gut in PD even in its early stages has led to the evaluation of enteric α-synuclein as a possible biomarker of early PD. The clinical manifestations of gastrointestinal dysfunction in PD include malnutrition, oral and dental disorders, sialorrhea, dysphagia, gastroparesis, constipation, and defecatory dysfunction. These conditions are quite distressing for the patients and require relevant investigations and adequate management. Treatment usually involves both pharmacological and non-pharmacological measures. One important aspect of gut dysfunction is its contribution to the clinical fluctuations in PD. Dysphagia and gastroparesis lead to inadequate absorption of oral anti-PD medications. These lead to response fluctuations, particularly delayed-on and no-on, and there is significant relationship between levodopa pharmacokinetics and gastric emptying in patients with PD. Therefore, in such cases, alternative routes of administration or drug delivery systems may be required.
Sequence comparisons of complementary DNAs encoding aequorin isotypes (1987)

Aequorin is the Ca2+-activated photoprotein which participates in the bioluminescence from the circumoral ring of the hydromedusa Aequorea victoria. The nucleotide sequences of five aequorin cDNAs have been compared and shown to code for three aequorin isoforms. The cDNA AEQ1 contains the entire protein coding region of 196 amino acids. The other four cDNAs contain only 70-90% of the coding region and apparently code for at least two other isoforms whose amino acid sequences differ significantly from that encoded by AEQ1. The nucleotide sequences coding for the three isotypes differ at a minimum of 54 positions out of a total of 588 nucleotides necessary to code for apoaequorin. Of these nucleotide differences, 24 account for 23 amino acid replacements, substantiating the microheterogeneity observed during sequencing of purified native aequorin [Charbonneau, H., Walsh, K.A., McCann, R.O., Prendergast, F.G., Cormier, M.J., & Vanaman, T.C. (1985) Biochemistry 24, 6762-6771]. Comparison of the deduced cDNA translations with the native protein sequences suggests the loss of seven residues from the amino terminus during purification of aequorin from Aequorea. Aequorin rapidly extracted from the jellyfish using conditions to minimize proteolysis is shown to have a larger molecular weight than that of purified native aequorin. Escherichia coli expressed aequorin encoded by AEQ1 is shown to have the same molecular weight and isoelectric point as those of one of the isotypes rapidly extracted from Aequorea.
The high-quality spectral fingerprint of glucose captured by Raman spectroscopy in non-invasive glucose measurement (2011)

Optical spectroscopy has the inherent advantage of directly measuring glucose levels by means of the unique nature of a spectral fingerprint for the target analyte, glucose, which is determined in the form of a calibration spectrum (a product of multivariate analysis method). The literature is replete with claims of successful in-vivo glucose measurements in terms of Clark error grid analysis. However, all of them fail to demonstrate an in vivo glucose-specific calibration spectrum. In this study we use Raman spectroscopy to capture a high quality spectral fingerprint of the glucose molecule noninvasively and demonstrate calculated correlation coefficients between a pure glucose spectrum and calibration spectra at over 0.8.
Binding of human fibronectin to antigen-antibody complexes. (1986)

We examined the capacity of human fibronectin (FN) to bind to antigen-antibody (IgG) complexes (IC) in the absence of complement components. Binding of FN to IC was not significantly different at 37 degrees C and 4 degrees C and reached equilibrium after 60 minutes of incubation. The binding was markedly enhanced by decreasing the ionic strength and lowering the pH of the incubation media. The effect of ionic strength on binding was caused at least in part by an increase in the percent of the total FN able to bind to IC. Binding of radiolabeled FN to IC was saturable and was inhibited by the addition of an excess of unlabeled FN. In addition, soluble IC prepared in antigen excess but not antigen or antibody alone inhibited the binding of FN to precipitable IC. FN binding to precipitable IC increased with increasing antibody concentrations in the IC. Heparin and gelatin, which bind to specific locations in the FN molecule, did not inhibit the binding of FN to IC. In conclusion, human FN binds to IC in the absence of C1q, and the binding is enhanced under conditions of antibody excess.
Dynamics of the IncW genetic backbone imply general trends in conjugative plasmid evolution (2006)

Plasmids cannot be understood as mere tools for genetic exchange: they are themselves subject to the forces of evolution. Their genomic and phylogenetic features have been less studied in this respect. Focusing on the IncW incompatibility group, which includes the smallest known conjugative plasmids, we attempt to unveil some common trends in plasmid evolution. The functional modules of IncW genetic backbone are described, with emphasis on their architecture and relationships to other plasmid groups. Some plasmid regions exhibit strong phylogenetic mosaicism, in striking contrast to others of unusual synteny conservation. The presence of genes of unknown function that are widely distributed in plasmid genomes is also emphasized, exposing the existence of ill-defined yet conserved plasmid functions. Conjugation is an essential hallmark of IncW plasmid biology and special attention is given to the organization and evolution of its transfer modules. Genetic exchange between plasmids and their hosts is analysed by following the evolution of the type IV secretion system. Adaptation of the trw conjugative machinery to pathogenicity functions in Bartonella is discussed as an example of how plasmids can change their host modus vivendi. Starting from the phage paradigm, our analysis articulates novel concepts that apply to plasmid evolution.
A Receptor-binding Region in Escherichia coli α-Haemolysin (2003)

Escherichia coli alpha-hemolysin (HlyA) is a 107-kDa protein toxin with a wide range of mammalian target cells. Previous work has shown that glycophorin is a specific receptor for HlyA in red blood cells (Cortajarena, A. L., Goñi, F. M., and Ostolaza, H. (2001) J. Biol. Chem. 276, 12513-12519). The present study was aimed at identifying the glycophorin-binding region in the toxin. Data in the literature pointed to a short amino acid sequence near the C terminus as a putative receptor-binding domain. Previous sequence analyses of several homologous toxins that belong, like HlyA, to the so-called RTX toxin family revealed a conserved region that corresponded to residues 914-936 of HlyA. We therefore prepared a deletion mutant lacking these residues (HlyA Delta 914-936) and found that its hemolytic activity was decreased by 10,000-fold with respect to the wild type. This deletion mutant was virtually unable to bind human and horse red blood cells or to bind pure glycophorin in an affinity column. The peptide Trp914-Arg936 had no lytic activity of its own, but it could bind glycophorin reconstituted in lipid vesicles. Moreover, the peptide Trp914-Arg936 protected red blood cells from hemolysis induced by wild type HlyA. It was concluded that amino acid residues 914-936 constitute a major receptor-binding region in alpha-hemolysin.
Synaptic Pathways to Phrenic Motoneurons Are Enhanced by Chronic Intermittent Hypoxia after Cervical Spinal Cord Injury (2003)

Spinal hemisection at C2 reveals caudal synaptic pathways that cross the spinal midline (crossed phrenic pathways) and can restore inspiratory activity in ipsilateral phrenic motoneurons. Intermittent hypoxia induces plasticity in the cervical spinal cord, resulting in enhanced inspiratory phrenic motor output. We hypothesized that chronic intermittent hypoxia (CIH) (alternating 11% O(2) and air; 5 min periods; 12 hr per night; 7 nights) would strengthen crossed phrenic pathways. Experiments were performed on anesthetized, vagotomized, paralyzed, ventilated, and spinally injured (C2 hemisection) rats that were exposed to either normoxia or CIH before acute injury (preconditioning) or after chronic injury (postconditioning). Spontaneous inspiratory bursts or compound action potentials evoked via stimulation of the ventrolateral funiculus (contralateral to injury) were recorded in both phrenic nerves. Spontaneous or evoked activity in crossed phrenic pathways were minimal or absent in all acutely injured rats regardless of preconditioning. In rats postconditioned with normoxia, crossed phrenic inspiratory bursts were observed occasionally during baseline conditions and always during chemoreceptor stimulation (hypoxia and hypercapnia). However, CIH postconditioned rats had substantially larger crossed phrenic inspiratory bursts during baseline, hypoxia, and hypercapnia (all p < 0.05 vs normoxic group). Short-latency (0.7 msec) evoked crossed phrenic potentials were also enhanced by CIH conditioning in chronically injured rats (p < 0.05). We conclude that CIH induced spinal cord plasticity-enhanced phrenic motor output. This plasticity required preconditions established by chronic spinal injury.
Conducting Carbon Wires in Ordered, Nanometer-Sized Channels (1994)

The encapsulation of graphite-type carbon wires in the regular, 3-nanometer-wide hexagonal channels of the mesoporous host MCM-41 is reported. Acrylonitrile monomers are introduced through vapor or solution transfer and polymerized in the channels with external radical initiators. Pyrolysis of the intrachannel polyacrylonitrile results in filaments whose microwave conductivity is about 10 times that of bulk carbonized polyacrylonitrile. The MCM host plays a key role in ordering the carbon structure, most likely through the parallel alignment of the precursor polymer chains in the channels. The fabrication of stable carbon filaments in ordered, nanometer-sized channels represents an important step toward the development of nanometer electronics.
Introduction to Computational Molecular Biology (1997)

Preface 1. Basic Concepts of Molecular Biology 2. Strings, Graphs, and Algorithms 3. Sequence Comparison and Database Search 4. Fragment Assembly of DNA 5. Physical Mapping of DNA 6. Phylogenetic Trees 7. Genome Rearrangements 8. Molecular Structure Prediction 9. Epilogue: Computing with DNA Answers to Selected Exercises / References / Index