gebhart/patrepeval huggingface dataset:
Functional Characterization of a Mucus-Specific LPXTG Surface Adhesin from Probiotic Lactobacillus rhamnosus GG (2011)

In spite of the wealth of clinical evidence supporting the health benefits of Lactobacillus rhamnosus GG in humans, there is still a lack of understanding of the molecular mechanisms behind its probiosis. Current knowledge suggests that the health-promoting effects of this probiotic strain might be partly dependent on its persistence in the intestine and adhesion to mucosal surfaces. Moreover, L. rhamnosus GG contains mucus-binding pili that might also explain the occupation of its ecological niche as a comparatively less stringent allochthonous intestine-dwelling bacterium. To uncover additional surface proteins involved in mucosal adhesion, we investigated the adherence properties of the only predicted protein (LGG_02337) in L. rhamnosus GG that exhibits homology with a known mucus-binding domain. We cloned a recombinant form of the gene for this putative mucus adhesin and established that the purified protein readily adheres to human intestinal mucus. We also showed that this mucus adhesin is visibly distributed throughout the cell surface and participates in the adhesive interaction between L. rhamnosus GG and mucus, although less prominently than the mucus-binding pili in this strain. Based on primary structural comparisons, we concluded that the current annotation of the LGG_02337 protein likely does not accurately reflect its predicted properties, and we propose that this mucus-specific adhesin be called the mucus-binding factor (MBF). Finally, we interpret our results to mean that L. rhamnosus GG MBF, as an active mucus-specific surface adhesin with a presumed ancillary involvement in pilus-mediated mucosal adhesion, plays a part in the adherent mechanisms during intestinal colonization by this probiotic.
Generating Permissive Site-Specific Unnatural Aminoacyl-tRNA Synthetases (2010)

Genetically incorporated unnatural amino acid (UAA) technologies are powerful tools that are greatly enhancing our ability to study and engineer biological systems. Using these techniques, researchers can precisely control the position and number of novel chemical moieties in a protein, via introducing the novel R group of UAAs, that are genetically encoded in the protein's primary structure. The substrate recognition properties of a natural aminoacyl-tRNA synthetase (aaRS) must be modified in order to incorporate UAAs into proteins. Protocols to do so are technically simple but require time and optimization, which has significantly limited the accessibility of this important technology. At present, engineered unnatural aminoacyl-tRNA synthetases (UaaRS) are evaluated on their translational efficiency (the extent to which they allow for incorporation of UAAs into protein) and fidelity (the extent to which they prevent incorporation of natural amino acids). We propose that a third parameter of substrate recognition, permissivity, is equally important. Permissive UaaRSs, whose relaxed substrate recognition properties allow them to incorporate multiple unnatural amino acids (but not natural amino acids), would eliminate the need to generate new UaaRSs for many new UAAs. Here, we outline methods for quickly and easily assessing the permissivity of existing UaaRSs and for generating permissive UaaRSs. In proof of principle experiments, we determined the degree of permissivity of two UaaRSs for a family of structurally related fluorinated UAAs ((19)F-UAAs). We then increased the permissivity of the initial UaaRSs to allow for incorporation of the family of (19)F-UAAs. Finally, we validated the utility of these new (19)F-UAAs as probes for fluorine NMR studies of protein structure and dynamics. We expect that results of this work will increase the accessibility of UAA technology and the use of new UAAs in proteins.
Anomalous hairpin formation in an oligodeoxyribonucleotide (1985)

An accurate method for deriving molar absorptivity-temperature profiles applied to a set of single-stranded oligodeoxyribonucleotides shows that the undecamer CGAGTTTGACGp exists in a hairpin conformation involving Watson-Crick base pairing between the two terminal CG dinucleotides. The hairpin, which has a transition midpoint of 40 degrees C in 0.115 M Na+, is unusually stable in comparison with previously reported hairpins. A non-linear least squares analysis of the undecamer's profile in terms of a two-state equilibrium model indicates that the hairpin-to-coil transition occurs with an enthalpy change about twice that expected if only combinations of Watson-Crick base-paired stacking interactions are considered. The analogous hairpin structure (containing an identical CG/CG stem) assignable to the complementary strand CGTCAAACTCGp does not form above 0 degrees C. Measurements on the two undecamers indicate that variation in non Watson-Crick interactions within the loops of two similar hairpins can produce a difference in stability of at least 2.2 kcal/mol (25 degrees C, 0.115 M Na+), roughly equal to the amount contributed to a double helix by a 5'-CG-3'/5'-CG-3' base-paired stacking interaction.
Impact of Economic Condition on Obesity (2016)

Prevalence of obesity has increased with alarming rate in the last two or three decades worldwide. The prevalence statistics shows that obesity pandemic is all-pervading even in the developing nations like India. In the present study an attempt has been made to report the prevalence of obesity on the basis of body mass index among school girls of Punjab, total 6000 students were selected with stratified random sampling technique, ranging in age from 10-17 years. The data was obtained from various government and private schools of Punjab based on economic status (1009 from high economic status, 2228 from middle economic status & 2763 from low economic status group). Height of each individual is measured with anthropometric rode and the body mass index (BMI) was calculated by the bio electrical impedance machine with scale HBF-361. Further analysis of variance (Anova) and Scheffe’s post hoc test was employed for testing the hypothesis; the level of significance was set at 0.05 levels. The results show that overweight & obesity was more prevalent among those girls who are associated from high economic status families & vice versa.
Ein erwartungsgesteuerter Koordinator zur partiellen Textanalyse (1993)

In dieser Papier wird die koordinierende Komponente eines Systems zur erwartungsgesteuerten Textanalyse auf der eingeschränkten Domäne deutscher Geschäftsbriefdokumente vorgestellt: Dazu wurden wesentliche Konzepte und Datenstrukturen zur Modellierung der Domäne, das Nachrichtenmodell, entwickelt (siehe [Gores & Bleisinger 92]). Mit diesem Nachrichtenmodell steuert die Komponente die Textextraktion der Informationen eines vorliegenden Briefdokumentes. Sie wird in ihrer Arbeit von Spezialisten, sogenannten Substantiierern, unterstützt, die auf dem Text arbeiten. Dazu muß intensiver Nutzen von den Informationen eines Lexikons gemacht werden. Die Repräsentation des Ergebnisses erfolgt in einer Form, die eine weitere Verarbeitung, wie die semantische Interpretation und eine darauf aufbauende Generierung neuer Aktionen begünstigt.
The LIM-Homeobox Gene<i>Islet-1</i>Is Required for the Development of Restricted Forebrain Cholinergic Neurons (2008)

Forebrain cholinergic neurons modulate complex mammalian behaviors such as reward-related learning and cognitive functions. Although their dysfunction is implicated in various psychiatric and neurodegenerative diseases, the factors governing cholinergic neuron differentiation and diversity are mostly unknown. We tested the role of the LIM-homeobox gene Isl1 in the development of forebrain cholinergic neurons by conditionally deleting Isl1 using a Six3-cre transgene. A depletion of cholinergic interneurons in the dorsal and ventral striatum, and cholinergic projection neurons in the nucleus basalis is observed and is ascribed to an early and persistent defect in cholinergic neuron differentiation. Notably, cholinergic innervation to the neocortex is abolished, whereas that to the hippocampus is unaltered. The unique pattern of cholinergic hypoinnervation encountered is supported by the presence of cholinergic projection neurons in the medial septum, the magnocellular preoptic area, and the substantia innominata. Together, these results demonstrate the requirement for Isl1 in the development of restricted telencephalic cholinergic neurons and link the development of cholinergic neurons in anatomically disparate sites to Isl1 function.
Responses of Japanese Eels to Oral Challenge with<i>Edwardsiella tarda</i>after Vaccination with Formalin-Killed Cells or Lipopolysaccharide of the Bacterium (1994)

Vaccination with formalin-killed cells (FKC) or the lipopolysaccharide (LPS) of Edwardsiella tarda was evaluated for its effectiveness against edwardsiellosis in orally challenged Japanese eels Anguilla japonica. The vaccination procedure was an intramuscular injection of 10 mg FKCs/ 100 g body weight or 1 mg LPS/ 100 g body weight, and a booster of the same type and dose 7 d later. The oral challenge with viable E. tarda was performed with 105-106 colony-forming units per fish 21 d after vaccination. At this time, agglutination titers of serum antibody ranged from 1:1,280 to 1:2,560 in the FKC-vaccinated fish and from 1:3,840 to l:5,120 in the LPS-vaccinated fish. In the FKC experiment, mortality of vaccinated fish ranged from 60 to 87.5%, whereas the unvaccinated control group had 80–100% mortality; these results indicated slight efficacy of the vaccine. The FKC-vaccinated fish showed bacterial phagocytosis by macrophages, a process that contributes to a slight decrease in mortality. In the LPS experiment, mortality of vaccinated fish ranged from 40 to 57%, whereas 80–90% mortality occurred in the controls. The LPS-vaccinated fish displayed demarcation by inflammatory cells against E. tarda in the intestine where E. tarda penetrated, as well as marked bacterial phagocytosis by macrophages, which contributed to a slight increase in survival.
IN VITRO INHIBITORY EFFECTS OF CHEUBULINIC ACID ON THE CONTRACTILE RESPONSES OF CARDIOVASCULAR MUSCLES (1996)

1. The effects of chebulinic acid, which has been shown to elicit blood pressure lowering effect in rats, on aortic vascular contraction as well as cardiac contraction were studied in rats. 2. Chebulinic acid had no effect on KCl-induced aortic contraction, but irreversibly inhibited the contractile responses to phenylephrine in an apparently non-competitive manner. Chebulinic acid also inhibited contractile responses of rat aorta to 5-hydroxytryptamine and angiotensin II. 3. Chebulinic acid inhibited the binding of [3H]-prazosin to dog aortic microsomal membranes in a concentration-dependent manner with an IC50 value of 0.34 mmol/L. Results of saturation binding experiments suggest a mixed mode of inhibition by chebulinic acid (i.e. a decrease in both the maximal number of binding sites and the affinity for prazosin). 4. Chebulinic acid concentration-dependently and reversibly inhibited the maximal left ventricular pressure of rat heart in a Langendorff preparation with 50% inhibition occurring at a concentration of 0.3 nmol/L. 5. We conclude that chebulinic acid exerts non-specific inhibitory actions in vascular preparations. Its inhibitory effect on cardiac contraction was reversible and three orders of magnitude more potent than that on vascular contraction. We suggest that the hypotensive effect of chebulinic acid is probably mediated via the decrease in cardiac output resulting from reduced left ventricular contraction.
Anomaly-Based Intrusion Detection Systems Utilizing System Call Data (2012)

Abstract : This research aims at the enhancement of computer defenses by making them invulnerable to new, mutating and obfuscated malware. It offers a semantic approach to system behavior analysis, centered on the concept of functionality. Functionality is the highest level of the behavior semantics, it is defined by the specific goal of computer operations, not by its software realization. This allows for identifying some classes of malware achieving the same specific malicious operations. Colored Petri nets are proposed as a basis for behavioral signatures representing particular functionalities, both legitimate and malicious. Special techniques are proposed to address three interrelated aspects: signature expressiveness, behavioral obfuscation and run-time signature matching efficiency. A signature based approach for detecting malicious functionalities in the system call domain is developed. It has been implemented in a prototype software and tested. It is superior to existing behavior based techniques in addressing behavioral obfuscations and multiple functionality realizations. The experiments results indicate low rate of false positives and negatives, and low execution overhead. Such results suggest that detecting malicious functionality presents a sufficiently dependable and efficient method for distinguishing malware from benign software.
Homologous expression and characterization of Cel61A (EG IV) of <i>Trichoderma reesei</i> (2001)

There are currently four proteins in family 61 of the glycoside hydrolases, from Trichoderma reesei , Agaricus bisporus , Cryptococcus neoformans and Neurospora crassa . The enzymatic activity of these proteins has not been studied thoroughly. We report here the homologous expression and purification of T. reesei Cel61A [previously named endoglucanase (EG) IV]. The enzyme was expressed in high amounts with a histidine tag on the C‐terminus and purified by metal affinity chromatography. This is the first time that a histidine tag has been used as a purification aid in the T. reesei expression system. The enzyme activity was studied on a series of carbohydrate polymers. The only activity exhibited by Cel61A was an endoglucanase activity observed on substrates containing β‐1,4 glycosidic bonds, e.g. carboxymethylcellulose (CMC), hydroxyethylcellulose (HEC) and β‐glucan. The endoglucanase activity on CMC and β‐glucan was determined by viscosity analysis, by measuring the production of reducing ends and by following the degradation of the polymer on a size exclusion chromatography system. The formation of soluble sugars by Cel61A from microcrystalline cellulose (Avicel; Merck), phosphoric acid swollen cellulose (PASC), and CMC were analysed on a HPLC system. Cel61A produced small amounts of oligosaccharides from these substrates. Furthermore, Cel61A showed activity against cellotetraose and cellopentaose. The activity of Cel61A was several orders of magnitude lower compared to Cel7B (previously EG I) of T. reesei on all substrates. One significant difference between Cel61A and Cel7B was that cellotriose was a poor substrate for Cel61A but was readily hydrolysed by Cel7B. The enzyme activity for Cel61A was further studied on a large number of carbohydrate substrates but the enzyme showed no activity towards any of these substrates.
Identification of a gene on chromosome 12q22 uniquely overexpressed in chronic lymphocytic leukemia (2005)

The pathogenesis of chronic lymphocytic leukemia (CLL) is unknown but may involve aberrant activation of signaling pathways. Somatic hypermutations in rearranged immunoglobulin heavy-chain (IgVH) genes allow a division of CLL patients into 2 categories: mutated IgVH genes are associated with an indolent disease, whereas unmutated IgVH genes define an aggressive form. Using differential display to compare gene expression in CLL cells with and without IgVH hypermutations, we identified a novel gene, CLL up-regulated gene 1 (CLLU1), that was highly up-regulated in CLL cells without IgVH hypermutations. CLLU1 mapped to chromosome 12q22, within a cluster of genes that are active in germinal center B cells. However, appreciable levels of CLLU1 were detectable only in CLL cells and not in a panel of normal tissue extracts or in any other tested hematologic malignancy. High expression of CLLU1 in CLL samples occurred irrespective of trisomy 12 or large chromosomal rearrangements. CLLU1 encodes 6 mRNAs with no sequence homology to any known gene, and most transcripts appear to be noncoding. Two transcripts, however, potentially encode a peptide with remarkable structural similarity to human interleukin 4. These data, in particular the unique and restricted expression pattern, suggest that CLLU1 is the first disease-specific gene identified in CLL.
3D-Printable Bioactivated Nanocellulose–Alginate Hydrogels (2017)

We describe herein a nanocellulose-alginate hydrogel suitable for 3D printing. The composition of the hydrogel was optimized based on material characterization methods and 3D printing experiments, and its behavior during the printing process was studied using computational fluid dynamics simulations. The hydrogel was biofunctionalized by the covalent coupling of an enhanced avidin protein to the cellulose nanofibrils. Ionic cross-linking of the hydrogel using calcium ions improved the performance of the material. The resulting hydrogel is suitable for 3D printing, its mechanical properties indicate good tissue compatibility, and the hydrogel absorbs water in moist conditions, suggesting potential in applications such as wound dressings. The biofunctionalization potential was shown by attaching a biotinylated fluorescent protein and a biotinylated fluorescent small molecule via avidin and monitoring the material using confocal microscopy. The 3D-printable bioactivated nanocellulose-alginate hydrogel offers a platform for the development of biomedical devices, wearable sensors, and drug-releasing materials.
Novel Mechanism of N‐Solanesyl‐N,N′‐bis(3,4‐dimethoxybenzyl)ethylenediamine in Potentiation of Antitumor Drug Action on Multidrug‐resistant and Sensitive Chinese Hamster Cells (1991)

The mechanism of the synthetic isoprenoid N-solanesyl-N,N'-bis(3,4-dimethoxybenzyl)ethylenediamine (SDB-ethylenediamine) in potentiating antitumor drug action against multidrug-resistant cells was comparatively studied with other potentiators such as verapamil and cepharanthine. SDB-ethylenediamine increased the accumulation of [3H]daunorubicin (DNR) in Chinese hamster V79 (V79/S) and its multidrug-resistant mutant (V79/ADM) cells. Even after SDB-ethylenediamine was removed from the medium, its effect continued. But when verapamil was removed from the medium, its effect disappeared immediately. Unlike verapamil and cepharanthine, SDB-ethylenediamine did not greatly inhibit the efflux of [3H]DNR from V79/ADM, the binding of [3H]vinblastine to membrane vesicles of V79/ADM, or the binding of [3H]azidopine to P-glycoprotein in the cytoplasmic membrane of V79/ADM. It did stimulate the influx of [3H]DNR into the ATP-depleted cells of V79/S and V79/ADM. Thus, SDB-ethylenediamine uniquely potentiates antitumor drugs. The increased intracellular accumulation of antitumor drugs in the presence of SDB-ethylenediamine is due not only to the inhibition of active efflux but also to the stimulation of the influx of antitumor drugs.
Extended-Phase-Shift Control of Isolated Bidirectional DC–DC Converter for Power Distribution in Microgrid (2011)

This paper points out a phenomenon of power backflow in traditional phase-shift (TPS) control of isolated bidirectional full-bridge DC–DC converter (IBDC), and analyzes the effects which backflow power act on power circulating flow and current stress. On this basis, the paper proposes a novel extended-phase-shift (EPS) control of IBDC for power distribution in microgrid. Compared with TPS control, EPS control not only expands regulating range of transmission power and enhances regulating flexibility, but also reduces current stress and improves the system efficiency. The operation principle of EPS control and the operation modes of IBDC are analyzed in the paper. By establishing mathematical models of transmission power, backflow power, and current stress, the paper comparatively analyzes control performances of TPS and EPS control. At last, experimental results verify the excellent performance of EPS control and correctness of the theoretical analysis.
Synthesis of New 4‐Heteroaryl‐2‐Phenylquinolines and Their Pharmacological Activity as NK‐2/NK‐3 Receptor Ligands (2007)

Substituted 4-heteroaryl-2-phenylquinolines were synthesized and tested on NK-2 and NK-3 receptors in order to get a better insight in the structure-activity relationship. On the whole, these molecules, which can be regarded as bioisosters of the NK-3 antagonist SB 218795, displayed a lower activity than the template. Ring electronic distribution and H-bond donor and acceptor positions played some role in selectivity, 2-imidazolyl substituted 2a showing affinity mainly towards NK-3 while 3-pyrazolyl substituted 4 displayed a preferential interaction with NK-2 receptor. Structural characterization of the synthesized compounds was achieved by NMR and mass techniques. Bidimensional 1H-NOESY experiments were a helpful tool for the assignment of the isomeric structures of compounds 9 and llb-c.
Process Yield and Reliability of 0.65 mm Pitch Technology in Surface Mounting (1994)

This paper describes the influence of soldering parameters on solder joint quality and reliability of 0.65 mm pitch QFP technology. Soldering process parameters such as soldering temperature, conveyor speed and board size have systematically been varied using factorial experimental analysis. Solder joint quality has been characterised in terms of solder ball formation, open joints and porosity behaviour. Equipment used includes microfocus X‐ray non‐destructive testing apparatus, optical and scanning electron microscope. The reliability of solder joints has been investigated by temperature cycling from −55 to + 125°C for 1000 cycles. The time per cycle was approximately 1 hour. The results from the present work show that pad layout on the printed circuit board (PCB) and the quality of pretinning during PCB production have a considerable influence on the solder joint yield. No failures have been observed during temperature cycling. This indicates that 0.65 mm (25 mil) pitch QFP components have very high reliability in respect of temperature cycling and are extremely compliant for absorbing the thermal stress developed during temperature cycling.
Mobile terminal antennnas implemented by using direct coupling (2006)

The current trend in mobile terminals is an increasing number of systems. The volume occupied by the antennas of the radio systems is becoming more and more problematic and new low-volume antenna solutions are needed. Since the EMC shielding and the ground plane operate as the main radiating structure especially below 1 GHz, a very small antenna structure can be achieved by using a direct feed, i.e. galvanically inducing currents on the surface of the chassis. The feed can be placed over an impedance discontinuity, e.g. formed by a slot. Using this approach, an antenna structure for a small handheld digital television (DVB-H) receiver is presented. The antenna gain exceeds the specification by a 4-dB margin. The introduced antenna structure can also be used for multi-system terminals.