gebhart/patrepeval huggingface dataset:
Defining Amino Acid Residues Involved in DNA−Protein Interactions and Revelation of 3‘-Exonuclease Activity in Endonuclease V (2005)

Endonuclease V is an enzyme that initiates a conserved DNA repair pathway by making an endonucleolytic incision at the 3' side one nucleotide from a deaminated base lesion. Site-directed mutagenesis analysis was conducted at seven conserved motifs of the thermostable Thermotoga maritima endonuclease V to probe for residues that affect DNA-protein interactions. Y80, G83, and L85 in motif III, H116 and G121 in motif IV, A138 in motif V, and S182 in motif VI affect binding of both the double-stranded inosine-containing DNA substrate and the nicked double-stranded inosine-containing DNA product, resulting in multiple enzymatic turnovers. The substantially reduced DNA cleavage activity observed in G113 in motif IV and G136 in motif V can be partly attributed to their defect in metal cofactor coordination. Alanine substitution at amino acid 118 primarily reduces the level of binding to the nicked product, suggesting that R118 plays a significant role in postcleavage DNA-protein interaction. Binding and cleavage analyses of multiple mutants at positions Y80 and H116 underscore the role these residues play in protein-DNA interaction and implicate their potential involvement as a hydrogen bond donor in recognition of deaminated DNA bases. DNA cleavage analysis using mutants defective in DNA binding reveals a novel 3'-exonuclease activity in endonuclease V. An alternative model is proposed that entails lesion specific cleavage and endonuclease to 3'-exonuclease mode switch by endonuclease V for removal of deaminated base lesions during endonuclease V-mediated repair.
A placebo controlled trial of bismuth salicylate in Helicobacter pylori associated gastritis. (1990)

In a placebo controlled prospective clinical trial of bismuth salicylate in helicobacter pylori associated gastritis, 52 adult patients were randomly allocated to treatment with bismuth salicylate or placebo. Helicobacter pylori were totally cleared in 77% patients in bismuth group but none in placebo group (P less than 0.001). Resolution of gastritis (P less than 0.001) and improvement of symptoms (P less than 0.01) were significantly better in patients where H. pylori infection cleared as compared to patients where the infection persisted.
Functional magnetic resonance imaging evidence of augmented pain processing in fibromyalgia (2002)

The fact that comparable subjectively painful conditions resulted in activation patterns that were similar in patients and controls, whereas similar pressures resulted in no common regions of activation and greater effects in patients, supports the hypothesis that FM is characterized by cortical or subcortical augmentation of pain processing.
IL-6 and sIL-6R concentration in the cerebrospinal fluid and serum of MS patients. (2002)

IL-6 and its soluble receptors are involved in a complex immunological reaction that is characteristic for MS. However, the significant differences in the results obtained here from those reported in other studies make it rather unlikely that IL-6 and its receptors could be used as surrogate markers of MS activity.
System-Level Performance and Characterization of Counter-Phase Optical Interference Cancellation (2010)

In this paper, we report on the performance of the second implementation of the optical counter-phase RF interference cancellation technique. Referred to as the opto-cancellation system, it has demonstrated narrowband-signal cancellation exceeding 80 dB. Also, broadband signals of 80-MHz bandwidth, whose center frequencies ranged from 1 GHz-20 GHz, were cancelled down to the system noise floor; where that cancellation was approximately uniform over the full bandwidth of each signal. It is not known that other interference cancellation systems can achieve such low cancellation depths, over such a wide frequency bandwidth, at the time of this writing. In addition to describing the system's performance in terms of experimental results, we also characterize the system's performance analytically. Although the sensitivity, gain, linearity, and noise figure of the current system implementation are known, the analysis presented here will be useful for future implementations of the optical counter-phase RF interference cancellation technique. The analysis will also aid in understanding the trade-offs and limitations of the current system implementation, as well as future implementations.
Prehospital hemostatic resuscitation to achieve zero preventable deaths after traumatic injury (2017)

Prehospital hemostatic resuscitation has the potential to significantly reduce preventable death from hemorrhage.
An Evidence-Based Systematic Review of Stevia by the Natural Standard Research Collaboration (2010)

The objective of this study was to evaluate the scientific evidence on stevia, including expert opinion, folkloric precedent, history, pharmacology, kinetics/dynamics, interactions, adverse effects, toxicology, and dosing. This review serves as a clinical support tool. Electronic searches were conducted in 10 databases, 20 additional journals (not indexed in common databases), and bibliographies from 50 selected secondary references. No restrictions were placed on the language or quality of the publications. All literature collected pertained to efficacy in humans, dosing, precautions, adverse effects, use in pregnancy and lactation, interactions, alteration of laboratory assays, and mechanisms of action. Standardized inclusion and exclusion criteria were used for selection. Grades were assigned using an evidence-based grading rationale. Based on the availability of scientific data, two indications are discussed in this review: hypertension and hyperglycemia. Evaluation of two long-term studies (1 and 2 years in length, respectively) indicates that stevia may be effective in lowering blood pressure in hypertensive patients, although data from shorter studies (1-3 months) did not support these findings. A pair of small studies also report positive results with respect to glucose tolerance and response, although the relatively low methodological rigor of these experiments limits the strength of these findings. Further investigation is warranted in both indications.
The Structure of a 19-Residue Fragment from the C-loop of the Fourth Epidermal Growth Factor-like Domain of Thrombomodulin (1995)

The solution structure has been determined for a 19-residue peptide that is fully folded at room temperature. The sequence of this peptide is based on the C-loop, residues 371-389, of the fourth epidermal growth factor-like domain of thrombomodulin, a protein that acts as a cofactor for the thrombin activation of protein C. Despite its small size, the peptide forms a compact structure with almost no repeating secondary structure. The results indicate the structure is held together by hydrophobic interactions, which in turn stabilize the two beta-turns in the structure. The first beta-turn in the C-loop represents a conserved motif that is found in the published structures of five other epidermal growth factor-like proteins. The critical role of Phe376 in the stabilization of the first beta-turn is consistent with mutagenesis data with soluble thrombomodulin. The results also show that a small subdomain of a larger protein can fold independently, and therefore it could act as an initiation site for further folding.
INTERACTIONS BETWEEN CANNABINOID AND OPIOID RECEPTOR SYSTEMS IN THE MEDIATION OF ETHANOL EFFECTS (2004)

Over the past few years, advances in the investigation of the neurochemical circuits involved in the development and treatment of alcohol dependence have identified peptides and receptors as potential key targets in the treatment of problems related to alcohol consumption. The endogenous opioid system is modified by alcohol intake in areas of the brain related to reward systems, and differential basal levels of opioid gene expression are found in rodents with a high preference for ethanol. This suggests a greater vulnerability to alcohol consumption in relation to differences in genetic background. Further evidence of the involvement of opioid peptides in alcohol dependence is the ability of the opioid antagonist naltrexone to reduce alcohol intake in animal models of dependence and in alcohol-dependent patients. Abundant evidence indicates that the activation of cannabinoid receptors stimulates the release of opioid peptides, therefore the cannabinoid receptor antagonists may presumably alter opioid peptide release, thus facilitating the reduction of ethanol consumption. However, little is known about the effects of ethanol on the endogenous cannabinoid system, the vulnerability of cannabinoid receptors to alcohol intake or their neurochemical implications in reducing consumption of alcohol. In this paper, we review the role of opioid and cannabinoid receptor systems, their vulnerability to alcohol intake and the development of dependence, and the targeting of these systems in the treatment of alcoholism.
Stability Indicating RP-HPLC Method for the Determination of Dronedarone Hydrochloride and Its Potential Process-Related Impurities in Bulk Drug and Pharmaceutical Dosage Form (2013)

Simple, sensitive and accurate stability indicating analytical method for dronedarone has been developed and validated using RP-HPLC technique. Developed method is used to evaluate the assay and related substances of dronedarone drug substance and tablets (Multaq?). The drug substance was subjected to the stress conditions such as hydrolysis (acid and base), oxidation, photolysis and thermal degradation as per International Conference on Harmonization (ICH) pre- scribed stress conditions to show the stability-indicating the nature of the method. Significant degradation was observed during acid and base hydrolysis, and peroxide degradation. The major degredants were identified by LC-MS, FTIR and 1H NMR spectral analysis. The chromatographic conditions were optimized using an impurity-spiked solution and the samples generated from forced degradation studies. In the developed HPLC method, the resolution between dronedar- one, process-related impurities, (namely Imp-1, Imp-2, Imp-3, Imp-4, Imp-5, Imp-6, Imp-7, Imp-8, Imp-9, Imp-10 and Imp-11) and degradation products were found to be greater than 1.5. The eleven potential process related impurities were separated on an Ascentis? Express C18 column (4.6 × 10 cm i.d., particle size 2.7 μm) at a flow rate of 1.2 mL.min-1. The LC method employed a linear gradient elution and the detection wavelength at 220 nm. The chroma- tographic behavior of all the impurities was examined under variable compositions of different solvents, temperatures and pH values.
Shifts in the concentrations of magnesium and calcium in early porcine and rat wound fluids activate the cell migratory response. (1995)

Accruing evidence indicates that the levels of extracellular Mg2+ and Ca2+ can have a distinct impact on the adhesive and migratory activities of many cell types. The physiological relevance of these observations, however, has remained largely unexplored. In the present study, wound fluids collected throughout the early stages of cutaneous wound repair were examined for possible Mg2+ and Ca2+ fluctuations. Early in the process, when cell migration into the wound site is initiated, Mg2+ is elevated and Ca2+ is reduced (Mg2+:Ca2+ = 1). As wound healing progresses, wound fluid concentrations of Mg2+ and Ca2+ begin to return to normal plasma levels (Mg2+:Ca2+ = 0.4). When macrophages, keratinocytes, fibroblasts, and endothelial cells were exposed to dialyzed wound fluid, the migration stimulated by undialyzed wound fluid was lost. Addition back to dialyzed wound fluid of 24 h, postinjury concentrations of Mg2+ and Ca2+ restored all migratory stimulus. This observed migration is approximately twofold greater than when normal plasma Mg2+ and Ca2+ concentrations are present. Changes in the levels of Mg2+ and Ca2+ in wound fluid occur during the same period that inflammatory cells, keratinocytes, fibroblasts, and neovasculature have been shown to migrate during wound healing in vivo. Together, these data suggest that the impact of these changes on integrins and E-cadherin may play a direct role in the activation and maintenance of the migratory phenotypes of the cells involved in the wound healing process.
Multiplexed phase-encoded lenses written on spatial light modulators (1989)

We report the writing of Fresnel phase-encoded lenses onto programmable spatial light modulators (SLM's). When the product of the phase-encoded lens and the two-dimensional Fourier transform of a desired output spatial pattern is written onto the SLM, the desired spatial pattern is focused at programmable distances from the SLM. More importantly the inverted version of the desired pattern normally produced is encoded onto a diverging beam and is not imaged. Theoretical analysis and experimental results using the magneto-optic SLM are presented.
In vitro Anti‐tumor Activity of Anti‐c‐erbB‐2 × Anti‐CD3ɛ Bifunctional Monoclonal Antibody (1992)

With the aim of developing an effective cancer immunotherapy for common epithelial cancer, a new class of bifunctional antibody (BFA) was developed; one arm of this BFA recognized c-erbB-2 gene product, and the other arm recognized CD3 epsilon, a T-cell specific surface antigen. Application of this BFA with human peripheral blood lymphocytes exhibited specific anti-tumor activity in vitro on a breast tumor cell line, ZR-75-1, which expressed abundant c-erbB-2 gene product on its cell surface. These results indicate that BFA recognizing an oncogene product on cell surface is a potential new agent for cancer immunotherapy.
Inhibitory Effects on Mushroom Tyrosinase by Some Alkylbenzaldehydes (2003)

The inhibition kinetics on the diphenolase activity of mushroom tyrosinase by some alkylbenzaldehydes has been investigated. The results show that the alkylbenzaldehydes assayed can lead to reversible inhibition to the enzyme; o-tolualdehyde and m-tolualdehyde are mixed-type inhibitors and p-alkylbenzaldehydes are uncompetitive inhibitors. For the p-alkylbenzaldehydes, the inhibition potency follows the order: p-tolualdehyde < p-ethylbenzaldehyde < p-propylbenzaldehyde = p-Isopropylbenzaldehyde < p-tert-butylbenzaldehyde = p-butylbenzaldehyde < p-pentylbenzaldehyde < p-hexylbenzaldehyde > p-heptylbenzaldehyde > p-octylbenzaldehyde, indicating the hydrophobic p-alkyl group played an important role in inhibition to the enzyme. The inhibitory effects of alkylbenzaldehydes on the monophenolase activity have also been studied. The results show that o-tolualdehyde and m-tolualdehyde can lengthen the lag time and decrease the steady-state activity of the enzyme, but p-alkylbenzaldehydes only decrease the steady-state activity and do not lengthen the lag time, indicating that their inhibitory mechanisms are different.
New evidence in trauma resuscitation - is 1:1:1 the answer? (2013)

Traumatic injury is a common problem, with over five million worldwide deaths from trauma per year. An estimated 10 to 20% of these deaths are potentially preventable with better control of bleeding. Damage control resuscitation involves early delivery of plasma and platelets as a primary resuscitation approach to minimize trauma-induced coagulopathy. Plasma, red blood cell and platelet ratios of 1:1:1 appear to be the best substitution for fresh whole blood; however, the current literature consists only of survivor bias-prone observational studies.
Production and characterization of poly‐3‐hydroxybutyrate from biodiesel‐glycerol by Burkholderia cepacia ATCC 17759 (2009)

Glycerol, a byproduct of the biodiesel industry, can be used by bacteria as an inexpensive carbon source for the production of value-added biodegradable polyhydroxyalkanoates (PHAs). Burkholderia cepacia ATCC 17759 synthesized poly-3-hydroxybutyrate (PHB) from glycerol concentrations ranging from 3% to 9% (v/v). Increasing the glycerol concentration results in a gradual reduction of biomass, PHA yield, and molecular mass (M(n) and M(w)) of PHB. The molecular mass of PHB produced utilizing xylose as a carbon source is also decreased by the addition of glycerol as a secondary carbon source dependent on the time and concentration of the addition. (1)H-NMR revealed that molecular masses decreased due to the esterification of glycerol with PHB resulting in chain termination (end-capping). However, melting temperature and glass transition temperature of the end-capped polymers showed no significant difference when compared to the xylose-based PHB. The fermentation was successfully scaled up to 200 L for PHB production and the yield of dry biomass and PHB were 23.6 g/L and 7.4 g/L, respectively.
Expression of the hair stem cell-specific keratin 15 in pilar tumors of the skin. (1999)

Keratin 15 (K15) was recently shown to be a specific marker of stem cells of the hair-follicle bulge. We studied the reactivity of an antibody to the CD8 antigen (C8/144B), recognizing K15, on 66 cutaneous tumors with known or alleged pilar differentiation, in order to assess its usefulness in the diagnosis of this group of tumors. 2/2 basal cell nevi, 5/8 trichoepitheliomas and 1/3 trichofolliculomas showed substantial reactivity. Much weaker reactivity was observed in cases of trichilemmal tumors (trichilemmomas and trichilemmal cysts); by contrast, all cases of pilomatricomas, basal cell carcinomas and epidermoid cysts were completely unreactive. These results are in keeping with the admitted differentiation of the tumors studied, and suggest further that basal cell carcinomas do not differentiate towards hair bulge cells. From a practical point of view, immunostaining for K15 seems to be an additional useful adjunct for the differential diagnosis between basal cell carcinoma and trichoepithelioma.
ChemInform Abstract: THE P‐NITROPHENYLETHYL (NPE) GROUP. A VERSATILE NEW BLOCKING GROUP FOR PHOSPHATE AND AGLYCONE PROTECTION IN NUCLEOSIDES AND NUCLEOTIDES (1984)

Abstract Die Synthese von neuen Monomer‐Bausteinen, die die Titelgruppe sowohl für den Phosphat‐ wie für den AgIykon‐Schutz enthalten, für die OligonucIeotid‐Synthese nach dem Phosphotriester‐Verfahren wird beschrieben.
Gut microbiota in autism and mood disorders (2015)

The hypothesis of an important role of gut microbiota in the maintenance of physiological state into the gastrointestinal (GI) system is supported by several studies that have shown a qualitative and quantitative alteration of the intestinal flora in a number of gastrointestinal and extra-gastrointestinal diseases. In the last few years, the importance of gut microbiota impairment in the etiopathogenesis of pathology such as autism, dementia and mood disorder, has been raised. The evidence of the inflammatory state alteration, highlighted in disorders such as schizophrenia, major depressive disorder and bipolar disorder, strongly recalls the microbiota alteration, highly suggesting an important role of the alteration of GI system also in neuropsychiatric disorders. Up to now, available evidences display that the impairment of gut microbiota plays a key role in the development of autism and mood disorders. The application of therapeutic modulators of gut microbiota to autism and mood disorders has been experienced only in experimental settings to date, with few but promising results. A deeper assessment of the role of gut microbiota in the development of autism spectrum disorder (ASD), as well as the advancement of the therapeutic armamentarium for the modulation of gut microbiota is warranted for a better management of ASD and mood disorders.
Spectroscopic Diagnosis of Arsenic Contamination in Agricultural Soils (2017)

This study investigated the abilities of pre-processing, feature selection and machine-learning methods for the spectroscopic diagnosis of soil arsenic contamination. The spectral data were pre-processed by using Savitzky-Golay smoothing, first and second derivatives, multiplicative scatter correction, standard normal variate, and mean centering. Principle component analysis (PCA) and the RELIEF algorithm were used to extract spectral features. Machine-learning methods, including random forests (RF), artificial neural network (ANN), radial basis function- and linear function- based support vector machine (RBF- and LF-SVM) were employed for establishing diagnosis models. The model accuracies were evaluated and compared by using overall accuracies (OAs). The statistical significance of the difference between models was evaluated by using McNemar's test (<i>Z</i> value). The results showed that the OAs varied with the different combinations of pre-processing, feature selection, and classification methods. Feature selection methods could improve the modeling efficiencies and diagnosis accuracies, and RELIEF often outperformed PCA. The optimal models established by RF (OA = 86%), ANN (OA = 89%), RBF- (OA = 89%) and LF-SVM (OA = 87%) had no statistical difference in diagnosis accuracies (<i>Z</i> < 1.96, <i>p</i> < 0.05). These results indicated that it was feasible to diagnose soil arsenic contamination using reflectance spectroscopy. The appropriate combination of multivariate methods was important to improve diagnosis accuracies.
Pharmacologically active sulfoximides: 5-hexyl-7-(S-methylsulfonimidoyl)xanthone-2-carboxylic acid, a potent antiallergic agent (1979)

The antiallergic activity of some xanthone derivatives containing a sulfoximide substitutent has been investigated. While 2-(S-methylsulfonimidoyl)xanthone itself was found to be inactive, a series of 7-(S-methylsulfonimidoly)-xanthone-2-carboxylic acids showed good levels of activity in the passive cutaneous anaphylaxis screen. N-Substituted sulfoximide derivatives were, without exception, less active than the corresponding unsubstituted compounds. The activity of the 7-(S-methylsulfonimidoyl)xanthone-2-carboxylic acids could be enhanced by the introduction of an alkyl or alkoxy substituent at C-5. As a result of these studies, 5-hexyl-7(S-methylsulfonimidoyl)xanthone-2-carboxylic acid has been selected for further investigation as an antipasthmatic agent.
Why B-pictures work: a theory of multi-hypothesis motion-compensated prediction (2002)

This paper presents a theoretical analysis of multi-hypothesis motion-compensated prediction for hybrid video coders. The power spectrum of the prediction error is related to the displacement error PDFs of an arbitrary number of hypotheses in a closed form expression. It is shown that, if the residual noise level is low, doubling the number of (equally good) hypotheses can yield a gain of up to 0.5 bits/sample and that doubling the accuracy of motion compensation (such as going from integer-pel to 1/2-pel accuracy) can additionally reduce the bit-rate by up to 0.5 bits/sample independent of N. With realistic residual noise levels, the introduction of B-frames or overlapped block motion compensation typically provides larger gains than doubling the motion compensation accuracy.