jimnoneill/paper-to-field-training huggingface dataset:
Structural Insights of WBmDapE and Deciphering of Potent Anti-filarial Inhibitors: A State-of-Art Computational Approach

Field: Pharmacology, Toxicology and Pharmaceutics (Life Sciences)

Lymphatic filariasis (LF) stands as a debilitating tropical ailment, impacting a considerable global populace. Existing drug therapies for LF exhibit limited effectiveness across all parasite stages, thereby accentuating the imperative for novel anti-filarial medications characterized by enhanced prognostic attributes and minimized adverse reactions. A promising avenue involves targeting the microbial enzyme WBmDapE, pivotal in worm survival and intricately linked to the lysine biosynthetic pathway and peptidoglycan cell wall construction. This investigation employs in silico methodologies encompassing molecular docking, Molecular Dynamics Simulation (MDS), conformational analysis, Shape-Based Virtual Screening (SBVS), ADMETox, MMGBSA, and Density Functional Theory (DFT) calculations to discern potential inhibitors of WBmDapE. Through discerning the conformational shifts of the WBmDapE-bound substrate and product, key amino acids implicated in substrate binding (Arg182 and Asp248) are unveiled. While the apo and substrate-bound structures exhibit an open conformation, the product-bound structure displays marked conformational alterations, including shifts within the catalytic domain and the cofactor in the dimerization domain, suggestive of an active and closed conformation. From the prism of shape-based virtual screening, two preeminent compounds (ZINC42784280 and ZINC84308049) have surfaced as potential hits. These compounds evince heightened binding affinity, optimal binding free energy, pivotal hydrogen bond interactions, and akin attributes to the product-bound complex. Subsequently, these compounds emerge as prospective candidates for filariasis treatment. In summation, our study furnishes invaluable insights into the fabrication of innovative WBmDapE inhibitors, potentially serving as anti-filarial agents. Rigorous experimental substantiation and fine-tuning of these compounds are requisite for prospective therapeutic interventions against LF.
Representations of stack triangulations in the plane

Field: Mathematics (Physical Sciences)

Stack triangulations appear as natural objects when defining an increasing family of triangulations by successive additions of vertices. We consider two different probability distributions for such objects. We represent, or "draw" these random stack triangulations in the plane $\R^2$ and study the asymptotic properties of these drawings, viewed as random compact metric spaces. We also look at the occupation measure of the vertices, and show that for these two distributions it converges to some random limit measure.
Effects of age at vaccination on efficacy of Brucella abortus strain RB51 to protect cattle against brucellosis

Field: Veterinary (Health Sciences)

Abstract Objective To establish that female calves vaccinated with Brucella abortus strain RB51 at 3, 5, and 7 months of age are protected against infection and abortion when challenged exposed during their first pregnancy. Animals Polled Hereford heifer calves obtained from a brucellosis-free herd. Procedure Calves were inoculated SC at 3, 5, or 7 months of age with strain RB51 (n = 26), strain 19 (n = 16), or sterile saline solution (n = 15). Calves were bred at 16 to 17 months of age and challenged exposed during the first pregnancy with virulent B abortus strain 2308. Results After vaccination, none of the heifers given strain RB51 developed serum antibodies that reacted in the standard tube agglutination test, but reacted in a dotblot assay, using RB51 antigen. B abortus was cultured from biopsy specimens of superficial cervical lymph nodes in the RB51 and S19 vaccinates at 10 weeks, but not at 12 weeks after vaccination. All 4 heifers that had been vaccinated with RB51 at 3 months of age were protected against infection and abortion when challenged exposed. Vaccination at 5 and 7 months of age gave equivalent protection. Heifers given strain 19 were 95% protected and controls (given saline solution) had a high incidence of infection and abortion. Conclusions Strain RB51 is protective at doses comparable to those of strain 19 in calves 3 to 10 months of age. Clinical Relevance Immunogenicity and failure to induce antibodies that interfere with the serologic diagnosis of field infections of B abortus make strain RB51 an effective vaccine. ( Am J Vet Res 1996;57:1153—1156)
Review Article A Road Map for the Global Elimination of Congenital Syphilis

Field: Medicine (Health Sciences)

Copyright © 2010 Mary L. Kamb et al. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. Congenital syphilis is the oldest recognized congenital infection, and continues to account for extensive global perinatal morbidity and mortality today. Serious adverse pregnancy outcomes caused by maternal syphilis infection are prevented with screening early in pregnancy and prompt treatment of women testing positive. Intramuscular penicillin, an inexpensive antibiotic on the essential medicine list of nations all over the world, effectively cures infection and prevents congenital syphilis. In fact, at a cost of $11–15 per disability adjusted life year (DALY) averted, maternal syphilis screening and treatment is among the most cost-effective public health interventions in existence. Yet implementation of this basic public health intervention is sporadic in countries with highest congenital syphilis burden. We discuss the global burden of this devastating disease, current progress and ongoing challenges for its elimination in countries with highest prevalence, and next steps in ensuring a world free of preventable perinatal deaths caused by syphilis. 1.
Molecular Characterization of Klebsiella Pneumonia in Clinical Isolates with High Resistance toward Carbapenemases

Field: Immunology and Microbiology (Life Sciences)

Carbapenem-resistant Enterobacteriaceae (CRE) is spreading in worldwide and has become endemic in several countries, including Italy . In this report we present the phenotypic and molecular characterizations of KPC-producing carbapenem-resistant K. pneumoniae clinical isolates in an Italian hospital.
Theory of engineering flat bands in graphene using doubly-periodic electrostatic gating

Field: Materials Science (Physical Sciences)

We explore the use of applied electrical potentials to induce band flattening in graphene for bands near zero energy. We consider various families of doubly periodic potentials and simulate their effect on the electronic band structure using a tight-binding and a continuum approach. From these families, we find that an applied potential with symmetries of wallpaper group 17, in particular a Kagome potential, works best for inducing a high degree of band flattening for a range of realistic potential amplitudes and periods. Our work indicates that it should be possible to engineer the band structure of graphene using electrostatic gating, thus enabling a new approach to the development of graphene-based metamaterials.
Concrete TLP's in Water Depths Beyond 3,000 ft

Field: Engineering (Physical Sciences)

Abstract Concrete hull TLP's are established as a viable concept for field development in water depths up to 3,000 ft. The first platform is now under construction for the norwegian Heidrun field. However, as the water depth increases, the platform natural periods tend to increase, which also will increase the tether fatigue. Is there a limit for the concrete hull? This paper describes a large size platform for Gulf of Mexico conditions at different water depths. A comparison is made with a steel hull alternative, under identical functional requirements. In particular, the tether extreme and fatigue responses are analyzed. The results demonstrate that concrete hull platforms are competitive also beyond 3,000 ft. High natural periods can be acceptable for the tether system provided that the platform geometry gives low excitation at roll/pitch resonance as well as low responses at higher periods. Introduction In the last few years, concrete has been introduced as a construction material also for floating production platforms. The concrete hull TLP has been found feasible and economically attractive in water depths up to 3,000 ft, as demonstrated by Wilson /1/ and Lokken /2/. The tether system, that moors the platform, is typically designed for extreme storm condition, which also provides adequate fatigue life (assuming appropriate component design). As the water depth increases, the fatigue life becomes more critical, as the tether stiffness decreases and the natural periods increase. In order to reduce the response at resonance, the natural periods can be reduced by increasing the tether stiffness. This means that the tether system is no longer designed for stress, but for stiffness (steel cross sectional area) " For Gulf of Mexico conditions, a practice is about to emerge, which claims that the natural periods in heave, roll and pitch should not exceed four (4) seconds. This paper sets about to investigate the relevance of such a limit, which may be questioned on the basis that the tether responses are a function of the platform geometry. For comparison, a concrete and a steel hull are analyzed with identical tether system. Design Basis The environmental conditions for this study are based on published information, the extreme conditions presented in Table 1 are taken from Brewer /3/, while the fatigue conditions, the wave scatter diagram, is taken from Kinra and Marshall /4/. Three waterdepths are considered; 3,000 ft, 4,500 ft and 6,000 ft. The platform requirements represent a large size Gulf of Mexico field. The topside mass, including payload and deck structure, is 30,000 tons (27,216 metric tonnes). This carrying capacity is defined for 3,000 ft (914 m), as the hull geometry is kept identical for larger water depths, the deck weight has to be reduced to allow for the increased tether weight. The total riser tension is 14,000 kips (62.3 MN). The riser tension is taken as independent of water depth (assumes that buoyancy is attached in very deep waters).
Additional file 1 of Integrated metabolomic and transcriptomic analyses of the synergistic effect of polymyxin–rifampicin combination against Pseudomonas aeruginosa

Field: Pharmacology, Toxicology and Pharmaceutics (Life Sciences)

Additional file 1: Table S1. Significantly changed metabolites at 15 min. Table S2. Significantly changed metabolites at 1 h. Table S3. Significantly changed metabolites at 4 h. Table S4. Significantly changed metabolites at 24 h. Table S5. DEGs induced by polymyxin B at 1 h. Table S6. DEGs induced by rifampicin B at 1 h. Table S7. DEGs induced by the combination of polymyxin B and rifampicin at 1 h. Table S8. DEGs induced by polymyxin B at 24 h. Table S9. DEGs induced by rifampicin at 24 h. Table S10. DEGs induced by the combination of polymyxin B and rifampicin at 24 h.
BIOCHEMISTRY OF THE LENS

Field: Biochemistry, Genetics and Molecular Biology (Life Sciences)

The possible functions of glutathione in the lens as well as in the rest of the body have been a matter of discussion since the discovery of this substance by Hopkins. 1 Although much experimental work has been done on the glutathione in the lens, its actual isolation from this organ was only recently accomplished by two of us. 2 That glutathione has an important function in the metabolism of the lens appears likely from the work of Adams, 3 who showed that the oxygen uptake of a lens extract became nil when glutathione was dialyzed out ; readdition of glutathione to the extract caused a resumption of its oxygen uptake. It was indicated that this substance is a constituent of an auto-oxidation system in which the sulfhydryl can act as a hydrogen donor, being oxidized to the disulfide form, which in turn can accept hydrogen from a thermostable residue. It
Adsorption of Polymer and Surfactant from Their Binary Mixtures on Alumina

Field: Chemistry (Physical Sciences)

The adsorption of water-soluble polymers and surfactants on positively charged alumina has been investigated. In the case of same charged adsorbates, such as sodium poly (styrenesulfonate) (PSS) and sodium dodecyl sulfate (SDS), the competitive adsorption between PSS and SDS on alumina occurs, where the adsorption strength of SDS is much greater than that of PSS. The adsorption from opposite charged adsorbates of PSS and hexadecyltrimethylammonium chloride (HTAC) shows enhancement of HTAC adsorption by PSS due to a formation of their complexes on alumina surface, which provides a lower micropolarity compared with those of respective adsorbates. In the case of neutral polymer and anionic surfactants, such as poly(vinylpyrrolidone) (PVP) and lithium dodecyl sulfate (LiDS), lithium perfluorooctanesulfonate (LiFOS), and sodium bis (2-ethylhexyl)sulfosuccinate(AOT), the adsorption of anionic surfactants enhances remarkably the adsorption of PVP at low surfactant concentrations due to a formation of PVP-surfactant complexes. However, at high surfactant concentrations, the adsorption of
<title>Purification of organic contaminants in seepage water of a landfill by UV/ozone technique</title>

Field: Environmental Science (Physical Sciences)

Seepage water of landfills, where toxic waste is deposited, has high concentrations of chlorinated phenols (CP), polychlorinated biphenyls (PCB), and polycyclic aromatic hydrocarbons (PAH). The concentrations of polychlorinated dibenzo-p-dioxins (PCDD) and dibenzofurans (PCDF) are usually found at ppq-level. Typical purification methods based on physical techniques produce highly contaminated residues, which have to be removed by combustion or deposition in a landfill. An alternative way is to destruct these contaminants by biological and chemical treatment. The behavior of the trace contaminants during UV/ozone treatment is described. Results show no significant effect for PCB and PCDD/PCDF. The CP and PAH were mostly reduced by UV/ozone treatment to a degradation ratio greater than 90%. An influence of the pH value on the UV/ozone treatment of seepage water could not be detected. A further experiment showed the degradability of PCDD/PCDF in pure water solution. To reach better results for the degradation of organic trace contaminants the seepage water first can be treated with biological methods. Thus the high TOC-concentration of 3 g/l is reduced to 50 - 70%. A combination of biological and oxidative techniques diminishes the treatment costs and better exploitation of the oxidants is reached. Because of high light absorbance of the seepage water between 200 nm and 300 nm we developed a falling-film- photo-reactor to ensure, that every volume of the solution is exposed to UV-radiation.
Machine Learning Prediction of H Adsorption Energies on Ag Alloys

Field: Computer Science (Physical Sciences)

Adsorption energies on surfaces are excellent descriptors of their chemical properties, including their catalytic performance. High-throughput adsorption energy predictions can therefore help accelerate first-principles catalyst design. To this end, we present over 5000 DFT calculations of H adsorption energies on dilute Ag alloys and describe a general machine learning approach to rapidly predict H adsorption energies for new Ag alloy structures. We find that random forests provide accurate predictions and that the best features are combinations of traditional chemical and structural descriptors. Further analysis of our model errors and the underlying forest kernel reveals unexpected finite-size electronic structure effects: embedded dopant atoms can display counterintuitive behavior such as nonmonotonic trends as a function of composition and high sensitivity to dopants far from the adsorbing H atom. We explain these behaviors with simple tight-binding Hamiltonians and d-orbital densities of states. We also use variations among forest leaves to predict the uncertainty of predictions, which allows us to mitigate the effects of larger errors.
Histological and Immunohistochemical Study on Human Placental Tissue in Normal Pregnancy and Preeclampsia

Field: Medicine (Health Sciences)

Background: Preeclampsia is a serious disorder affecting the mother. It may be responsible for more than 50,000 maternal deaths worldwide each year. It is a major killer of both mother and fetus. Aim: To demonstrate the morphological changes of human placental tissue in pre-eclamptic pregnancies compared with the normal by using histological and immunohistochemical techniques. Materials & Methods: Twenty pregnant women were included in this study. 10 of them were diagnosed as having moderate pre-eclampsia and considered as the pre-eclamptic (PE) group, while 10 women were clinically normal and considered as the control group. Placental specimens were obtained after either vaginal delivery or caesarian section and processed for H&E and Masson's trichrome stains, as well as for immunohistochemical stains for eNOS and HIF-1α. Morphometric measurement of number of syncytial knots, area % of collagen fibers, eNOS and HIF-1α.were done followed by statistical analysis. Results: PE group revealed thickened wall of fetal blood capillaries, crowded degenerating villi with decreased intervillous spaces, intravillous and perivillous fibrinoid deposition. Numerous syncytial knots and exfoliated trophoblast cells were also observed. There was thickened layer of subchorionic fibrinoid. Increased area% of collagen fibers, HIF-1α. immunoreactivity and decreased area% of eNOS immunoexpression were found. Conclusions: As evidenced by the previous results, this study concluded various placental changes detected by histological and histochemical techniques. The findings have clarified a significant correlation between eNOS and HIF-1α immunoexpression and pre-eclampsia. Whether this relation is causal or effect relationship, this may need further investigations for better management and avoidance of consequences of pre-eclampsia.
Temperature Modeling Study for High Precision Gyroscope Based on Neural Network

Field: Computer Science (Physical Sciences)

In the study, neural network theory was used to build a nonlinear model for high precision gyroscope reflecting the relationship between temperature and drift.The result shows that types of neural network and input sample have great influence on model precision. High precision gyroscope is sensitive to temperature. The input sample must take account of the continuous temperature and mean temperature value in a period of time can not be used for model. The model of multi-input and single-output is better than the model of single-input and single-output in the same neural network. Genetic algorithm(GA) can optimizes Back-Propagation(BP) neural network. GA-BP and BP neural network can't achieve the precision request. Radial basis function(RBF) neural network has good precision whose relative error is about 10-6. RBF neural network can achieve model request.
Streptococcal nucleases. V. Specificities of deoxyribonuclease action of the A, B, C, and D enzymes

Field: Biochemistry, Genetics and Molecular Biology (Life Sciences)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTStreptococcal nucleases. V. Specificities of deoxyribonuclease action of the A, B, C, and D enzymesWalid G. Yasmineh and Ernest David. GrayCite this: Biochemistry 1968, 7, 1, 105–113Publication Date (Print):January 1, 1968Publication History Published online1 May 2002Published inissue 1 January 1968https://pubs.acs.org/doi/10.1021/bi00841a014https://doi.org/10.1021/bi00841a014research-articleACS PublicationsRequest reuse permissionsArticle Views16Altmetric-Citations2LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-Alertsclose Get e-Alerts
The experiment of male China oak silkworm liquid's obviating function on alcoholic fatty liver in rats

Field: Pharmacology, Toxicology and Pharmaceutics (Life Sciences)

Objective It is to observe the China oak silkworm liquid's function of obviating alcoholic fatty degeneration.Methods 40 Kunming rats were divided into 4 groups randomly.The China oak male silkworm liquid of high and low dosage was given to the rats in the treatment groups everyday(the dilution was 1∶2 and 1∶4).20 days later,all the rats were put to death 12 hour after fasting diet to get their vein blood and liver tissue.The tissue under microscope was observed and scored.TG,TC,ALT,AST in blood serum were determined,and the content of MDA,activity of SOD in mitochondria of liver cells were determined by TBA method.Results In model group,the fatty degeneration of liver tissue was obvious,and the levels of ALT,AST,MDA were obviously higher and the activity of SOD was lower than that in normal group(P0.05).Compared win model group,fatty degeneration in China oak silkworm liquid group was obviously improved(P0.05),especially in the low dosage group(P0.01).The level of MDA lowed down and the activity of SOD rose up(P0.05).Compared with model group,the contents of ALT and AST decreased in low dose group(P0.05),but in high dose group there was no significant difference(P0.05).Conclusion The male China oak silkworm liquid can improve lipid peroxidation of mitochondria in liver cells,and has a certain extent protecting function on fatty degeneration induced by alcohol.
Phylogenetic reconstructions of Micromonas commoda RCC299 light stress response proteins from the manuscript "Phosphate limitation responses in marine green algae are linked to reprogramming of the tRNA epitranscriptome and codon usage bias"

Field: Agricultural and Biological Sciences (Life Sciences)

Phylogenetic reconstructions of Micromonas commoda RCC299 light stress response proteins in nexus (*.tre) and pdf format (*.pdf), corresponding to Fig. 4, Fig. S5 and Dataset S3 in the manuscript "Phosphate limitation responses in marine green algae are linked to reprogramming of the tRNA epitranscriptome and codon usage bias". Trees were inferred using IQ-TREE, using the best LG model identified for each alignment separately, node support was calculated using 1000 ultrafast bootstrap replicates. Filenames for phylogenies contain, in that order, the Micromonas commoda RCC299 protein ID(s), the name of the gene(s) as described in the manuscript and the model used for tree reconstruction.