Miracle-dz/UniFAR-FTUs huggingface dataset:
Evolutionary dynamics of the vapD gene in Helicobacter pylori and its wide distribution among bacterial phyla

The vapD gene is present in microorganisms from different phyla and encodes for the virulence-associated protein D (vapD). In some microorganisms, it has been suggested that vapD participates in either protecting the bacteria from respiratory burst within the macrophage or in facilitating the persistence of the microorganism within the respiratory epithelial cell. The aim of this study was to define the phylogenetic relationship of the Helicobacter pylori vapD gene with other vapD genes of different bacterial species from different phyla and to estimate the genealogy of vapD gene within H. pylori species. Sixteen sequences of Helicobacter pylori vapD gene obtained from Mexican patients and 211 vapD sequences from 72 species of six bacterial phyla were analysed. Our results showed that the vapD region is a hot spot that presents a greater diversity in the Mexican strains of H. pylori to that previously reported. Rearrangements in the vapD region led to the formation of new ORFs in Mexican strains, which were not seen as being fortuitous, suggesting that these chromosomal rearrangements might provide some type of advantage to the bacteria. Phylogenetic analysis, codon usage bias and GC content indicated that vapD was acquired by horizontal gene transfer. Then, in some H. pylori strains it was incorporated and fixed into the bacterial chromosome and maintained in these strains in a similar fashion as an essential gene. Genealogical analysis of the H. pylori vapD gene showed two divisions: one that grouped most of the strains from different parts of the world and the other that grouped only Mexican strains together with the 60190 and 26695 reference strains. Keywords: vapD gene; Helicobacter pylori; Genealogy; Phylogeny; Horizontal Gene Transfer.
A comprehensive review on phytochemistry and pharmacological activities of Vernonia amygdalina

Vernonia amygdalina Delile is a small tree with brittle branches, up to 10 m tall and commonly called as bitter leaf due to its bitter taste. It is native of tropical Africa but widely found on riverside and lakes areas, in woodland and grassland up to 2800 m altitude, in areas where the average rainfall is 750-2000 mm. The plant is considered as a medicinal herb and mostly used in traditional medicine system. The principal phytoconstituents of the plant are oxalate, phytates, tannins, saponins, flavonoids, cyanogenic glycosides, alkaloids, terpenes, anthraquinone, steroid, coumarins, lignans, xanthones, edotides and sesquiterpenes and phenol. The plant attributed with anti-cancer, antidiabetic, anti-malarial, anti-inflammatory, cathartic, hepatoprotective, antimicrobial, antioxidant, chemo protective and cytotoxic, Analgesic, anthelmintic, Anti-pyretic, hypolipidaemic properties and also used as Hemolytic, Antimutagenic, Anti-leishmanial, Spermatogenic, anti-platelet and abortifacient agent. The plant was traditionally used as appetizer and against the problems like constipation and diarrhoea. It is considered as a treatment for alcohol induced hepatotoxicity.
Intake of different chemical species of dietary arsenic by the japanese, and their blood and urinary arsenic levels

We calculated the intake of each chemical species of dietary arsenic by typical Japanese, and determined urinary and blood levels of each chemical species of arsenic. The mean total arsenic intake by 35 volunteers was 195±235 (15.8-1039) μg As day−1, composed of 76% trimethylated arsenic (TMA), 17.3% inorganic arsenic (Asi), 5.8% dimethylated arsenic (DMA), and 0.8% monomethylated arsenic (MA): the intake of TMA was the largest of all the measured species. Intake of Asi characteristically and invariably occurred in each meal. Of the intake of Asi, 45-75% was methylated in vivo to form MA and DMA, and excreted in these forms into urine. The mean measured urinary total arsenic level in 56 healthy volunteers was 129±92.0 μg As dm−3, composed of 64.6% TMA, 26.7% DMA, 6.7% Asi and 2.2% MA. The mean blood total arsenic level in the 56 volunteers was 0.73±0.57 μg dl−1, composed of 73% TMA, 14% DMA and 9.6% Asi. The urinary TMA levels proved to be significantly correlated with the whole-blood TMA levels (r = 0.376; P<0.01).
LONG-TERM AND RESIDUAL EFFECTS OF CATTLE MANURE APPLICATION ON DISTRIBUTION OF P IN SOIL AGGREGATES

Applying excessive amounts of livestock manure to agricultural land may increase the risk of P loading to surface water, particularly through smaller-sized aggregates that are more susceptible to wind and water erosion. The objective of this study was to determine the long-term and residual effects of livestock manure on aggregate size distribution and P content. Soil samples were collected from rain-fed and irrigated blocks of land. Solid cattle feedlot manure had been applied to the rain-fed block at rates of 0 (Treatment M0), 30 (M30), 60 (M60), and 90 (M90) Mg ha−1 yr−1 for 28 years or for 14 years followed by 14 years of no application (R30, R60, and R90) and to the irrigated block at rates of 0 (M0), 60 (M60), 120 (M120), and 180 (M180) Mg ha−1 yr−1 for 28 years or for 14 years followed by 14 years of no application (R60, R120, and R180). Feedlot manure had no significant effect on aggregate size distribution, geometric mean diameter, and wind erodible fraction even after 28 annual applications, but it significantly increased total P (TP), soil test P (STP), and water-soluble P (WP) content in the whole soil and in all aggregate sizes. The TP content increased from <1123 mg kg−1 in M0 to 3278 mg kg−1 for M90 and 4942 mg kg−1 for M180. Similarly, STP content increased from <162 mg kg−1 in M0 to 1178 mg kg−1 for M90 and 1823 mg kg−1 for M180; and WP content increased from <30 mg kg−1 in M0 to 129 mg kg−1 in M90 and 156 mg kg−1 in M180. The increases in TP and STP contents were greater in larger than in smaller (<0.177 mm) aggregates. Irrigation had no significant effect on soil P content, but it did increase the size and reduce the wind erodible fraction of soil aggregate. The effects of manure application on soil P (TP, STP, and WP contents) were long lasting, as indicated by the residual effects still measurable 14 years after manure application was discontinued. When P-enriched soil aggregates are deposited on surface water as a result of erosion, they have an immediate effect through their high WP and STP content and a long lasting effect through the slow release of the remaining TP over time. When using livestock manure on agricultural land, it is necessary to consider application rate, application frequency, residual effects, and farm management practices to protect surface water and to minimize environmental impacts.
Optimization of Nannochloropsis oculata growth using the response surface method

Optimization of Nannochloropsis oculata growth was undertaken using the Response Surface Method. A central composite design was defined to study the effects of temperature, pH, incident light intensity and aeration rate on the maximum growth rate of the microalga. Using statistical analysis, the first model calculated to fit results was twice improved. The final model obtained was used to clarify the effects of each factor and their interactions on the growth of Nannochloropsis oculata. The optimum growth conditions of this microorganism were also estimated as 21°C, 52 µmol photons.m-2.s-1, pH 8.4 and 14.7 VVH of aeration rate. These conditions were tested and validated experimentally since the maximum growth rate achieved with these parameters, 0.0359h-1, is the best reported in this study.
The advertisement calls of Epipedobates anthonyi (Noble, 1921) and Epipedobates tricolor (Boulenger, 1899) (Anura: Dendrobatidae: Colostethinae): intra- and interspecific comparisons

Vocal communication is the main mechanism to exchange information in many groups of animals, and anurans represent an impressive example of complex acoustic communication signals. To date several calls with different and partly multiple meanings have been described for numerous species. Anuran calls were found to be species-specific, providing important taxonomic information, and advertisement calls are frequently used for systematic assignments. The closely related poison dart frogs Epipedobates anthonyi and Epipedobates tricolor inhabit geographically disjunct areas in Ecuador and Peru. Both species are very similar in appearance and have frequently been confused. Consequently, multiple scientific publications on E. tricolor refer to E. anthonyi instead and vice versa. This is also true for the descriptions of the species’ advertisement call. So far, no comparative study on the species’ calls exists. Here we analyze and compare the calls of E. anthonyi and E. tricolor. We found the advertisement calls of both species to be very similar in general but to differ in pulse frequency and interval. Thus, they can be distinguished with certainty. However, a comparison of characteristic call patterns between populations revealed intraspecific variation to be higher than interspecific variation, which questions the usefulness of calls for species delimitation of frogs for the genus Epipedobates.
The reactions of copper and zinc with calcium carbonate surfaces

SUMMARY The reaction of copper and zinc were studied by adding the metal nitrate to a 4g:50ml suspension of calcite and water which had been equilibrated for two days, and then equilibrating for a further three days. Zinc behaved in a similar manner to cadmium in forming a surface-solid solution of ZnχCa1-χCO3 as a result of adsorption, and the pIAP of the equilibrium solutions were close to those expected from the Thorstenson & Plummer equation. However, the continuity from adsorption to precipitation was broken by the formation of Zn5(OH)6(CO3)2 which has a higher stability than ZnCO3. The CaCO3 surface appears to constrain the adsorbed Zn to conform to a carbonate structure despite its lower stability than the hydroxy carbonate. The adsorption data for Cu can also be explained in terms of a surface-solid solution of CuχCa1-XCO3, but CuCO3 is not found naturally because of much greater stability of Cu(OH)2, and so there is no independent value for the solubility of a CuCO3 end-member if a surface-solid solution is formed. Secondary reactions are more likely to occur for Cu, especially close to the adsorption-precipitation boundary. Continuity from adsorption to precipitation again was not found. Theory predicts that Cu is less likely to form a surface-solid solution than Zn. Upper Chalk (calcite with 4% other minerals, mostly quartz) behaved in a similar way but with increased adsorption due to its higher surface area.
Flow Characteristics in an Airlift Membrane Bioreactor

Effect of changing the liquid level in an airlift membrane bioreactor of 0.7 m height, 0.24 m width and 0.18 m depth was studied both experimentally and by simulation. Three-dimensional simulations of the airlift membrane bioreactor were carried out at two different liquid levels above the membrane. The simulations were based on the two-fluid model with the standard k? model for the turbulence. The results showed that by lowering the liquid level, the quality of mixing and uniformity of the velocity distribution of liquid phase in the riser would be improved while the shear stress on the membrane surface would be reduced. Higher shear stress on the membrane surface at high levels of liquid minimizes the extent to which particles settle on the membrane, thus, fouling will be reduced and flux of liquid through membrane will be enhanced. Moreover, it was shown that by lowering the liquid level, the fraction of air in the downcomers becomes lower.
CHARACTERIZATION OF THE INTERACTIONS BETWEEN NATURAL FLAVONOID COMPOUNDS AND BOVINE SERUM ALBUMIN BY CAPILLARY ELECTROPHORESIS AND FLUORESCENCE METHOD

The interactions of three flavonoid compounds isolated from natural products: Puerarin, (−)-Epicatechin, (−)-Epigallocatechin gallate with bovine serum albumin (BSA) are investigated by two methods: affinity capillary electrophoresis (ACE) and fluorescence quenching method. ACE gives binding constants (Kb) and thermodynamic parameters. The thermodynamic parameters indicate that van der Waals interactions and hydrogen bond played important roles. The result also implies that in spite of the relatively small difference in the chemical structures, large differences are observed in their binding capacity. The fluorescence quenching method gains quenching constant Ksv, binding site number n and Kb. The fluorescence results indicate that BSA fluorescence quenching mechanism is mainly a static quenching process. The results of the two methods show the flavonoids had a fairly strong interaction with BSA. The Kb obtained from ACE is similar with that obtained from the fluorescence method. Our work might give an insight on the high throughput screening active components in natural products.
Online Assortment Optimization for Two-sided Matching Platforms

Motivated by online labor markets, we consider the online assortment optimization problem faced by a two-sided matching platform that hosts a set of suppliers waiting to match with a customer. Arriving customers are shown an assortment of suppliers, and may choose to issue a match request to one of them. After spending some time on the platform, each supplier reviews all the match requests he has received and, based on his preferences, he chooses whether to match with a customer or to leave unmatched. We study how platforms should design online assortment algorithms to maximize the expected number of matches in such two-sided settings. We show that, when suppliers do not immediately accept/reject match requests, our problem is fundamentally different from standard (one-sided) assortment problems, where customers choose over a set of products. We establish that a simple greedy algorithm is 1/2-competitive against an optimal clairvoyant algorithm that knows in advance the full sequence of customers' arrivals. However, unlike related online assortment problems, no randomized algorithm can achieve a better competitive ratio, even in asymptotic regimes. To advance beyond this general impossibility, we consider structured settings where suppliers' preferences are described by the Multinomial Logit and Nested Logit choice models. We develop specialized balancing algorithms, which we call preference-aware, that leverage general information about the suppliers' choice models. In certain settings, the resulting competitive ratios are provably larger than the standard "barrier" of 1-1/e in the adversarial arrival model. Our results suggest that the shape and timing of suppliers' choices play critical roles in designing online two-sided assortment algorithms.
Coherent electron quantum transport in In 0.53 Ga 0.47 As/ GaAs Sb 0.49 double barrier resonant tunnelling structures

In this work, we have modelled and computed the transport properties of the double-barrier InGaAs/GaAsSb structure from the resonant tunnelling point of view. Based on the clas-sical Tsu-Esaki formula for the tunnelling current, we have calculated the current density-voltage characteristic of a Al-free type-II In 0.53 Ga 0.47 As/GaAs 0.51 Sb 0.49 structure at different cryogenic and elevated temperatures. The tunnelling coefficient has been calculated in the framework of effective mass approximation with nonparabolicity included, using the transfer matrix approach. A good qualitative agreement of the position of resonant current peaks with the existing experimental data was achieved. Our calculation shows a very high sensitivity of the tunnelling current peak on monolayer-scale layer structure fluctuation which strongly affects peak to valley ratio in the resonant tunnelling structure.
Multi-Modality Imaging in the Assessment of Cardiovascular Toxicity inthe Cancer Patient

Ma Cancer therapy can be associated with both cardiac and vascular toxicity. Advanced multi-modality imaging can be used to stratify patient risk, identify cardiovascular injury during and after therapy, and forecast recovery. Echocardiography continues to be the mainstay in the evaluation of cardiac toxicity. Particularly, echocardiography-based strain imaging is useful for risk stratification of patients at baseline, and detection of subclinical left ventricle (LV) dysfunction during therapy. Cardiac magnetic resonance (CMR) serves a complementary role in the patient with poor echocardiographic or equilibrium radionuclide angiographic image quality or in situations where a more accurate and precise LV ejection fraction measurement is needed to inform decisions regarding discontinuation of chemotherapy. New CMR techniques like T1 and T2 mapping and positron emission tomography (PET) imaging will help us better understand the structural, pathological, and metabolic myocardial changes associated with ventricular dysfunction or release of serum biomarkers. CMR may also be helpful in the evaluation of vascular complications of cancer therapy. Stress echocardiography, stress CMR, computed tomography, and PET are excellent imaging options in the evaluation of ischemia in patients receiving therapies that could potentially cause vasospasm or accelerated atherosclerosis. (J Am Coll Cardiol Img 2018;11:1173–86) © 2018 the American College of Cardiology Foundation. Published by Elsevier. All rights reserved.
Effect of green manuring and fly ash on the growth and grain yield of rice (Oryza sativa L.)

A field experiment was planned and carried out with entitled “Effect of soil moisture and agrochemical A field experiment entitled “Effect of green manuring and fly ash on the growth and grain yield of rice (Oryza sativa L.)” was conducted during kharif 2018 at Research Farm, Guru Kashi University, Talwandi Sabo, Bathinda (Punjab). The experiment was laid out in split plot design comprising two green manuring levels viz., control (0 t/ha), and 25 t/ha incorporation in main plots and three fly ash doses viz., control (0 t/ha), 10 and 20 t/ha in sub plot plots. It is clearly concluded that there is a good scope of increasing crop yields through the use of green manuring and fly ash. It is extremely important for sustaining production and improving the fertility of soils. Green manuring significantly increased the plant growth viz., plant height, dry matter and number of tillers/plant and yield attributing characters viz., number of grains/panicle and test weight and seed cotton yield, straw yield and harvest index in rice. Incorporation of green manuring @ 25 t/ha recorded 8.70% more grain yield than control. Fly ash @ 10 t ha and 20 t ha resulted in the statistically similar plant growth, yield attributes and grain yield in rice. Fly ash @ 10 t ha and 20 t ha recorded 9.40 and 6.75%, respectively higher grain yield than control.
Discharges in air from point electrodes in the presence of dielectric plates-theoretical analysis

The authors investigate the onset of DC corona from a point electrode as influenced by a nearby dielectric plate as well as the charging of the plate by the corona space charge. The electric field in the vicinity of the point is influenced by surface charges building up on the dielectric plate during voltage application. The field is calculated using the charge simulation technique where the electrodes are simulated by discrete charges and the dielectric plate by area charges. The potential and field in the vicinity of the stressed electrodes as well as the maximum surface charge on the dielectric plate are determined by applying suitable boundary conditions during voltage application. The distribution of surface charge on the dielectric plate is measured by means of an electrometer with a specially designed electrostatic probe. The calculated onset voltages and surface charge distributions are compared with those measured experimentally. >
Extremes floods of Venice : characteristics , dynamics , past and 1 future evolution 2 3 4

21 Floods in the Venice city centre result from the superposition of several factors: astronomical tides, seiches and 22 atmospherically forced fluctuations, which include storm surges, meteotsunamis, and surges caused by planetary waves. 23 All these factors can contribute to positive sea-level anomalies individually and can also result in extreme sea-level events 24 when they act constructively. The largest extreme sea level events have been mostly caused by storm surges produced by 25 the Sirocco winds. This leads to a characteristic seasonal cycle, with the largest and most frequent events occurring from 26 November to March. Storm surges can be produced by cyclones whose centers are located either north or south of the 27 Alps. The most intense historical events have been produced by cyclogenesis in the western Mediterranean, to the west 28 of the main cyclogenetic area of the Mediterranean region in the Gulf of Genoa. Only a small fraction of the interannual 29 variability of extreme sea levels is described by fluctuations in the dominant patterns of atmospheric circulation variability 30 over the Euro-Atlantic sector. Therefore, decadal fluctuations of sea-level extremes remain largely unexplained. In 31 particular, the effect of the 11-year solar cycle appears to be small, non-stationary or masked by other factors. The historic 32 increase in the frequency of extreme sea levels since the mid 19 Century is explained by relative sea level rise, with no 33 long term trend in the intensity of the atmospheric forcing. Analogously, future regional relative mean sea level rise will 34 be the most important driver of increasing duration and intensity of Venice floods through this century, overwhelming 35 the small decrease in marine storminess projected during the 21 century. Consequently, the future increase of extreme sea 36 levels covers a large range, partly reflecting the highly uncertain mass contributions to future mean sea level rise from 37 the melting of Antarctica and Greenland ice-sheets, especially towards the end of the century. In conclusion, for a high 38 emission scenario the magnitude of 1-in-100 year sea level events at the North Adriatic coast is projected to increase up 39 to 65% and 160% in 2050 and 2100, respectively, with respect to the present value, and subject to continued increase 40 https://doi.org/10.5194/nhess-2020-359 Preprint. Discussion started: 13 November 2020 c © Author(s) 2020. CC BY 4.0 License.
The tonsils of the soft palate do not mediate the 1 response of pigs to oral vaccination with heat 2 inactivated Mycobacterium bovis 3

10 1 SaBio IREC (CSIC-UCLM-JCCM), Ronda de Toledo s/n, 13005 Ciudad Real, Spain. 11 2 Centro de Vigilancia Sanitaria Veterinaria (VISAVET), Universidad Complutense de Madrid, 12 Avenida de Puerta de Hierro s/n, 28040, Madrid, Spain 13 3 Department of Veterinary Pathobiology, Center for Veterinary Health Sciences, Oklahoma 14 State University, Stillwater, OK 74078, USA. 15 4 NEIKER-Tecnalia, Animal Health Department, C/Berreaga 1, E-48160, Derio, Bizkaia, Spain. 16 5 Hospital General Universitario Gregorio Marañón, C/Doctor Esquerdo 46, 28007, Madrid, 17 Spain 18 6 Chembio Diagnostic Systems Inc., Medford, New York, 11763, United States of America 19 20 21 22 23 *Corresponding author at: SaBio IREC (CSIC-UCLM-JCCM), Ronda de Toledo s/n, 13005 Ciudad 24 Real, Spain. Email address: Christian.Gortazar@uclm.es (Christian Gortázar) 25 26
Interpretation of “Neural Network as the World”

Recently a controversial series of paper ends up proposing the possibility that the universe be a neural network by observing that with an irreversible thermodynamics model of the learning process of the neural network, it might appear possible to model quantum and quantum physics as well as observe emergence of a General Relativity space time and gravity, and the plausibility to construct a generalized holographic principle beyond the AdS/CFT correspondence conjecture. The approach has been received with some skepticism. In this paper, we present our suggestions to interpret the results including how NN models could relate to the Wigner wonder at why mathematics describe the Physical world.