For the KdV-Burgers equations on cylindrical and spherical waves the development of a regular profile starting from an equilibrium under a periodic perturbation at the boundary is studied. The equations describe a medium which is both dissipative and dispersive. Symmetries, invariant solutions and conservation laws are investigated. For an appropriate combination of dispersion and dissipation the asymptotic profile looks like a periodical chain of shock fronts with a decreasing amplitude (sawtooth waves). The development of such a profile is preceded by a head shock of a constant height and equal velocity which depends on spatial dimension as well as on integral characteristics of boundary condition; an explicit asymptotic for this head shock and a median of the oscillating part is found.

In this study we investigate the formation of dynamical energy cascades in higher order KdV-type equations. In the beginning we recall what is known about the dynamic cascades for the classical KdV (quadratic) and mKdV (cubic) equations. Then, we investigate further the mKdV case by considering a richer set of initial perturbations in order to check the validity and persistence of various facts previously established for the narrow-banded perturbations. Afterwards we focus on higher order nonlinearities (quartic and quintic) which are found to be quite different in many respects from the mKdV equation. Throughout this study we consider both the direct and double energy cascades. It was found that the dynamic cascade is always formed, but its formation is not necessarily accompanied by the nonlinear stage of the modulational instability. Direct cascade structure remains invariant regardless the size of the spectral domain. In contrast, the double cascade shape can depend on the size of the spectral domain, even if the total number of cascading modes remains invariant. Results obtained in this study can be potentially applied to plasmas, free surface and internal wave hydrodynamics.

In this study, we investigate the formation of dynamical energy cascades in higher-order KdV-type equations. In the beginning, we recall what is known about the dynamic cascades for the classical KdV (quadratic) and mKdV (cubic) equations. Then, we investigate further the mKdV case by considering a richer set of initial perturbations in order to check the validity and persistence of various facts previously established for the narrow-banded perturbations. Afterwards, we focus on higher-order nonlinearities (quartic and quintic) which are found to be quite different in many respects from the mKdV equation. Throughout this study, we consider both the direct and double energy cascades. It was found that the dynamic cascade is always formed, but its formation is not necessarily accompanied by the nonlinear stage of the modulational instability. Direct cascade structure remains invariant regardless of the size of the spectral domain. In contrast, the double cascade shape can depend on the size of the spectral domain, even if the total number of cascading modes remains invariant. Results obtained in this study can be potentially applied to plasmas, free surface and internal wave hydrodynamics.

The space time fractional Korteweg-de Vries equation, modified Equal Width equation and Benney-Luke Equations are solved by using simple hyperbolic tangent Ansatz method. A simple compatible wave transformation in one dimension is employed to reduce the governing equations to integer ordered ODEs. Then, the ansatz approximation is used to derive exact solutions. Some illustrative examples are presented for some particular choices of parameters and derivative orders.

Formulating a relativistic equation for particles with arbitrary spin remains an open challenge in theoretical physics. In this study, the main algebraic approaches used to generalize the Dirac and Kemmer–Duffin equations for particles of arbitrary spin are investigated. It is proved that an irreducible relativistic equation formulated using spin matrices satisfying the commutation relations of the de Sitter group leads to inconsistent results, mainly as a consequence of violation of unitarity and the appearance of a mass spectrum that does not reflect the physical reality of elementary particles. However, the introduction of subsidiary conditions resolves the problem of unitarity and restores the physical meaning of the mass spectrum. The equations obtained by these approaches are solved and the physical nature of the solutions is discussed.

The objective of this study was to evaluate the drying kinetics of the mass of jambu leaves and mass of jambu leaves in foam mat at different temperatures (50, 60 and 70 °C and thickness of 1.0 cm). The physicochemical characterization of the materials was performed before and after drying. Twelve different drying models were fitted to the drying kinetics data and the thermodynamic properties were calculated. The physicochemical parameters for the mass of leaves and foam after drying were moisture content from 2 to 7%, ash from 13 to 17%, protein content from 22 to 30%, lipids from 0.6 to 4% and total titratable acidity from 0.20 to 0.28% of tartaric acid. Wang & Singh and Midilli models were recommended for describing the drying kinetics. The use of foam mat promoted higher values of effective diffusion coefficient and activation energy and lower values of enthalpy and entropy, thus enhancing the reduction of drying time.

It is shown that, for a de Sitter Universe, the Hartle-Hawking (HH) wave function can be obtained in a simple way starting from the Friedmann- Lemaitre-Robertson-Walker (FLRW) line element of cosmological equations. An oscillator having imaginary time is indeed derived starting from the Hamiltonian obtaining the HH condition. This proposes again some crucial matter on the meaning of complex time in cosmology. In order to overcome such difficulties, we propose an interpretation of the HH framework based on de Sitter Projective Holography.

This article aimed at providing some extension of the modal square of opposition in the 1 light of Ockham’s account of the modal operators. Moreover, we shall set forth some significant 2 remarks on the de re-de dicto distinction and on the modal operator of contingency by means of a 3 Boolean algebra called Bitstring Semantics. This generalisation starting from Ockham’s account of 4 modalities will allow us to take into consideration whether Ockham’s thought on this matter holds 5 water or not, and in which case it should be changed in order to make it coherent.

A theoretical description of quantum jumps at the level of elementary particles is proposed, based on a micro-cosmological interpretation of their de Broglie phase. The third quantization formalism proposed in current literature for the description of baby universes in quantum cosmology is used here to describe the breakdown of unitarity in the transition from the pre-jump to the post-jump wave function. The corpuscular aspect manifested by the particle in the micro-interaction that originates the jump is represented by a pair of evanescent "micro-universes", respectively pre- and post-jump, connected by a wormhole. The latter represents the actual implementation of the interaction that leads to the projection on the outgoing state; this interaction is always local, even when the selected outgoing state is entangled. Therefore, the decoherence which leads to the emergence of classicality is originated by the same fundamental interactions of the Standard Model involved in the unitary evolution of the wave function. The objective nature of the reduction process admits implications on the possibility of using the formalism in the cosmological context, which are briefly discussed.

The signature of chaotic systems can be characterized either by the sensitivity of the initial conditions or by the change of its parameters. This feature can be used for manufacturing high sensitivity sensors. Sensors based on chaotic circuits have already been used for measuring water salinity, inductive effects, and both noise and weak signals. This article investigates an impedance sensor based on the Van der Pol and Duffing damped oscillators. The calibration process is a key point and therefore the folding behavior of signal periods was also explored. A sensitivity of 0.15 kΩ/Period was estimated over a range from 89.5 to 91.6 kΩ. This range can be adjusted according to the application by varying the gain of the operational amplifier used in this implementation. The development of this type of sensor might be used in medical and biological engineering for skin impedance measurements, for example. This type of chaotic sensor has the advantage of sensing small disturbances and then detect small impedance changes within biological materials which, in turn, may not be possible with other detectors.

Uncertainty relations in hydrodynamics are numerically studied. We first give a review for the formulation of the generalized uncertainty relations in the stochastic variational method (SVM), following the work by two of the present authors [Phys.\ Lett.\ A\textbf{382}, 1472 (2018)]. In this approach, the origin of the finite minimum value of uncertainty is attributed to the non-differentiable (virtual) trajectory of a quantum particle and then both of the Kennard and Robertson-Schr\"{o}dinger inequalities in quantum mechanics are reproduced. The same non-differentiable trajectory is applied to the motion of fluid elements in the Navier-Stokes-Fourier equation or the Navier-Stokes-Korteweg equation. By introducing the standard deviations of position and momentum for fluid elements, the uncertainty relations in hydrodynamics are derived. These are applicable even to the Gross-Pitaevskii equation and then the field-theoretical uncertainty relation is reproduced. We further investigate numerically the derived relations and find that the behaviors of the uncertainty relations for liquid and gas are qualitatively different. This suggests that the uncertainty relations in hydrodynamics are used as a criterion to classify liquid and gas in fluid.

We are using information from a paper deriving a Lorentz-violating energy-momentum relation entailing an exact mo_mentum cutof as stated by G. Salesi . Salesi in his work allegedly defines Pre Planckian physics, whereas we restrict our given application to GW generation and DE formation in the first 10^-39s to 10^-33s or so seconds in the early universe. This procedure is inacted due to an earlier work whereas referees exhibited puzzlement as to the physical mechanism for release of Gravitons in the very early universe. The calculation is meant to be complementary to work done in the Book “Dark Energy” by M. Li, X-D. Li, and Y. Wang, and also a calculation for Black hole destruction as outlined by Karen Freeze, et. al. The GW generation will be when there is sufficient early universe density so as to break apart Relic Black holes but we claim that this destruction is directly linked to a Lorentz violating energy-momentum G. Salesi derived, which we adopt, with a mass m added in the G. Salesi energy momentum results proportional to a tiny graviton mass, times the number of gravitons in the first 10^-43 seconds

This article aims to approach the Mudejar architecture developed in Mexico during the 16th and 17th centuries. The subject has been little studied although both general and specific contributions have been made by the author’s research group. At the methodological level, this study is based on the existing bibliography as well as archive and field research which allow an accurate scientific approach and results. The article analyses the social and productive conditions in Mexico during the Viceregal period along with the systematization carried by the Viceroy Antonio de Mendoza, the guild ordinances and the architectural typologies. The perception of territory and the use of constructive models by the Viceregal authorities would justify the use of the Mudejar style as cultural and unity criteria

In the same way as the realization of some of the famous gedanken experiments imagined by the founding fathers of quantum mechanics has recently led to the current renewal of the interpretation of quantum physics, it seems that the most recent progresses of observational astrophysics can be interpreted as the realization of some cosmological gedanken experiments such as the removal from the universe of the whole visible matter or the cosmic time travel leading to a new cosmological standard model. This standard model involves two dark components of the universe, dark energy and dark matter. Whereas dark energy is usually associated with the cosmological constant, we propose to explain dark matter as a pure QCD effect, namely a gluonic Bose Einstein condensate, following the transition from the quark gluon plasma phase to the colorless hadronic phase. Our approach not only allows us to assume a ratio Dark/Visible equal to 11/2 but also provides gluons and (anti-)quarks with an extra mass of vibrational nature. Such an interpretation would comfort the idea that, apart from the violation of the matter/antimatter symmetry satisfying the Sakharov’s conditions, the reconciliation of particle physics and cosmology needs not the recourse to any ad hoc fields, particles or hidden variables.

An explanation of the origin of dark matter is suggested in this work. The argument is based on symmetry considerations about the concept of mass. In the Wigner's view, the rest mass and the spin of a free elementary particle in flat space-time are the two invariants that characterize the associated unitary irreducible representation of the Poincar\'e group. The Poincar\'e group has two and only two deformations with maximal symmetry. They describe respectively the de Sitter (dS) and Anti de Sitter (AdS) kinematic symmetries. Analogously to their shared flat space-time limit, two invariants, spin and energy scale for de Sitter and rest energy for Anti de Sitter, characterize the unitary irreducible representation associated with dS and AdS elementary systems. While the dS energy scale is a simple deformation of the Poincaré rest energy and so has a purely mass nature, AdS rest energy is the sum of a purely mass component and a kind of zero-point energy derived from the curvature. An analysis based on recent estimates on the chemical freeze-out temperature marking in Early Universe the phase transition quark-gluon plasma epoch to the hadron epoch supports the guess that dark matter energy might originate from an effective AdS curvature energy.

This article focuses on the comparison and perception of the potential of water’s surface in selected parts of the waterfront in two contrasting cities. The aim is to define the potential of the water’s surface in terms of psychology and its effects on climate. The analysis was performed on the example of Prague with its waterfront on the river Vltava, and Santa Cruz de Tenerife with its Atlantic coastline. Data was sourced from maps, questionnaire surveys and interviews with waterfront users during October 2020. The research showed a higher importance of the water’s surface for users in Prague, than in Santa Cruz. The main finding is that the psychological perception of the waterfront by its the users is affected by the possibility of a visual contact with the water’s surface, the design and composition of the space, and the climate situation of a site affected by the presence of an urban heat island (UHI). The results promote an adherence to ecosystem-based approaches in future design projects and modifications of existing public spaces. The purpose of the work is to open a broader debate on the sustainability of the potential of waterfronts and their positive impact on human health.

The prevalence and incidence of cardiac pro-arrhythmic disorders are often influenced by sex due to specific effects on the QT interval. Androgens shorten QT, which may be protective against acquired long QT syndromes and their related arrhythmias in men such as torsade de pointes (TdP). On the other hand, androgens can potentiate Brugada and early repolarization syndromes, which are most prevalent in men. In this case series, we highlight four male patients with aborted SCD in the setting of abnormal testosterone status; two patients with TdP in a setting of testosterone deprivation (of which one drug-induced) and 2 patients with ventricular fibrillation associated with exogenous androgenic booster (Tribulus terrestris) intake. From this case series, we review the current available literature of the effects of androgen as a double-edged sword on the QTc interval and emphasize the importance of QTc monitoring in this subset of patients.

The origin of SARS-CoV-2 is debated, even after 18 months into the COVID-19 pandemic and a special investigation conducted by the World Health Organization. The RaTG13 sequence has been a highlight of discussions surrounding the origin of SARS-CoV-2. Here we express our opinion about the need for better reporting standards for information about sequencing data, especially for pathogens, citing our findings with the reported RaTG13 genome.

A thin-shell wormhole is crafted by the cut-and-paste method of two Bardeen de-Sitter black holes using Darmois-Israel formalism. Energy conditions are considered for different values of magnetic charge while both mass and cosmological constant are fixed. The attractive and repulsive characteristics of the throat of the thin-shell wormhole are also examined through the radial acceleration. Dynamics and stability of the wormhole are studied around the static solutions of the linearized radial perturbations at the throat of the wormhole. The regions of stability are determined by checking out the condition of concavity of the potential as a function in the throat radius for different values of magnetic charges.

This paper discusses the impact of orthographic manuals on the state of literacy, i.e. the relation of orthographic literacy and orthographic standardisation. The established hypothesis claims that frequent changes of orthographic rules during the pupils’ primary and secondary education do not have any considerable impact on their orthographic habits. In other words, the quantity of orthographic mistakes observed during a longer period of time and in conditions of changed orthographic rules would not show significant oscillations in their spelling. In order to confirm the hypothesis, a questionnaire was conducted encompassing 41 tests among 526 students of a technical study programme during four consecutive academic years, pursuant to whose results a writing uniformity index and a categorisation of orthographic controversy into six classes is established. The Croatian language has been selected for the observation due to multiple orthographic changes in the last 30 years in the three major orthographic points: writing of the covered r, writing of d and t in front of c and č in declination of words ending in -tak, -tac, -dak and -dac, and the issue of compound or separate spelling of the negation particle and the auxiliary biti (to be). Moreover, the paper methodologically and quantitatively establishes criteria according to which the second established hypothesis on evolutionary orthographic literacy can be confirmed. The conclusions are expected to be able to contribute to the better understanding of orthographic planning and application of orthographic norms in schools.

Biofilter application for treatment of stormwater containing de-icing chemicals commonly applied in airports, propylene glycol and potassium formate, was investigated. Lab-scale adsorption tests using filter media made of crushed clay (Filtralite) and granular activated carbon showed that adsorption was unsuitable for removal of propylene glycol and potassium formate. Column filtration experiment testing two different crushed clay size ranges was conducted. The results showed that DOC removal was dependent on a number of factors. This study investigated the impact of filter depth, nutrients addition, and filtration rate. DOC removal suggested that DOC degradation occurred on the top filter layer. It was shown that the most active separation occurred in the first ~20 cm of filter depth. This was confirmed by results from water quality analysis (i.e. DOC removal and ATP measurement) and calculations based on a filtration performance analysis (Iwasaki model) and filter hydraulic evaluation (Lindquist diagram). It was shown that for the highest C:N:P ratio tested (molar ratio of 24:7:1), 50-60% DOC removal was achieved. Addition of nutrients was found important and determining the biofilter performance.

With the advancement of long-read sequencing technologies and their more widespread use for bacterial genomics, several methods for generating genome assemblies from error-prone long reads have been developed. These are complemented by various tools for assembly polishing using either long reads, short reads, or reference genomes. End users are therefore left with a plethora of possible combinations of programs for obtaining a final trusted assembly. Hence, there is also the need for measuring completeness and accuracy of such assemblies, for which, again, several evaluation methods implemented in various programs are available. In order to automatically run all these programs, I developed two workflows for the workflow management system Snakemake for bacterial genome assembly and evaluation of assemblies, which provide end users with an easy-to-run method for both tasks. The workflows are available as open source software under the MIT license at https://github.com/pmenzel/ont-assembly-snake and https://github.com/pmenzel/score-assemblies.

We report on the study of ultrafast laser-induced plasma expansion dynamics in a gas microjet. To this purpose, we focused femtosecond laser pulses on a nitrogen jet produced through a homemade De Laval micronozzle. The laser excitation leads to plasma excitation with a characteristic spectral line emission at 391 nm. By following the emitted signal with a detection system based on an Intensified Charge-Coupled Device (ICCD) we captured the two-dimensional spatial evolution of the photo-excited nitrogen ions with a temporal resolution on the nanosecond time scale. We fabricated the micronozzle on fused silica substrate by femtosecond laser micromachining. This technique enables high accuracy and three-dimensional capabilities, thus providing an ideal platform for developing glass-based microfluidic structures for application to plasma physics and ultrafast spectroscopy.

Philip Phenix’s (1964) book Realms of meaning started the ever growing movement concerned with how school education might help young people in their search for meaning in times of rapid social change. Today, in globalised, digital, secularised, de-traditionalised culture, the importance and urgency of this role have never been greater. Cultural change has accelerated exponentially, and for many – including students in religious/Catholic schools – traditional religious sources of meaning are no longer prominent or plausible reference points. Catholic schools, whether independent or semi-state institutions because of government funding, can make a valuable contribution young people’s spiritual/moral education, no matter what their level of religious affiliation or practice. This article argues that such a contribution requires change to the discourse or narrative of Catholic school Religious Education, with corresponding adjustments to content and pedagogy. Its present trajectory, which is excessively concerned with promoting a Catholic identity in students, needs to be modified. Both the religious and non-religious students, especially in the senior classes, would derive greater spiritual and religious benefit from the inclusion of more life-relevant and issue-related content, together with a critical, research-oriented pedagogy. Such an approach proposes that the Catholic Church’s schools should offer unconditionally a meaningful spiritual/moral education that is relevant to all students, rather than a traditional one which seemed to presume that all students are, or should be practising Catholics. This does not minimise attention to the Catholic tradition, but it allows for a study of how people negotiate the task of constructing meaning and values in a complex culture. The article also looks at the ‘headwinds’ that hinder the implementation of this approach. The article is focused specifically on the Australian context where Catholic schools are semi-state institutions because they are funded by both state and federal governments. The issues are still likely to be pertinent to Catholic education in other countries, while taking into account significant contextual differences.

As more cases of COVID-19 are studied and treated world-wide, it had become apparent that lethal and most severe cases of pneumonia are due to an out-of-control inflammatory response to the SARS-CoV2 virus. I explored the putative causes of this specific feature through a detailed genomic comparison with the closest SARS-CoV-2 relatives isolated from bats, as well as previous coronavirus strains responsible for the previous epidemics (SARS-CoV, and MERS-CoV). The high variability region of the nsp3 protein was confirmed to exhibit the most variations between closest strains. It was then studied in the context of physiological and molecular data available in the literature. A number of convergent findings point out de-mono-ADP-ribosylation (de-MARylation) of STAT1 by the SARS-CoV-2 nsp3 as a likely cause of the cytokine storm observed in the most severe cases of COVID-19. This may suggest new therapeutic approaches and an assay to predict the virulence of naturally circulating SARS-like animal coronaviruses.

The fluid flow field at the upper airways is highly complex due to the complex structure of the airway. The inhaled particle flow, the air streamline and the interaction of the continuum and discrete phase could significantly affect the transport behaviour of the inhaled particles. A range of analytical, mathematical and computational fluid dynamics (CFD) models analyzed the airflow and particle transport in different idealized and asymmetric airway models. A precise understanding of the continuum and discrete phase interaction in realistic human airways is missing, and this study aims to develop a CFD-DEM model for particle transport in realistic airways. This study uses the CFD model for the continuum phase and the discrete element method (DEM) for the discrete phase. A soft sphere approach is used for the interaction of the discrete phase. Proper validation is performed for particle transport efficiency. The CFD-DEM model analyzed the particle transport in an idealized and realistic airway model, and different methods are used to analyze the transport behaviour. During the particle-particle interaction, a stagnation point and a high-pressure zone are observed at the airway model's carinal angle. The numerical results report higher deposition efficiency (DE) for particle-particle interaction than without interaction. The flow field becomes highly complex with the spring constant values, and higher DE is found for high spring constant values. The spring dashpot friction-dshf method shows higher deposition at the upper part of the airways than other interaction methods. The findings of this study and more case-specific analysis would improve the knowledge of aerosol transport in airways and the health risk assessment of the patient.

QTc interval measurement is a widely used screening tool to assess the risk of cardiac diseases, arrhythmias, and is a useful biomarker for pharmacovigilance. However, interpretation of QTc is difficult in neonates due to hemodynamic maturational changes and uncertainties on reference values. To describe trends in QTc values throughout infancy (1 year of life), and to explore the impact of (non)-maturational changes and medicines exposure, a structured systematic review (PROSPERO CRD42022302296) was performed. In term neonates, a decrease was observed over the first week of life, whereafter values increased until two months of age, followed by a progressive decrease until six months. A similar pattern, with longer QTc values was observed in preterms. QTc is influenced by cord clamping, hemodynamic changes, therapeutic hypothermia, illnesses and sleep, not by sex. Cisapride, domperidone and doxapram result in QTc prolongation in neo-nates. Further research in this age category is needed to improve primary screening practices, earlier detection of risk factors and precision pharmacovigilance.

The genus Rhodotorula includes basidiomycetous oleaginous yeast species. R. babjevae can produce compounds of biotechnological interest such as lipids, carotenoids and biosurfactants from low value substrates such as lignocellulose hydrolysate. High-quality genome assemblies are needed to develop genetic tools and to understand fungal evolution and genetics. Here, we combined short- and long-read sequencing to resolve the genomes of two R. babjevae strains, CBS 7808 (type strain) and DBVPG 8058 at chromosomal level. Both genomes have a size of 21 Mbp and a GC content of 68.2%. Allele frequency analysis indicated tetraploidy in both strains. They harbor 21 putative chromosomes with sizes ranging from 0.4 to 2.4 Mb. In both assemblies, the mitochondrial genome was recovered in a single contig, which shared 97% pairwise identity. The pairwise identity between the majority of chromosomes ranges from 82% to 87%. We found indications for strain-specific extrachromosomal endogenous DNA. 7,591 protein-coding genes and 7,607 associated transcripts were annotated in CBS 7808 and 7,481 protein-coding genes and 7,516 associated transcripts in DBVPG 8058. CBS 7808 has accumulated a higher number of tandem duplications than DBVPG 8058. We identified large translocation events between putative chromosomes and a high genetic divergence between the two strains.

Docking the tail of lambs is a standard husbandry procedure and is achieved through several techniques including clamps, hot or cold knives and latex rings, the last of which is the most popular. All tail docking methods cause acute pain which can be reduced by application of local anesthetic, however precise anatomical injection for optimal efficacy requires considerable skill. This pen trial evaluated the ability of local anesthetic delivered with a dual function ring applicator / injector to alleviate acute tail docking pain. Thirty ewe lambs were assigned to one of three treatment groups (n = 10 per group): ring plus local anesthetic (Ring LA), ring only (Ring) and sham handled control (Sham). Lambs were videoed and behavior categorized every 5 minutes for the first hour and every 10 min for the subsequent 2 hours after treatment. There was a significant effect (p < 0.001) of treatment on total active pain related behaviors in the first hour, with Ring lambs showing higher counts compared to Ring LA or Sham. Ring lambs also displayed a significantly higher count of combined abnormal postures (p < 0.001) than Ring LA or Sham lambs. Delivery of 1.5ml of 2% lignocaine via the dual action device abolished abnormal behaviors and signs of pain in Ring LA lambs. However, lambs in the Ring LA group spent less time attempting to suckle compared to Ring and Sham lambs, suggesting that some residual discomfort remained.

Currently, with a large number of fatality rates, coronavirus disease-2019 (COVID-19) has emerged as a potential threat to human health worldwide. It has been well-known that severe acute respiratory syndrome-coronavirus-2 (SARS-CoV-2) is responsible for COVID-19 and World Health Organization (WHO) proclaimed the contagious disease as a global pandemic. Researchers from different parts of the world amalgamate together inquest of remedies for this deadly virus. Recently, it has been demonstrated that the spike glycoprotein (SGP) of SARS-CoV-2 is the mediator behind the entrance into the host cells. Our group has comprehensibly analyzed the SGP of SARS-CoV-2 through multiple sequence analysis along with the phylogenetic analysis. Further, this research work predicted the most immunogenic epitopes for both B-cell and T-cell. Notably, we focused mainly on major histocompatibility complex (MHC) class I potential peptides and predicted two epitopes; WTAGAAAYY and GAAAYYVGY, that bind with the MHC class I alleles which are further validated by molecular docking analysis. Furthermore, this study also proposed that the selected epitopes were shown availability in a greater range of the population. Hence, our study comes up with a strong base for the implementation of designing novel vaccine candidates against SARS-CoV-2, however adequate laboratory works will need to be conducted for the appropriate application.

There is crescent demand for knowledge improvement of the integrated water vapor (IWV) distribution in regions affected by heat islands that are associated with extreme rainfall events such as in the metropolitan area of Rio de Janeiro (MARJ). This work assessed the suitability and distribution of IWV in the MARJ using products from the Global Navigation Satellite Systems (GNSS), MODerate Resolution Imaging Spectroradiometer (MODIS), and radiosonde. GNSS data were collected by the tracking station named RDJN, from the cooperation of the International GNSS Monitoring and Assessment System (iGMAS) and the National Observatory of Brazil (Observatório Nacional - ON), and the tracking stations ONRJ, RIOD, and RJCG belonging to the Brazilian Network for Continuous Monitoring (RBMC) in the period of January 2015–August 2018. High variability of the near surface air temperature (T) and relative humidity (RH) were observed among eight meteorological sites considered. The mean T differences between sites, up to 4.4 °C, led to mean differences as high as 3.1 K for weighted mean temperature (Tm) and hence 0.83 mm for IWV differences. The performance of the MODIS MOD07 and MYD07 products provided a reasonably good representation of the mean spatial distribution of IWV, especially during the daylight passages of the satellites TERRA and AQUA. Local grid points of MODIS IWV estimates had relatively good agreement with the GNSS-derived IWV, with mean differences from -2.4–1.1 mm considering only daytime passages of the satellites TERRA and AQUA. During nighttime, MODIS underestimated IWV (from -9–-3 mm) with respect to GNSS, due to attenuation of IR radiation by clouds. A contrasting behavior was found in the radiosonde IWV estimates compared with the estimates from GNSS. There were dry biases of 1.4 mm (3.7% lower than expected) by radiosonde IWV during the daytime considering that all other estimates were unbiased and the differences between IWV GNSS and IWV RADS were consistent. Based on the IWV comparisons between radiosonde and GNSS at nighttime, the atmosphere over the radiosonde site is about 1.2 (2.3) mm wetter than over RIOD (RDJN) station. The long time series of the comparisons between IWVRDJN and IWVRIOD showed that the highest values of IWV occurred from the afternoon to nocturnal hours. Further, the atmosphere over the site RIOD was consistently about 1 mm wetter than over RDJN. These results showed the feasibility of the iGMAS RDJN station data compared with the RBMC, MODIS, and radiosonde data to investigate IWV in a region with occurrence of heat islands, and the peculiar physiographic and meteorological characteristics as in the MARJ. This work recommended the usage of complete meteorological station data collocated near every GNSS receiver aiming improvements of local GNSS IWV estimates and serving as additional support for operational numerical assimilation, weather forecast, and nowcast of extreme rainfall events.

To assess the degree to which it has met its commitments under the Paris Agreement, Morocco is called upon to carry out carbon assessments and transparent evaluations. Within the forestry sector, little is known about the role of Morocco’s forests in contributing to carbon uptake. With this aim, we applied for the first time in literature the 3-PG model to Cedrus atlantica ((Endl.) Manetti ex Carrière, 1855), which represents about 131.800 ha of Morocco’s forest area (i.e. Azrou forest). Through the Differential Evolution - Markov Chains (DE-MC) we tested and assessed the sensitivity and calibrated the 3-PG model. This process-based model provided significant results regarding the carbon sequestration capacity. The results showed the following: i- Parameters related to stand properties, canopy structure, and processes, as well as biomass partitioning, are the most important or sensitive for the performance of the model; ii- The DE-MC method optimized the values of the 3-PG parameters which was confirmed by the means of Gelman-Rubin convergence test; iii- According to the predictions of the calibrated 3-PG, the Net Primary Production in the pure Azrou forest varies between 0.32 and 7.88 tC.ha−1.yr−1, it is equal in average to 4.9 tC.ha−1.yr−1, which given the total area corresponds to 7078 tC.yr−1.

Canola is the major oilseed crop of Canada. The de-oiled material is an important by-product due to its rich phenolic profile and high protein content. This co-processing stream from canola is primarily utilized as animal feed but represents an invaluable source of nutraceuticals. Microwave-assisted solvent extraction (MAE), as a green extraction method, has received considerable attention in recent times. The ease of use and application of many solvents at the same time makes the MAE one of the best methods for studying multiple solvents at the same time. The formation of canolol, from sinapine and sinapic acid, is primarily dependant on temperature which favors the decarboxylation reaction. Hence, MAE using green extractants can be used to enhance the yield of canolol. This study examined the effects of different pre-treatment temperature-time combinations of 140, 150, 160, and 170℃ for 5, 10, 15, 20 and 30 minutes on the extraction of canolol and other canola endogenous phenolic compounds. Three antioxidant assays assessed the antioxidant activity of the different extracts obtained by MAE confirming the microwave as a novel and versatile instrument for enhancing the yield of canolol. Improvements in the antioxidant activity of the different extracts further established the efficacy of the current method for isolating important natural phenolic derivatives for utilization by the nutraceutical industry.

The issue of being pro-gender is still a controversial topic to be debated in Indonesian society. However, in the 21st Century, many women have been able to break through barriers and participate in the public sphere. It is a form of self-existence as proposed by Simone de Beauvoir on existentialist feminism. Based on these problems, this study aims to find out and answer questions about how Indonesian women exist in the public sphere in the 21st Century and find out how Indonesian women exist in the public sphere through Simone de Beauvoir's existentialist feminism paradigm. The research method used is descriptive-qualitative through a literature review of 23 journal articles, websites, and data reports with a range of 2019-2021. This study found that based on Simone de Beauvoir's feminist paradigm, Indonesian women in the 21st Century are no longer a figure other than complete. Furthermore, the data collected by the researcher shows that several gender indicators have shown that Indonesian women have been able to occupy public spaces in various aspects. Based on these results, it is hoped that it can provide information about Simone de Beauvoir's existentialist feminism thought and its relevance to the existence of Indonesian women in the public sphere in the 21st Century. However, this research has limitations, those are only about women in Indonesia, and the paradigm of feminism is limited to Simone de Beauvoir's existentialist feminism.

In this paper we will show that standard physics to a large degree consists of derivatives of a deeper reality. This means standard physics is both overly complex and also incomplete. Modern physics has typically started from working with first understanding the surface of the world, that is typically the macroscopic world, and then forming theories about the atomic and subatomic world. And we did not have much of a choice, as the subatomic world is very hard to observe directly, if not impossible to observe directly at the deepest level. Despite the enormous success of modern physics, it is therefore no big surprise that we at some point have possibly taken a step in the wrong direction. We will claim that one such step came when one thought that the de Broglie wavelength represented a real matter wavelength. We will claim that the Compton wavelength is the real matter wavelength. Based on such a view we will see that many equations in modern physics are only derivatives of much simpler relations. Second, we will claim that in today’s physics one uses two different mass definitions, one mass definition that is complete or at least more complete, embedded in gravity equations without being aware of it, as it is concealed in GM, and the standard, but incomplete, kg mass definition in non-gravitational physics. First, when this is understood, and one uses the more complete mass definition that is embedded in gravity physics, not only in gravity physics, but in all of physics, then one has a chance to unify gravity and quantum mechanics. Our new theory shows that most physical phenomena when observed over a very short timescale are probabilistic for masses smaller than a Planck mass and dominated by determinism at or above Planck mass size. Our findings have many implications. For example, we show that the Heisenberg uncertainty principle is rooted in a foundation not valid for rest-mass particles, so the Heisenberg uncertainty principle can say nothing about rest-masses. When re-formulated based on a foundation compatible with a new momentum that is also compatible with rest-masses, we obtain a re-defined Heisenberg principle that seems to become a certainty principle in the special case of a Planck mass particle. Furthermore, we show that the Planck mass particle is linked to gravity and that we can easily detect the Planck scale from gravity observations. The Planck mass particle is unique as it only lasts the Planck time, and in that very short time period it can only be observed directly from itself, and it therefore closely linked to absolute rest.

With the development of deep learning technology, various structures and research methods for super-resolution restoration of natural images and document images have been introduced. In particular, a number of recent studies have been conducted and developed in image restoration using generative adversarial network. Super-resolution restoration is ill-posed problem because of some complex restraints such as a lot of high-resolution images being restored for the same low-resolution image and also difficulty in restoring noises like edges, light smudging, and blurring. In this study, we utilized the spatially adaptive de-normalization (SPADE) structure for document image restoration to solve previous problems such as edge unclearness, hardness to catch features of texts, and the image color transition. Consequently, it can be confirmed that the edge of the character and the ambiguous stroke are restored more clearly when contrasting with the other previously suggested methods. Also, the proposed method’s PSNR and SSIM scores are geting 8% and 15% higher, respectively, compared to the previous methods.

The widespread integration and growing dependence among currency, stock and commodity markets make these markets often very vulnerable to shocks and at risk of collapse at the same time. As a result, these trends threaten the sustainability of the entire financial system. In this study, we explore the spillovers and nonlinear dependences between the seven major foreign ex-change rates, crude oil and gold prices, a global stock price index, and oil and stock implied volatility indices as proxy variables for global risk factors by em-ploying directional spillover network approach. We also use multi-scale de-composition method and nonlinear causality test between these variables to capture multi-level relationships at short and long horizons. Major findings are summarized as follows. First, from the multi-scale decomposition analysis, we identify that Granger causality test results and the direction and strength of return spillovers change with the level of decomposition. Second, the results of nonlinear causality tests show variation in both the significance and direction of Granger causality relationships between the decomposed currency and other series at different timescales, especially for the decomposed oil, gold, and OVX series. Third, the measured directional spillover indices identify the EUR as the largest contributor of connectedness to the other series. The central role of the EUR is a net transmitter of connectedness to gold, oil, the GBP, JPY, and CHF.

Scale invariance is expected in empty Universe models, while the presence of matter tends to suppress it. As shown recently, scale invariance is certainly absent in cosmological models with densities equal to or above the critical value ρ_c = 3(H₀)²/(8πG). For models with densities below ρc, the possibility of limited effects remains open. If present, scale invariance would be a global cosmological property. Some traces could be observable locally. For the Earth-Moon two-body system, the predicted additional lunar recession would be increased by 0.92 cm/yr, while the tidal interaction would also be slightly increased. The Earth-Moon distance is the most systematically measured distance in the Solar System, thanks to the Lunar Laser Ranging (LLR) experiment active since 1970. The observed lunar recession from LLR amounts to 3.83 (±0.009) cm/yr; implying a tidal change of the length-of-the-day (LOD) by 2.395 ms/cy. However, the observed change of the LOD since the Babylonian Antiquity is only 1.78 ms/cy, a result supported by paleontological data, and implying a lunar recession of 2.85 cm/yr. The significant difference of (3.83-2.85) cm/yr = 0.98 cm/yr, already pointed out by several authors over the last two decades, corresponds well to the predictions of the scale-invariant theory, which is also supported by several other astrophysical tests.

Autonomous weapons systems (AWS), sometimes referred to as “killer robots”, are receiving evermore attention, both in public discourse as well as by scholars and policymakers. Much of this interest is connected with emerging ethical and legal problems linked to increasing autonomy in weapons systems, but there is a general underappreciation for the ways in which existing law might impact on these new technologies. In this paper, we argue that as AWS become more sophisticated and increasingly more capable than flesh-and-blood soldiers, it will increasingly be the case that such soldiers are “in the power” of those AWS which fight against them. This implies that such soldiers ought to be considered hors de combat, and not targeted. In arguing for this point, we draw out a broader conclusion regarding hors de combat status, namely that it must be viewed contextually, with close reference to the capabilities of combatants on both sides of any discreet engagement. Given this point, and the fact that AWS may come in many shapes and sizes, and can be made for many different missions, we argue that each particular AWS will likely need its own standard for when enemy soldiers are deemed hors de combat. We conclude by examining how these nuanced views of hors de combat status might impact on meaningful human control of AWS.

The Astyanax species complex has two morphs: a blind, depigmented morph which inhabits caves in México and an eyed, pigmented surface-dwelling morph. The eyed morph can also be found in caves, sometimes hybridizing with the cave morph. This species complex has arguably become the most prominent model system among cave organisms for the study of evolutionary development and genomics. Before this study, 32 caves were known to be inhabited by the cave morph, 30 of them within the El Abra region. The purpose of this study was to conduct new surveys of the area and to assess some unconfirmed reports of caves presumably inhabited by troglomorphic fish. We describe two new localities, Sótano del Toro #2 and Sótano de La Calera. These two caves make a single hydric system together with the previously described cave of Sótano del Toro. The system is inhabited by a mixed population of troglomorphic, epigeomorphic and presumably hybrid fish. Furthermore, Astyanax cavefish and the mysid shrimp Spelaeomysis quinterensis show a phylogeographic convergence that supports the notion that the central Sierra de El Abra is a biogeographical region that has influenced the evolutionary history of its aquatic community across species. The presumptive location of its boundaries, which may limit cave-to-cave or surface-to-cave gene flow, are identified.

Mutations, especially those at the protein-protein interaction (PPI) interface, have been associated with various diseases. Meanwhile, though de novo mutations (DNMs) have been proven important in neuropsychiatric disorders, such as developmental delay (DD), the relationship between PPI interface DMNs and DD has not been well studied. Here we curated developmental delay DNM datasets from the PsyMuKB database and showed that DD patients showed a higher rate and deleteriousness in DNM missense on the PPI interface than sibling control. Next, we identified 302 DD-related PsychiPPIs, defined as PPI harboring a statistically significant number of DNM missenses at their interface, and 42 DD candidate genes from PsychiPPI. We then observed that PsychiPPIs preferentially affected hub proteins in the human protein interactome network. When analyzing DD candidate genes using gene ontology and gene spatio-expression, we found that PsychiPPI genes carrying PPI interface mutations, such as FGFR3 and ALOX5, were enriched in development-related pathways and the development of the neocortex, and cerebellar cortex, suggesting their potential involvement in the etiology of DD. Our results demonstrated that DD patients carried an excess burden of PPI-truncating DNM, which could be used to efficiently search for disease-related genes and mutations in large-scale sequencing studies. In conclusion, our comprehensive study indicated the significant role of PPI interface DNMs in developmental delay pathogenicity.

ALDH+ H1975 lung adenocarcinoma stem cells (LSCs) are a rare cell population identified in lung adenocarcinoma (LUAD). LSCs can self-renew, drive tumor initiation, growth, metastasis, and recurrence, and are also the predominant cause of poor prognosis due to their intrinsic resistance to drugs and chemotherapy. Consequently, LSCs are a promising target for LUAD therapy. Noncoding RNAs (ncRNAs), including microRNAs (miRNAs), long noncoding RNAs (lncRNAs), and circular RNAs (circRNAs), exert many significant regulatory functions in the pathogenesis of human cancers, showing the necessity for a comprehensive understanding of the mechanisms that underlie lung carcinogenesis. Nonetheless, research on many known transcripts and messenger RNAs (mRNAs) has already generated new information. Unknown biomarkers in ncRNAs and systematic and comprehensive interrelation with unknown ncRNAs and mRNAs may provide further insights into the biology of LUAD. Herein, a set of novel ncRNAs that include miRNAs, lncRNAs, circRNAs, were identified and differentially expressed patterns of ncRNAs and mRNAs in LSCs and ALDH- H1975 LUAD tumor cells (LTCs) were obtained using stringent bioinformatics pipelines. Through a meta-analysis of the identified landscapes, novel competitive endogenous RNA (ceRNA) networks were constructed to reveal the potential molecular mechanisms that regulate the hallmarks of LSCs and LTCs. This study presents a summary of novel ncRNAs and the fundamental roles of differentially expressed ncRNAs implicated in the activity of LSCs and LTCs. In addition, the study also provides a comprehensive resource for the future identification of diagnostic, therapeutic, and prognostic biomarkers in LUAD.

To guide analysts to select the right tool and parameters in differential gene expression analysis of single-cell RNA sequencing (scRNA-seq) data, we developed a novel simulator that recapitulates the data characteristics of real scRNA-seq datasets while accounting for all the relevant sources of variation in a multi-subject, multi-condition scRNA-seq experiment: the cell-to-cell variation within a subject, the variation across subjects, the variability across cell types, the mean/variance relationship of gene expression across genes, library size effects, group effects, and covariate effects. By applying it to benchmark 12 differential gene expression analysis methods (including cell-level and pseudo-bulk methods) on simulated multi-condition, multi-subject data of the 10x Genomics platform, we demonstrated that methods originating from the negative binomial mixed model such as glmmTMB and NEBULA-HL outperformed other methods. Utilizing NEBULA-HL in a statistical analysis pipeline (https://github.com/interactivereport/scRNAseq_DE) for single cell analysis will enable scientists to better understand cell-type specific transcriptomic response to disease or treatment effects and to discover new drug targets. Further, application to two real datasets showed the outperformance of our differential expression (DE) pipeline, with unified findings of differentially expressed genes (DEG) and a pseudo-time trajectory transcriptomic result. In the end, we made recommendations of filtering strategies of cells and genes based on simulation results to achieve optimal experimental goals.

Temperature-index modeling is used to determine the magnitude of temperature depression on the Blanca Massif, Colorado, required to maintain steady-state mass balances of nine reconstructed glaciers at their extent during the Last Glacial Maximum (LGM). The mean temperature depression thus determined is ~8.6 +0.7/–0.9 °C where the uncertainties account for those inherent in the glacier reconstructions, in model parameters (e.g. melt factors), and possible modest changes in LGM precipitation. Associated equilibrium-line altitudes (ELAs) exhibit a statistically significant directional dependency being lower toward the north and east. Under the assumption that regional temperature change was uniform, required changes in precipitation vary systematically – also exhibiting a directional dependency coinciding with that in ELAs – and indicate increases (over modern) occurred on the eastern side of the massif while decreases occurred on the western side. This disparity represents a strengthening of a precipitation asymmetry, particularly winter precipitation, that exists today. The modern precipitation asymmetry may be a consequence of snow being blown over to the eastern side of the massif (advective transport) by southwesterly flow. Intensification of this flow during the LGM would have enhanced advection, and augmented snow accumulation on glaciers, thus explaining the lower ELAs and increased precipitation on that side of the massif.

In this paper we perform numerous numerical studies for the problem of low-rank matrix completion. We compare the Bayesian approaches and a recently introduced de-biased estimator which provides a useful way to build confidence intervals of interest. From a theoretical viewpoint, the de-biased estimator comes with a sharp minimax-optimal rate of estimation error whereas the Bayesian approach reaches this rate with an additional logarithmic factor. Our simulation studies show originally interesting results that the de-biased estimator is just as good as the Bayesian estimators. Moreover, Bayesian approaches are much more stable and can outperform the de-biased estimator in the case of small samples. However, we also find that the length of the confidence intervals revealed by the de-biased estimator for an entry is absolutely shorter than the length of the considered credible interval. These suggest further theoretical studies on the estimation error and the concentration for Bayesian methods as they are being quite limited up to present.

We report on the application of femtosecond laser micromachining to the fabrication of complex glass microdevices, for high-order harmonic generation in gas. The three-dimensional capabilities and extreme flexibility of femtosecond laser micromachining allow us to achieve accurate control of gas density inside the micrometer interaction channel. This device gives a considerable increase in harmonics generation efficiency if compared with traditional harmonic generation in gas jets. We propose different chip geometries that allow to control the gas density and driving field intensity inside the interaction channel to achieve quasi-phase matching conditions in the harmonic generation process. We believe that these glass micro-devices will pave the way to future downscaling of High-order Harmonic Generation beamlines.

Chile faces a serious crisis on housing affordability given that most of the population is unable to secure a house. While housing prices between 2008 increased by 70.96%, wages only increased by 20.43%. This article presents the analysis of the housing prices configuration for the main district in the country: Santiago Centro. The assessment focuses on verticalised housing buildings constructed between 2015 and 2019. The article develops an exploratory study on the price of housing in the city of Santiago de Chile, to generate a diagnosis to identify the role played by expectations of profitability when configuring that price. Based on the information generated, we seek to contribute to the discussion on public policies that advance towards the development of affordable housing for households in central communes with high urban value, as is the case of Santiago Centro. We hypothesize that profitability expectations of real estate developers play a key role in the housing prices and an adjustment in the profit ratios may increase the affordability keeping the housing market over profitable rates. The research is relevant due to the lack of data transparency in the Chilean housing market, where access to investment costs, land values, yields and house price formation are not part of the public discussion, even though this implies that many households are facing severe difficulties in paying for access to decent housing.

DNA methylation, one of the major epigenetic mechanisms, plays critical roles in regulating gene expression, genomic stability and cell lineage commitment. Establishment and maintenance of DNA methylation in mammals is achieved by two groups of DNA methyltransferases: DNMT3A and DNMT3B, which are responsible for installing DNA methylation patterns during gametogenesis and early embryogenesis, and DNMT1, which is essential for propagating DNA methylation patterns during replication. Both groups of DNMTs are multi-modular proteins, containing a large N-terminal regulatory region in addition to the C-terminal methyltransferase domain. Recent structure-function investigations of the individual domains or large fragments of DNMT1 and DNMT3A have revealed the molecular basis for their substrate recognition and specificity, intramolecular domain-domain interactions, as well as their crosstalk with other epigenetic mechanisms. These studies highlight a multifaceted regulation for both DNMT1 and DNMT3A/3B, which is essential for the precise establishment and maintenance of lineage-specific DNA methylation patterns in cells. This review summarizes current understanding of the structure and mechanism of DNMT1- and DNMT3A-mediated DNA methylation, with emphasis on the functional cooperation between the methyltransferase and regulatory domains.

Background Hydroxychloroquine (HCQ) combined with azithromycin (AZM) has been widely administered to patients with COVID-19 despite scientific controversies. In particular the potential to prolong cardiac repolarisation by using this combination has been discussed. Materials and methods We report a pragmatic and simple safety approach which we implemented in the first patients treated for COVID-19 in our center early 2020. Treatment contraindications were the presence of severe structural or electrical heart disease, baseline corrected QT interval (QTc) >500 ms, hypokalaemia, or other drugs prolonging QTc that could not be interrupted. Electrocardiogram and QTc was evaluated at admission and re-evaluated after 48 hours of the initial prescription. Results Among 424 consecutive adults (mean age 46.3 ± 16.1 years; 216 women). Patients were followed in conventional wards (21.5%) or in a day-care unit (78.5%). A total of 11 patients (2.6%) had contraindications to HCQ-AZ combination. In the remaining 413 treated patients, there were no arrhythmic events in any patient during the 10-day treatment regimen. QTc was slightly but statistically significantly prolonged by 3.75 ± 25.4 ms after two days (p=0.003). Ten patients (2.4%) developed QTc prolongation >60 ms, and none had QTc >500 ms. Conclusions This report do not aim to contribute to knowledge of the efficacy of treating COVID-19 with HCQ-AZ. However, a simple initial assessment of patient medical history, ECG and kalaemia identifies contraindicated patients and enables the safe treatment by HCQ-AZ of COVID-19 patients. QT-prolonging anti-infective drugs can be used safely in acute life-threatening infections, provided that a strict protocol and close collaboration between infectious disease specialists and rhythmologists are followed.

The acquired immunodeficiency syndrome (AIDS) caused by the human immunodeficiency virus (HIV) continues to be a public health problem. In 2020, 680,000 people died from HIV-related causes, and 1.5 million people were infected. Antiretrovirals are only a way to control HIV infection but not to cure AIDS. As such, effective treatment must be developed to control AIDS. Developing a drug is not an easy task, and there is an enormous amount of work and economic resources invested. For this reason, it is highly convenient to employ computer-aided drug design methods, which can help generate and identify novel molecules. Using the de novo design, new novel molecules can be developed using fragments as building blocks. In this work, we develop a virtual-focused compound library of HIV-1 viral protease inhibitors from natural product fragments. Natural products are characterized by a large diversity of functional groups, many sp3 atoms, and chiral centers. Pseudo-natural products are a combination of natural products fragments that keep the desired structural characteristics from different natural products. An interactive version of chemical space visualization of virtual compounds focused on HIV-1 viral protease inhibitors from natural product fragments is freely available at https://figshare.com/s/ceb58d58e8f5585ce67e.

Despite advances in algorithms and computational platforms, de-novo genome assembly remains a challenging process. Due to the constant innovation in sequencing technologies (Sanger, SOLiD, Illumina, 454, PacBio and Oxford Nanopore), genome assembly has evolved to respond to the changes in input data type. This paper includes a broad and comparative review of the most recent short-read, long-read and hybrid assembly techniques. In this review, we provide (1) an algorithmic description of the important processes in the workflow that introduces fundamental concepts and improvements; (2) a review of existing software that explains possible options for genome assembly; and (3) a comparison of the accuracy and the performance of existing methods executed on the same computer using the same processing capabilities and using the same set of real and synthetic datasets. Such evaluation allows a fair and precise comparison of accuracy in all aspects. As a result, this paper identifies both the strengths and weaknesses of each method. This comparative review is unique in providing a detailed comparison of a broad spectrum of cutting-edge algorithms and methods.

In this paper, a local meshless method (LMM) based on radial basis functions (RBFs) is utilized for the numerical solution of various types of PDEs, due to the flexibility with respect to geometry and high order of convergence rate. In case of global meshless methods, the two major deficiencies are the computational cost and the optimum value of shape parameter. Therefore, research is currently focus towards localized radial basis function approximations, as the local meshless method is proposed here. The local meshless procedures is used for spatial discretization whereas for temporal discretization different time integrators are employed. The proposed local meshless method is testified in terms of efficiency, accuracy and ease of implementation using regular and irregular domains.

The New Zealand brushtail possum (Trichosurus vulpecula), introduced from Australia in the 1850s, is an invasive species that is widespread throughout New Zealand and forms the largest self-sustained reservoir of bovine tuberculosis (Mycobacterium bovis) in the wild. Conservation and agricultural authorities regularly apply a series of population control measures to suppress brushtail possum populations. The evolutionary consequence of more than half a century of intensive population control operations on the species genomic diversity and population structure is hindered by a paucity of available genomic resources for the species. This study is the first to characterise the functional content and diversity of brushtail possum liver and brain cerebral cortex transcriptomes. Raw sequences from hepatic cells and cerebral cortex were assembled into 58,001 and 64,735 transcripts in hepatic cells and cerebral cortex, respectively. Functional annotation and polymorphism assignment of the assembled transcripts demonstrated a considerable level of variation in the core metabolic pathways that represent potential targets for selection pressure exerted by chemical toxicants. This study suggests that the brushtail possum population in New Zealand harbours considerable levels of variation in metabolic pathways that could potentially promote the development of tolerance against chemical toxicants.

Recently, the properties of bouncing oil droplets, also known as `walkers', have attracted much attention because they are thought to offer a gateway to a better understanding of quantum behaviour. They indeed constitute a macroscopic realization of wave-particle duality, in the sense that their trajectories are guided by a self-generated surrounding wave. The aim of this paper is to try to describe walker phenomenology in terms of de Broglie-Bohm dynamics and of a stochastic version thereof. In particular, we first study how a stochastic modification of the de Broglie pilot-wave theory, à la Nelson, affects the process of relaxation to quantum equilibrium, and we prove an H-theorem for the relaxation to quantum equilibrium under Nelson-type dynamics. We then compare the onset of equilibrium in the stochastic and the de Broglie-Bohm approaches and we propose some simple experiments by which one can test the applicability of our theory to the context of bouncing oil droplets. Finally, we compare our theory to actual observations of walker behavior in a 2D harmonic potential well.

The BRFSS is an annual survey conducted by each state and designed to identify trends in a representative sample of the resident population. In its 2019 field survey, the U.S. state of Georgia tested a new 3 – item module to measure the numbers of bereaved, resident adults. Bereavement means that participants answered, ‘Yes’ to the item ‘Have you experi-enced the death of a family member or close friend in the years 2018 or 2019?’. This analysis addresses two questions. Can estimates for bereavement prevalence be derived without large sampling errors, low precision, and small subsamples? Can multiple imputation techniques be applied to overcome non-response and missing data to support multivari-ate modeling? Analyses in this study were conducted under two scenarios. Scenario 1 ap-plies the complex sample weights created by the Centers for Disease Control and imputes values for missing responses. Scenario 2 treats the data as a panel – no weighting com-bined with removal of persons with missing data. Scenario 1 reflects the use of BRFSS data for public health and policy, while Scenario 2 reflects data as it is commonly used in so-cial science research. The bereavement item has a response rate (RR) of 70.8% (5206 of 7534 persons). Subgroups have RR of 55% or more. Under Scenario 1, the prevalence of bereavement is 45.38%, meaning that 3,739,120 adults reported bereaved in 2018 or 2019. The prevalence is 46.02% with Scenario 2 which removes persons with any missing data (4,289 persons). Scenario 2 overestimates the bereavement prevalence by 1.39%. An il-lustrative logistic model is included to show the performance of exposure to bereavement under each scenario. Recent bereavement can be ascertained in a surveillance survey without biases in response. This survey is limited to one US state in a single year and ex-cludes persons aged 17 years and younger.

G protein-coupled receptors (GPCRs) are amongst the most pharmaceutically relevant and well-studied protein targets, yet unanswered questions in the field leave significant gaps in our understanding of their nuanced structure and function. 3D pharmacophore models are powerful computational tools in silico drug discovery, presenting myriad opportunities for the integration of GPCR structural biology and cheminformatics. This review highlights success stories in the application of 3D pharmacophore modeling to de novo drug design, discovery of biased and allosteric ligands, scaffold hopping, QSAR analysis, hit-to-lead optimization, GPCR de-orphanization, mechanistic understanding of GPCR pharmacology and elucidation of ligand-receptor interactions. Furthermore, advances in the incorporation of dynamics and machine learning will be highlighted. The review will analyze challenges in the field of GPCR drug discovery, detailing how 3D pharmacophore modeling can be used to address them. Finally, we will present opportunities afforded by 3D pharmacophore modeling in the advancement of our understanding and targeting of GPCRs.

– Every physical theory involving quantum fields does require a model of the quantum vacuum. The vacuum associated to quantum gravity must incorporate the prescriptions from both the theory of relativity and quantum physics. In this work, starting from the hypothesis of nucleation of sub-Planckian bubbles from a de Sitter vacuum, we study the necessary conditions to obtain baby universes, black holes and particles. The de Sitter-Planck background is described by an “infinite” Quantum Boltzmann statistics that generates fermions and bosons, and manifests itself as a deformation of the geometry that leads to a generalized uncertainty principle and a unified expression for the generalized Compton wavelength and event horizon size, drawing a connection between quantum black holes and elementary particles, the latter seen as a collective organization of the bubbles of the vacuum described by the generalized Compton wavelength. The quantum thermodynamics of black holes is then outlined and the physical history of each bubble is found to depend on the cosmological constant described in terms of thermodynamic pressure. Finally, a suggestive treatment of the Casimir effect is provided in the de Sitter-Planck background with Quantum-Boltzmann statistics and wormholes are explored as bubble coalescence processes.

The underlying physical concept of computing out-of-time-ordered correlation (OTOC) is a significant new tool within the framework of quantum field theory, which now-a-days is treated as a measure of random fluctuations. In this paper, by following the canonical quantization technique we demonstrate a computational method to quantify the two different types of Cosmological auto-correlated OTO functions during the epoch when the non-equilibrium features dominates in Primordial Cosmology. In this formulation, two distinct dynamical time scales are involved to define the quantum mechanical operators arising from cosmological perturbation scenario. We have provided detailed explanation regarding the necessity of this new formalism to quantify any random events generated from quantum fluctuations in Primordial Cosmology. We have performed an elaborative computation for the two types of two-point and four-point auto-correlated OTO functions in terms of the cosmological perturbation field variables and its canonically conjugate momenta to quantify random auto-correlations in the non-equilibrium regime. For both the cases we found significantly distinguishable non-chaotic, but random behaviour in the OTO auto-correlations, which was not pointed before in this type of studies. Finally, we have also demonstrated the classical limiting behaviour of the mentioned two types of auto-correlated OTOC functions from the thermally weighted phase space averaged Poisson Brackets, which we found exactly matches with the large time limiting behaviour of the auto-correlations in the super-horizon regime of the cosmological scalar mode fluctuation.

Plant-parasitic nematodes cause expressive annual yield losses to worldwide agricultural production. Most cultivated plants have no known resistance against nematodes and the few bearing a resistance gene can be overcome by certain species. The chemical methods that have been deployed to control nematodes were largely banned from use due to their poor specificity and high toxicity. Hence, there is an urgent need for the development of cleaner and more specific control methods. Recent advances in nematode genomics, including in phytoparasitic species, provide an unprecedented opportunity to identify genes and functions specific to these pests. Using phylogenomics, we compared 61 nematode genomes, including 16 for plant-parasitic species and identified more than 24,000 protein families specific to these parasites. In the genome of Meloidogyne incognita, one of the most devastating plant parasites, we found ca. 10,000 proteins with orthologs restricted only to phytoparasitic species and no further homology in protein databases. Among these phytoparasites-specific proteins, ca. 1,000 shared the same properties as known secreted effectors involved in essential parasitic functions. Of those, 68 were novel and showed strong expression during the endophytic phase of the nematode life cycle, based on both RNA-seq and RT-qPCR analyses. Besides effector candidates, transcription-related and neuro-perception functions were enriched in phytoparasites-specific proteins, revealing interesting targets for nematode control methods. This phylogenomics analysis, constitutes an unprecedented resource for the further understanding of the genetic basis of nematode adaptation to phytoparasitism and for the development of more efficient control methods.

We suggest that momentum should be redened in order to help make physics more consistent and more logical. In this paper, we propose that there is a rest-mass momentum, a kinetic momentum, and a total momentum. This leads directly to a simpler relativistic energy momentum relation. As we point out, it is the Compton wavelength that is the true wavelength for matter; the de Broglie wavelength is mostly a mathematical artifact. This observation also leads us to a new relativistic wave equation and a new and likely better QM. Better in terms of being much more consistent and simpler to understand from a logical perspective.

For the majority of lipophilic compounds adipose tissue is traditionally considered as storage depot and only rarely as a target organ. Meanwhile, abnormalities in adipose tissue physiology induced by chemical exposures may contribute to the current epidemic of obesity and metabolic diseases. Polybrominated diphenyl ethers (PBDEs) is a group of lipophilic flame retardants found in majority of human samples in North America. Their ability to alter physiology of adipose tissue is unknown. We exposed pregnant mice to 0.2 mg/kg body weight/day of BDE-47 perinatally. Transcriptomic changes in gonadal adipose tissue were analyzed in male offspring using RNA-seq approach with subsequent bioinformatic analysis. Genes of coagulation and complement cascade, de novo lipogenesis, and xenobiotic metabolism were altered in expression in response to BDE-47 exposure. The affected molecular network included the following hubs: PPARα, HNF1A and HNF4. These findings suggest that adipose tissue should be considered a target tissue for BDE-47, in addition to its role as a storage depot. This study also builds a background for a targeted search of sensitive phenotypic endpoints of BDE-47 exposure, including lipid profile parameters and coagulation factors in circulation. Additional studies are needed to investigate the role of PBDEs as an obesogen.

We introduce the Hermite based poly-Bernoulli polynomials with a q parameter and give someof their basic properties including not only addition property, but also derivative properties and integralrepresentations. We also de.ne the Hermite based λ -Stirling polynomials of the second kind, and thenprovide some relations. Moreover, we derive several correlations and identities including the Hermite-Kampéde Fériet (or Gould-Hopper) family of polynomials, the Hermite based poly-Bernoulli polynomials with a qparameter and the Hermite based λ -Stirling polynomials of the second kind.

We outline and test a new methodology for genuine simulation of stochastic processes with any dependence and any marginal distribution. We reproduce time dependence with a generalized, time symmetric or asymmetric, moving-average scheme. This implements linear filtering of non-Gaussian white noise, with the weights of the filter determined by analytical equations in terms of the autocovariance of the process. We approximate the marginal distribution of the process, irrespective of its type, using a number of its cumulants, which in turn determine the cumulants of white noise in a manner that can readily support the generation of random numbers from that approximation, so that it be applicable for stochastic simulation. The simulation method is genuine as it uses the process of interest directly without any transformation (e.g. normalization). We illustrate the method in a number of synthetic and real-world applications with either persistence or antipersistence, and with non-Gaussian marginal distributions that are bounded, thus making the problem more demanding. These include distributions bounded from both sides, such as uniform, and bounded form below, such as exponential and Pareto, possibly having a discontinuity at the origin (intermittence). All examples studied show the satisfactory performance of the method.

A relationship between the functional Schr\"odinger representation and the precanonical quantization of a nonlinear scalar field theory is extended to arbitrary curved space-times. The canonical functional derivative Schr\"odinger equation is derived from the manifestly covariant precanonical Schr\"odinger equation in a singular limiting case when the ultraviolet parameter $\varkappa$ introduced by precanonical quantization is identified with the invariant delta-function at equal spatial points. In the same limiting case, the Schr\"odinger wave functional is expressed as the trace of the multidimensional product integral of Clifford-algebra-valued precanonical wave functions restricted to a certain field configuration. Thus the standard QFT in curved space-time in functional Schr\"odinger representation emerges from the precanonical formulation of quantum fields as a singular limiting case.

Physical processes play important roles in controlling eutrophication and oligotrophication. In stratified lakes, internal waves can cause vertical transport of heat and nutrients without breaking the stratification, through boundary mixing events. Such is the case in tropical Valle de Bravo (VB) lake, where strong diurnal winds drive internal waves, boundary mixing and hypolimnetic warming during stratification periods. We monitored VB during 18 years (2001-2018) when important water-level fluctuations (WLF) occurred, affecting mixing and nutrient flux. Mean hypolimnetic temperature increase (0.06–1.04°C month-1) occurred in all the stratifications monitored. We analyzed temperature distributions and modeled the hypolimnion heat budget to assess vertical mixing between layers (26,618–140,526 m-3h-1), vertical diffusivity coefficient KZ (6.2x10-7–3.3x10-6 m2s-1) and vertical nutrient entrainment to epilimnion on monthly scale. Stability also varied as a function of WLF. Nutrient flux to the epilimnion ranged 0.36–5.99 mg m-2d-1 for soluble reactive phosphorus (SRP) and 5.8–97.1 mg m-2d-1 for dissolved inorganic nitrogen (DIN). During low water-level years, vertical nutrient fluxes increase and can account for up to >40% of the total external nutrients load to the lake. Vertical mixing changes related to WLF affect nutrient recycling, their flux to sediments, ecosystemic metabolic balance and planktonic composition of VB.

Behavior of supported alloyed and de-alloyed platinum-copper catalysts, which contained 14% - 27% wt. of Pt, was studied in the reactions of methanol electrooxidation (MOR) and oxygen electroreduction (ORR) in 0.1 M HClO4 solutions. Alloyed PtCux/C catalysts were prepared by a multistage sequential deposition of copper and platinum onto a Vulcan XC72 dispersed carbon support. De-alloyed PtCux-y/C catalysts were prepared by PtCux/C materials pretreatment in acid solutions. The effects of the catalysts initial composition and the acid treatment condition on their composition, structure, and catalytic activity in MOR and ORR were studied. Functional characteristics of platinum-copper catalysts were compared with those of commercial Pt/C catalysts when tested, both in an electrochemical cell and in H2/Air membrane-electrode assembly (MEA). It was shown that the acid pretreatment of platinum-copper catalysts practically does not have negative effect on their catalytic activity, but it reduces the amount of copper passing into the solution during the subsequent electrochemical study. The activity of platinum-copper catalysts in the MOR and the current-voltage characteristics of the H2/Air PEMFC MEAs measured in the process of their life tests were much higher than those of the Pt/C catalysts.

We study C*-algebraic versions of following conjectures/theorems: (1) Bieberbach conjecture (de Branges theorem) (2) Robertson conjecture (3) Lebedev-Milin conjecture (4) Zalcman conjecture (5) Krzyz conjecture (6) Corona conjecture (Carleson theorem). We prove that the C*-algebraic Bieberbach Conjecture for invertible coefficients is true for second degree C*-algebraic polynomials.

We review consequences for the radiation and dark sectors of the cosmological model arising from the postulate that the CMB is governed by an SU(2) rather than a U(1) gauge principle. We also speculate on the possibility of actively assisted structure formation due to the de-percolation of lump-like configurations of condensed ultralight axions with a Peccei-Quinn scale comparable to the Planck mass. The chiral-anomaly induced potential of the axion condensate receives contributions from SU(2)/SU(3) Yang-Mills factors of hierarchically separated scales which act in a screened (reduced) way in confining phases.

Noise reduction in medical images is a perplexing undertaking for the researchers in digital image processing. Noise generates maximum critical disturbances as well as touches the medical images quality, ultrasound images in the field of biomedical imaging. The image is normally considered as gathering of data and existence of noises degradation the image quality. It ought to be vital to reestablish the original image noises for accomplishing maximum data from images. Medical images are debased through noise through its transmission and procurement. Image with noise reduce the image contrast and resolution, thereby decreasing the diagnostic values of the medical image. This paper mainly focuses on Gaussian noise, Pepper noise, Uniform noise, Salt and Speckle noise. Different filtering techniques can be adapted for noise declining to improve the visual quality as well as reorganization of images. Here four types of noises have been undertaken and applied on medical images. Besides numerous filtering methods like Gaussian, median, mean and Weiner applied for noise reduction as well as estimate the performance of filter through the parameters like mean square error (MSE), peak signal to noise ratio (PSNR), Average difference value (AD) and Maximum difference value (MD) to diminish the noises without corrupting the medical image data.

As an important follow-up report on the latest study of the first author (H.S.) on an off-shell quantum field causing a dressed photon and dark energy, we further discuss a couple of intriguing subjects based on our new theory. One is the dressed photon constant. If we use it, in addition to h¯ and c, as the third component of natural units, then it is defined as the geometric mean of the smallest and the largest lengths: Planck length and that relating to the cosmological constant. Interestingly, this length (≈ 50 nanometers) seems to give a rough measure of the Heisenberg cut for electromagnetic phenomena. The other is a new perspective on cosmology that combines two original notions, i.e., twin universes and conformal cyclic cosmology, proposed respectively by Petit and Penrose, into one novel picture where universes expand self-similarly. We show the possibility that twin universes having a dual structure of [matter with (dark energy & matter)] vs. corresponding anti-entities, separated by an event horizon embedded in the geometric structure of de Sitter space, undergo endless cyclic processes of birth and death, as in the case of the pair creation and annihilation of elementary particles through the intervention of a conformal light field.

With the rise of long-read sequencers and long-range technologies, delivering high-quality plant genome assemblies is no longer reserved to large consortia. Indeed, sequencing techniques but also computer algorithms have reached a point where the reconstruction of assemblies at the chromosome-scale is now feasible at the laboratory scale. Current technologies, and especially long-range technologies, are numerous and selecting the most promising one for the genome of interest is crucial to obtain optimal results. In this study, we resequenced the genome of the yellow sarson, Brassica rapa cv. Z1, using the Oxford Nanopore PromethION sequencer and assembled the sequenced data using current assemblers. To reconstruct complete chromosomes, we used and compared three long-range techniques, optical mapping, Omni-C and Pore-C sequencing libraries commercialized by Bionano Genomics, Dovetail Genomics and Oxford Nanopore Technologies respectively, or a combination of the three, in order to evaluate the capability of each technology.

The Gilles de la Tourette syndrome (GTS) and Non-Coeliac Gluten Sensitivity (NCGS) may be associated. We analyse the efficacy of a gluten-free diet (GFD) in 29 patients with GTS (23 children; 6 adults) in a prospective pilot study. All of them followed a GFD for one year. The YGTSS, Y-BOCS/CY-BOCS and GTS-QOL questionnaires were compared before and after the GFD. 74% of children and 50% of adults were males, not significant (NS). At the beginning of the study, 69% of children and 100% of adults had associated OCD (NS). At baseline, the YGTSS scores were 55.0 ± 17.5 (children) and 55.8 ± 19.8 (adults) (NS), the Y-BOCS/CY-BOCS scores were 15.3 (SD = 12.3) (children) and 26.8 (9.2) (adults) (p = 0.043), and the GTS-QOL scores were 42.8 ± 18.5 (children) and 64 ± 7.9 (adults) (p = 0.000). NCGS was frequent in both groups, with headaches reported by 47.0% of children and 83.6% of adults (p = 0.001). After one year on a GFD there was a marked reduction in measures of tics (YGTSS) (p = 0.001), and the intensity and frequency of OCD (Y-BOCS/CY-BOCS) (p = 0.001), along with improved QOL (p = 0.001) in children and adults. In conclusion, a GFD maintained for one year in GTS patients led to a marked reduction in tics and OCD both in children and adults.

Applying a procedure similar to that of E.S. Bring, by using a 4^th degree Tschirnhaus transformation, it was possible to transform the Bring-Jerrard normal quintic (BJQ) equation into a De Moivre form (DMQ), so that it could be solved by radicals. The general solution by radicals of the De Moivre equations of any degree is presented. By the same procedure the BJSx (normal sextic) equation was taken to another one without the 2^nd, 4^th and 6^th terms which was transformed into a cubic (solvable) equation. By applying a 6^th degree Tschirnhaus transformation to the BJSp (normal septic) equation its binormal (without the 2^nd, 3^rd, 4^th and 5^th terms) form was obtained.

Applying a procedure similar to that of E.S. Bring, by using a 4^th degree Tschirnhaus transformation, it was possible to transform the Bring-Jerrard normal quintic (BJQ) equation into a De Moivre form (DMQ), so that it could be solved by radicals. The general solution by radicals of the De Moivre equations of any degree is presented. By the same procedure the BJSx (normal sextic) equation was taken to another one without the 2^nd, 4^th and 6^th terms which was transformed into a cubic (solvable) equation. By applying a 6^th degree Tschirnhaus transformation to the BJSp (normal septic) equation its binormal (without the 2^nd, 3^rd, 4^th and 5^th terms) form was obtained.

Applying a procedure similar to that of E.S. Bring, by using a 4^th degree Tschirnhaus transformation, it was possible to transform the Bring-Jerrard normal quintic (BJQ) equation into a De Moivre form (DMQ), so that it could be solved by radicals. The general solution by radicals of the De Moivre equations of any degree is presented. By the same procedure the BJSx (normal sextic) equation was taken to another one without the 2^nd, 4^th and 6^th terms which was transformed into a cubic (solvable) equation. By applying a 6^th degree Tschirnhaus transformation to the BJSp (normal septic) equation its binormal (without the 2^nd, 3^rd, 4^th and 5^th terms) form was obtained.

Applying a procedure similar to that of E.S. Bring, by using a 4^th degree Tschirnhaus transformation, it was possible to transform the Bring-Jerrard normal quintic (BJQ) equation into a De Moivre form (DMQ), so that it could be solved by radicals. The general solution by radicals of the De Moivre equations of any degree is presented. By the same procedure the BJSx (normal sextic) equation was taken to another one without the 2^nd, 4^th and 6^th terms which was transformed into a cubic (solvable) equation. By applying a 6^th degree Tschirnhaus transformation to the BJSp (normal septic) equation its Bring-Jerrard binormal (without the 2^nd, 3^rd, 4^th and 5^th terms) form was obtained.

The paper briefly reviews the Clifford algebras of space Cl(3,0) and anti-space Cl(0,3) with a particular focus on the paravector representation, emphasizing the fact that both algebras have an isomorphic center represented just by two coordinates. Since the paravector representation allows assigning the scalar element of grade 0 to the time coordinate, we consider the relativity in such two-dimensional spacetime for a uniformly accelerated frame with the constant acceleration 3Hc. Using the Rindler coordinate transformations in two-dimensional spacetime and then applying it to Minkowski coordinates, we obtain the FLRW metric, which in the case of the Clifford algebra of space Cl(3,0) corresponds to the anti-de Sitter (AdS) flat (k=0) case, the negative cosmological term and an oscillating model of the universe. The approach with anti-Euclidean Clifford algebra Cl(0,3) leads to the de Sitter model with the positive cosmological term and the exact form of the scale factor used in modern cosmology.