bluuebunny/crossref_metadata_2025 huggingface dataset:
The method of approximate inverse for the normal Radon transform operator
Authors: Svetov I E , Polyakova A P
Published: January 2021

We propose an approach for reconstructing a three-dimensional function from the known values of the Radon transform. The approach is based on the method of approximate inverse. The result obtained is the basis of two approaches for reconstructing a potential part of the vector and symmetric 2-tensor fields from the known values of the normal Radon transform. The first approach allows the recovery of components of the potential part of fields, and the second one reconstructs a potential of the potential part of fields.
Towards Optimizing Cloud Computing Using Residue Number System
Authors: Kucherov N , Kuchukova E , Tchernykh A , Kuchukov V , Babenko M
Published: January 2021

In the work methods for building systems of distributed data storage based on the system of residual classes are considered. The use of direct conversion of data from the positional system of calculation to the residue number system will have a large computational complexity, the use of modules of a particular type allows you to solve this problem. The operation of scaling and expansion of the base system, which is necessary to restore the number of stored parts in case of failure of one or more cloud servers, is considered.
Application of the Dorovsky model for taking into account the fluid saturation of geological media
Authors: Golubev V I , Shevchenko A V , Petrov I B
Published: January 2021

The discovery of oil deposits with complex internal structures requires an improvement of available seismic survey methods. The development of modern high-performance computing systems provides an opportunity to use more sophisticated mathematical models. This paper aims to investigate seismic wave propagation in porous fluid-saturated media. The Dorovsky three velocity model was formulated in the two-dimensional case and its numerical solution was obtained with the grid-characteristic method. The computational domain consisted of three layers with different rheology: a water layer, a porous fluid-saturated layer, and an elastic layer. Explicit contact conditions were derived between them and successfully applied with the help of Riemann invariants. The curvature of geological layers was taken into consideration by means of structured hexahedral grids. The time evolution of the spatial distribution of stress tensors and material velocity vectors were calculated and analyzed. These signals contain a mixture of volume, surface, transmitted and reflected waves.
The numerical solution of the problem of the contact interaction in models with gas pockets
Authors: Stognii P.V. , Khokhlov N.I. , Petrov I.B.
Published: January 2021

We present the solution to the problem of detecting the gas layers in the Arctic conditions through the numerical modelling of the seismic waves spread in the heterogeneous media. The grid-characteristic method of the third order of accuracy is used in all the computations. We build the models with the different numbers of the gas layers and analyze the full wave fields in the heterogeneous media and the anomalous fields, excluding the seismic reflections from all the geological layers except for the gas layers. The results demonstrate the possibility of applying the grid-characteristic method to solving these problems. The result seismograms allow us to determine the location of the gas layers through collecting the time moments of the coming reflections from the gas layers to the seismic receivers.
Statistical simulation of radiation transfer in horizontally inhomogeneous stratus clouds
Authors: Kablukova E G , Prigarin S M
Published: January 2021

The aim of the paper is to analyze the influence of a cloud layer horizontal inhomogeneity on radiation fluxes in the atmosphere using the models based on observation data of the optical thickness for stratus clouds. To reproduce the correlation structure and one-dimensional distributions of the observed stratus optical thickness fields we have developed numerical stochastic cloud models based on the inverse distribution function method and autoregressive schemes. We used Monte Carlo methods to simulate the radiation fluxes for visible and infrared ranges of wavelength.
Monte Carlo simulation of the laser pulse propagation in water layers with reflection on boundaries
Authors: Mironova D E , Prigarin S M
Published: January 2021

By Monte Carlo method we study peculiarities of scattering of short laser pulses in the water media with reflection from the underlying and water-air boundaries. The results of numerical modeling show that the ring-shaped structures of light may appear in the water layers.
On vortex sheet intensity reconstruction in meshless vortex particle method for two-dimensional flows simulation
Authors: Soldatova I , Kuzmina K , Yakutina M
Published: January 2021

The problem of numerical solution of the boundary integral equation arising in 2D Lagrangian meshless vortex particle methods is considered. The Viscous vortex domains method used for viscous flow simulation, that leads to a large number of vortex particles in the flow domain, especially in the near-wall region. From a mathematical point of view, it leads, in turn, to the fast oscillating right-hand side of the integral equation. An original correction technique is developed that permits one to obtain a numerical solution with high resolution without grid refining. It is based on the Galerkin approach where additional terms are included in numerical solution expansion, that correspond to the subgrid-scale of the solution variation.
Building ontologies for solving compute-intensive problems
Authors: Glinskiy B M , Zagorulko Y A , Zagorulko I M Kulikov G B , Sapetina A F , Titov P A , Zhernyak G F
Published: January 2021

The aim of the study, results of which are presented in this paper, is to analyse methods and tools for constructing an ontology related to solving compute-intensive problems and to form algorithms of its use. This problem arises from the need to solve problems using modern and future supercomputers, containing millions and, in the long term, billions of simultaneously operating computing cores and having a huge degree of parallelism. In solving such problems, the researcher should be well versed in both computational methods for solving the problem and modern supercomputer technologies, which is not always the case. One of the solutions to this problem is the creation of a knowledge base that includes ontological descriptions of methods for solving compute-intensive problems and architectures of supercomputers that can be used to solve them. The development of ontologies for a given subject area is one of the most important stage in creating an intelligent support system for solving specific compute-intensive problems. The paper discusses the methods and tools that are used to build the ontology. The paper also presents examples of the development of ontologies for astrophysics and geophysics problems.
A fractional numerical study on advection-dispersion equation with fractional order
Authors: Fadugba SE , Edogbanya HO , Ogunyebi SN , Babalola BT , Okunlola JT
Published: January 2021

This paper proposes a fractional numerical study on Advection-Dispersion Equation (ADE) with Fractional Order (FO) via the Caputo Fractional Reduced Differential Transform Method (CFRDTM). CFRDTM is the combination of the Caputo Fractional Derivative (CFD) and the well known Transform Method (RDTM). A convergent series solution for ADE with FO is obtained via CFRDTM. The performance of CFRDTM is tested on two illustrative examples. Hence, CFRDTM is found to be accurate and efficient.
Diagnosis of COVID-19 using artificial intelligence based model
Authors: Omoniyi TA , Alabere HO , Sule E E
Published: January 2021

Scientists have shown that early diagnosis of COVID-19 and self-isolation can help curb the spread of the virus. Hence, there is a need to develop methods for early and fast diagnosis of the disease. This research focuses on the development and use of an AI based model that would help medical professionals in easy and fast detection of COVID-19 that can be found in X-ray images, CT scan images, and patient symptoms. The model would then be deployed to the web for easy accessibility. To increase the confident level of decision made by the model, different data augmentation technique was deployed to create variance to the dataset and thereby increasing the accuracy and validation of the model. This project proposes the use of Convolutional Neural Network for classification purpose of both the X-ray image of the Lung of a positive and negative pneumonia patient. Further processes were done with CT scan images of both positive and negative COVID-19 patients. This eliminated biasness of the model. Lastly, symptoms of the disease were added to the model as conditional statement convolutional neural network model. The model was able to reach an overall accuracy of 95% for Pneumonia X-ray image and 89.65% for CT scan image of unseen data (test/evaluation). Artificial intelligence based model is therefore, encouraged for better, easier and more accurate diagnosis of COVID-19. Also, the accuracy of the model can further be improved by certain feature engineering technique and adding more complex deep neural network technique known as ensembles.
Iterative methods for approximate solution of the Ornstein-Uhlenbeck process with normalised brownian motion
Authors: Ogundile O. P. , Edeki S. O.
Published: January 2021

This work considers the concept of the Normalised Brownian motion for the solutions of the Ornstein-Uhlenbeck process using the Daftardar-Jafari Method (DJM) and Picard Iterative Method (PIM) as the approximate-analytical methods of solutions. The results obtained from DJM are compared with those of the PIM. The obtained results, therefore, show the effectiveness of the proposed methods.
Analysis and applicability of a new quartic polynomial one-step method for solving COVID-19 model
Authors: Fadugba S E , Shaalini V J , Ibrahim A A
Published: January 2021

This paper presents the Quartic Polynomial One-Step Method (QPOSM) based on quartic polynomial interpolating function for solving first order Ordinary Differential Equations (ODEs). The validity of the paper is analysed through consistency, order of convergence and stability. Also, the stability polynomial of this method is derived and the corresponding stability region is obtained. The applicability of the method has been demonstrated by COVID-19 model.
Application of the shooting method for the solution of second order boundary value problems
Authors: Edun Ifeoluwa F. , Akinlabi Grace O.
Published: January 2021

Due to the applications of Boundary Value Problems (BVPs) in real-life phenomena, the shooting method has proven itself useful and efficient in handling BVP. The shooting method works by first reducing the BVP to an Initial Value Problem (IVP), then one/two initial value guesses are made. The IVPs are then solved using an iterative solution, and this process is then repeated until the second boundary condition is reached to a satisfactory level. The iterative formula used in this study is the Euler’s method while the initial value estimation method used is the Secant method (interpolation formula).
Demulsification of a Nigerian crude emulsion using ethoxylated-resoles and their xylene modified blends
Authors: Efeovbokhan Vincent E. , Chibuzor Chukwuebuka C. , Babalola Rasheed , Abatan Olubunmi G. , Oladimeji Temitayo E.
Published: January 2021

Demulsification is a method used to reduce or disrupt the water - crude oil emulsion system without uttering the initial composition of the crude oil. This process is done by the introduction of chemicals called demulsifiers, which break the emulsion into aqueous and organic phases. In this study, the demulsifier formulated was the base-catalyzed phenol-formaldehyde resin known as the resoles, with the ratios of phenol to formaldehyde, varied between 1.0:1.2 and 1.0:2.0. The different samples of resoles where then ethoxylated to make them more hydrophilic using different weights (10, 15 & 20 g) of polyethylene glycol (PEG). Screening of the ethoxylated demulsifiers was done using the established bottle test procedure, at 70 °C, the concentration of 50 ppm, and 20 minutes of residence or separation time, in order to select the most effective demulsifier, based on the amount of water removed from the emulsion. The best chemical-demulsifier produced was the ethoxylated resole, which was then blended with xylene at varying percentages (0, 20, 40, 50, and 80 % weight/weight) and was further screened, using the bottle test method. From the analysis, it was obtained that the most effective ethoxylate-xylene demulsifier blend was sample DR3, and made of formaldehyde to phenol ratio of 1.8:1, 20 g of PEG 400 blended with 20 % xylene. The demulsifier gave a water separation efficiency of 85.7 %, compared with the commercial demulsifier, which yielded 72.7 %. The result indicates the practical significance of solvent modified demulsifiers for separating crude oil emulsions in the petroleum industries.
A feedforward artificial neural network model for classification and detection of type 2 diabetes
Authors: Frimpong Enoch A. , Oluwasanmi Ariyo , Baagyere Edward Y. , Zhiguang Qin
Published: January 2021

Efforts to enhance accuracy in medical diagnostics in molecular medicine have contributed to the wide use of artificial neural network (ANN) algorithms for disease detection due to its ability to process large medical datasets and integrate them into characterized outputs to avoid misdiagnosis. Typically, the application of ANNs have proven useful in sample analyses of patients with diabetes and in decision support systems. Over the years, various ANN models have been utilized in medical diagnostics; however, these approaches still maintain certain levels of error and have lesser training and testing accuracies in disease detection. In this study, we propose a Feedforward Artificial Neural Network (FFANN) model with a dense neural network architecture suitable for processing numeric and textual dataset. We carefully designed our model structure to have the ability to maximize the number of layers and nodes required to learn every feature of the dataset and also to perform effective computations but avoiding model under fitting and overfitting which occurs when less or more layers are used respectively. This approach puts our model ahead of other state-of-the-art prediction models which have been proposed in terms of performance as it achieved 97.27% and 96.09% training and testing accuracies, respectively, for type 2 diabetes detection on Pima Indian Diabetes dataset.
Effect of snail shell ash on black cotton soil
Authors: Ofuyatan O , Olowofoyeku A , Oluwafemi J
Published: January 2021

Black cotton soil stabilization with various agricultural additives has attained a lot of success due to increase in the demand for agricultural products. The engineering properties of black cotton soil due to the swelling and shrinkage problem, a research was carried out on the effect of snail shell ash in the black cotton soil properties such as the Optimum moisture content (OMC), Maximum dry density (MDD), Atterberg limit, Shrinkage limit, and California bearing ratio (CBR) were studied. It has been observed by the experiments conducted on the sample by using snail shell ash of varying percentages (0%, 4%, 8%, 12%, 16% and 20%) by weight of dry soil. Based on the results from the various tests carried out-(Specific gravity, Atterberg limit, Compaction test, Hydrometer Analysis, Shrinkage limit and California bearing ratio) it shows that the black cotton soil under the AASHTO soil classification and USCS soil classification, the black cotton soil is highly organic, so that leads to the use of hydrometer analysis-calibration method. The natural liquid limit value of the soil before the stabilization process is 54.8%, at 16% SSA it decreases to 40.4%. The OMC of its natural state is 18.82%, so at 12% SSA it decreases to 11.72%, while the MDD at the natural state is 1357Kg/m3, so at 16% SSA it increases to 1738 Kg/m3. The CBR value of the soil in natural state is 27.19, so at 16% SSA it increases to 40. The results demonstrated the positive effect of snail shell ash in black cotton soil at 16% snail shell ash improving the strength of the engineering properties.
KPI measurement on the 4G network within the University of Ilorin
Authors: Oje A. A , Edeki S. O.
Published: January 2021

The present work seeks to address the following question which serves a key motivation behind this research: ‘What if there is a guide on the University of Ilorin website or in the weekly published magazine within the school, guiding the student on which MNO is best for internet connectivity based on the location which they are at any point in time?″. This research is key to answering the question. Data was gathered through a walk test using TEMS Investigation 16.3.4 and analyzed using TEMS Discovery Device 10. The test was based on internet access on the 4G Network by users who are subscribed to the various MNOs that are serving within the school premises.
Performance analysis of service users’ perception of mobile network quality in the learning settings
Authors: Oje A. A , Edeki S. O.
Published: January 2021

This paper aims to provide information about the mobile network operators as presented by the users. The research tool used is a questionnaire that was distributed physically as well as online using google forms. One hundred fifty (150) questionnaires were distributed, and 101 recovered. There were 50 respondents online. The results obtained about the number of subscribers per Mobile Network Operator (MNO) reflects the data published by the Nigeria Communication Commission (NCC), this by interpretation, proves the validity of the research data.
Design and implementation of electronic biomedical device for monitoring heartbeat rate and blood oxygen
Authors: Gabriella Igebu Anesi , Somefun Tobiloba , Olajube Ayobami , Samuel Isaac
Published: January 2021

The ongoing innovative advancements in remote correspondence, low-power processors and electronic gadgets make the Internet of Things (IoT) a reality. With recent pandemic due to COVID-19, several industries have integrated IoT into their systems in order to aid continuous production and delivery of their service. In this study, an electronic biomedical sensor which is used to detect heartbeat rate and blood oxygen is synchronised with IoT to aid delivery of service of the healthcare sector to patients that can be placed under the category of outpatient. Furthermore, an app is designed using AdobeXD and developed using Flutter to communicate with electronic biomedical sensor for patients’ data record and emergency communication.
A new approach for the solution of the Black-Scholes equation with barrier option constraints
Authors: Fadugba SE , Edeki SO
Published: January 2021

This paper introduces an efficient approach to solve the Black-Scholes Partial Differential Equation (BSPDE) with Barrier Option Constraints (BCOs). The approach of the Laplace–Adomian Decomposition Method (LADM), which is the combination of the Laplace Transform Method (LTM) and the Adomian Decomposition Method (ADM) is employed. The LTM is applied to the BSPDE, and the ADM is used for decomposing the solution of BSPDE into an infinite series. Moreover, the approximate solution obtained via LADM is expressed in the form of a convergent series with computed components. An illustrative example is presented, and the results are compared with the Analytical Value (AV). Hence, LADM is found to be effective and a powerful technique for obtaining an approximate solution of BSPDE with BCOs.
Analysis and multiple control measures for a typhoid fever disease model
Authors: Collins O C , Okeke J E
Published: January 2021

Typhoid fever is one of the diseases that is affecting humanity globally especially in the developing countries where access to clean environment and food are limited. We formulate a dynamical system model to study the effects of multiple control measures (i.e, vaccination, treatment and environmental sanitation) in mitigating typhoid fever disease. The qualitative analysis of our model was carried out accordingly. The impact of introducing the control measures were estimated using appropriate mathematical analysis and numerical simulations.
External acoustic control of the laminar vortex shedding past a bluff body
Authors: Lemke Mathias , Citro Vincenzo , Giannetti Flavio
Published: January 2021

This paper deals with the active control of the compressible flow past a bluff-body by means of external acoustic sources. We successfully suppress the transition leading to the von-Karman vortex street. The derived adjoint-based framework allows the determination of the corresponding acoustic sources for generic bluff-body shapes. In particular, we determine the optimal spatial position for the control, i.e. where the acoustic source is most efficient, and the associated temporal signal. For the proposed example, a two-dimensional cylindrical body, the resulting acoustic actuation is anti-symmetric and harmonic. We found that the limits of our control approach are related to the limits of linear acoustics. The methodology and the results proposed in this paper can be used to design a control strategy coupled with a continuation procedure able to obtain the unstable solutions beyond the critical threshold.
Pannexin 1 mutation found in melanoma tumor reduces phosphorylation, glycosylation, and trafficking of the channel-forming protein
Authors: Nouri-Nejad Daniel , O’Donnell Brooke L. , Patil Chetan S. , Sanchez-Pupo Rafael E. , Johnston Danielle , Sayedyahossein Samar , Jurcic Kristina , Lau Rebecca , Gyenis Laszlo , Litchfield David W. , Jackson Michael F. , Gloor Gregory B. , Penuela Silvia
Published: January 2021

In this study, we discovered the first mutation in a phosphorylation site of pannexin 1 (PANX1) that affects phosphorylation, glycosylation, and trafficking of PANX1 channels in a melanoma patient tumor. We also reported on the ancestral allele of PANX1 that is the most representative variant within human populations.
Integrin-linked kinase tunes cell–cell and cell-matrix adhesions to regulate the switch between apoptosis and EMT downstream of TGFβ1
Authors: Kilinc Ayse Nihan , Han Siyang , Barrett Lena A. , Anandasivam Niroshan , Nelson Celeste M.
Published: January 2021

Integrin-linked kinase regulates the switch between epithelial-mesenchymal transition and apoptosis downstream of transforming growth factor 1 by controlling the balance between cell–matrix and cell–cell adhesions in mammary epithelial cells.
Modeling the dynamic behaviors of the COPI vesicle formation regulators, the small GTPase Arf1 and its activating Sec7 guanine nucleotide exchange factor GBF1 on Golgi membranes
Authors: Sager Garrett , Szul Tomasz , Lee Eunjoo , Kawai Ryoichi , Presley John F. , Sztul Elizabeth
Published: January 2021

The initial reactions regulating cis-Golgi vesicle biogenesis are analyzed using FRAP paired with a Monte Carlo simulation. We demonstrate how these reactions qualitatively behave and predict the exact mechanism driving various molecular mutations. Furthermore, we outline a rigorous FRAP analysis that captures qualitative features of FRAP data.
Perceived versus objective sleep quality in long-stay hospitalised older adults—a mixed methods study
Authors: Aluzaite Kristina , Wu Harry , Hyslop Brent , Young Jessica , Schultz Michael , Brockway Ben
Published: January 2021

Background

Hospital inpatients experience substantial sleep problems that have been linked with worse health outcomes, poor quality of life and the post-hospital syndrome. However, little is known about assessing sleep issues in older hospitalised patients.

Objective

To conduct an in-depth investigation on hospitalised older adults’ sleep challenges and methods of sleep assessment.

Design

Cross-sectional observational study.

Setting

Public hospital inpatient unit.

Subjects

Long-stay hospitalised older adults.

Methods

Data were collected using validated sleep questionnaires, actigraphy devices and qualitative interviews. Quantitative data were analysed with descriptive statistics, multiple logistic regression and Cohen’s Kappa. Qualitative data were analysed with qualitative content analysis; findings compared to the quantitative assessments.

Results

We collected data on 33 older long-stay hospital inpatients, who were mean (SD) 80.2(7.4) years old, 57.6% female and were hospitalised following stroke, medical illness and orthopaedic fracture. Mean (SD) total sleep time and actigraphic sleep efficiency were 480.6(73.6) minutes and 81.5(11.2)%, respectively. About, 57.6% were poor sleepers (Pittsburgh Sleep Quality Index [PSQI]) and 30.8% had indicators of clinical depression/low quality of life (WHO-5 well-being index). Three main themes were identified: “sleep assessment”; “factors that affect sleep”; “expectations of sleep”. Bad sleepers were more likely to feel a lack of control over their sleep, while good sleepers spoke about the ability to adjust and accept their circumstances.

Conclusions

We found high levels of sleep problems and identified substantial discrepancies between the validated sleep questionnaire and qualitative response data. Our findings indicate that standard assessment tools, such as PSQI, may not be suitable to assess sleep in hospitalised older adults and call for further investigations to build more appropriate methods. Further exploring psychological factors and expectations could potentially lead to novel interventions to improve sleep in this setting.
Is the US Gender Gap in Depression Changing Over Time? A Meta-Regression
Authors: Platt Jonathan M , Bates Lisa , Jager Justin , McLaughlin Katie A , Keyes Katherine M
Published: January 2021

The depression gap refers to higher rates of depression among women than men. Change in the depression gap over time might elucidate social causes of this disparity—such as unequal college attendance or employment status. We conducted a meta-regression analysis to estimate variation in the depression gap over time by age, accounting for potential sources of variation between studies. Electronic databases and bibliographies were searched for English-language studies from January 1980 through October 2019; 144 independent estimates from US-representative samples met selection criteria (n = 813,189). The depression gap was summarized as prevalence ratios among studies using diagnostic instruments and as standardized mean differences among symptom-based studies. Primary study measures were baseline study year (range, 1982–2017) and age (age groups ranging, in years, from 10–59 and 60 or older). Compared with respondents aged ≥60 years, depression prevalence was greater among respondents aged 10–19 (prevalence ratio = 1.26, 95% confidence interval: 1.02, 1.56). Over time, the depression gap did not change among adults, but it increased among adolescents (age-by-time interaction prevalence ratio = 1.05, 95% confidence interval: 1.01, 1.08). Results were similar for symptom-based studies. The present study finds no evidence of a change in the depression gender gap for US adults; however, the gap increased among adolescents. Greater attention to factors driving this widening disparity in adolescent depression is needed.
Extensin, an underestimated key component of cell wall defence?
Authors: Castilleux Romain , Plancot Barbara , Vicré Maité , Nguema-Ona Eric , Driouich Azeddine
Published: January 2021

Background

Extensins are plant cell wall hydroxyproline-rich glycoproteins known to be involved in cell wall reinforcement in higher plants, and in defence against pathogen attacks. The ability of extensins to form intra- and intermolecular cross-links is directly related to their role in cell wall reinforcement. Formation of such cross-links requires appropriate glycosylation and structural conformation of the glycoprotein.

Scope

Although the role of cell wall components in plant defence has drawn increasing interest over recent years, relatively little focus has been dedicated to extensins. Nevertheless, new insights were recently provided regarding the structure and the role of extensins and their glycosylation in plant–microbe interactions, stimulating an interesting debate from fellow cell wall community experts. We have previously revealed a distinct distribution of extensin epitopes in Arabidopsis thaliana wild-type roots and in mutants impaired in extensin arabinosylation, in response to elicitation with flagellin 22. That study was recently debated in a Commentary by Tan and Mort (Tan L, Mort A. 2020. Extensins at the front line of plant defence. A commentary on: ‘Extensin arabinosylation is involved in root response to elicitors and limits oomycete colonization’. Annals of Botany 125: vii–viii) and several points regarding our results were discussed. As a response, we herein clarify the points raised by Tan and Mort, and update the possible epitope structure recognized by the anti-extensin monoclonal antibodies. We also provide additional data showing differential distribution of LM1 extensin epitopes in roots between a mutant defective in PEROXIDASES 33 and 34 and the wild type, similarly to previous observations from the rra2 mutant defective in extensin arabinosylation. We propose these two peroxidases as potential candidates to specifically catalyse the cross-linking of extensins within the cell wall.

Conclusions

Extensins play a major role within the cell wall to ensure root protection. The cross-linking of extensins, which requires correct glycosylation and specific peroxidases, is most likely to result in modulation of cell wall architecture that allows enhanced protection of root cells against invading pathogens. Study of the relationship between extensin glycosylation and their cross-linking is a very promising approach to further understand how the cell wall influences root immunity.
Geographic patterns of genomic diversity and structure in the C4 grass Panicum hallii across its natural distribution
Authors: Palacio-Mejía Juan Diego , Grabowski Paul P , Ortiz Edgardo M , Silva-Arias Gustavo Adolfo , Haque Taslima , Des Marais David L , Bonnette Jason , Lowry David B , Juenger Thomas E
Published: January 2021

Geographic patterns of within-species genomic diversity are shaped by evolutionary processes, life history and historical and contemporary factors. New genomic approaches can be used to infer the influence of such factors on the current distribution of infraspecific lineages. In this study, we evaluated the genomic and morphological diversity as well as the genetic structure of the C4 grass Panicum hallii across its complex natural distribution in North America. We sampled extensively across the natural range of P. hallii in Mexico and the USA to generate double-digestion restriction-associated DNA (ddRAD) sequence data for 423 individuals from 118 localities. We used these individuals to study the divergence between the two varieties of P. hallii, P. hallii var. filipes and P. hallii var. hallii as well as the genetic diversity and structure within these groups. We also examined the possibility of admixture in the geographically sympatric zone shared by both varieties, and assessed distribution shifts related with past climatic fluctuations. There is strong genetic and morphological divergence between the varieties and consistent genetic structure defining seven genetic clusters that follow major ecoregions across the range. South Texas constitutes a hotspot of genetic diversity with the co-occurrence of all genetic clusters and admixture between the two varieties. It is likely a recolonization and convergence point of populations that previously diverged in isolation during fragmentation events following glaciation periods.
MBG: Minimizer-based sparse de Bruijn Graph construction
Authors: Rautiainen Mikko , Marschall Tobias
Published: January 2021

Motivation

De Bruijn graphs can be constructed from short reads efficiently and have been used for many purposes. Traditionally, long-read sequencing technologies have had too high error rates for de Bruijn graph-based methods. Recently, HiFi reads have provided a combination of long-read length and low error rate, which enables de Bruijn graphs to be used with HiFi reads.

Results

We have implemented MBG, a tool for building sparse de Bruijn graphs from HiFi reads. MBG outperforms existing tools for building dense de Bruijn graphs and can build a graph of 50× coverage whole human genome HiFi reads in four hours on a single core. MBG also assembles the bacterial E.coli genome into a single contig in 8 s.

Availability and implementation

Package manager: https://anaconda.org/bioconda/mbg and source code: https://github.com/maickrau/MBG.

Supplementary information

Supplementary data are available at Bioinformatics online.
Pain in Parkinson’s disease and the role of the subthalamic nucleus
Authors: Mostofi Abteen , Morgante Francesca , Edwards Mark J , Brown Peter , Pereira Erlick A C
Published: January 2021

Pain is a frequent and poorly treated symptom of Parkinson’s disease, mainly due to scarce knowledge of its basic mechanisms. In Parkinson’s disease, deep brain stimulation of the subthalamic nucleus is a successful treatment of motor symptoms, but also might be effective in treating pain. However, it has been unclear which type of pain may benefit and how neurostimulation of the subthalamic nucleus might interfere with pain processing in Parkinson’s disease. We hypothesized that the subthalamic nucleus may be an effective access point for modulation of neural systems subserving pain perception and processing in Parkinson’s disease. To explore this, we discuss data from human neurophysiological and psychophysical investigations. We review studies demonstrating the clinical efficacy of deep brain stimulation of the subthalamic nucleus for pain relief in Parkinson’s disease. Finally, we present some of the key insights from investigations in animal models, healthy humans and Parkinson’s disease patients into the aberrant neurobiology of pain processing and consider their implications for the pain-relieving effects of subthalamic nucleus neuromodulation. The evidence from clinical and experimental studies supports the hypothesis that altered central processing is critical for pain generation in Parkinson’s disease and that the subthalamic nucleus is a key structure in pain perception and modulation. Future preclinical and clinical research should consider the subthalamic nucleus as an entry point to modulate different types of pain, not only in Parkinson’s disease but also in other neurological conditions associated with abnormal pain processing.
The Pin1-CaMKII-AMPA Receptor Axis Regulates Epileptic Susceptibility
Authors: Hou Xiaojun , Yang Fan , Li Angcheng , Zhao Debao , Ma Nengjun , Chen Linying , Lin Suijin , Lin Yuanxiang , Wang Long , Yan Xingxue , Zheng Min , Lee Tae Ho , Zhou Xiao Zhen , Lu Kun Ping , Liu Hekun
Published: January 2021

Pin1 is a unique isomerase that regulates protein conformation and function after phosphorylation. Pin1 aberration contributes to some neurological diseases, notably Alzheimer’s disease, but its role in epilepsy is not fully understood. We found that Pin1-deficient mice had significantly increased seizure susceptibility in multiple chemical inducing models and developed age-dependent spontaneous epilepsy. Electrophysiologically, Pin1 ablation enhanced excitatory synaptic transmission to prefrontal cortex (PFC) pyramidal neurons without affecting their intrinsic excitability. Biochemically, Pin1 ablation upregulated AMPA receptors and GluA1 phosphorylation by acting on phosphorylated CaMKII. Clinically, Pin1 was decreased significantly, whereas phosphorylated CaMKII and GluA1 were increased in the neocortex of patients with epilepsy. Moreover, Pin1 expression restoration in the PFC of Pin1-deficient mice using viral gene transfer significantly reduced phosphorylated CaMKII and GluA1 and effectively suppressed their seizure susceptibility. Thus, Pin1-CaMKII-AMPA receptors are a novel axis controlling epileptic susceptibility, highlighting attractive new therapeutic strategies.
Intestinal Ultrasound to Assess Disease Activity in Ulcerative Colitis: Development of a novel UC-Ultrasound Index
Authors: Bots Steven , Nylund Kim , Löwenberg Mark , Gecse Krisztina , D’Haens Geert
Published: January 2021

Introduction

Intestinal ultrasound [IUS] is useful to assess inflammation in ulcerative colitis [UC] patients. We aimed to develop an ultrasonographic activity index using endoscopy as the reference standard.

Methods

Patients were included consecutively. IUS was performed within 3 weeks from endoscopy. IUS parameters and endoscopy were compared for each colonic segment [except the rectum]. The best parameters were used to construct a UC-IUS index, which was correlated with endoscopic disease activity using the Spearman’s rank test.

Results

In 60 patients, 207 colonic segments were evaluated endoscopically. Bowel wall thickness [BWT] > 2.1 mm was optimal to discriminate between Mayo 0 and Mayo 1–3 (sensitivity 82.6%; specificity 93.0%; area under the curve [AUC] 0.910), a cut-off of 3.2 mm was optimal to discriminate between Mayo 0–1 and Mayo 2–3 [sensitivity 89.1%; specificity 92.3%; AUC 0.946] and BWT > 3.9 mm was optimal for detection of Mayo 3 [sensitivity 80.6%; specificity 84.1%; AUC 0.909]. The presence of colour Doppler signal [CDS] predicted active disease, stretches of CDS were associated with Mayo 2–3, lack of haustrations predicted active disease and fat wrapping was associated with severe disease. Inter- and intra-rater intraclass correlation for BWT was substantial. Inter-rater agreement for CDS was substantial and ranged from slight to substantial for haustrations. Intra-rater agreement for CDS was substantial and ranged from moderate to almost perfect for haustrations. The index showed strong correlation with endoscopic disease activity [Mayo: ρ 0.830; p < 0.001, UCEIS: ρ 0.759; p < 0.001].

Conclusion

We developed an UC-IUS index which showed strong correlation with endoscopic disease activity using internal validation. It is currently being validated in prospective studies.
The starlet sea anemone, Nematostella vectensis, possesses body region-specific bacterial associations with spirochetes dominating the capitulum
Authors: Bonacolta Anthony M , Connelly Michael T , M. Rosales Stephanie , del Campo Javier , Traylor-Knowles Nikki
Published: January 2021

Sampling of different body regions can reveal highly specialized bacterial associations within the holobiont and facilitate identification of core microbial symbionts that would otherwise be overlooked by bulk sampling methods. Here, we characterized compartment-specific associations present within the model cnidarian Nematostella vectensis by dividing its morphology into three distinct microhabitats. This sampling design allowed us to uncover a capitulum-specific dominance of spirochetes within N. vectensis. Bacteria from the family Spirochaetaceae made up 66% of the community in the capitulum, while only representing 1.2% and 0.1% of the communities in the mesenteries and physa, respectively. A phylogenetic analysis of the predominant spirochete sequence recovered from N. vectensis showed a close relation to spirochetes previously recovered from wild N. vectensis. These sequences clustered closer to the recently described genus Oceanispirochaeta, rather than Spirochaeta perfilievii, supporting them as members of this clade. This suggests a prevalent and yet uncharacterized association between N. vectensis and spirochetes from the order Spirochaetales.
TRANSDUCTIONAL INSTABILITY OF Tn5-INDUCED MUTATIONS: GENERALIZED AND SPECIALIZED TRANSDUCTION OF Tn5 BY BACTERIOPHAGE P1
Authors: Berg Claire M , Grullón Carmen A , Wang Aoquan , Whalen William A , Berg Douglas E
Published: January 2021

Generalized transduction is commonly used to move transposon-induced mutations among bacterial strains by selecting for inheritance of a transposonencoded resistance determinant. Although complete cotransduction of the resistance determinant and the chromosomal mutation might be expected, it is often found that when Tn5(Kan) insertion mutations are transduced by bacteriophage P1 most of the nonmutant kanamycin-resistant transductants are due to specialized transduction of Tn5. Such P1::Tn5 specialized transducing phage are not found when a mutant Tn5 element lacking a functional transposase is employed.
FINE STRUCTURE MAPPING OF THE am (GDH) LOCUS OF NEUROSPORA
Authors: Rambosek John A , Kinsey John A
Published: January 2021

Utilizing a combination of flanking marker analysis and deletion mapping we have constructed a fine structure map of the am locus which includes 63 point mutants and ten unique deletions. Positions of point mutants can be rapidly assigned to one of 13 segments within the gene on the basis of crosses to nine deletion strains.
ROLE OF BIASED GENE CONVERSION IN ONE-LOCUS NEUTRAL THEORY AND GENOME EVOLUTION
Authors: Walsh James Bruce
Published: January 2021

The implications of biased gene conversion acting on selectively neutral alleles are investigated for a single diallelic locus in a finite population. Even a very slight conversion bias can significantly alter fixation probabilities. We argue that most newly arising mutants will be at a conversion disadvantage, resulting in a potentially greatly decreased substitution rate of new alleles compared with predictions from strict neutral theory. Thus, conversion bias potential allows for conservation of particular alleles without having to invoke selection. Conversely, we also show that bias can be important in the maintenance of repeated gene families without altering the substitution rate at other loci that experience the same amount of conversion bias, provided that the number of genes in the family is sufficiently large. Bias can, therefore, be important at the genomic level and yet be unimportant at the populational level. Finally, we discuss the role of biased gene conversion in speciation events, concluding that this type of molecular turnover acting independently at many individual loci is very unlikely to decrease the time required for two allopatric populations to speciate.
ENHANCED GENE CONVERSION AND POSTMEIOTIC SEGREGATION IN PACHYTENE-ARRESTED SACCHAROMYCES CEREVISIAE
Authors: Davidow Lance S , Byers Breck
Published: January 2021

Previous study has demonstrated that incubation of yeast cells of strain AP-1 in sporulation medium at 36° permits them to begin meiosis but that they become arrested at pachytene and undergo enhanced intragenic recombination between ade2 heteroalleles. Tetrad analysis was undertaken to characterize the altered program of meiotic recombination more widely. In one set of experiments, pachytene-arrested cells were permitted to resume sporulation upon transfer to the permissive temperature. In the resulting asci, both postmeiotic segregation and gene conversion were increased several-fold at a number of loci relative to unarrested controls, whereas reciprocal recombination increased two- to threefold. Another set of experiments analyzed the genetic consequences of inducing the pachytene-arrested cells to revert directly to mitotic growth without completion of meiosis. The appearance of homozygous sectors from heterozygous markers revealed that these cells had become committed to appreciable recombination but that reciprocal exchange was less frequent than in normal asci. Taken together, the data indicate that pachytene arrest rendered the cells committed to enhanced recombination upon resumption of sporulation but that most of the crossing over did not occur until release from the arrest. —The genetic basis of pachytene arrest by AP-1 was investigated by mating each of its parents with progeny of strain Y55, which is able to sporulate at 36°. Both of these diploids sporulated at 36°, and asci from the one studied further exhibited 2:2 segregation of the sporulation defect, indicating that pachytene arrest is dependent on a recessive, temperature-sensitive allele at a chromosomal locus.
MEASURING GENE FLOW AMONG POPULATIONS HAVING HIGH LEVELS OF GENETIC FRAGMENTATION
Authors: Larson Allan , Wake David B , Yanev Kay P
Published: January 2021

We present an analysis of the genetic structures of 22 species of salamanders, with regard to levels of gene flow among populations. We estimate the gene flow parameter, Nm (the product of the effective population number and rate of migration among populations) using two alternative methods described by Wright and Slatkin. For most species, these two methods give approximately congruent estimates of Nm; when estimates differ, the method of Wright produces values slightly larger than those derived by the method of Slatkin. We analyze these results in light of independently derived historical inferences of the fragmentation of populations. This analysis suggests that the Nm values calculated from protein polymorphisms may contain information more relevant to historical patterns of gene exchange than to the current population dynamics; moderately large values of Nm may be calculated for species containing populations known to be no longer exchanging genes. Application of a method for estimating the maximum possible rate of gene exchange among populations indicates that, for most species studied here, gene flow among populations probably is no greater than the mutation rate. We suggest that most plethodontid species cannot be viewed as units whose cohesion is maintained by continuing gene exchange. Furthermore, we suggest that phenotypic uniformity among populations is not easily explained by hypotheses of continual stabilizing selection and propose that future work concentrate upon clarification of the genetic and epigenetic factors conferring self-maintenance or autopoietic properties on living systems.
MONOZYGOTIC VS. DIZYGOTIC TWIN BEHAVIOR IN ARTIFICIAL MOUSE TWINS
Authors: Baunack E , Falk U , Gärtner K
Published: January 2021

Adult inbred mice of an isogenic strain (AKR/NHan or C57BL/6J Han) differ in social (sexual and agonistic), emotional and psychomotoric behavior, depending on the kind of manipulation to which they were subjected at an early ontogenetic stage. Monozygotic twins (MZT) from eight-cell stages halved and transferred to uterine foster mothers were compared with dizygotic twins (DZT) from nonreduced but transferred eight-cell stages and with naturally born animals (NBA). Generally, early embryonic conditions predict the behavioral characteristics of the adult animals to a high degree. The MZT are motorially less active, less emotional, less aggressive and less socially interested than DZT and NBA. In tests of spontaneous social behavior (allogrooming, anogenital licking, mounting, fighting), as well as in tests for emotionality (open field: crossed fields and defecation), these behavioral patterns occurred less frequently in MZT than in DZT; the NBA were mostly intermediate. The copulatory pattern of male MZT differs from that of male DZT by a shortage of intromission latency and duration; furthermore, MZT pairs do not build up a steady rank order in competitive copulation tests, as opposed to DZT and NBA pairs. In a test for psychomotoric behavior (swimming), the MZT prefer "floating" as a survival strategy, wheras the DZT and NBA prefer "adult swimming." Therefore, it can be concluded that these behavioral differences may be caused by the particular psychosocial environment in which the twins grow up or may be due to early prenatal peculiarities, such as inadequate synchronization of the developmental status of uterus and embryo.