bluuebunny/crossref_metadata_2025 huggingface dataset:
Comparative Analysis of Machine Learning techniques for Network Traffic Classification
Authors: Jonathan Oluranti , Misra Sanjay , Osamor Victor
Published: February 2021

Network traffic classification is the operation of giving appropriate identification to the every traffic flowing through a network. Several methods have been applied in the past to achieve network traffic classification including port-based, payload-based, behavior based and so on. These methods have been found to one limitation or the other. Nowadays, attention is now on Machine Learning(ML) methods that rely on the statistical properties of the traffic flows generated. However, ML methods do not perform well when confronted with large-scale traffic data having large number of features and instances. Feature selection is employed to remove non-relevant and redundant features before passing the data to ML classifiers. In this study, network traffic classification using ML methods is demonstrated from two perspectives: one that involves feature selection and one that does not. A number of performance metrics are considered including runtime, accuracy, recall, precision and F- score. The experimental results indicate that the classification without features has an average accuracy and runtime of 94.14% and 0.52 seconds respectively. On the other hand, the method with feature selection has accuracy of 95.61% and average of 0.25 seconds for the runtime. The improvement obtained reflects the importance of applying only relevant and non-redundant features to the ML methods. Thus it recommended that feature selection be included in the network classification process to guarantee an optimal accuracy result.
A two-stage coupling process for the recovery of base oils from used lubricating oils
Authors: Ayeni Augustine O. , Tagwai Sarah , Dick Deima T. , Agboola Oluranti , Ayoola Ayodeji A. , Babatunde Damilola E. , Oni Babalola A.
Published: February 2021

This study aims to apply a two-stage solvent extraction and adsorption principles for base oil recovery from used lubricating oils (UBO). Methyl-ethyl ketone was utilized as the solvent for extraction and activated carbon (AC) from unripe plantain peels as the adsorbent. The activities of the solvent to oil proportions from 1:1 to 5:1 on lube oil recovery were analyzed in terms viscosity of the oil, total base number (TBN) of lubricating oil, and percent weight of metallic contents removal from used oil. The results confirm that solvent to oil ratio of 3:1 gave excellent efficiencies relating the UBO to a treated base oil (TBO) with the highest removal of contaminants, increased viscosity, high TBN after the two-stage treatments. The results after solvent extraction at varying temperatures of 30, 45, 60 °C showed the TBN increased to 32% (10.21 mgKOH/g from an initial UBO value of 6.90 mgKOH/g) at 60 °C extraction temperature. After the adsorption stage, the removal of metallic contaminants at the 60 °C extractive temperature and AC 15 wt% loading was 91% for calcium and over 91% for zinc. The optimum solvent to oil ratio of 3:1 at 60 °C yielded a base oil with a kinematic viscosity of 90.23 centiStokes, a flashpoint of 203 °C, the density of 0.909 g/ml and sulphur content of 0.64 wt%. This refined base oil obtained had close similarities with fresh Ram SN500 base oil.
Wireless power transfer: a review
Authors: Okoyeigbo O. , Olajube A. A. , Shobayo O. , Aligbe A. , Ibhaze A. E.
Published: February 2021

- The ubiquitous nature and the proliferation of mobile devices has made wireless power transfer (WPT) a very important area of research. The flexibility and cost effectiveness of charging these enormous devices in our world without having to connect physically to any electrical port especially when the user is indisposed to do so is a very attractive characteristic of WPT. Conventional means of charging the batteries of these mobile devices are wired which invariably meansthey requirephysical connection to power sources through electrical cables. Electric power istransmitted wirelessly when a magnetic field produced by the inductive coupling of coils or electrical field produced by the capacitive coupling between electrodes is transferred over a short distance through the air interface and later received by an antenna for utilisation. This article gives a detailed review of the existing wireless power transfer technologies, principles of operation, applications and the opportunities for future research in this area of emerging technology. However, WPT has some drawbacks but it is a disruptive technology with the ability to revolutionise the dynamics of mobile wireless systems, internet of things and otherallied future technologies.
Study of surface evolution via Modified Ion Beam Sputtering Semi-Empirical Model (MIBSEM)
Authors: Oyewande Oluwole E. , Awelewa Samuel A. , Omotoso T.V.
Published: February 2021

An Ion Beam Sputtering Monte Carlo Model (IBSM) was modified to study the effect of different surface diffusion mechanics on the surface height and surface roughness of materials when bombarded with energetic ions. The extension was done by incorporating Seahet al.’s semi-empirical ion sputtering equations into the sputter erosion algorithm of the MC model and by enforcing curvature dependence of sputter yield. Also, TRansport of Ions in Matter (TRIM) software, was used to calculate the sputter yield and the values obtained were compared with those obtained from Seahet al.’s semi-empirical model and the sputter yield obtained from sputtering experiments. Our studies show that the surface diffusion mechanics that occurs during a sputtering process controls the substrate surface height and its roughness while curvature dependence of sputter yield has little or no contribution to the target surface height and its roughness. Our comparison of the calculated sputter yield values of TRIM and Seahet al.’s model with experimental sputter yield values show that Seahet al.’s model gives sputter yield values closer to experimental values than TRIM at a normal angle of incidence while TRIM gives sputter yield values closer to experimental values at 60°angle of incidence.
Diagnostic reference levels for adult’s abdominal computed tomography in a referral centre in Nigeria
Authors: Joseph D.Z. , Mansur I.S. , Garba I. , Umar M.S. , Nkubli F.B. , Shem B. S.
Published: February 2021

To address the limitation of CTDIvol, the American Association of Physicists in Medicine recently published a report on SSDE in body CT, where a patient’s size is used to compute an estimate of patient dose from CTDIvol. This study estimates patients’ radiation dose in abdominal computed tomography examination by considering patient size and established a facility diagnostic reference levels (DRLs) based on CTDI, DLP and SSDE for the purpose of dose optimization. A prospective cross-sectional study was carried out at Aminu Kano Teaching Hospital (AKTH), Kano-Northwestern Nigeria from April 2019 to September 2019. The study reviewed Fifty-five patients for abdominal Computed Tomography based on the recommendation of ICRP for DRLs. The study considered CTDIvol, DLP and SSDE. The SSDE is based on the anterior-posterior and lateral diameters of the patients; and a conversion factor (f). Statistical Package for Social Sciences (SPSS) Version 23.0 was used to analysed the mean, median, standard deviation and interquartile range of the radiation dose received. Independent Student t-test was used to determine the relationship between CTDIvol, DLP and SSDE by taking SSDE as an independent variable. The mean and standard deviation values of the estimated SSDE for 18-27, 28-37, 38-47, 48-57, 58-67 and 68-77 patients’ age groups are 12.9, 13.74, 13.22, 13.49, 10.44 and 12.43mGy and 4.15, 5.71, 5.21, 4.05, 3.14 and 5.24 respectively. The established DRL values for CTDI, DLP and SSDE are 11.50, 620.30 and 16.85 respectively. There was no statistical significance difference (P<0.05) between reported CTDI and DLP and the estimated SSDE. There is good optimization of radiation dose in Aminu Kano teaching hospital, with regard to CT abdomen but still patients’ size needs to be considered.
Assessment of environmental impact of telecommunication base transceivers stations in residential areas
Authors: Elehinafe F. B , Ayeni A. O. , Mamudu A. O , Odunlami O. A , Abatan O. G , Folayan A. J , Sonibare J. A.
Published: February 2021

This paper assessed the environmental impact of a telecommunication base transceiver stations (BTS) located at Cardoso Close, Apapa, Lagos State, Nigeria with the coordinates 6°4392’N, 3°3126’E. The ambient air quality parameters: SO2, NO, CO, CH4 and total suspended particulates (TSP) were measured using the ITX Emission Analyzer at four sampling points within the base station. The concentrations of SO2, NO, CO and TSP atthe base station ranged between 0.3-0.5 ppm, 1.9-2.2 ppm, 5.5-7.5 ppm, 101-110 µg/m3 respectively for 24-hour averaging period. CH4 was not detected at any of the sampling points. A digital Realistic Sound Level Meter was used in measuring the noise level. The measured average noise levels in all the four sampling points at the BTS studied ranged between 83.1-88.7 dB (A). Samples of water were collected from boreholes around the base station and were subjected tophysico-chemical examinations using the ‘standard methods for water and waste water’ 14th edition prepared by American Public Health Association (APHA). The analyses of the water samples showed that all the parameters are within limits. To measure the electromagnetic radiation emitted from the station during the field study, the SPECTRAN HF-4049 RF, an in-situ dosimeter for radio frequency measurement was used. The results obtained showed that, the measured averageradiation levels in all the four sampling points within the BTS studied ranged between 0.051-0.054 µW/m2. All the measured parameters are within safety margins apart from SO2 and NO. SO2 was not traceable to the BTS while NO was only partly connected with the fossil-fuelled electricity generating sets. The parameters of the physico-chemical analysis of the borehole water were significantly below limits.
Detection of Concealed Mineral Deposits using Magnetic Data in part of Osun State and its Environs, South-western Nigeria
Authors: Lawal T.O. , Omar D.M. , Salami M.K. , Adewumi T. , Sunday J.A. , Fawale O.
Published: February 2021

Magnetic data of part of Osun State and its Environs, Southwestern Nigeria has been studied with the aim of identifying structures concealing mineral deposits through some enhancement techniques. These techniques are Analytic signal, Euler deconvolution, Center for exploration targeting and porphyry analysis. In this work we were have applied Analytic signal to identify edges and distribution of magnetic sources that are equivalent to concealed mineral deposits, Euler deconvolution was used to identify and estimate depth to various magnetic source geometries using prescribed structural indices of 0.0, 1.0 and 2.0 respectively and lastly, the center for exploration targeting and porphyry analysis was used to obtain magnetic lineaments and porphrytic intrusives that may serve as structures concealing mineral deposits. From this study, we were able to identify several volcanic intrusions which appeared beyond surface exposure and at the same time of Cenozoic era. These intrusions resulted from the high magnetic content which serves as a contributing factor for the presence of positive magnetic anomalies in the area. In conclusion, we have been able use magnetic data of Osun State and its environs to delineate structures concealing mineral deposits.
Radiometric survey of natural radioactivity concentration and risk assessment on dwellers around Ijako active dumpsite in Ogun State
Authors: Adagunodo T.A. , Enemuwe C. A. , Usikalu M.R. , Orosun M. M. , Adewoyin O.O. , Akinwumi S.A. , Oloke O.C. , Lukman A.F. , Adeniji A.A. , Adewoye A.O.
Published: February 2021

Radiometric assessment of natural radioactivity concentration around Ijako dumpsite was done using hand held gamma spectrometer. A total of 10 in situ measurements were taken at the site. The U-238, Th-232, and K-40 radioactivity concentration obtained were used to assess the radiological hazard level in the area. Comparing the mean results of radiological parameter obtained with world average; Radium equivalent was far less than 370Bqkg-1, External hazard was less than 1, Annual effective dose equivalent was less than 0.08mSvy-1, Gamma index was less than 1, and Excess life cancer risk was less than 0.29 × 10-3. This implies that Ijako dumpsite poses no radiological hazard to the general public.
Remote Sensing and Land Use Management in Nigeria: a Review
Authors: Ajibola M. O. , Oluwunmi A. O. , Iroham C. O. , Ayedun C. A.
Published: February 2021

Land is essential for man’s existence, and its use involves the management and modification of the natural environment into built environments such as recreational, transportation, agricultural, residential, and commercial. The global population increase is exerting more pressure and demand on this limited natural resource. Accompanying man’s need is the grievous depletion of the natural environment and the extent of this depletion and conversion has yet to be fully determined by the application of traditional approaches. Therefore, the focus of this study is on how to apply remote sensing principles to land use and its management in Nigeria. Secondary data, the literature on land use, and remote sensing were adopted in the study. The study revealed that in the South West land use for settlements increased from 107.3ha in 1986 to 210.96 in 2003, while other land uses reduced in sizes – cropland (6021ha to 5,351.10ha). In Abuja, urban/built-up land increased from 36.8km2 (1987) to 385.4km2 (2017). The study further revealed that land management, using remote sensing, fosters inventory and management, periodic monitoring, and effective allocation and coordination of land resources. It provides automated techniques for integrating both quantitative and qualitative data in land information management that helps better decision-making processes, efficient policy formulation, and monitoring in land-related problems across local and global scales. The study therefore recommends the integration of remote sensing into land management and policy decision in Nigeria.
Human-wildlife conflicts and rural livelihood in Okomu national park, Edo state, Nigeria
Authors: Akinsorotan Oluseun A. , Odelola Veronica A. , Olaniyi Oluwatobi E. , Oguntuase Bukola G.
Published: February 2021

Human-wildlife conflict remains a major challenge in wildlife conservation. This study explored the occurrence of human-wildlife conflict and its impact on the subsistence of rural communities’ adjoining Okomu National Park (ONP), Edo State, Nigeria. A semi-structured questionnaire (for villagers and law enforcement staff of Okomu National Park) and focus group discussion were employed to establish the occurrence and impact of human-wildlife conflict in ONP from January to April 2019. A total of 5 villages were purposively sampled of which 160 villagers, 70 rangers and 3 focused groups (comprising 7 individuals per group) were surveyed. The results revealed that Monkey (Cercopithecus erythrogaster), Buffalo (Syneruscafer), Elephant (Loxodontacylotis), Duikers (Philatombamaxwelli), and Porcupine (Histrixcristata)causes significant problem (χ2 =102.28, P= 0.000; χ2=10.592, P=0.000; χ2=15.454, P= 0.001; χ2= 10.213, P= 0.001; χ2=27.815, P= 0.007 respectively). Also, the occurrence of human-wildlife conflict was higher in villages within 2km radius to park boundary. The livelihood of villagers was negatively affected as they lose their crops to wild animals with no intervention from the park authorities. Management of conservation areas should ensure clear boundary demarcation to reduce the rate of encroachment into the park. Besides, management strategies that aid in the preservation of ecological integrity of the site and human well-being should be taken into account. Improved conservation education and compensation for the loss incurred to crop-raiding should be designed and implemented.
Elucidating local pollution and site representativeness at the Jungfraujoch, Switzerland through parallel aerosol measurements at an adjacent mountain ridge
Authors: Bukowiecki Nicolas , Brem Benjamin T. , Wehrle Günther , Močnik Griša , Affolter Stéphane , Leuenberger Markus , Coen Martine Collaud , Hervo Maxime , Baltensperger Urs , Gysel-Beer Martin
Published: February 2021

Many long-term air pollution and climate monitoring stations face the issue of increasing anthropogenic activities in their vicinity. Furthermore, the spatial representativeness of the sites is often not entirely understood especially in mountainous terrain with complex topographic features. This study presents a 5-year comparison of parallel aerosol measurements (total particle number concentration and equivalent black carbon mass concentration) at the Jungfraujoch in the Swiss Alps (JFJ, 3580 m a.s.l.), and an adjacent mountain ridge, the Jungfrau East Ridge (JER, 3705 m a.s.l.), in 1000 m air-line distance to the main site. The parallel aerosol measurements reveal characteristic differences in the diurnal variations between the two sites under certain specific meteorological conditions. Our analysis estimates that on 20%–40% of the days local activities at the Jungfraujoch have a clear influence on the measured time series of the total aerosol number concentration and the equivalent black carbon mass concentration. This influence is mainly seen in form of strong isolated spikes rather than by an increase in the on-site background concentration. They can thus be flagged during the data quality assurance process and filtered from those measurement parameters available at high time resolution. Removing the spikes from the original time series results in daily mean values for the total aerosol number concentration and equivalent black carbon mass concentration that are 5%–10% lower compared to the original signals. During nighttime with hardly any local pollution sources that cause spikes this percentage decreases towards 0%. The signal baselines at the Jungfraujoch and Jungfrau East Ridge correlate well during more than 50% of the days.
Effect of the use of volcanic pozzolan from Mbepit Massif (West-Cameroon) on the mechanical properties of mortar and composite cements production
Authors: Mahomed Aziz Mounjouohou , Moundi Amidou , Dawai Daouda , Ntieche Benjamin , Koungang Bernard Morino Ganou , Michel Frederic
Published: February 2021

The rise in industrialization and infrastructural development is increasing leading to a constant need for construction materials; however, some of these materials continue to pose a problem to the concerned environments. There is a need to search for materials that will reduce environmental degradation and ensure sustainability. Natural pozzolanic materials possess certain characteristics such that their use in mortar and cement production could reduce the emission of carbon dioxide (CO2) due to the transformation of limestone (CaCO3) into lime for production of Portland cements. Colossal deposits of volcanic pozzolan outcrop in the Njimbouot II locality and the characterization of those materials is vital in deciphering their suitability in cement production as a construction material for sustainable development. Grinding is the only treatment performed on pozzolans in order to increase their specific surface area and reactivity. The rate of substitution of cement with pozzolan in the samples varied from 0%, 10%, and 15% to 25%. Mechanical tests were carried out after 7, 28 and 90 days on mortar specimens (4 × 4 × 16 cm3). Results revealed the presence of amorphous phases. The activity index obtained was approximately 75% and the lapilli and volcanic ash in this area are classified as pozzolans (classification ASTM C618). Regardless of the rate of substitution, the mechanical proprieties of mortars are observed to increase with age. The compressive strength values changed from 33.72 to 52.5 MPa while the flexural strength evolved from 5.62 to 8.29 MPa revealing that the Njimbouot II Pozzolan are advantageous in the manufacture of ecological cements.
On best approximations to compact operators
Authors: Sain Debmalya
Published: February 2021

We study best approximations to compact operators between Banach spaces and Hilbert spaces, from the point of view of Birkhoff-James orthogonality and semi-inner-products. As an application of the present study, some distance formulae are presented in the space of compact operators. The special case of bounded linear functionals as compact operators is treated separately and some applications to best approximations in reflexive, strictly convex and smooth Banach spaces are discussed. An explicit example is presented in

ℓ
p

n

\ell _p^{n}

spaces, where

1
>
p
>
∞
,

1 > p > \infty ,

to illustrate the applicability of the methods developed in this article. A comparative analysis of the results presented in this article with the well-known classical duality principle in approximation theory is conducted to demonstrate the advantage in the former case, from a computational point of view.
The Heterogonic Life Cycles of Oak Gall Wasps Need to Be Closed: A Lesson From Two Species ofDryophanta(Hymenoptera: Cynipidae: Cynipini)
Authors: Ide Tatsuya , Abe Yoshihisa
Published: February 2021

In heterogonic gall wasps, the gall structure, phenology, and adult morphology differ between the asexual and sexual generations, even within the same species. Dryophanta japonica Ashmead and Dryophanta mitsukurii Ashmead were described in 1904, but their heterogonic life cycles were uncertain. To match their asexual and sexual generations, we compared the type specimens of both species with specimens of gall wasps reared to demonstrate heterogonic life cycles. This revealed that these two species are the respective asexual and sexual generations of a single heterogonic species. Based on the morphological characteristics, we transferred D. japonica to Cerroneuroterus Melika and Pujade-Villar as Cerroneuroterus japonicus (Ashmead, 1904) comb. nov. and treated the sexual generation as a junior synonym: Dryophanta mitsukuriiAshmead, 1904syn. nov. Moreover, we examined the type specimens of other species previously suggested to be synonymous with D. mitsukurii. This showed that Neuroterus vonkuenburgiDettmer, 1934syn. nov. (and N. vonkuenburgi wakayamensisMonzen, 1954syn. nov.) is the asexual generation of C. japonicus and that Neuroterus bonihenriciDettmer, 1934syn. nov. is the sexual generation. Judging from the original descriptions, Andricus asakawaeShinji, 1943syn. nov., Andricus kanagawaeShinji, 1943syn. nov., Andricus asakawaeShinji, 1944syn. nov., Andricus kanagawaeShinji, 1944syn. nov., and Neoneuroterus kashiyamaiMonzen, 1954syn. nov. were also regarded as the sexual generation of C. japonicus. Finally, we discussed how matching asexual and sexual generations in heterogonic gall wasps not only avoids taxonomic confusion but also contributes to progress in gall wasp biology.
Skin Reactions to Personal Protective Equipment among First-Line COVID-19 Healthcare Workers: A Survey in Northern Morocco
Authors: Marraha Farah , Al Faker Ibtissam , Charif Faiza , Chahoub Hanane , Benyamna Youness , Rahmani Najlaa , Kabbou Soukaina , Rkiek Yasmine , Najdi Adil , Gallouj Salim
Published: February 2021

Objectives

Health care workers (HCWs) adopted several protective measures, including hand hygiene and wearing personal protective equipment (PPE) during the COVID-19 outbreak. However, the frequent use of these preventive measures can lead to skin reactions. Our study aimed to determine the frequency of these reactions in Northern Morocco. In addition, we also looked at the risk factors and the consequences of these injuries on work efficiency and performance.

Materials and Methods

An anonymous online survey was used to collect data, which was sent to 500 health workers in the study region. Descriptive and inferential statistics were used to analyze the data on IBM SPSS software.

Results

In total, 273/500 responded to the questionnaire (55%). For the participants’ profession, 41% were doctors, 32% were nursing staff, and 26% held other jobs. The general prevalence rate of adverse reactions for all health workers was (80%), including skin problems: after wearing goggles (58%), after wearing surgical masks and respirators (57%), after handwashing and wearing gloves (45%), after wearing a face shield (23%), and after wearing protective clothing (11%). Bleach immersion was highly significantly associated with hand reaction (OR: 2.9, 95% CI: 1.77–4.90; P < 0.001). Moreover, we found a statistically significant association between hand cream use more than twice daily and fewer reactions (OR: 1.9, 95% CI: 0.98–3.77; P = 0.038). The skin reactions related to goggles use were also significantly associated with use duration (OR: 1.7, 95% CI: 0.988–3.12; P = 0.05). Similarly, wearing masks and N95 respirators and their related adverse reactions were significantly associated with use duration (OR: 0.5, 95% CI: 0.20–0.7; P = 0.02). In addition, adverse reactions of regular use of protective clothing were related to the frequency of its use per shift (OR: 3.5, 95% CI: 1.47–8.54; P = 0.05).

Conclusions

Our survey-based study showed that the prevalence of these skin reactions in our context should not be neglected. The length of daily wearing time and the frequency of PPE uses were the most implicated factors. More attention must be paid to these reactions for better care of HCWs during these critical times.
An efficient heterologousEscherichia coli-based expression system for lectin production fromPleurocybella porrigens
Authors: Suzuki Tomohiro , Nakamura Luna , Inayoshi Satomi , Tezuka Yuki , Ono Akiko , Choi Jae-Hoon , Dohra Hideo , Sasanami Tomohiro , Hirai Hirofumi , Kawagishi Hirokazu
Published: February 2021

In this study, we report a more efficient heterologous expression of lectin from Pleurocybella porrigens (PPL) using an Escherichia coli-based expression system. The yield (9.3 mg/L culture broth) of recombinant PPL (rPPL) using this expression system was increased approximately 9-fold compared to our previous study. The rPPL obtained in this study exhibited the same biochemical properties as the native PPL.
Chemotactic disruption as a method to control bacterial wilt caused by Ralstonia pseudosolanacearum
Authors: Tunchai Mattana , Hida Akiko , Oku Shota , Tajima Takahisa , Kato Junichi
Published: February 2021

We have demonstrated that chemotaxis to l-malate facilitated motility of Ralstonia pseudosolanacearum MAFF 106611, a causative agent of bacterial wilt, to plant roots. Here, we evaluated the assumption that the disruption of chemotaxis to l-malate leads to inhibition of plant infection by R. pseudosolanacearum MAFF 106611. Chemotactic assays revealed that chemotaxis to l-malate was completely or partially inhibited in the presence of l-, d-, and dl-malate, respectively. Moreover, l-malate served as a carbon and energy source for R. pseudosolanacearum MAFF 106611, while d-malate inhibited the growth of this bacterium. In the sand-soak inoculation virulence assay for tomato plants, the addition of l-, d-, and dl-malate to sand suppressed the plant infection. We concluded that supplementation of l- and dl-malate suppresses tomato plant infection with R. pseudosolanacearum MAFF 106611 by disrupting its chemotaxis to l-malate, while d-malate suppresses it by both the disruption of l-malate chemotaxis and inhibition of growth.
A modeling framework for embedding-based predictions for compound–viral protein activity
Authors: Mall Raghvendra , Elbasir Abdurrahman , Almeer Hossam , Islam Zeyaul , Kolatkar Prasanna R. , Chawla Sanjay , Ullah Ehsan
Published: February 2021

Motivation

A global effort is underway to identify compounds for the treatment of COVID-19. Since de novo compound design is an extremely long, time-consuming and expensive process, efforts are underway to discover existing compounds that can be repurposed for COVID-19 and new viral diseases.

We propose a machine learning representation framework that uses deep learning induced vector embeddings of compounds and viral proteins as features to predict compound-viral protein activity. The prediction model in-turn uses a consensus framework to rank approved compounds against viral proteins of interest.

Results

Our consensus framework achieves a high mean Pearson correlation of 0.916, mean R2 of 0.840 and a low mean squared error of 0.313 for the task of compound-viral protein activity prediction on an independent test set. As a use case, we identify a ranked list of 47 compounds common to three main proteins of SARS-COV-2 virus (PL-PRO, 3CL-PRO and Spike protein) as potential targets including 21 antivirals, 15 anticancer, 5 antibiotics and 6 other investigational human compounds. We perform additional molecular docking simulations to demonstrate that majority of these compounds have low binding energies and thus high binding affinity with the potential to be effective against the SARS-COV-2 virus.

Availability and implementation

All the source code and data is available at: https://github.com/raghvendra5688/Drug-Repurposing and https://dx.doi.org/10.17632/8rrwnbcgmx.3. We also implemented a web-server at: https://machinelearning-protein.qcri.org/index.html.

Supplementary information

Supplementary data are available at Bioinformatics online.
BERT4Bitter: a bidirectional encoder representations from transformers (BERT)-based model for improving the prediction of bitter peptides
Authors: Charoenkwan Phasit , Nantasenamat Chanin , Hasan Md Mehedi , Manavalan Balachandran , Shoombuatong Watshara
Published: February 2021

Motivation

The identification of bitter peptides through experimental approaches is an expensive and time-consuming endeavor. Due to the huge number of newly available peptide sequences in the post-genomic era, the development of automated computational models for the identification of novel bitter peptides is highly desirable.

Results

In this work, we present BERT4Bitter, a bidirectional encoder representation from transformers (BERT)-based model for predicting bitter peptides directly from their amino acid sequence without using any structural information. To the best of our knowledge, this is the first time a BERT-based model has been employed to identify bitter peptides. Compared to widely used machine learning models, BERT4Bitter achieved the best performance with an accuracy of 0.861 and 0.922 for cross-validation and independent tests, respectively. Furthermore, extensive empirical benchmarking experiments on the independent dataset demonstrated that BERT4Bitter clearly outperformed the existing method with improvements of 8.0% accuracy and 16.0% Matthews coefficient correlation, highlighting the effectiveness and robustness of BERT4Bitter. We believe that the BERT4Bitter method proposed herein will be a useful tool for rapidly screening and identifying novel bitter peptides for drug development and nutritional research.

Availabilityand implementation

The user-friendly web server of the proposed BERT4Bitter is freely accessible at http://pmlab.pythonanywhere.com/BERT4Bitter.

Supplementary information

Supplementary data are available at Bioinformatics online.
Novel mineral regulatory pathways in ovine pregnancy: I. phosphate, klotho signaling, and sodium-dependent phosphate transporters
Authors: Stenhouse Claire , Halloran Katherine M , Newton Makenzie G , Gaddy Dana , Suva Larry J , Bazer Fuller W
Published: February 2021

Appropriate mineralization of the fetal skeleton requires an excess of phosphate in the fetus compared to the mother. However, mechanisms for placental phosphate transport are poorly understood. This study aimed to identify phosphate regulatory pathways in ovine endometria and placentae throughout gestation. Suffolk ewes were bred with fertile rams upon visual detection of estrus (Day 0). On Days 9, 12, 17, 30, 70, 90, 110, and 125 of pregnancy (n = 3–14/Day), ewes were euthanized and hysterectomized. Phosphate abundance varied across gestational days in uterine flushings, allantoic fluid, and homogenized endometria and placentae (P < 0.05). The expression of mRNAs for sodium-dependent phosphate transporters (SLC20A1 and SLC20A2) and klotho signaling mediators (FGF7, FGF21, FGF23, FGFR1–4, KL, KLB, ADAM10, and ADAM17) were quantified by qPCR. Day 17 conceptus tissue expressed SLC20A1, SLC20A2, KLB, FGF7, FGF21, FGF23, FGFR1, and FGFR2 mRNAs. Both sodium-dependent phosphate transporters and klotho signaling mediators were expressed in endometria and placentae throughout gestation. Gestational day influenced the expression of SLC20A1, ADAM10, ADAM17, FGF21, FGFR1, and FGFR3 mRNAs in both endometria and placentae (P < 0.05). Gestational day influenced endometrial expression of FGF7 (P < 0.001), and placental expression of FGF23 (P < 0.05). Immunohistochemistry confirmed that both FGF23 and KL proteins were expressed in endometria and placentae throughout gestation. The observed spatiotemporal profile of KL-FGF signaling suggests a potential role in the establishment of pregnancy and regulation of fetal growth. This study provides a platform for further mechanistic investigation into the role for KL-FGF signaling in the regulation of phosphate transport at the ovine maternal–conceptus interface.
Being the Gatekeeper: How Thinking about Sharing Affects Neural Encoding of Information
Authors: Chan Hang-Yee , Scholz Christin , Baek Elisa C , O’Donnell Matthew B , Falk Emily B
Published: February 2021

Information transmission in a society depends on individuals’ intention to share or not. Yet, little is known about whether being the gatekeeper shapes the brain’s processing of incoming information. Here, we examine how thinking about sharing affects neural encoding of information, and whether this effect is moderated by the person’s real-life social network position. In an functional magnetic resonance imaging study, participants rated abstracts of news articles on how much they wanted to read for themselves (read) or—as information gatekeepers—to share with a specific other (narrowcast) or to post on their social media feed (broadcast). In all conditions, consistent spatial blood oxygen level-dependent patterns associated with news articles were observed across participants in brain regions involved in perceptual and language processing as well as higher-order processes. However, when thinking about sharing, encoding consistency decreased in higher-order processing areas (e.g., default mode network), suggesting that the gatekeeper role involves more individualized processing in the brain, that is, person- and context-specific. Moreover, participants whose social networks had high ego-betweenness centrality (i.e., more likely to be information gatekeeper in real life) showed more individualized encoding when thinking about broadcasting. This study reveals how gatekeeping shapes our brain’s processing of incoming information.
A System-Wide Understanding of the Human Olfactory Percept Chemical Space
Authors: Kowalewski Joel , Huynh Brandon , Ray Anandasankar
Published: February 2021

The fundamental units of olfactory perception are discrete 3D structures of volatile chemicals that each interact with specific subsets of a very large family of hundreds of odorant receptor proteins, in turn activating complex neural circuitry and posing a challenge to understand. We have applied computational approaches to analyze olfactory perceptual space from the perspective of odorant chemical features. We identify physicochemical features associated with ~150 different perceptual descriptors and develop machine-learning models. Validation of predictions shows a high success rate for test set chemicals within a study, as well as across studies more than 30 years apart in time. Due to the high success rates, we are able to map ~150 percepts onto a chemical space of nearly 0.5 million compounds, predicting numerous percept–structure combinations. The chemical structure-to-percept prediction provides a system-level view of human olfaction and opens the door for comprehensive computational discovery of fragrances and flavors.
Isotopic niche provides an insight into the ecology of a symbiont during its geographic expansion
Authors: González-Ortegón Enrique , Perez-Miguel Marta , Navas Jose I , Drake Pilar , Cuesta Jose A
Published: February 2021

The study of the recent colonization of a symbiont and its interaction with host communities in new locations is an opportunity to understand how they interact. The use of isotopic ratios in trophic ecology can provide measurements of a species’ isotopic niche, as well as knowledge about how the isotopic niches between symbiont and host species overlap. Stable isotope measurements were used to assess the sources of carbon assimilated by the host species (the bivalves Mytilus galloprovincialis and Scrobicularia plana) and their associated symbiont pea crab Afropinnotheres monodi, which occurs within these bivalves’ mantle cavities. The mixing model estimates suggest that all of them assimilate carbon from similar sources, particularly from pseudofaeces and particulate organic matter in this symbiotic system based on filter feeding. The symbiotic species occupy comparable trophic levels and its association seems to be commensal or parasitic depending on the duration of such association. The pea crab A. monodi reflects a sex-specific diet, where males are more generalist than the soft females because the latter’s habitat is restricted to the host bivalve. The high isotopic overlap between soft females and M. galloprovincialis may reflect a good commensal relationship with the host.
The role of pharmacogenomics in contemporary cardiovascular therapy: a position statement from the European Society of Cardiology Working Group on Cardiovascular Pharmacotherapy
Authors: Magavern Emma Forton , Kaski Juan Carlos , Turner Richard M , Drexel Heinz , Janmohamed Azara , Scourfield Andrew , Burrage Daniel , Floyd Christopher N , Adeyeye Elizabeth , Tamargo Juan , Lewis Basil S , Kjeldsen Keld Per , Niessner Alexander , Wassmann Sven , Sulzgruber Patrick , Borry Pascal , Agewall Stefan , Semb Anne Grete , Savarese Gianluigi , Pirmohamed Munir , Caulfield Mark J
Published: February 2021

There is a strong and ever-growing body of evidence regarding the use of pharmacogenomics to inform cardiovascular pharmacology. However, there is no common position taken by international cardiovascular societies to unite diverse availability, interpretation, and application of such data, nor is there recognition of the challenges of variation in clinical practice between countries within Europe. Aside from the considerable barriers to implementing pharmacogenomic testing and the complexities of clinically actioning results, there are differences in the availability of resources and expertise internationally within Europe. Diverse legal and ethical approaches to genomic testing and clinical therapeutic application also require serious thought. As direct-to-consumer genomic testing becomes more common, it can be anticipated that data may be brought in by patients themselves, which will require critical assessment by the clinical cardiovascular prescriber. In a modern, pluralistic and multi-ethnic Europe, self-identified race/ethnicity may not be concordant with genetically detected ancestry and thus may not accurately convey polymorphism prevalence. Given the broad relevance of pharmacogenomics to areas, such as thrombosis and coagulation, interventional cardiology, heart failure, arrhythmias, clinical trials, and policy/regulatory activity within cardiovascular medicine, as well as to genomic and pharmacology subspecialists, this position statement attempts to address these issues at a wide-ranging level.
WhatsApp as part of an EFL programme: participation and interaction
Authors: Mackay Jessica , Andria Maria , Tragant Elsa , Pinyana Àngels
Published: February 2021

This study examines the results of an intervention conducted with adult EFL learners in Barcelona, Spain, to foster engagement with the target language outside class time. As part of the programme, the messaging service WhatsApp was used to carry out a range of voluntary communicative tasks, in learners’ own time. Familiarity with this tool made it easy to use, and learner feedback was positive. Analysis of the resulting chat transcript indicated that (1) off-task participation increased as learners appropriated the space as a vehicle for their own communication, (2) off-task interactions fell predominantly into two categories: administrative and social, and (3) despite being voluntary and unevaluated, with minimum teacher intervention, English was overwhelmingly the language of choice within these interactions. We hope this study can serve as an example of the possibilities offered by the WhatsApp medium in an EFL context.
Factors associated with A1C reduction with GLP-1 agonist or SGLT-2 inhibitor use
Authors: Davis Hanifah , Heilmann Rachel , Milchak Jessica , Delate Thomas
Published: February 2021

Background

While use of glucagon-like peptide-1 (GLP-1) agonists and sodium-glucose cotransporter-2 (SGLT-2) inhibitors reduces the risk of atherosclerotic cardiovascular disease outcomes and lowers glycosylated haemoglobin (A1C), evidence on patient characteristics associated with clinically relevant A1C reduction is lacking.

Objective

The objective of this retrospective cohort study was to identify patient characteristics associated with A1C reduction with initial GLP-1 or SGLT-2 use.

Methods

Patients with type 2 diabetes and a baseline A1C ≥7% who were dispensed a GLP-1 or SGLT-2 between 01/01/10 and 12/31/17 were included. Patients were categorized as having a ≥1% or <1% A1C reduction during the 90–365 days after GLP-1/SGLT-2 initiation. Patient characteristics were collected during the 180 days prior to initiation. Multivariable logistic and linear regression modelling was performed to identify characteristics associated with a ≥1% A1C reduction and absolute change in A1C, respectively.

Results

Five hundred and seventy-two patients were included with 261 (46%) and 311 (54%) having and not having an ≥1% A1C reduction. Patients were primarily middle-aged, female, white, non-Hispanic and had a high burden of chronic disease. Characteristics associated with a ≥1% A1C reduction included: GLP-1/SGLT-2 persistence, congestive heart failure comorbidity, phentermine dispensing, care management team (CMT) enrollee and higher baseline A1C. Characteristics associated with absolute A1C reduction included: age, baseline A1C, CMT enrollee, GLP-1/SGLT-2 persistence and a phentermine dispensing.

Conclusions

The results of this study provide practitioners with guidance on the patients who are most likely to have a clinically relevant A1C reduction with GLP-1 or SGLT-2 use.
Modelling growing stock volume of forest stands with various ALS area-based approaches
Authors: Parkitna Karolina , Krok Grzegorz , Miścicki Stanisław , Ukalski Krzysztof , Lisańczuk Marek , Mitelsztedt Krzysztof , Magnussen Steen , Markiewicz Anna , Stereńczak Krzysztof
Published: February 2021

Airborne laser scanning (ALS) is one of the most innovative remote sensing tools with a recognized important utility for characterizing forest stands. Currently, the most common ALS-based method applied in the estimation of forest stand characteristics is the area-based approach (ABA).

The aim of this study was to analyse how three ABA methods affect growing stock volume (GSV) estimates at the sample plot and forest stand levels. We examined (1) an ABA with point cloud metrics, (2) an ABA with canopy height model (CHM) metrics and (3) an ABA with aggregated individual tree CHM-based metrics. What is more, three different modelling techniques: multiple linear regression, boosted regression trees and random forest, were applied to all ABA methods, which yielded a total of nine combinations to report. An important element of this work is also the empirical verification of the methods for estimating the GSV error for individual forest stand. All nine combinations of the ABA methods and different modelling techniques yielded very similar predictions of GSV for both sample plots and forest stands. The root mean squared error (RMSE) of estimated GSV ranged from 75 to 85 m3 ha−1 (RMSE% = 20.5–23.4 per cent) and from 57 to 64 m3 ha−1 (RMSE% = 16.4–18.3 per cent) for plots and stands, respectively. As a result of the research, it can be concluded that GSV modelling with the use of different ALS processing approaches and statistical methods leads to very similar results. Therefore, the choice of a GSV prediction method may be more determined by the availability of data and competences than by the requirement to use a particular method.
Genome announcement ofSteinernema khuongiand its associated symbiont from Florida
Authors: Baniya Anil , DiGennaro Peter
Published: February 2021

Citrus root weevil (Diaprepes abbreviates) causes significant yield loss in citrus, especially in Florida. A promising source of control for this pest is biological control agents, namely, native entomopathogenic nematodes (EPNs) within the genus Steinernema. Two species of endemic EPN in Florida are S. diaparepesi, abundant within the central ridge, and S. khuongi, dominating the flatwood regions of the state. These citrus-growing regions differ significantly in their soil habitats, which impacts the potential success of biological control measures. Although the genome sequence of S. diaprepesi is currently available, the genome sequence of S. khuongi and identity of the symbiotic bacteria is still unknown. Understanding the genomic differences between these two nematodes and their favored habitats can inform successful biological control practices. Here, MiSeq libraries were used to simultaneously sequence and assemble the draft genome of S. khuongi and its associated symbionts. The final draft genome for S. khuongi has 8,794 contigs with a total length of ∼82 Mb, a largest contig of 428,226 bp, and N50 of 46 kb; its BUSCO scores indicate that it is > 86% complete. An associated bacterial genome was assembled with a total length of ∼3.5 Mb, a largest contig at 116,532 bp, and N50 of 17,487 bp. The bacterial genome encoded 3,721 genes, similar to other Xenorhabdus genomes. Comparative genomics identified the symbiotic bacteria of S. khuongi as Xenorhabdus poinarii. These new draft genomes of a host and symbiont can be used as a valuable tool for comparative genomics with other EPNs and its symbionts to understand host range and habitat suitability.
Religious Involvement and Cognitive Functioning at the Intersection of Race–Ethnicity and Gender Among Midlife and Older Adults
Authors: Henderson Andrea K , Walsemann Katrina M , Ailshire Jennifer A
Published: February 2021

Objectives

To investigate the association between religious involvement and cognitive functioning at the intersections of race–ethnicity and gender among midlife and older adults, and to determine if psychosocial factors help explain this relationship.

Method

The sample included 14,037 adults aged 50+ from the Health and Retirement Study (HRS). We utilized measures from the HRS 2010 and 2012 Core interviews and Leave-Behind questionnaires and estimated our models using linear regression.

Results

Compared to individuals who frequently attended religious services, infrequent religious service attendance was related to poorer cognitive functioning. Religiosity was inversely associated with cognitive functioning at baseline, but the relationship varied by race/gender subgroup. Greater religiosity was associated with better cognitive functioning among Black women, but lower cognitive functioning among White men and women. Psychosocial factors did little to explain the inverse association between religiosity and cognitive functioning.

Discussion

Results suggest the association between religious involvement and cognitive functioning is varied and complex, and largely dependent on important social identities. The findings have important implications for investigating health-protective factors, like religious involvement, using an intersectional perspective.