bluuebunny/crossref_metadata_2025_split huggingface dataset:
Malaria protection due to sickle haemoglobin depends on parasite genotype
Authors: Band Gavin , Leffler Ellen M. , Jallow Muminatou , Sisay-Joof Fatoumatta , Ndila Carolyne M. , Macharia Alexander W. , Hubbart Christina , Jeffreys Anna E. , Rowlands Kate , Nguyen Thuy , Gonçalves Sónia , Ariani Cristina V. , Stalker Jim , Pearson Richard D. , Amato Roberto , Drury Eleanor , Sirugo Giorgio , d’Alessandro Umberto , Bojang Kalifa A. , Marsh Kevin , Peshu Norbert , Saelens Joseph W. , Diakité Mahamadou , Taylor Steve M. , Conway David J. , Williams Thomas N. , Rockett Kirk A. , Kwiatkowski Dominic P. 
Published: December 2021

AbstractHost genetic factors can confer resistance against malaria1, raising the question of whether this has led to evolutionary adaptation of parasite populations. Here we searched for association between candidate host and parasite genetic variants in 3,346 Gambian and Kenyan children with severe malaria caused by Plasmodium falciparum. We identified a strong association between sickle haemoglobin (HbS) in the host and three regions of the parasite genome, which is not explained by population structure or other covariates, and which is replicated in additional samples. The HbS-associated alleles include nonsynonymous variants in the gene for the acyl-CoA synthetase family member2–4PfACS8 on chromosome 2, in a second region of chromosome 2, and in a region containing structural variation on chromosome 11. The alleles are in strong linkage disequilibrium and have frequencies that covary with the frequency of HbS across populations, in particular being much more common in Africa than other parts of the world. The estimated protective effect of HbS against severe malaria, as determined by comparison of cases with population controls, varies greatly according to the parasite genotype at these three loci. These findings open up a new avenue of enquiry into the biological and epidemiological significance of the HbS-associated polymorphisms in the parasite genome and the evolutionary forces that have led to their high frequency and strong linkage disequilibrium in African P. falciparum populations.
Estimation of COVID-19 recovery and decease periods in Canada using delay model
Authors: Paul Subhendu , Lorin Emmanuel 
Published: December 2021

AbstractWe derive a novel model escorted by large scale compartments, based on a set of coupled delay differential equations with extensive delays, in order to estimate the incubation, recovery and decease periods of COVID-19, and more generally any infectious disease. This is possible thanks to some optimization algorithms applied to publicly available database of confirmed corona cases, recovered cases and death toll. In this purpose, we separate (1) the total cases into 14 groups corresponding to 14 incubation periods, (2) the recovered cases into 406 groups corresponding to a combination of incubation and recovery periods, and (3) the death toll into 406 groups corresponding to a combination of incubation and decease periods. In this paper, we focus on recovery and decease periods and their correlation with the incubation period. The estimated mean recovery period we obtain is 22.14 days (95% Confidence Interval (CI) 22.00–22.27), and the 90th percentile is 28.91 days (95% CI 28.71–29.13), which is in agreement with statistical supported studies. The bimodal gamma distribution reveals that there are two groups of recovered individuals with a short recovery period, mean 21.02 days (95% CI 20.92–21.12), and a long recovery period, mean 38.88 days (95% CI 38.61–39.15). Our study shows that the characteristic of the decease period and the recovery period are alike. From the bivariate analysis, we observe a high probability domain for recovered individuals with respect to incubation and recovery periods. A similar domain is obtained for deaths analyzing bivariate distribution of incubation and decease periods.
The prevalence of unintended pregnancy and its association with HIV status among pregnant women in South Africa, a national antenatal survey, 2019
Authors: Woldesenbet Selamawit , Kufa Tendesayi , Lombard Carl , Manda Samuel , Morof Diane , Cheyip Mireille , Ayalew Kassahun , Puren Adrian 
Published: December 2021

AbstractTo describe the prevalence of unintended pregnancy and its association with HIV status among pregnant women in South Africa. A cross-sectional survey was conducted between October and mid-November 2019 among pregnant women aged 15–49 years in 1589 selected public antenatal care facilities. Pregnancy intention was assessed using two questions from the London Measure of Unplanned Pregnancy. Survey logistic regression examined factors associated with unintended pregnancy. Among 34,946 participants, 51.6% had an unintended pregnancy. On multivariable analysis, the odds of unintended pregnancy was higher among women who knew their HIV-positive status before pregnancy but initiated treatment after the first antenatal visit (adjusted odds ratio [aOR], 1.5 [95% confidence interval (CI):1.2–1.8]), women who initiated treatment before pregnancy (aOR, 1.3 [95% CI:1.2–1.3]), and women with a new HIV diagnosis during pregnancy (aOR, 1.2 [95% CI:1.1–1.3]) compared to HIV-negative women. Women who were single, in a non-cohabiting or a cohabiting relationship, and young women (15–24 years) had significantly higher risk of unintended pregnancy compared to married women and women aged 30–49 years, respectively. A comprehensive approach, including regular assessment of HIV clients’ pregnancy intention, and adolescent and youth-friendly reproductive health services could help prevent unintended pregnancy.
Predicting deleterious missense genetic variants via integrative supervised nonnegative matrix tri-factorization
Authors: Arani Asieh Amousoltani , Sehhati Mohammadreza , Tabatabaiefar Mohammad Amin 
Published: December 2021

AbstractAmong an assortment of genetic variations, Missense are major ones which a small subset of them may led to the upset of the protein function and ultimately end in human diseases. Various machine learning methods were declared to differentiate deleterious and benign missense variants by means of a large number of features, including structure, sequence, interaction networks, gene disease associations as well as phenotypes. However, development of a reliable and accurate algorithm for merging heterogeneous information is highly needed as it could be captured all information of complex interactions on network that genes participate in. In this study we proposed a new method based on the non-negative matrix tri-factorization clustering method. We outlined two versions of the proposed method: two-source and three-source algorithms. Two-source algorithm aggregates individual deleteriousness prediction methods and PPI network, and three-source algorithm incorporates gene disease associations into the other sources already mentioned. Four benchmark datasets were employed for internally and externally validation of both algorithms of our predictor. The results at all datasets confirmed that, our method outperforms most state of the art variant prediction tools. Two key features of our variant effect prediction method are worth mentioning. Firstly, despite the fact that the incorporation of gene disease information at three-source algorithm can improve prediction performance by comparison with two-source algorithm, our method did not hinder by type 2 circularity error unlike some recent ensemble-based prediction methods. Type 2 circularity error occurs when the predictor annotates variants on the basis of the genes located on. Secondly, the performance of our predictor is superior over other ensemble-based methods for variants positioned on genes in which we do not have enough information about their pathogenicity.
Retrospective study of the differences in patient characteristics and revenue between male and female surgeons in Taiwan
Authors: Cheng Weiming , Lin Shu-Yi , Fan Yu-Hua , Chen Sheng-Wen 
Published: December 2021

AbstractSurgery is traditionally a male-dominated field, and gender differences exist despite the growing numbers of female surgeons. A handful of studies have evaluated the condition in Asian societies. We aimed to examine the difference between female and male surgeons in urology, general surgery, and gynecology by analyzing a nationwide, population-based database. We identified surgeons with a clinical experience of six to thirteen years between 1995 to 2013 from the National Health Insurance Research Database. We collected patient numbers and revenue per month in outpatient and inpatient care, as well as monthly numbers of surgeries conducted by female and male surgeons in urology, general surgery, and gynecology, for analysis. Original student’s t-test and wilcoxon rank sum test was used to compare the differences between female and male surgeons, and p values less than 0.05 were considered statistically significant. Female urologists and general surgeons had a significantly higher ratio of female patients in Taiwan. Female urologists had patient numbers, revenues, and numbers of surgeries comparable to male urologists. In contrast, female general surgeons had significantly less involvement in outpatient and inpatient care and had low monthly revenues. Female general surgeons contradictorily performed more oncological surgeries per month than males. However, the difference in numbers of oncological surgeries was not significant after excluding breast cancer surgeries. Female gynecologists had a similar amount of outpatients and outpatient revenue but significantly less inpatient care and numbers of surgeries per month. A gender-based gap exists among surgeons in Taiwan. The gap between females and males appeared narrower in urology than in general surgery and gynecology. Management of diseases related to female sex organs, including breast, were more common among female surgeons. Efforts should be made to decrease gender stereotypes, to ensure that patients receive the best care regardless of the sex of the surgeons.
8 Sydnone-Based Cycloadditions in Click Chemistry
Authors: Friscourt F. 
Published: December 2021

AbstractThe 1,3-dipolar cycloaddition of sydnones (1,2,3-oxadiazolium-5-olates) with dipolarophiles, such as alkynes, has recently emerged as a versatile click reaction, with applications ranging from the mild and regioselective preparation of polysubstituted pyrazoles for drug discovery to the metal-free bioorthogonal ligation of biomacromolecules in living cells. This chapter reviews the importance of metal catalysis for controlling the regioselectivity of the copper-mediated reaction (CuSAC), as well as the development of fluorogenic probes, the click and release strategy, and photo-triggered ligations based on strain-promoted sydnone–alkyne cycloadditions (SPSAC).
Rapid assessment of perfect time for transferring wells to water injection for pressure maintenance in low-permeable sediments of Tyumen suite of LLC «RN-Uvatneftegas» oilfields
Authors: Shevchenko B S , Ziazev R R 
Published: December 2021

Abstract
A significant part of the initial geological reserves of LLC “RN-Uvatneftegas” oilfields are concentrated in deposits with abnormally low reservoir properties (porosity, permeability). The organization strategy of pressure maintenance of such oilfields significantly affect to the economic profitability of the reservoir development. One of the major tasks to achieve this goal is to determine the perfect time for application injection wells in oil production before forming the pressure maintenance system. Often, the solution to this issue turns out to be labor-intensive. In this regard, the analytical tool has been developed that allows rapidly assess the perfect time for transferring wells to water injection for pressure maintenance forming. The developed tool is based on a statistical analysis of the decline rate of horizontal wells fluid rates at the RN-Uvatneftegas oilfields. And also a comparative analysis of the results of the developed tool and other existing methods was carried out. The analysis showed that the developed tool is distinguished by its accuracy, simplicity and efficiency of work.
Coral diseases of mushroom coral (Fungiidae) in Pari Island, Kepulauan Seribu, Jakarta
Authors: Subhan B , Zamani N P , Rahmawati F , Arafat D , Bramandito A , Khairudi D , Santoso P , Royhan Q M , Madduppa H , Rizqydiani M 
Published: December 2021

Abstract
Coral disease is one of the causes of the decline in the condition of coral reef ecosystems. This study aims to measure coral health based on the abundance and prevalence of coral health categories. The research was conducted in the Pari Island Cluster, Seribu Islands at four stations. The Belt Transect method with 2 × 100 meters was used to calculate coral health and a 30 m Line Intercept Transect (LIT) with three replications to determine substrate cover. The condition of coral reefs can be categorized as moderate to good based on this percentage value. The study results found five genera from the Fungiidae, namely Fungia, Ctenactis, Herpolitha, Heliofungia, and Sandalolitha. The most commonly found genus is the genus Fungia. The health condition of Fungiidae corals in Pari Island is divided into two categories, namely 35% healthy and 65% unhealthy, consisting of changes in tissue color - white (coral bleaching), changes in tissue color - not white (yellow band disease), and compromised health (damage by sedimentation). Yellow band disease is only found in the genus ˆ and is not found in other genera.
Illuminating species diversity of nudibranch in Indonesian coral reef ecosystem using molecular identification
Authors: Dharmawan I G W D , Bengen D G , Setyobudiandi I , Subhan B , Verawati I , Sani L M I , Madduppa H 
Published: December 2021

Abstract
Nudibranch has high species diversity with complex morphological characters and is challenging to identify at the species level. The lack of knowledge about nudibranchs makes it difficult to identify conventionally using morphological characters. This study aims to identify nudibranchs at the species level using the DNA barcoding method from the mitochondrial cytochrome oxidase 1 (CO1) gen. The results of DNA barcoding using the Cytochrome Oxidase I (COI) gene showed 18 species of 51 samples analyzed. The phylogenetic tree reconstruction revealed 11 main clades belonging to 11 genera. The genetic distance between and within species clearly shows the difference between individuals. Interspecific genetic distance shows the lowest value between species was found between Chromodoris annae and Chromodoris magnifica is 0.075, and the largest genetic distance observed between species Glossodoris rufomarginata and Tritonidae sp is 0.354. This study shows molecular analysis can be used to identify nudibranch up to species level, which will be a source of information in knowing the distribution and the genetic distance.
Internal solitary waves propagation speed estimation in the northern-part of Lombok Strait observed by Sentinel-1 SAR and Himawari-8 images
Authors: Chonnaniyah  , Karang I W G A , Osawa T 
Published: December 2021

AbstractRemotely sensed data, both Synthetic Aperture Radar (SAR) and optical sensors, significantly contribute to the study and understanding internal solitary wave (ISW) dynamics in the ocean. Pairs of SAR and optical sensors were analyzed to estimate the ISW propagation speed in the northern-part of Lombok Strait. ISW propagation speed estimation used an image from Sentinel-1 SAR and three image pairs of Himawari-8 on 29 October 2018 with a time difference of 409 minutes. Sentinel-1 wide-swath imagery (250 km x 400 km) from two adjacent scenes can provide information on multiple ISW packets evolution in the northern-part of Lombok Strait. ISW propagation speed estimation on Sentinel-1 SAR image using the simple estimation by measuring the interpacket distance and dividing by the semidiurnal tidal period. The high temporal resolution of the optical sensor from Himawari-8 can estimate the ISW propagation speed using two different approaches. ISW propagation speed estimation using the semidiurnal tidal period from Sentinel-1 and Himawari-8 showed almost similar values. Sentinel-1 estimation results are 2.69 m.s−1(Lombok Strait) and 1.30 m.s−1(northern-part area), Himawari-8 results are 2.52 m.s−1(Lombok Strait) and 1.27 m.s−1(northern-part area). ISW propagation speed variability in the northern-part of the Lombok Strait shown in this study.
Influence of river discharge on circulation and tidal process in the Java Sea, Indonesia
Authors: Ramadhan H , Nugroho D , Nurjaya I W , Atmadipoera A S 
Published: December 2021

Abstract
This study investigates the effect of river discharge in transport and tidal processes in the Java Sea using the Coastal and Regional Ocean Community (CROCO) hydrodynamic model. The model has 20 vertical layers and a horizontal resolution of 1/18 degrees. The oceanic and atmospheric forcing of this model is taken from the global Copernicus Marine Environment Monitoring Service (CMEMS) model and the fifth generation ECMWF atmospheric reanalysis (ERA5) hourly data. Daily Global Flood Awareness System (GloFAS) data has been successfully implemented as river flow data for this study. Two scenarios have been applied, namely, with and without river discharge. This study shows that the two scenarios and the satellite observational data agree in terms of water level with Root Mean Square Difference RMSD) about 4 cm, Sea Surface Temperature with RMSD about 0.29 °C, and Sea Surface Salinity with RMSD about 0.39 psu. The model was also validated using seven tide gauges and produced a good agreement. River discharge increase eastward transport in the eastern part of the Java Sea up to 0.1 Sv (1 Sv= 106 m3s−1). Both scenarios produce similar tidal amplitude and phase and agree well with previous studies and other tidal data sources.
Modeling small-pelagic fish biomass in the Indonesian seas: climate variability and climate change impacts
Authors: Koropitan A F , Nabil  , Osawa T 
Published: December 2021

AbstractThe present study uses the Community Earth System Model, version 1– Biogeochemistry [CESM1(BGC)] to examine the influence of climate variability and climate change on small pelagic fish biomass in the Indonesian seas. The fish biomass was calculated based on a fish production model according to primary production and energy transfer at the tropic level. The primary production data were obtained from results of CESM1(BGC) model from 1850 to 2015. Empirical orthogonal function (EOF) analysis of the calculated fish biomass identifies three regions in the Indonesian seas that are associated with coastal upwelling. These regions are located in (1) southern coast of Central Java Province until west-coast of West Sumatra Province, (2) southern coast of Central Java Province until the southern coast of Bali Province, and (3) Banda-Arafura Seas. Fish production variability in these regions exhibits semi-annual, annual, and IOD-ENSO related signals. Climate change impact for RCP 4.5 scenario produces ‘fish stock increase status’ in 2025 for the three regions, while the ‘fish stock current status’ will reoccur in 2050, except for the western part of Sumatra (part of region-1) which alters to ‘fish stock decrease status’.
Convention and idiosyncrasy
Authors: Caplan David 
Published: December 2021

Abstract
“Convention and idiosyncrasy” shows how the successful use of recognizable artistic conventions can help a poet to enter a literature and a culture that seeks to exclude them. It can moderate skepticism, even hostility, and sanction an outsider’s admittance into a community. At the same time, respect for poetic convention hardly reigns uncontested in American literary culture. With several notable exceptions, American poetry and, even more so, its scholarly discussions value a different quality. American poets and readers alike often appreciate idiosyncrasy and the associated values of disruption, originality, innovation, strangeness, and surprise. Poets as different Phillis Wheatley, Emily Dickinson, Adrienne Rich, Charles Bernstein, and Maggie Smith consider the competing imperatives of convention and idiosyncrasy.
Habitat and developmental constraints drove 330 million years of horseshoe crab evolution
Authors: Bicknell Russell D C , Kimmig Julien , Budd Graham E , Legg David A , Bader Kenneth S , Haug Carolin , Kaiser Dorkas , Laibl Lukáš , Tashman Jessica N , Campione Nicolás E 
Published: December 2021

Abstract
Records of evolutionary stasis over time are central to uncovering large-scale evolutionary modes, whether by long-term gradual change or via enduring stability punctuated by rapid shifts. The key to this discussion is to identify and examine groups with long fossil records that, ideally, extend to the present day. One group often regarded as the quintessential example of stasis is Xiphosurida, the horseshoe crabs. However, when, how and, particularly, why stasis arose in xiphosurids remain fundamental, but complex, questions. Here, we explore the protracted history of fossil and living xiphosurids and demonstrate two levels of evolutionary stability: developmental stasis since at least the Pennsylvanian and shape stasis since the Late Jurassic. Furthermore, shape and diversity are punctuated by two high-disparity episodes during the Carboniferous and Triassic – transitions that coincide with forays into habitation of marginal environments. In an exception to these general patterns, body size increased gradually over this period and, thus, cannot be described under the same, often-touted, static models of evolution. Therefore, we demonstrate that evolutionary stasis can be modular and fixed within the same group at different periods and in different biological traits, while other traits experience altogether different evolutionary modes. This mosaic in the tempo and mode of evolution is not unique to Xiphosurida but likely reflects variable mechanisms acting on biological traits, for example transitions in life modes, niche occupation and major evolutionary radiations.
Understanding the Voices of Disability Advocates in Physician-Assisted Suicide Debates
Authors: Stahl Devan 
Published: December 2021

Abstract
Christians have an obligation to attend to the voices of persons who are crying out that their dignity and very lives are in jeopardy when physician-assisted suicide (PAS) becomes legalized. The following essay begins with an account of the concept of “disability moral psychology,” which elucidates the unique ways persons with disabilities perceive the world, based on their phenomenological experience. The author then explores the disability critique of PAS and the shared social conditions of persons who are chronically disabled and terminally ill. Finally, the author positions the disability critique within Christian moral deliberations on PAS to unearth its significance for Christian ethics. To bear witness to a compassionate God, theological and ethical judgments concerning PAS must seek perspectives from persons who claim that their dignity and even their lives are in jeopardy by the practice.