Altmetrics and their relationship with citation counts: a case of journal articles in physics

Purpose The first purpose of the present study is to investigate the coverage of journal articles in Physics in various sources of altmetrics. Secondly, the study investigates the relationship between altmetrics and citations. Finally, the study also investigates whether the relationship between citations and altmetrics was stronger or weaker for those articles that had been mentioned at least once in the sources of altmetrics. Design/methodology/approach The journal articles in Physics having at least one author from an Indian Institution and published during 2014–2018 in sources of altmetrics have been investigated. Altmetric.com was used for collecting altmetrics data. Spearman’s rank correlation coefficient (ρ) has been used as the data found to be skewed. Findings The highest coverage was found on Twitter (22.68%), followed by Facebook (3.62%) and blogs (2.18%). The coverage in the rest of the sources was less than 1%. The average Twitter mentions for journal articles tweeted at least once was found to be 4 (3.99) and for Facebook mentions, it was found to be 1.48. Correlations between Twitter mentions–citations and Facebook mentions–citation were found to be statistically significant but low to weak positive. Research limitations/implications The study concludes that due to the low coverage of journal articles, altmetrics should be used cautiously for research evaluation keeping in mind the disciplinary differences. The study also suggests that altmetrics can function as complementary to citation-based metrics. Originality/value The study is one of the first large scale altmetrics studies dealing with research in Physics. Also, Indian research has not been attended to in the altmetrics literature and the present study shall fill that void.

Genotype calling and haplotype inference from low coverage sequence data in heterozygous plant genome using HetMap

Many software packages and pipelines had been developed to handle the sequence data of the model species. However, Genotyping from complex heterozygous plant genome needs further improvement on the previous methods. Here we present a new pipeline available at https://github.com/Ncgrhg/HetMapv1) for variant calling and missing genotype imputation from low coverage sequence data for heterozygous plant genomes. To check the performance of the HetMap on the real sequence data, HetMap was applied to both the F1 hybrid rice population which consists of 1495 samples and wild rice population with 446 samples. Four high coverage sequence hybrid rice accessions and two high coverage sequence wild rice accessions, which were also included in low coverage sequence data, are used to validate the genotype inference accuracy. The validation results showed that HetMap archived significant improvement in heterozygous genotype inference accuracy (13.65% for hybrid rice, 26.05% for wild rice) and total accuracy compared with other similar software packages. The application of the new genotype with the genome wide association study also showed improvement of association power in two wild rice phenotypes. It could archive high genotype inference accuracy with low sequence coverage with a small population size with both the natural population and constructed recombination population. HetMap provided a powerful tool for the heterozygous plant genome sequence data analysis, which may help the discover of new phenotype regions for the plant species with complex heterozygous genome.

Comparison of Genotype Imputation for SNP Array and Low-Coverage Whole-Genome Sequencing Data

Genotype imputation is the term used to describe the process of inferring unobserved genotypes in a sample of individuals. It is a key step prior to a genome-wide association study (GWAS) or genomic prediction. The imputation accuracy will directly influence the results from subsequent analyses. In this simulation-based study, we investigate the accuracy of genotype imputation in relation to some factors characterizing SNP chip or low-coverage whole-genome sequencing (LCWGS) data. The factors included the imputation reference population size, the proportion of target markers /SNP density, the genetic relationship (distance) between the target population and the reference population, and the imputation method. Simulations of genotypes were based on coalescence theory accounting for the demographic history of pigs. A population of simulated founders diverged to produce four separate but related populations of descendants. The genomic data of 20,000 individuals were simulated for a 10-Mb chromosome fragment. Our results showed that the proportion of target markers or SNP density was the most critical factor affecting imputation accuracy under all imputation situations. Compared with Minimac4, Beagle5.1 reproduced higher-accuracy imputed data in most cases, more notably when imputing from the LCWGS data. Compared with SNP chip data, LCWGS provided more accurate genotype imputation. Our findings provided a relatively comprehensive insight into the accuracy of genotype imputation in a realistic population of domestic animals.

Promosi Kesehatan tentang Pencegahan Kanker Serviks Melalui Pemanfaatan Media Online Health Promotion of Cervical Cancer Prevention Using Online Media

ABSTRAKKanker serviks adalah penyebab kematian tertinggi keempat pada wanita di dunia. Tingginya angka kesakitan dan kematian wanita akibat kanker serviks di Indonesia, juga menunjukkan rendahnya angka cakupan pemeriksaan papsmear dan imunisasi HPV di Indonesia. Oleh karena itu dibutuhkan metode promosi kesehatan untuk mendorong wanita untuk aktif dalam melakukan pencegahan kanker serviks. Kegiatan ini merupakan salah satu bentuk pengabdian masyarakat yang dilakukan dengan cara penyuluhan melalui metode ceramah dan diskusi dengan aplikasi zoom dan whatsapp. Peserta yang mendaftar dalam kegiatan ini sejunlah 41 orang dengan rentang usia 20-35 tahun. Peserta berasal dari berbagai daerah antara lain, Jakarta, Lampung, Surabaya, Malang, Palu dan Banjarmasin. Materi yang telah disampaikan menyatakan bahwa pencegahan kanker serviks dapat dilakukan sedini mungkin. Dibandingkan dengan metode penyuluhan yang dilakukan secara langsung, pemanfaatan media sosial terbukti efektif dalam mencapai jangkauan keluasan sasaran. Kata kunci: kanker serviks, pencegahan, deteksi dini, HPV ABSTRACTCervical cancer is the fourth main cause of death in women in the world and the main cause of death for women in developing countries. The high morbidity and mortality rates for women due to cervical cancer in Indonesia also shows the low coverage rates for Pap smear test and HPV immunization in Indonesia. Therefore a health promotion is needed to encourage women to be active in preventing cervical cancer. This event is a form of counseling through lectures and discussions with zoom and WhatsApp applications. The number of participants who participated in this activity was 41 people in age 20-35 years from various provinces including Jakarta, Lampung, Surabaya, Malang, and Banjarmasin. The subject that has been presented states that cervical cancer prevention can be done as early as possible. Compared to conventional health promotion methods, the use of social media has proven to be effective in reaching a broad target. Keywords: cervical cancer, prevention, early detection, HPV

Predicting the impact of COVID-19 vaccination campaigns - a flexible age-dependent, spatially-stratified predictive model, accounting for multiple viral variants and vaccines

Background: After COVID-19 vaccines received approval, vaccination campaigns were launched worldwide. Initially, these were characterized by a shortage of vaccine supply, and specific risk groups were prioritized. Once supply was guaranteed and vaccination coverage saturated, the focus shifted from risk groups to anti-vaxxers, the underaged population, and regions of low coverage. At the same time, hopes to reach herd immunity by vaccination campaigns were put into perspective by the emergence and spread of more contagious and aggressive viral variants. Particularly, concerns were raised that not all vaccines protect against the new-emerging variants. Methods and findings: A model designed to predict the effect of vaccination campaigns on the spread of viral variants is introduced. The model is a comprehensive extension of the model underlying the pandemic preparedness tool CovidSim 2.0 (http://covidsim.eu/). The model is age and spatially stratified, incorporates a finite (but arbitrary) number of different viral variants, and incorporates different vaccine products. The vaccines are allowed to differ in their vaccination schedule, vaccination rates, the onset of vaccination campaigns, and their effectiveness. These factors are also age and/or location dependent. Moreover, the effectiveness and the immunizing effect of vaccines are assumed to depend on the interaction of a given vaccine and viral variant. Importantly, vaccines are not assumed to immunize perfectly. Individuals can be immunized completely, only partially, or fail to be immunized against one or many viral variants. Not all individuals in the population are vaccinable. The model is formulated as a high-dimensional system of differential equations, which is implemented efficiently in the programming language Julia. As an example, the model was parameterized to reflect the epidemic situation in Germany until November 2021 and predicted the future dynamics of the epidemic under different interventions. In particular, without tightening contact reductions, a strong epidemic wave is predicted. At the current state, mandatory vaccination would be too late to have a strong effect on reducing the number of infections. However, it would reduce mortality. An emergency brake, i.e., an incidence-based stepwise lockdown would be efficient to reduce the number of infections and mortality. Furthermore, to specifically account for mobility between regions, the model was applied to two German provinces of particular interest: Saxony, which currently has the lowest vaccine rollout in Germany and high incidence, and Schleswig-Holstein, which has high vaccine rollout and low incidence. Conclusions: A highly sophisticated and flexible but easy-to-parameterize model for the ongoing COVID-19 pandemic is introduced. The model is capable of providing useful predictions for the COVID-19 pandemic, and hence provides a relevant tool for epidemic decision-making. The model can be adjusted to any country, to derive the demand for hospital and ICU capacities as well as economic collateral damages.

Use of Simple Mobile Technology to Create an Electronic Vaccination Registry in Kenya

Vaccination is one of the high-impact public health interventions against the spread of disease. Over time, developed countries have been able to reduce the burden of disease through improving access to vaccination and achieving high vaccine coverage. In low-income countries, the situation is different as most countries still report low coverages of less than 90%, which is the global target recommended by the World Health Organization. The main reasons for this low coverage include poor access to vaccination, stock-outs, and poor documentation and targeting for vaccination services. To address these problems, we developed an electronic vaccine registry using Unstructured Supplementary Service Data (USSD) technology that registered births, vaccines administered and sent short message reminders to mothers about their clinic dates. The study was conducted in Nyandarua County, Kenya, between June 2018 to March 2019. To participate in the study, mothers had to reside within the jurisdiction of the study site. Mothers who moved into the study site also had their children registered and previous vaccines updated. A total of 4,823 births and 20,515 vaccines administered were captured into the system. The system sent 12,554 short message reminders to mothers; 3 days before the due day and on the due day. Additionally, it generated a birth register, vaccination register, defaulter list, dropout rate report, vaccine coverage, and timeliness reports. The intervention improved vaccination coverage and timeliness of vaccination by up to 8.7%.

hapCon: Estimating contamination of ancient genomes by copying from reference haplotypes

Human ancient DNA (aDNA) studies have surged in recent years, revolutionizing the study of the human past. Typically, aDNA is preserved poorly, making such data prone to contamination from other human DNA. Therefore, it is important to rule out substantial contamination before proceeding to downstream analysis. As most aDNA samples can only be sequenced to low coverages (<1x average depth), computational methods that can robustly estimate contamination in the low coverage regime are needed. However, the ultra low-coverage regime (0.1x and below) remains a challenging task for existing approaches. We present a new method to estimate contamination in aDNA for male individuals. It utilizes a Li&Stephen's haplotype copying model for haploid X chromosomes, with mismatches modelled as genotyping error or contamination. We assessed an implementation of this new approach, hapCon, on simulated and down-sampled empirical aDNA data. Our results demonstrate that hapCon outperforms a commonly used tool for estimating male X contamination (ANGSD), with substantially lower variance and narrower confidence intervals, especially in the low coverage regime. We found that hapCon provides useful contamination estimates for coverages as low as 0.1x for SNP capture data (1240k) and 0.02x for whole genome sequencing data (WGS), substantially extending the coverage limit of previous male X chromosome based contamination estimation methods.

Zirconium-Based Metal Organic Frameworks for the Capture of Carbon Dioxide and Ethanol Vapour. A Comparative Study

This paper reports on the comparison of three zirconium-based metal organic frameworks (MOFs) for the capture of carbon dioxide and ethanol vapour at ambient conditions. In terms of efficiency, two parameters were evaluated by experimental and modeling means, namely the nature of the ligands and the size of the cavities. We demonstrated that amongst three Zr-based MOFs, MIP-202 has the highest affinity for CO2 (−50 kJ·mol−1 at low coverage against around −20 kJ·mol−1 for MOF-801 and Muc Zr MOF), which could be related to the presence of amino functions borne by its aspartic acid ligands as well as the presence of extra-framework anions. On the other side, regardless of the ligand size, these three materials were able to adsorb similar amounts of carbon dioxide at 1 atm (between 2 and 2.5 µmol·m−2 at 298 K). These experimental findings were consistent with modeling studies, despite chemisorption effects, which could not be taken into consideration by classical Monte Carlo simulations. Ethanol adsorption confirmed these results, higher enthalpies being found at low coverage for the three materials because of stronger van der Waals interactions. Two distinct sorption processes were proposed in the case of MIP-202 to explain the shape of the enthalpic profiles.

Genomic prediction using low-coverage portable Nanopore sequencing

Most traits in livestock, crops and humans are polygenic, that is, a large number of loci contribute to genetic variation. Effects at these loci lie along a continuum ranging from common low-effect to rare high-effect variants that cumulatively contribute to the overall phenotype. Statistical methods to calculate the effect of these loci have been developed and can be used to predict phenotypes in new individuals. In agriculture, these methods are used to select superior individuals using genomic breeding values; in humans these methods are used to quantitatively measure an individual’s disease risk, termed polygenic risk scores. Both fields typically use SNP array genotypes for the analysis. Recently, genotyping-by-sequencing has become popular, due to lower cost and greater genome coverage (including structural variants). Oxford Nanopore Technologies’ (ONT) portable sequencers have the potential to combine the benefits genotyping-by-sequencing with portability and decreased turn-around time. This introduces the potential for in-house clinical genetic disease risk screening in humans or calculating genomic breeding values on-farm in agriculture. Here we demonstrate the potential of the later by calculating genomic breeding values for four traits in cattle using low-coverage ONT sequence data and comparing these breeding values to breeding values calculated from SNP arrays. At sequencing coverages between 2X and 4X the correlation between ONT breeding values and SNP array-based breeding values was > 0.92 when imputation was used and > 0.88 when no imputation was used. With an average sequencing coverage of 0.5x the correlation between the two methods was between 0.85 and 0.92 using imputation, depending on the trait. This suggests that ONT sequencing has potential for in clinic or on-farm genomic prediction, however, further work to validate these findings in a larger population still remains.

THE RELATIONSHIP BETWEEN BREAST CARE IMPLEMENTATION AND POST PARTUM MOTHER'S MILK PRODUCTION AT PMB VERONIKA SINAGA BATAM CITY

Breast care is one of the most important efforts for post partum mothers with the aim of facilitating the production of breast milk.In order to reduce child morbidity and mortality, the United Nations Children's Fund (UNICEF) and the World Health Organization (WHO) in 2005 recommended that infants be breastfed for at least six months.The success rate of breastfeeding in Indonesia in 2013 was 54.3%,(Kemenkes RI, 2014). The success rate of breastfeeding in the Riau Islands in 2013 was 52.6%,(Kemenkes RI, 2014).Exclusive Breast Milk Coverage in Batam City 47% in 2017. The low coverage of exclusive breastfeeding may be due to the low awareness of the importance of breast care to support the production of breast milk,(Dinas Kesehatan Kota Batam, 2018).The purpose of this study was to explain the relationship between the implementation of breast care and the expenditure of breast milk in post partum mothers.The method used by the author is a descriptive type, in the form of research with a case study method or approach, with visits during the postpartum period to respondents aged 25 years P2A1 at PMB Veronika Sinaga Batam City and carried out 3 times.From the results of the study, it was shown that the breast care provided to the respondents went smoothly and there was an increase in the expenditure of breast milk after breast care was carried out.The conclusion in this study based on the results of the assessment and examination it was found that breast care for postpartum mothers was very influential, respondents were able to carry out breast care independently well, and the authors were able to apply midwifery care through a midwifery management approach and documented by the SOAP method.