Sri Lankan Footprint in Global Aquatic Science Research: A Scientometric Analysis

The present study summarizes the research productivity and international collaboration in aquatic studies conducted by Sri Lankan scholars during 2000-2019. The study was based on the SCOPUS® database. R programming language, package bibliometrix and Vosviewer software were employed in the analysis. Results of the present study indicate that increasing growth trend in the annual number of publications. A significant correlation (p<0.05) between the number of articles and per capita GDP (Gross Domestic Production) was also observed. Senior authors dominated in terms of the article count, citation count, h index, and other author productivity indices. Journal of the National Science Foundation of Sri Lanka had the highest article count (n=33). Aquatic studies in Sri Lanka were more locally funded. Sri Lanka had strong research collaborations with Japan, South Korea and Australia. During 2000-2019, the transition of aquatic studies from lacustrine field studies to molecular lab-based studies were observed. The findings of the present study may provide a comprehensive understanding on the current context and future directions of aquatic studies in Sri Lanka.

Variability of Rainfall Over the Coastal Area In Bangladesh by Using Climate Model

The study attempt to understand the variability of rainfall by looking into the previous and future climate of the coastal area in Bangladesh from 1850 to 2100 by using the climate model (CMCC-CM- the Centro Euro-Mediterraneo Sui Cambiamenti Climatici Climate Model) of the Fifth Assessment Report (AR5) of the Intergovernmental Panel on Climate Change (IPCC). Rainfall data were collected from CMCC-CM by R programming for two GHGs emission scenarios (RCP 4.5 and RCP 8.5) referred to as ‘Representative Concentration Pathways (RCPs)’. The analysis has been conducted based on four seasons and an annual basis by plotting model data in MS Excel and R programming. The model shows that the average annual rainfall will increase from 1055.6 mm (during 1850-1900) to 1368.1mm (during 2051-2100) for RCP 4.5 while it will reach 1569.7mm (during 2050-2100) for RCP 8.5. Rainfall is also increasing for all seasons except winter. In winter season, the average rainfall will increase from 35.37mm (during 1850-1900) to 41.75mm (during 2051-2100) for RCP 4.5, where it will decrease from 35.37mm (during 1850-1900) to 22.55mm (during 2051-2100) for RCP 8.5 in the study area. The increasing and decreasing trend are more in high GHGs emission scenarios than in the medium, which will be alarming. Accordingly, this projection will be helpful to understand the adverse impacts of climatic elements and take short and long-term planning of decision-makers in that area. J. Asiat. Soc. Bangladesh, Sci. 47(2): 149-160, December 2021

SNPfiltR: an R package for interactive and reproducible SNP filtering

Here I describe the novel R package SNPfiltR and demonstrate its functionalities as the backbone of a customizable, reproducible SNP filtering pipeline implemented exclusively via the widely adopted R programming language. SNPfiltR extends existing SNP filtering functionalities by automating the visualization of key parameters such as depth, quality, and missing data, then allowing users to set filters based on optimized thresholds, all within a single, cohesive working environment. All SNPfiltR functions require a vcfR object as input, which can be easily generated by reading a SNP dataset stored as a standard vcf file into an R working environment using the function read.vcfR() from the R package vcfR. Performance benchmarking reveals that for moderately sized SNP datasets (up to 50M genotypes with associated quality information), SNPfiltR performs filtering with comparable efficiency to current state of the art command-line-based programs. These benchmarking results indicate that for most reduced-representation genomic datasets, SNPfiltR is an ideal choice for investigating, visualizing, and filtering SNPs as part of a cohesive and easily documentable bioinformatic pipeline. The SNPfiltR package can be downloaded from CRAN with the command [install.packages(“SNPfiltR”)], and a development version is available from GitHub at: (github.com/DevonDeRaad/SNPfiltR). Additionally, thorough documentation for SNPfiltR, including multiple comprehensive vignettes, is available at the website: (devonderaad.github.io/SNPfiltR/).

Identification of a shared, common haplotype cosegregating with an SGCB c.544A>C mutation in Indian patients affected with sarcoglycanopathy

Background Sarcoglycanopathies (SG) is the most frequent form of autosomal recessive limb-girdle muscular dystrophies (LGMD) leading to progressive muscle wasting and weakness, predominantly characterized by limb-girdle weakness. LGMDR4 is caused by mutations in SGCB encoding for the beta-sarcoglycan proteins. In this study, we describe a shared, common haplotype cosegregating in 14 SG cases from 13 unrelated families with the likely pathogenic homozygous mutation c.544A>C (p.Thr182Pro) in SGCB. Methods The genotypes of five selected markers (rs10009426, rs6824707, rs2271046, rs35414474 and rs17611952) surrounding the c.544A>C (p.Thr182Pro) were extracted from the variant call format (VCF) generated from whole-exome sequencing (WES) of 14 cases and 14 related family members as controls. The linkage data file was constructed and linkage disequilibrium (LD) plots were generated using HaploView to visualize patterns of LD. Further, haplotype reconstructions based on the 6 markers were conducted using PLINK1.9. using the expectation-maximization (EM) algorithm, an iterative method to find maximum likelihood. Subsequently, the R programming language was used to determine and compare plots of the haplotype frequencies and percentages for both groups to infer the risk haplotypes. Results Four strong LD blocks were identified in control group: rs10009426 to rs6824707 (0.27 kb), rs6824707 to rs2271046 (41.6 kb), rs10009426 to rs2271046 (41.8 kb) and rs35414474 to rs17611952 (0.17 kb) which were absent in the case group. Similarly, a total of nine haplotypes were estimated in cases and controls of which haplotype H1= G, A, T, G, G, T showed significant statistical difference in the frequency between cases and controls. H1 is also observed to cosegregate with c.544A>C (p.Thr182Pro) in the pedigrees of all the cases. Conclusion The identification of c.544A>C (p.Thr182Pro) mutation in 14 cases from India indicates a probable event of founder effect. Further, the H1 haplotype, cosegregating with this mutation, convincingly sheds light on the recent developments in population genetics allowing insights into demographic and population history. This haplotype can also be used as a genetic marker to screen individuals with genetic susceptibility as carriers and provide genetically informed risk stratification and management in the prevention of SG.

Ensuring Scalability of a Cognitive Multiple-Choice Test through the Mokken Package in R Programming Language

This study investigated the scalability of a cognitive multiple-choice test through the Mokken package in the R programming language for statistical computing. A 2019 mathematics West African Examinations Council (WAEC) instrument was used to gather data from randomly drawn K-12 participants (N = 2866; Male = 1232; Female = 1634; Mean age = 16.5 years) in Education District I, Lagos State, Nigeria. The results showed that the monotone homogeneity model (MHM) was consistent with the empirical dataset. However, it was observed that the test could not be scaled unidimensionally due to the low scalability of some items. In addition, the test discriminated well and had low accuracy for item-invariant ordering (IIO). Thus, items seriously violated the IIO property and scalability criteria when the HT coefficient was estimated. Consequently, the test requires modification in order to provide monotonic characteristics. This has implications for public examining bodies when endeavouring to assess the IIO assumption of their items in order to boost the validity of testing.

Yugan Khanty Phonetic Features Based on the Experimental Data

The paper deals with the phonetics of Yugan idiom of Surgut Khanty. The research is a part of the project aimed at describing Surgut Khanty phonetics. The Yugan idiom has significant differences from the Tromyegan idiom described before. The analysis is based on the data collected during the expedition to the settlement Ugut in 2019. The experimental part includes 130 words list read out three times by four native speakers from different traditional settlements on the Malyi Yugan river and on the Bolshoi Yugan river. The research was conducted using experimental techniques: Praat, Emu-SDMS software. The main technique was a formant analysis that deals with resonant frequencies in vowel spectra to obtain data on articulation features. Statistical evaluations and visualization were established via R programming language. We found differences between the Malyi Yugan river and the Bol’shoi Yugan river idioms. 12 vowel phonemes were found in the Malyi Yugan idiom. Compared to the Tromyegan system the phoneme /ɔ/ (traditionally /ȯ̆/) is absent. It was replaced by /ɛ/ (traditionally /ȧ̆/) or /o/ (traditionally /ŏ/). The phoneme u̇ described in previous literature on the topic disappeared and was replaced by /iː/. The Bolshoi Yugan vowel system includes these phonemes and also diphthongs [ui], [ɔɛ]. They appear after [k] where etimological u̇, ȯ̆ used to be. They probably are the realizations of the phonemes /iː/, /ɛ/ in the position after labialized k, which has become a phoneme. Non-initial [w] is reported to be specific Jugan feature and appears to have parallels in Tromyegan idiom too. It is an evidence for the rearranging of the Surgut idioms. In this pronunciation type /w/ is realized as a labial approximant in an initial position and after not-rounded vowels in a non-final position. After not-rounded vowels in a final position it comes as an initial-voiced fricative evoking preceding vowel diphthongization. After rounded vowels it is labiovelar [γʷ] or non-syllabic [ʊ] (before consonants). This pronunciation type is similar to the Tromyegan type, but it differs from the Pim type where /w/ comes as a labial approximant consistently. The disappearance of labial fricatives is a new phenomenon which has not been described properly. Territorial and social factors for this process are given. The Malyi Yugan speakers use lateral fricatives /ł/, /ʎ̥/ and the Bolshoi Yugan speakers replace it by /t/, /c͡c̦/. In the settlement Ugut where Bolshoi and Malyi Yugan natives contact in Russian-spoken environment both variants are used with t-pronunciation evaluated by speakers as new and declining from the ‘'right’ speech.

A guide on extracting and tidying tweets with R

Social media platforms represent a deep resource for academic research and a wide range of untapped possibilities for linguists (D'ARCY; YOUNG, 2012). This rapidly developing field presents various ethical issues and unique challenges regarding methods to retrieve and analyze data. This tutorial provides a straightforward guide to harvesting and tidying Twitter data, focused mainly on the Tweets' text, by using the R programming language (R CORE TEAM, 2020) via Twitter's APIs. The R code was developed in Adams (2020), based on the rtweet package (KEARNEY, 2018), and successfully resulted in a script for corpora compilation. In this tutorial, we discuss limitations, problems, and solutions in our framework for conducting ethical research on this social networking site. Our ethical concerns go beyond what we "agree to" in terms of use and privacy policies, that is, we argue that their content does not contemplate all the concerns researchers need to attend to. Additionally, our aim is to show that using Twitter as a data source does not require advanced computational skills.

An Intelligent Data-Driven Analytics System for Operation Management, Budgeting, and Resource Allocation using Machine Learning and Data Analytics

This is a data science project for a manufacturing company in China [1]. The task was to forecast the likelihood that each product would need repair or service by a technician in order to forecast how often the products would need to be serviced after they were installed. That forecast could then be used to estimate the correct price for selling a product warranty [2]. The underlying forecast model in the R Programming language for all of the companies products is established. In addition, an interactive web app using R Shiny is developed so the business could see the forecast and recommended warranty price for each of their products and customer types [3]. The user can select a product and customer type and input the number of products and the web app displays charts and tables that show the probability of the product needing service over time, the forecasted costs of service, along with potential income and the recommended warranty price.

Reflections from Transitioning Carpentries Workshops Online

Objectives: As certified Carpentries instructors, the authors organized and co-taught the University of Montana’s first in-person Carpentries workshop focused on the R programming language during early 2020. Due to the COVID-19 pandemic, a repeated workshop was postponed to the fall of 2020 and was adapted for a fully online setting. The authors share their Carpentries journey from in-person to online instruction, hoping to inspire those interested in organizing Carpentries at their institution for the first time and those interested in improving their existing Carpentries presence. Methods: The authors reflected on their experience facilitating the same Carpentries workshop in-person and online. They used this unique opportunity to compare the effectiveness of a face-to-face environment versus a virtual modality for delivering an interactive workshop. Results: When teaching in the online setting, the authors learned to emphasize the basics, create many opportunities for feedback using formative assessments, reduce the amount of material presented, and include helpers who are familiar with technology and troubleshooting. Conclusions: Although the online environment came with challenges (i.e., Zoom logistics and challenges, the need to further condense curricula, etc.), the instructors were surprised at the many advantages of hosting an online workshop. With some adaptations, Carpentries workshops work well in online delivery.