bluuebunny/crossref_metadata_2025_split huggingface dataset:
Evaluation of RT-PCR assays for detection of SARS-CoV-2 variants of concern.
Authors: Dip Sourav Dutta , Sarkar Shovon Lal , Setu Md. Ali Ahasan , Pramanik Md. Hasan Ali , Das Prosanto Kumar , Alam A. S. M. Rubayet Ul , Al-Emran Hassan M. , Hossain M. Anwar , Jahid Iqbal Kabir 
Published: April 2022

Abstract
Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2) pandemic has been considered with great importance on correct screening procedure. The detection efficiency of recent variants of concern were observed by comparing 5 commercial RT-PCR kits and a SYBR-green method developed and validated in our laboratory. The RNA was extracted from nasopharyngeal samples from suspected COVID-19 patients as instructed by each manufacturer and RT-PCR was also done according to standard procedures according to manufacturers. We found that commercially available Maccura kit (sensitivity and specificity > 80%), TaqPath kit (sensitivity and specificity > 80%) and in house SYBR-Green method (sensitivity and specificity > 90%) showed a consistent detection result. We also found that detection kits targeting more genes show a better result than less target gene containing protocols which facilitates less false positive results (< 20%) and better diagnostic accuracy (> 80%). Our study also showed a significant difference (sig. <0.005) in Ct value reported for common target genes shared by the RT-PCR kits in relation with different variants, specifically the Variants of Concerns (VOCs) tends to report a higher Ct value than wild type SARS-CoV-2 and suggests to detect with more target genes for better accuracy and better assessment of COVID-19 infection.
Large-scale subduction controls three-dimensional mantle flow beneath the European Alps
Authors: Link Frederik , Rümpker Georg 
Published: April 2022

Abstract
The European Alps formed at the boundary between the European plate and Adriatic microplate within a complex system of collision and subduction. However, the large-scale three-dimensional mantle-flow field related to the underlying geodynamic processes has not yet been resolved. Here, we present the first analysis of layered anisotropy for the complete Alpine range from shear-wave splitting measurements at 591 seismic stations of the AlpArray experiment. Our findings suggest that a three-dimensional asthenospheric flow field is required to explain the complexities in the data which is in contrast to the previously reported models of single-layer anisotropy. The additional vertical resolution reveals the dominant role of the larger scale Mediterranean subduction systems, including the Apenninic and Hellenic slabs, on mantle dynamics. The splitting observations also provide supporting evidence that the European slab has broken off at its western and eastern boundaries and that the resulting gaps channel mantle flow from the European plate to the Apennines and Hellenic subduction systems. Among the features in this region, only the Rhine Graben shows evidence of significant distinct lithospheric anisotropy. The findings provide new constraints for the geodynamic processes involved in the formation of the European Alps and their modelling.
Printability Assessment of Three Dimensional Bioprinter modified from Filament Deposition Modeling Printer using Carboxy Methyl Cellulose – Gelatin as Model Bioink
Authors: Balaji Krithi Vishnu , Bhutoria Sumant , Nayak Sunita , PR Anil Kumar , Velayudhan Shiny 
Published: April 2022

Abstract
Three dimensional (3D) bioprinting is an innovative technology that can precisely fabricate functional tissue constructs or organs by accurately positioning living cells and biomaterial in a controlled manner. Given its high similarity to extracellular matrix of the cells, hydrogels are widely used biomaterial in bio-printing as bioink. Depositing bioink in 3D requires computer controlled dispensing system in layer-by-layer fashion using a bioprinter. The 3D bioprinter also plays crucial role in determining the printability of a bioink making the phenomenon as an ability determined by combination of properties of bioink and the bioprinter. Despite availability of expensive bioprinters commercially, efforts on modifying a conventional Filament Deposition Modelling (FDM) 3D printer is well-thought-out to develop economical 3D bioprinters. While using such custom 3D bioprinters, many factors such as the software used for computer Assisted Design (CAD) models, slicing and generation of movement co-ordinates influence the printability outcome. This study focuses on quantifying the printability of a hybrid hydrogel composed of sodium salt carboxymethyl cellulose (CMC) and gelatin using a 3D bioprinter based on RepRap prototyper. The 3D design and the slicing parameters were generated using opensource software and manually edited for good printability. The results of these experiments indicate the importance of printability evaluation of custom bioprinters and provide some key aspects about how to modify CAD design parameters for prinatbility evaluation. This approach can also be adopted to evaluate the printability of other hydrogels for bio-printing.
A Two-Step Pre-processing Tool to Remove Gaussian and Ectopic Noise for Heart Rate Variability Analysis
Authors: Saleem Shiza , Khandoker Ahsan H. , Alkhodari Mohanad , Hadjileontiadis Leontios J. , Jelinek Herbert F. 
Published: April 2022

Abstract
Artifacts in the Electrocardiogram (ECG) degrade the quality of the recorded signal and are not conducive to heart rate variability (HRV) analysis. The two types of noise most often found in ECG recordings are technical and physiological artifacts. Current preprocessing methods primarily attend to ectopic beats but do not consider technical issues that affect the ECG. A secondary aim of this study was to investigate the effect of increasing increments of artifacts on 24 of the most used HRV measures. A two-step preprocessing approach for denoising HRV is introduced which targets each type of noise separately. First, the technical artifacts in the ECG are eliminated by applying complete ensemble empirical mode decomposition with adaptive noise (CEEMDAN). The second step removes physiological artifacts from the HRV signal using a combination filter of single dependent rank order mean (SDROM) and an adaptive filtering algorithm (ADF). The performance of the two-step pre-processing tool showed a high correlation coefficient of 0.846 and RMSE value of 7.69 x10− 5 for 6% of added ectopic beats and 6dB Gaussian noise. All HRV measures studied except HF peak and LF peak are significantly affected by both types of noise. Frequecy measures of Total power, HF power, and LF power and fragmentation measures; PAS, PIP, and PSS are the most sensitive to both types of noise.
Delineating the ecotoxic effects of Chlorpyrifos and Dimethoate on Eisenia fetida
Authors: Srivast Vaibhav , Sahab Sinha , Singh Rajeev Pratap 
Published: April 2022

Abstract
Acute (14 DOE) and chronic toxicity (56 DOE) experiments were conducted to compare the lethal and sub-lethal effects of chlorpyrifos and dimethoate on earthworms (Eisenia fetida). Earthworms were cultured in test soil (agricultural soils + cow dung) spiked with various concentrations of these two organophosphorus pesticides of different half-life. The determined effects were avoidance response, biomass change, growth inhibition, mortality, biomass gain per unit feed, cocoon and hatchling production. The resulted order of effects for acute and chronic toxicity exposure periods for E. fetida was dimethoate > chlorpyrifos. The reported median lethal concentration (LC50) in present study was 17.45 and 228.06 mg kg-1 dry test soil for dimethoate and chlorpyrifos, respectively. Growth inhibition was more critically influenced in dimethoate as compare to chlorpyrifos. Rather than lesser growth inhibition in chlorpyrifos, cocoon and hatchling production is influenced greatly at higher concentrations. The cocoon and hatchling production is significantly affected at lower concentrations of dimethoate. All the tested parameters were found to be dose dependent. The present results showed that even a small concentration of dimethoate is potentially dangerous to earthworms than higher concentrations of chlorpyrifos. In comparison the chlorpyrifos was found safer than dimethoate at sub-lethal concentrations for the development and reproduction of E. fetida. Our study provides a clear insight of different antagonistic effects of two organophosphate pesticides with different half-life.
IFA utilization and factors associated with IFA utilization among pregnant women attending ANC at government health facilities and family guidance clinic in Hawassa city, South Ethiopia
Authors: Merse Fekadu , Fanta Amanuel , Kelbiso Lolemo 
Published: April 2022

Abstract
Background: Iron deficiency is the most common nutritional disorder in the world, and most prevalent in women of reproductive age. Iron supplementation is a common strategy currently used to control iron deficiency, and iron deficiency anemia in developing countries. However, it is not clear whether women actually ingest the supplements. Objectives: To assess IFA utilization and factors associated with IFA utilization among pregnant women attending ANC at government health facilities and family guidance clinic in Hawassa city, South Ethiopia.Methods: Facility based cross-sectional survey was conducted in March /2015. Sample size is determined by using single and double population proportion. Consecutive sampling technique was used to select study units. Data was collected by trained unemployed diploma nurses using a pretested structured questionnaire. It was cleaned and checked for completeness and then entered in to Epi-info 3.2.2 and exported to SPSS 16.o software for analysis. Predictors were found out using bivariate and multivariate logistic regression.RESULTS:A total of 412 pregnant women who came to attend ANC at least for the second time were interviewed in seven health facilities. Our study showed that 333 (81%, 95% CI: 77.2 −84.8) pregnant women reported taking IFA supplement and compliance was 37.7% (95%CI: 32.5-42.9). In multivariable analysis, side effects and low acceptance of the supplement were significantly associated with high compliance to IFA supplementation (P < 0.05). Conclusion: There was a better level of compliance towards IFA supplementation compared to other national data. Pregnant women should be counseled regarding how to manage the side effects of IFA supplement during ANC. Further research has to be done on the acceptability of the supplements.
Disparities in the offer of COVID-19 vaccination to migrants and non-migrants in Norway: a cross sectional survey study
Authors: Diaz Esperanza , Dimka Jessica , Mamelund Svenn-Erik 
Published: April 2022

Abstract
Background: Vaccination is key to reduce the spread and impacts of COVID-19 and other infectious diseases. Migrants, compared to majority populations, tend to have lower vaccination rates, as well as higher infection disease burdens. Previous studies have tried to understand these disparities based on factors such as misinformation, vaccine hesitancy or medical mistrust. However, the necessary precondition of receiving, or recognizing receipt, of an offer to get a vaccine must also be considered. Methods: We conducted a web-based survey in six parishes in Oslo that have a high proportion of migrant residents and were hard-hit during the COVID-19 pandemic. Logistic regression analyses were conducted to investigate differences in reporting being offered the COVID-19 vaccine based on migrant status. Different models controlling for vaccination prioritization variables (age, underlying health conditions, health-related jobs, and parish), socioeconomic and demographic variables, and variables specific to migrant status (language spoken at home and years lived in Norway) were conducted.Results: Responses from 5,442 participants (response rate of 9.1%) were included in analyses. The sample included 1,284 (23.6%) migrants. Fewer migrants than non-migrants reported receiving a vaccine offer (68.1% vs. 81.1%), and this difference was significant after controlling for prioritization variables (OR 0.66, 95% CI: 0.52-0.82). Subsequent models showed higher odds ratios for reporting having been offered the vaccine for females, and lower odds ratios for those with university education. There were few to no significant differences based on parish, language spoken at home, or among birth countries compared to each other. Duration of residence emerged as an important explanatory variable, as migrants who had lived in Norway for fewer years than 15 years were less likely to report offer of a vaccine.Conclusion: Results were consistent with studies that show disparities between non-migrants and migrants in actual vaccine uptake. While differences in receiving an offer cannot fully explain disparities in vaccination rates, our analyses suggest that receiving, or recognizing and understanding, an offer does play a role. Issues related to duration of residence, such as inclusion in census and health registries and health and digital literacy, should be addressed by policymakers and health services organizers.
Does ICT diffusion make human development sustainable in the era of globalization? An empirical analysis from SAARC economies
Authors: Verma Anushka , Giri Arun Kumar , Debata Byomakesh 
Published: April 2022

Abstract
This study intends to examine the impact of ICT diffusion, globalization, financial development, government effectiveness, and economic growth on sustainable human development (SHD) i.e., the development of human capital adjusted against the human ecological footprint, using 2005-2020 panel data of SAARC economies. The methodology involves econometric techniques robust to cross-sectional dependence (CSD) such as Pesaran’s CSD tests, second-generation unit root test, Pedroni, Kao, Westerlund cointegration tests, FMOLS, DCCE-MG, Driscoll-Kraay (DK) regression, and DH causality test. The findings of the cointegration tests demonstrate that the variables are cointegrated and have long run equilibrium relationship. The results from DCCE-MG and DK regression, indicate that ICT diffusion has a significant, favorable impact on SHD. Similarly, globalization and economic growth also have a significant positive impact on SHD. On the other hand, the impact of government effectiveness and financial development was found to be insignificant. In addition, the DH causality test results show the presence of a unidirectional causality running from ICT diffusion to SHD and globalization to SHD. A bidirectional causal link is detected between economic growth and SHD. Therefore, the study concludes that in order to resolve the undesirable consequences of environmental degradation on human development in the globalized era, it is essential for SAARC economies to tackle challenges for adequate ICT infrastructure, particularly: access and affordability. By eliminating these significant barriers to ICT access, CO2 emissions can be reduced, and human development can be sustained simultaneously.JEL code: C23, O15, 033, O40
Validity and Acceptance of Self vs Conventional Sampling for the Analysis of Human Papillomavirus and Pap Smear
Authors: Castanyer Maria Josep Gibert , Escudero Carmen Sánchez-Contador , Vives Guillem Artigues 
Published: April 2022

Abstract
Background:
The newest high-risk human papillomavirus (HPV) detection techniques were included for cervical cancer primary screening under the Spanish National Health System in 2019. These analyses allow changing population approaches to foster adherence to screening. Therefore, the validity of self versus conventional sampling for HPV and cytology analyses was appraised. Women's preferences concerning samples and devices were also evaluated.
Methods:
This is a diagnostic accuracy cross-sectional study among 120 women recruited from a colposcopy clinic at a general hospital in Illes Balears, Spain. Participants were given written information and asked for a self-sample. One of two sets containing two devices each were handed. One set was transported dry and the second in liquid medium. Next, clinicians collected vaginal samples that were our gold standards. The agreement between both techniques was examined with the Kappa coefficient (κ). Next, self-sampling evaluation and preferences for different vaginal devices were surveyed.
Results:
The agreement between self and conventional samples concerning HPV positivity was very good (κ 0.86 for Mía by XytoTest® and 0.83 for Viba-Brush®) or reasonable (κ 0.73 for Iune and 0.68 for viscose swab). Pap smears from self-samples exhibited moderate agreement (κ 0.41 for Mía® and 0.51 for Viba-Brush® respectively) for negative versus ASC-US and worse results. Most of the participants considered self-sampling as beneficial (110 or 91.7%) and the advantages were, in decreasing order, scheduling, comfort, privacy and less fear for pain or disturbance. The priority of choice for the devices was Mía® and viscose swab (chosen in first or second place) in opposition to Viba-Brush® and Iune (chosen in third or fourth place). If Viba-Brush® was to collect the best quality samples, 108 women (94.7%) switched their decisions.
Conclusions:
Our agreement between self and conventional samples was very good or reasonable for HPV, with the best values for devices in a liquid medium, and moderate for cytology. Even so, reflex cytology on self-samples is a valuable tool in promoting adherence. Self-sampling was widely accepted for smooth and thin devices. However, there is no resistance to change to others if a higher quality of the sample is obtained.
Comparison of Methods for Donor-Derived Cell-Free DNA Quantification in Plasma and Urine from Solid Organ Transplant Recipients
Authors: Küng Nicholas , Arcioni Séverine , Sandberg Fanny , Kuhn Christian , Banz Vanessa , Largiadèr Carlo R. , Sidler Daniel , Amstutz Ursula 
Published: April 2022

Abstract
Background
In allograft monitoring of solid organ transplant recipients, liquid biopsy has emerged as a novel approach using quantification of donor-derived cell-free DNA (dd-cfDNA) in plasma. Despite early clinical implementation and analytical validation of techniques, direct comparisons of dd-cfDNA quantification methods are lacking. Furthermore, data on dd-cfDNA in urine is scarce and high-throughput sequencing-based methods so far have not leveraged unique molecular identifiers (UMIs) for absolute dd-cfDNA quantification.
Methods
Different dd-cfDNA quantification approaches were compared in urine and plasma of kidney and liver recipients: A) Droplet digital PCR (ddPCR) using allele-specific detection of seven common HLA-DRB1 alleles and the Y chromosome; B) high-throughput sequencing (HTS) using a custom QIAseq DNA panel targeting 121 common polymorphisms; and C) a commercial dd-cfDNA quantification method (AlloSeq® cfDNA, CareDx). Dd-cfDNA was quantified as %dd-cfDNA, and for ddPCR and HTS using UMIs additionally as donor copies. In addition, relative and absolute dd-cfDNA levels in urine and plasma were compared in clinically stable recipients.
Results
The HTS method presented here showed a strong correlation of the %dd-cfDNA with ddPCR (R2 = 0.98) and AlloSeq® cfDNA (R2 = 0.99) displaying only minimal to no proportional bias. Absolute dd-cfDNA copies also correlated strongly (τ = 0.78) between HTS with UMI and ddPCR albeit with substantial proportional bias (slope: 0.25; 95%-CI: 0.19–0.26). Among 30 stable kidney transplant recipients, the median %dd-cfDNA in urine was 39.5% (interquartile range, IQR: 21.8–58.5%) with 36.6 copies/µmol urinary creatinine (IQR: 18.4–109) and 0.19% (IQR: 0.01–0.43%) with 5.0 copies/ml (IQR: 1.8–12.9) in plasma without any correlation between body fluids. The median %dd-cfDNA in plasma from eight stable liver recipients was 2.2% (IQR: 0.72–4.1%) with 120 copies/ml (IQR: 85.0-138) while the median dd-cfDNA copies/ml was below 0.1 in urine.
Conclusions
This first head-to-head comparison of methods for absolute and relative quantification of dd-cfDNA in urine and plasma supports a method-independent %dd-cfDNA cutoff and indicates the suitability of the presented HTS method for absolute dd-cfDNA quantification using UMIs. To evaluate the utility of dd-cfDNA in urine for allograft surveillance, absolute levels instead of relative amounts will most likely be required given the extensive variability of %dd-cfDNA in stable kidney recipients.
Transcriptional Responses to Long-term Salinity Stress and Acclimation in the Black Mussel, Mytilus Galloprovincialis
Authors: Icagasioglu Elif , Haznedaroglu Berat Z. , Civelek Ilkay , Bilgin Rasit 
Published: April 2022

Abstract
The black mussel Mytilus galloprovincialis is an ideal organism for studying adaptation as it inhabits highly variable environments. We examined its acclimation to long-term, time-series osmostress utilizing RNA-seq based transcriptomics approaches. In our results, osmotic homeostasis was enhanced by alterations of membrane permeability and nitrogen metabolism. Cholinergic ciliary stimulation and calcium signaling were involved in the response. Genes encoding protein turnover, carbohydrate metabolism/catabolism, nucleotide metabolism, arachidonic acid metabolism, aerobic and anaerobic energy metabolisms, and apoptosis were all inversely regulated with salinity. In addition to the existing literature, we encountered two important metabolic regulations; first, involvement of anaerobic to aerobic metabolism that was suggested in bivalves before, and second, regulation of PEPCK with OXPHOS and glycolysis genes. These two regulations attracted our attention, especially in terms of their similarities to the metabolic regulations seen in cancer cells. Although there are many types/causes of cancer, there are common adaptations that support survival/proliferation, such as the aforementioned metabolic regulations and apoptosis suppression. In our study, parallel with these metabolic regulations, p53 and p63 originated apoptosis were present with the participation of TP53 apoptosis effector (PERP), TLRs, and TNFSF14. Understanding genes/pathways/modifications that trigger the mechanism that sets off cell death in this context in our study can be promising for cancer and in developing therapeutic and protective products such as vaccines.
Dietary protein replacement of fish meal with black soldier fly larvae meal: Effects on growth, whole-body composition, digestive enzyme activity, muscle-growth-related gene expression and haemato-biochemical responses of juvenile goldfish, Carassius auratus
Authors: Kamalii ahilan , Antony Cheryl , Ahilan Baboonsundaram , Uma Arumugam , Prabu Elangovan 
Published: April 2022

Abstract
A 60-day indoor growth trial was carried out to investigate the effects of dietary replacement of fish meal (FM) protein with black soldier fly larvae meal (BSFLM) at graded concentrations on bio-growth parameters, whole-body chemical composition, digestive enzyme activity, muscle-growth-related gene expression and haemato-biochemical responses of goldish juveniles (Carassius auratus). Six isonitrogenous and isoenergetic diets were formulated with BSFLM to substitute FM protein at 0 (T0), 20 (T20), 40 (T40), 60 (T60), 80 (T80) and 100 percent (T100). The aquaria with 20 fishes in each replicate were fed with experimental diet twice a day. Gold fish juveniles fed T60 diet exhibited maximum growth performances and feed utilization. However, escalating the percentage of fishmeal substitution with BSFLM above 60 percentage led to significant reduction in growth and feed utilization of goldfish juveniles. The protease activity was high in T60 and T80, wherein the lipase and amylase activity were high in T100. The relative mRNA expression of GH and MyoD was significantly upregulated in fish fed T40 and T60 diets, while the myostatin was significantly downregulated fish fed T40 and T60 diets. Thus, the fishmeal protein substituted at 60 percent with BSFLM with an inclusion level of 20.1 g/kg of diet will be well suitable for the goldfish juveniles.