bluuebunny/crossref_metadata_2025_split huggingface dataset:
Application of Biochar on the runoff purification performance of porous asphalt pavement
Authors: Liu Jiawen , Li Hui , Harvey John , Zhang Hengji , Tian Yu 
Published: December 2021

Abstract
Biochar is currently applied in many low-impact development measures, such as biofilters and filter strips. However, its application in permeable pavement is limited. Due to the wide range of raw material sources, biochar may also contain nutrients and heavy metals. Whether its leachate will cause contamination during application remains unknown. Based on the static leachate contamination test, this study first evaluated the leachate contamination risks of three types of biochar and porous asphalt mixture (PA) with three biochar fillers. Through the pavement infiltration test, the purification performance of PA with biochar fillers and filter layers was further analysed. The results show that biochar contains nitrogen and phosphorus, and the leaching contamination of coconut shell is the most obvious; when the biochar is applied as a filler in PA, the leaching contamination decreases, while the pollutant purification performance is not obvious; when 3−5 mm rice straw biochar is used as a filter layer, the removal rate of total suspended solids can be 100%, but it is accompanied by more serious nitrogen and phosphorus leaching, and the greater the thickness, the more serious the degree of leaching. Deionized water cleaning can remove the phosphates contained in biochar, but have little effect on nitrogen. Therefore, before the application of biochar, cleaning measures should be taken to minimize its leaching contamination.
How is Exercise Prescribed for Hemodialysis Patients? A Scoping Review Protocol
Authors: Ribeiro Heitor S. , Andrade Francini P. , Leal Diogo V. , Oliveira Juliana S. , Wilund Kenneth R. , Viana João L. 
Published: December 2021

AbstractObjectiveThe objective of this scoping review is to describe how exercise has been prescribed for hemodialysis patients.IntroductionExercise interventions have received more attention from the nephrology community in the last few years. Despite some limitations in the findings, there is currently robust evidence suggesting that exercise is clinically important and provides benefits to hemodialysis patients. Even so, there is little evidence precisely detailing and describing how exercise can be prescribed and delivered for this population.Inclusion criteriaBased on the PCC framework, we will review and include evidence from hemodialysis patients (Participants); describing exercise interventions (Concept); in all settings and designs (Context). The evidence that included any other kidney replacement therapy other than hemodialysis will be excluded.MethodsThis review will follow the JBI methodology for scoping reviews and the PRISMA-ScR. We will perform a comprehensive literature search using MEDLINE, EMBASE, SPORTDiscuss, CINAHL, and LILACS databases without date or language restrictions from inception until December 2021. Websites, books, and guidelines from prominent societies and associations will also be searched. Experimental, quasi-experimental, observational, and protocol evidence from adults with chronic kidney disease (≥18 years) undergoing hemodialysis that prescribed exercise as an intervention will be considered. Two independent reviewers will screen title and abstract and perform the full-text review. Data extraction will be done by the main reviewer and checked by a second reviewer. Data characterizing the exercise interventions (e.g., type, setting, frequency, duration, intensity, volume, progression, periodization, professionals involved, etc.) will be extracted from selected evidence. The qualitative and quantitative results will be synthesized and presented in tables and figures along with a narrative summary.
Oral and gut microbiome biomarkers of susceptibility to respiratory tract infection in adults: a longitudinal cohort feasibility study
Authors: Woodall Claire A. , Hammond Ashley , Cleary David , Preston Andrew , Muir Peter , Pascoe Ben , Sheppard Samuel K. , Hay Alastair D. 
Published: December 2021

AbstractBackground and aimRespiratory tract infections (RTIs) are common in the community. There is some evidence that microbial biomarkers can be used to identify individuals most susceptible to RTI acquisition. We investigated the feasibility of recruiting healthy adults to collect at-home self-reported socio-demographic data and biological samples, saliva (oral) and stool (gut) at three time points (TPs): baseline/start of the study (TP-A), during an RTI (TP-B) and end of study (TP-C).MethodsHealthy adults were recruited from two urban Bristol GP practices. To identify respiratory pathogens in all saliva samples and RTI-S stool samples reverse transcriptase PCR (RT-PCR) was applied. We compared oral and gut samples from participants who developed RTI symptoms (RTI-S) and those who remained healthy (no-RTI) using 16S rRNA profiling microbiome analysis to identify the core microbiome, alpha and beta diversity, and biomarkers for susceptibility to RTIs from baseline samples (TP-A) when all participants were healthy.ResultsWe recruited 56 participants but due to the UK COVID-19 pandemic disruption we did not receive samples from 16 participants leaving 19 RTI-S and 21 no-RTI participants with socio-demographic and microbiome data. RT-PCR revealed coagulase-negative Staphylococcus carriage was significantly higher in RTI-S participants compared to those who remained healthy and RTI symptoms may have been due to viral influenzae and bacterial co-infection with Haemophilus influenzae. Core microbiomes of no-RTI participants contained a greater number of taxa compared to RTI-S participants. Microbial biomarkers of RTI susceptibility in the oral cavity were an increased abundance of the pathobiont Streptococcus sobrinus and decreased probiotic bacterium Lactobacillus salivarius whereas in the gut there was an increased abundance of the genus Veillonella and decreased abundance of Coprobacillus.ConclusionIn our feasibility study we found oral and gut microbial biomarkers for susceptibility to RTI acquisition. Strategies to identify those most vulnerable to RTI in the community could lead to novel interventions to decrease respiratory infection and associated health services burden.
Cochlear implantation restores cortical processing for spatial hearing in asymmetric hearing loss
Authors: Karoui C. , Strelnikov K. , Payoux P. , Salabert A.-S. , James C. , Deguine O. , Barone P. , Marx M. 
Published: December 2021

AbstractIn asymmetric hearing loss (AHL), the normal pattern of contralateral hemispheric dominance for monaural stimulation is modified, with a shift towards the hemisphere ipsilateral to the better ear. The extent of this shift has been shown to relate to sound localisation deficits. In this study, we examined whether cochlear implantation to treat AHL can restore the normal functional pattern of auditory cortical activity and whether this relates to improved sound localisation. We recruited 10 subjects with a cochlear implant for AHL (AHL-CI) and 10 normally-hearing controls. The participants performed a voice/non-voice discrimination task with binaural and monaural presentation of the sounds, and the cortical activity was measured using positron emission tomography (PET) brain imaging with a H215O tracer. The auditory cortical activity was found to be lower in the AHL-CI participants for all of the conditions. A cortical asymmetry index was calculated and showed that a normal contralateral dominance was restored in the AHL-CI patients for the non-implanted ear, but not for the ear with the cochlear implant. It was found that the contralateral dominance for the non-implanted ear strongly correlated with sound localisation performance (rho = 0.8, p < 0.05). We conclude that the restoration of binaural mechanisms in AHL-CI subjects reverses the abnormal lateralisation pattern induced by the deafness, and that this leads to improved spatial hearing. Our results suggest that cochlear implantation fosters the rehabilitation of binaural excitatory/inhibitory cortical interactions, which could enable the reconstruction of the auditory spatial selectivity needed for sound localisation.
Age-related changes, influencing factors and crosstalk between vaginal and gut microbiota: a cross-sectional comparative study of pre- and postmenopausal women
Authors: Yoshikata Remi , Yamaguchi Michiko , Mase Yuri , Tatuzuki Ayano , Myint Khin Z. , Ohta Hiroaki 
Published: December 2021

AbstractObjectiveThe ideal vaginal environment is maintained by Lactobacillus species, which keep the vagina clean and free of infections, including sexually transmitted diseases and human papilloma virus infection. Other reported health benefits of Lactobacillus include a favorable impact on fertility and immunity, leading to a reduced risk of gynecological malignancies. Age-related decline in estrogen affects the population of Lactobacillus, leading to dominance of pathogenic flora and increased diversity in vaginal microbiota. In this study, we compared the differences between the vaginal microbiota of premenopausal and postmenopausal women. In addition, we examined the relationships between vaginal and gut microbiota, as well as their relationships to sex hormones and equol producing ability.MethodsThis was a cross-sectional study of 35 premenopausal and 35 postmenopausal women, ranging from 27 to 76 years of age. We compared parameters such as the composition of the gut and vaginal microbiota, vaginal pH, sex hormones in the blood (estradiol and follicular stimulating hormone), and urinary equol concentration.ResultsIn the vaginal microbiota of premenopausal women, Lactobacillus species constituted approximately 71.98%, and pathogenic flora constituted approximately 16.87%. They were 10.08% and 26.78%, respectively, in the vaginal microbiota of postmenopausal women. Therefore, the proportion of Lactobacillus was significantly low, whereas microbial diversity and vaginal pH were significantly high (p<0.0001) in postmenopausal women. The compositions of the vaginal microbiota were significantly different in pre- and postmenopausal women. However, such differences were not noticeable in the gut microbiota. Urinary equol production had no significant correlation with vaginal microbiota, although it had significant relationships with gut microbiota in postmenopausal women. There were significant correlations among bacterial species in the gut and vaginal microbiota, especially in postmenopausal women. In both groups, the proportions of vaginal Lactobacillus were inversely correlated with vaginal microbial diversity and vaginal pH.ConclusionPostmenopausal women had significantly low Lactobacillus and high pathogenic flora in their vaginal flora, whereas such age-related differences were not identified in gut microbiota. There were significant correlations among the bacterial species inhabiting the gut and vaginal microbiota, especially in postmenopausal women, indicating potential crosstalk between each other.
Complete genomic profiles of 1,496 Taiwanese reveal curated medical insights
Authors: Wu Dung-Chi , Hsu Jacob Shu-Jui , Chen Chien-Yu , Shih Shang-Hung , Liu Jen-Feng , Tsai Ya-Chen , Lee Tung-Lin , Chen Wei-An , Tseng Yi-Hsuan , Lo Yi-Chung , Lin Hong-Ye , Chen Yi-Chieh , Chen Jing-Yi , Chang Darby Tien-Hao , Guo Wei-Hong , Mao Hsin-Hsiang , Chen Pei-Lung 
Published: December 2021

AbstractBackgroundTaiwan Biobank (TWB) project has built a nationwide database to facilitate the basic and clinical collaboration within the island and internationally, which is one of the valuable public datasets of the East Asian population. This study provided comprehensive genomic medicine findings from 1,496 WGS data from TWB.MethodsWe reanalyzed 1,496 Illumina-based whole genome sequences (WGS) of Taiwanese participants with at least 30X depth of coverage by Sentieon DNAscope, a precisionFDA challenge winner method. All single nucleotide variants (SNV) and small insertions/deletions (Indel) have been jointly called and recalibrated as one cohort dataset. Multiple practicing clinicians have reviewed clinically significant variants.ResultsWe found that each Taiwanese has 6,870.7 globally novel variants and classified all genomic positions according to the recalibrated sequence qualities. The variant quality score helps distinguish actual genetic variants among the technical false-positive variants, making the accurate variant minor allele frequency (MAF). All variant annotation information can be browsed at TaiwanGenomes (https://genomes.tw). We detected 54 PharmGKB-reported Cytochrome P450 (CYP) genes haplotype-drug pairs with MAF over 10% in the TWB cohort and 39.8% (439/1103) Taiwanese harbored at least one PharmGKB-reported human leukocyte antigen (HLA) risk allele. We also identified 23 variants located at ACMG secondary finding V3 gene list from 25 participants, indicating 1.67% of the population is harboring at least one medical actionable variant. For carrier status of all known pathogenic variants, we estimated one in 22 couples (4.52%) would be under the risk of having offspring with at least one pathogenic variant, which is in line with Japanese (JPN) and Singaporean (SGN) populations. We also detected 6.88% and 2.02% of carrier rates for alpha thalassemia and spinal muscular atrophy (SMA) for copy number pathogenic variants, respectively.ConclusionAs WGS has become affordable for everyone, a person only needs to test once for a lifetime; comprehensive WGS data reanalysis of the genomic profile will have a significant clinical impact. Our study highlights the overall picture of a complete genomic profile with medical information for a population and individuals.
An experimental feasibility study evaluating the adequacy of sportswear-type wearables for recording physical exercise intensity
Authors: Marutani Yoshihiro , Konda Shoji , Ogasawara Issei , Yamasaki Keita , Yokoyama Teruki , Maeshima Etsuko , Nakata Ken 
Published: December 2021

AbstractSportswear-type wearables with integrated inertial sensors and electrocardiogram (ECG) electrodes, have been developed. We examined the feasibility of using sportswear-type wearables to evaluate exercise intensity within a controlled laboratory setting. Six male college athletes were asked to wear a sportswear-type wearable while performing a treadmill test that reached up to 20 km/h. The magnitude of the filtered tri-axial acceleration signal, recorded by the inertial sensor, was used to calculate the acceleration index. The R-R intervals of ECG were used to determine heart rate; the external validity of the heart rate was then evaluated according to oxygen uptake, which is the gold standard physiological exercise intensity. Single regression analyses between treadmill speed and the acceleration index in each participant showed that the slope of the regression line was significantly greater than zero with a high coefficient of determination (walking, 0.95; jogging, 0.96; running, 0.90). Another single regression analyses between heart rate and oxygen uptake showed that the slope of the regression line was significantly greater than zero, with a high coefficient of determination (0.96). Together, these results indicate that sportswear-type wearables are a feasible technology for evaluating physical and physiological exercise intensity across a wide range of physical activities and sport performances.
Method versatility in RNA extraction-free PCR detection of SARS-CoV-2 in saliva samples
Authors: Allicock Orchid M. , Yolda-Carr Devyn , Earnest Rebecca , Breban Mallery I. , Vega Noel , Ott Isabel M. , Kalinich Chaney , Alpert Tara , Petrone Mary E. , Wyllie Anne L. 
Published: December 2021

AbstractEarly in the pandemic, a simple, open-source, RNA extraction-free RT-qPCR protocol for SARS-CoV-2 detection in saliva was developed and made widely available. This simplified approach (SalivaDirect) requires only sample treatment with proteinase K prior to PCR testing. However, feedback from clinical laboratories highlighted a need for a flexible workflow that can be seamlessly integrated into their current health and safety requirements for the receiving and handling of potentially infectious samples. To address these varying needs, we explored additional pre-PCR workflows. We built upon the original SalivaDirect workflow to include an initial incubation step (95°C for 30 minutes, 95°C for 5 minutes or 65°C for 15 minutes) with or without addition of proteinase K. The limit of detection for the workflows tested did not significantly differ from that of the original SalivaDirect workflow. When tested on de-identified saliva samples from confirmed COVID-19 individuals, these workflows also produced comparable virus detection and assay sensitivities, as determined by RT-qPCR analysis. Exclusion of proteinase K did not negatively affect the sensitivity of the assay. The addition of multiple heat pretreatment options to the SalivaDirect protocol increases the accessibility of this cost-effective SARS-CoV-2 test as it gives diagnostic laboratories the flexibility to implement the workflow which best suits their safety protocols.
Amplicon-based nanopore minion sequencing of patients with COVID-19 omicron variant from India
Authors: Kumar Somesh , Lomash Avinash , Faruq Mohammed , Siddiqui Oves , Kumar Suresh , Kapoor Seema , Suravajhala Prashanth , Polipalli Sunil K ,   SCOG_MAMC_ LNH
Published: December 2021

AbstractSARS-CoV-2 infection has been playing havoc with emerging omicron variants of concern (VoC). Here, we report sequencing of the omicron variant in 13 patients from India using Oxford Nanopore Technology (ONT) Minion, wherein a rapid amplicon based sequence analysis was performed to assess and compare with existing 34 mutations in spike glycoprotein. We highlight and discuss the nature of these mutations that are unique and common to other populations. This is perhaps the first report on omicron variants from India using a long read sequencing chemistry.
Detection of the omicron variant in international travellers and their family contacts in India
Authors: Potdar Varsha A. , Yadav Pragya D. , Lole Kavita , Cherian Sarah , Shastri Jayanti , Malhotra Bharati , Bharadwaj Sumit , Razdan Alpana , Choudhary M L , Gupta Nivedita , Abraham Priya ,   NIC team,   Bioinformatics team,   BSL4 team,   The Indian SARS-CoV-2 Genomics Consortium (INSACOG)
Published: December 2021

HighlightsWith the emergence of the Variant of Concern, omicron (B.1.1.529), India has enhanced genomic surveillance in international travellers. The omicron variant was detected in 59 cases from different States; 40 from Maharashtra, 17 from Rajasthan and one each from Gujrat and Tamil Nadu. The positive cases and their contacts were asymptomatic and genomic surveillance could identify two clusters, one from Maharashtra and another from Rajasthan.
Single-nuclei isoform RNA sequencing reveals combination patterns of transcript elements across human brain cell types
Authors: Hardwick Simon A , Hu Wen , Joglekar Anoushka , Fan Li , Collier Paul G , Foord Careen , Balacco Jennifer , Belchikov Natan , Jarroux Julien , Prjibelski Andrey , Mikheenko Alla , Luo Wenjie , Milner Teresa A , Ndhlovu Lishomwa C , Trojanowski John Q , Lee Virginia MY , Fedrigo Olivier , Tombácz Dóra , Ross M Elizabeth , Jarvis Erich , Boldogkői Zsolt , Gan Li , Tilgner Hagen U 
Published: December 2021

AbstractSingle-nuclei RNA-Seq is being widely employed to investigate cell types, especially of human brain and other frozen samples. In contrast to single-cell approaches, however, the majority of single-nuclei RNA counts originate from partially processed RNA leading to intronic cDNAs, thus hindering the investigation of complete isoforms. Here, using microfluidics, PCR-based artifact removal, target enrichment, and long-read sequencing, we developed single-nuclei isoform RNA-sequencing (‘SnISOr-Seq’), and applied it to the analysis of human adult frontal cortex samples. We found that exons associated with autism exhibit coordinated and more cell-type specific inclusion than exons associated with schizophrenia or ALS. We discovered two distinct modes of combination patterns: first, those distinguishing cell types in the human brain. These are enriched in combinations of TSS-exon, exon-polyA site, and distant (non-adjacent) exon pairs. Second, those with all isoform combinations found within one neural cell type, which are enriched in adjacent exon pairs. Furthermore, adjacent exon pairs are predominantly mutually associated, while distant pairs are frequently mutually exclusive. Finally, we observed that human-specific exons are as tightly coordinated as conserved exons, pointing to an efficient evolutionary mechanism underpinning coordination. SnISOr-Seq opens the door to single-nuclei long-read isoform analysis in the human brain, and in any frozen, archived or hard-to-dissociate sample.
Comparative proteomic analysis of Fusarium oxysporum f. sp. cubense strains (Foc R1 and Foc TR4) provides better insights into mechanisms of their virulence, habitat adaptation and pathogenesis
Authors: Raman Thangavelu , Kalaimughilan Kalaiponmani , Esack Edwin Raj 
Published: December 2021

AbstractFusarium oxysporum f. sp. cubense (Foc), a devastative soil-borne fungal pathogen causing vascular wilt (i.e. Panama disease) which leads to severe crop losses in most of the banana-growing regions of the world. As there is no single source of effective management practices available so far, understand the pathogenicity of the organism may help in designing effective control measures through molecular approaches. The study aims to compare the proteome of the two pathogenic Foc virulent strains, Race 1 (Foc R1) and tropical race 4 (Foc TR4) that are capable of infecting the Cavendish group of bananas using 2-dimensional (2-D) gel electrophoresis, MALDI-TOF/MS and MS/MS analysis. The results of the study revealed that the proteins, peroxiredoxins, NAD-aldehyde dehydrogenase (NAD-ALDH), MAPK protein, pH-response regulator protein palA/rim-20 and isotrichodermin C15 hydroxylase have shared homology with the fungal proteins, which regulate the osmotic stress response, signal transduction, root colonization and toxin biosynthesis. These are the important functions for the pathogen survival in an unfavourable environment, and successful establishment and infection of the banana host. The present study also identified several putative pathogenicity related proteins in both Foc R1 and Foc TR4. Specifically, certain Foc TR4 specific putative pathogenicity related proteins, phytotoxins biosynthesis gene, fructose 1,6-bisphosphate aldolase class II, Synembryn-like proteins found to contribute strong virulence. Overexpression or knockout of the elective genes could help in devising better control measures for the devastative pathogens in the future. To the best of our knowledge, this is the first report on the proteomics of Foc R1 and Foc TR4 strains of Indian origin that infect Cavendish bananas.