bluuebunny/crossref_metadata_2025_split huggingface dataset:
Genome Assembly of the Popular Korean Soybean Cultivar Hwangkeum
Authors: Kim Myung-Shin , Lee Taeyoung , Baek Jeonghun , Kim Ji Hong , Kim Changhoon , Jeong Soon-Chun 
Published: April 2021

AbstractMassive resequencing efforts have been undertaken to catalog allelic variants in major crop species including soybean, but the scope of the information for genetic variation often depends on short sequence reads mapped to the extant reference genome. Additional de novo assembled genome sequences provide a unique opportunity to explore a dispensable genome fraction in the pan-genome of a species. Here, we report the de novo assembly and annotation of Hwangkeum, a popular soybean cultivar in Korea. The assembly was constructed using PromethION nanopore sequencing data and two genetic maps, and was then error-corrected using Illumina short-reads and PacBio SMRT reads. The 933.12 Mb assembly was annotated 79,870 transcripts for 58,550 genes using RNA-Seq data and the public soybean annotation set. Comparison of the Hwangkeum assembly with the Williams 82 soybean reference genome sequence revealed 1.8 million single-nucleotide polymorphisms, 0.5 million indels, and 25 thousand putative structural variants. However, there was no natural megabase-scale chromosomal rearrangement. Incidentally, by adding two novel groups, we found that soybean contains four clearly separated groups of centromeric satellite repeats. Analyses of satellite repeats and gene content suggested that the Hwangkeum assembly is a high-quality assembly. This was further supported by comparison of the marker arrangement of anthocyanin biosynthesis genes and of gene arrangement at the Rsv3 locus. Therefore, the results indicate that the de novo assembly of Hwangkeum is a valuable additional reference genome resource for characterizing traits for the improvement of this important crop species.
Demographics of COVID19 vaccine hesitancy during the second wave of COVID-19 pandemic: A cross-sectional web-based survey in Saudi Arabia
Authors: Al-Mohaithef Mohammed , Padhi Bijaya Kumar , Ennaceur Soukaina Abdulmajed 
Published: April 2021

AbstractBackgroundThe Coronavirus disease 2019 (COVID-19) pandemic is considered a major global public health threat affecting across the life course and socioeconomic aspects of life. Globally acceptance to an effective vaccine is the most anticipated resolution. This study aims to evaluate intent to be vaccinated among public in Saudi Arabia during the second wave of COVID-19 pandemic.MethodsA cross-sectional web-based study was designed in Saudi Arabia. Study participants (N=658) were recruited through snowball sampling. SurveyMonkey platform was used to record the response. Cross-tabulation were performed by participants’ intention to vaccinate against COVID-19 virus with sociodemographic characteristics and respondents’ risk perception towards COVID-19, trust in the healthcare system, and their history of vaccine hesitancy behavior. Multivariable logistic regression analysis was performed to compute the predictors of vaccination intention among the study participants.Results658 participants were completed the survey (females = 47.4%). Of the 658 participants 351 (53.3%) have shown intent to be vaccinated. 519 (78.8%) of the participants were reported to be at high risk of COVID-19, and 307 (46.6%) were reported to trust the healthcare system in the country. The multivariable analysis shows respondents with a high-risk perception (OR: 2.27, 95% CI: 1.49-3.48); higher trust in the healthcare system (OR: 3.24, 95% CI: 2.32-4.61) was found to be the significant factor affecting the decision in acceptance of the COVID-19 vaccine in Saudi Arabia.ConclusionParticipants reported high knowledge towards COVID-19 virus, and vaccine developments. About half (46.6%) of the study participant reported refusal/hesitancy towards the vaccine during the second wave of the pandemic in Saudi Arabia. The study highlighted that higher risk perception and higher trust in the healthcare system were found to be the main reasons for participant’s intentions behind the vaccination.
Life on the leaf: Seasonal activities of the phyllosphere microbiome of perennial crops
Authors: Howe Adina C. , Stopnisek Nejc , Dooley Shane K. , Yang Fan , Grady Keara L. , Shade Ashley 
Published: April 2021

AbstractPlants and microorganisms form beneficial associations. Understanding plant-microbe interactions will inform microbiome management to enhance crop productivity and resilience to stress. Here, we apply a genome-centric approach to identify key leaf microbiome members on field-grown switchgrass and miscanthus, and quantify their activities for switchgrass over two growing seasons. We integrate metagenome and metatranscriptome sequencing from 192 leaf samples collected over key time points in crop phenology. We curated 40 focal metagenome-assembled-genomes (MAGs) and conservatively focus analysis on transcript recruitment to medium and high-quality MAGs that were <10% contaminated and >50% complete. Classes represented by these MAGs (Actinomycetia, Alpha- and Gamma-Proteobacteria, and Bacteroidota) were active and had seasonal dynamics in key functions, including enrichments in transcripts for of short chain dehydrogenase, molybdopterin oxioreductase, and polyketide cyclase in the late season. The majority of MAGs had activated stress-associated pathways, including trehalose metabolism, indole acetic acid degradation, betaine biosynthesis, and reactive oxygen species degradation, suggesting direct engagement with the host environment. We also detected seasonally activated biosynthetic pathways for terpenes (carotenoid and isoprenoids), and for various non-ribosomal peptide pathways that were poorly annotated. Overall, this study overcame laboratory and bioinformatic challenges associated with field-based leaf metatranscriptome analysis to inform potential key activities of these phyllosphere populations. These activities collectively support that leaf-associated bacterial populations are seasonally dynamic, responsive to host cues and interactively engage in feedbacks with the plant.
Comparison of Mucosal and Intramuscular Immunization against SARS-CoV-2 with Replication-Defective and Replicating Single-cycle Adenovirus Vaccines
Authors: Mudrick Haley E. , McGlinch Erin B. , Parrett Brian J. , Hemsath Jack R. , Barry Mary E. , Rubin Jeffrey D. , Uzendu Chisom , Hansen Michael J. , Erskine Courtney L. , VanKeulen Virginia P. , Drelich Aleksandra , Tseng Chien-Te Kent , Massey Shane , Fida Madiha , Suh Gina A. , Peikert Tobias , Block Matthew S. , Olivier Gloria R. , Barry Michael A. 
Published: April 2021

AbstractSARS-CoV-2 enters the body at mucosal surfaces, such as the nose and lungs. These events involve a small number of virions at these mucosal barriers and are therefore a strategic point to stop a COVID-19 infection before it starts. Despite this, most vaccines against COVID-19 are being injected into the muscle where they will not generate the highest levels of mucosal protection. The vaccines that are approved for use in humans are all replication-defective (RD) mRNA, DNA, or adenovirus (Ad) vaccines that do not amplify antigen transgenes. We developed single cycle adenovirus (SC-Ad) vectors that replicate antigen genes up to 10,000-fold in human cells, but that are disabled from producing infectious Ad particles. We show here that SC-Ad expressing the full-length SARS-CoV-2 spike protein produces 100-fold more spike protein than a matched RD-Ad-Spike vector. When Ad-permissive hamsters were immunized with these vaccines by intranasal (IN) or intramuscular (IM) routes, SC-Ad produced significantly stronger antibody responses as compared to RD-Ad against the spike protein that rose over 14 weeks after one immunization. Single IN or IM immunizations generated significant antibody responses in serum and in bronchoalveolar lavages (BALs). IN priming, but not IM priming, generated HLA-restricted CD8 T cell responses in BALs. SC-Ad-Spike generated antibodies that retain binding to spike receptor binding domains (RBDs) with mutations from new viral variants. These data suggest empowering the genomes of gene-based vaccines with the ability to amplify antigen genes can increase potency. This may be particularly advantageous when applying mucosal vaccines to combat mucosal pathogens like SARS-CoV-2.One Sentence SummaryArming adenovirus vaccines with the ability to replicate vaccine antigen genes may increase potency for systemic, or more importantly, mucosal immunization against mucosal pathogens.
Measuring Oxygen Access: lessons from health facility assessments in Nigeria
Authors: Graham Hamish R , Olojede Omotayo E , Bakare Ayobami A , Iuliano Agnese , Olatunde Oyaniyi , Isah Adamu , Osebi Adams , Ahmed Tahlil , Burgess Rochelle Ann , McCollum Eric D , Colbourn Tim , King Carina , Uchendu Obioma C , Falade Adegoke G 
Published: April 2021

ABSTRACTThe COVID-19 pandemic has highlighted global oxygen system deficiencies and revealed gaps in how we understand and measure “oxygen access”. We present a case study on oxygen access from 58 health facilities in Lagos state, Nigeria. We found large differences in oxygen access between facilities (primary vs secondary, government vs private) and describe four key domains to consider when measuring oxygen access.Use8/58 (14%) of facilities had a functional pulse oximeter for detecting hypoxaemia (low blood oxygen level) and guiding oxygen care. Oximeters were typically located in outpatient clinics (12/27, 44%), paediatric ward (6/27, 22%), or operating theatre (4/27, 15%), not suitable for children, and infrequently used.Availability34/58 (59%) facilities had a functional source of oxygen available on the day of inspection, of which 31 (91%) facilities had it available in a single ward area, typically the operating theatre or maternity ward.CostOxygen was free to patients at primary health centres, when available, but expensive in hospitals and private facilities, with the median cost for 2 days oxygen 13000 ($36 USD) and 27500 ($77 USD) naira, respectively.Patient accessNo facilities were adequately equipped to meet minimum oxygen demands for patients. We were unable to determine the proportion of hypoxaemic patients who received oxygen therapy with available data.We highlight the importance of a multi-faceted approach to measuring oxygen access that assesses access at the point-of-care, and ideally at the patient-level. We propose standard metrics to report oxygen access and describe how these can be integrated into routine health information systems and existing health facility assessment tools.SUMMARY BOXOxygen access is poorly understood and the most commonly used metrics (e.g. presence of an oxygen source) do not correlate well with actual access to patients.Pulse oximetry use is a critical indicator for the quality of oxygen services and may be a reasonable reflection of oxygen coverage to patients with hypoxaemia.Oxygen, and pulse oximeter, availability must be assessed at the point-of-care in all major service delivery areas, as intra-facility oxygen distribution is highly inequitable.Minimum functional requirements for oxygen sources must be assessed, as many oxygen concentrators and cylinders may be present without being in working order.
Human Taste Cells Express ACE2: a Portal for SARS-CoV-2 Infection
Authors: Doyle Máire E , Appleton Ashley , Liu Qing-Rong , Yao Qin , Mazucanti Caio Henrique , Egan Josephine M 
Published: April 2021

AbstractLoss and changes in taste and smell are well-reported symptoms of SARS-CoV-2 infection. The virus targets cells for entry by high affinity binding of its spike protein to cell-surface angiotensin-converting enzyme-2 (ACE2). It was not known whether ACE2 is expressed on taste receptor cells (TRCs) nor if TRCs are infected directly. Using anin-situhybridization (ISH) probe and an antibody specific to ACE2, it seems evident that ACE2 is present on a subpopulation of specialized TRCs, namely, PLCβ2positive, Type II cells in taste buds in taste papillae. Fungiform papillae (FP) of a SARS-CoV-2+ patient exhibiting symptoms of COVID-19, including taste changes, were biopsied. Based on ISH, replicating SARS-CoV-2 was present in Type II cells of this patient. Therefore, taste Type II cells provide a portal for viral entry that predicts vulnerabilities to SARS-CoV-2 in the oral cavity. The continuity and cell turnover of the FP taste stem cell layer of the patient were disrupted during infection and had not fully recovered 6 weeks post symptom onset. Another patient suffering post-COVID-19 taste disturbances also had disrupted stem cells. These results indicate that a COVID-19 patient who experienced taste changes had replicating virus in their taste buds and that SARS-CoV-2 infection results in deficient stem cell turnover needed for differentiation into TRCs.
Bank loan covenants, accrual quality and firms’ information environment
Authors: Chen Chao‐Jung , He Wen , Lu Chien‐Ju , Yu Xin 
Published: April 2021

AbstractWe examine whether initiations of bank loans with financial covenants motivate banks to monitor borrowers’ accounting practice and result in a higher quality of reported accruals and a better information environment for firms. We document that, relative to loans without financial covenants, loans with financial covenants lead to an improvement in accrual quality measured by the extent to which accruals can be mapped into cash flows. The effect of loan covenants on accrual quality is stronger when external monitoring by non‐bank stakeholders (i.e., institutional investors and financial analysts) is weaker. Furthermore, initiations of bank loans with financial covenants are related to subsequent improvements in analysts’ information environment. The evidence supports the view that bank monitoring improves accounting quality.
Words with Consistent Diachronic Usage Patterns are Learned Earlier: A Computational Analysis Using Temporally Aligned Word Embeddings
Authors: Cassani Giovanni , Bianchi Federico , Marelli Marco 
Published: April 2021

AbstractIn this study, we use temporally aligned word embeddings and a large diachronic corpus of English to quantify language change in a data‐driven, scalable way, which is grounded in language use. We show a unique and reliable relation between measures of language change and age of acquisition (AoA) while controlling for frequency, contextual diversity, concreteness, length, dominant part of speech, orthographic neighborhood density, and diachronic frequency variation. We analyze measures of language change tackling both the change in lexical representations and the change in the relation between lexical representations and the words with the most similar usage patterns, showing that they capture different aspects of language change. Our results show a unique relation between language change and AoA, which is stronger when considering neighborhood‐level measures of language change: Words with more coherent diachronic usage patterns tend to be acquired earlier. The results support theories positing a link between ontogenetic and ethnogenetic processes in language.
Contrast‐enhanced ultrasound combined with augmented reality medical technology in the treatment of rabbit liver cancer with high‐energy focused knife
Authors: Na Fengyu , Wang Li , Wu Cuicui , Ding Yan 
Published: April 2021

AbstractAugmented reality technology can enhance people's perception and interactive experience of real scenes due to its characteristics of fusion of virtual and real, and has become a popular technology in the field of computer science. This article mainly studies the application of contrast‐enhanced ultrasound combined with augmented reality medical technology in the treatment of rabbit liver cancer with high‐energy focused knife. Sixty healthy male New Zealand white rabbits were used in this study. Seldinger's method was used to superselective embolize the artery supplying tumor with the help of hepatic angiography, which can kill tumor cells to the greatest extent and reduce the damage to normal liver cells. At the same time, another assistant under the guidance of ultrasound inserted the temperature probe into the position 1 cm away from the microwave radiation source, and then started the microwave ablation (MWA) treatment. High intensity focused ultrasound (HIFU) treatment is carried out under general anesthesia, the breathing rhythm of patients is controlled by ventilator, the proper position is set before operation, the real‐time monitoring is carried out by ultrasound monitoring mediated by medium water, and the HIFU three‐dimensional scanning treatment system is used to accurately cover all tumor treatment areas from point to line and from line to surface, so as to kill tumor cells to the greatest extent. The data of each group were processed by SPSS17.0 statistical software, and the measurement data were expressed as mean ± SD. ANOVA analysis of variance was used to compare the differences among the groups, and LSD method was used to make pairwise comparison within the group. p < 0.05 was considered as having statistical difference. The growth rate of tumor was 56.1% and 60.3%, respectively. Contrast‐enhanced ultrasound combined with augmented reality medical technology provides a new way for the treatment of rabbit liver cancer.
Prevalence of the presystolic wave in echocardiography and its association with the extent of coronary artery disease in patients with chronic stable angina
Authors: Alimi Hedieh , Hamidi Fatemeh , Bigdelue Leila , Poorzand Hoorak , Ghaderi Fereshteh , Fazlinejad Afsoon , Muhebati Mohsen , Emadzadeh Maryam 
Published: April 2021

AbstractIntroductionSince mortality and morbidity of coronary artery disease are high, there is a need for non‐invasive diagnostic methods for early diagnosis and prediction of ischemic heart disease (IHD) outcome. This study aimed to assess the relationship between angiographic findings, the Presystolic wave (PSW) and some of the ischemic related parameters in echocardiography of the patients with chronic stable angina.Materials and methodsThis cross‐sectional study was conducted on the patients with chronic angina pectoris who referred to a tertiary hospital for coronary angiography in Mashhad, Iran. Demographic and medical history of the patients, as well as echocardiography findings, including ejection fraction (EF), regional wall motion abnormalities (RWMA), PSW and diastolic function were recorded. Angiographic findings, including SYNTAX score were also assessed.ResultsA total of 220 patients (132 males and 88 females) with the mean age of 62.43 ± 11.40 years old participated in this study. The prevalence of PSW was 49.1%. The absence of the PSW was related to more RWMA (P =.002), and higher stages of left ventricular diastolic dysfunction (LVDD) (P =.029) and higher SYNTAX score (P =.001). There was a significant association between the absence of the PSW and EF categories, especially in severe LV systolic dysfunction (LVEF < 30%) (P =.001).ConclusionsThe findings of this study revealed that PSW is strongly associated with the SYNTAX score. The absence of the PSW may indicate patients at high‐risk clinical status (higher SYNTAX score, severe systolic dysfunction, more RWMA, and higher stages of LVDD).
Modified recombinant human IgG1‐Fc is superior to natural intravenous immunoglobulin at inhibiting immune‐mediated demyelination
Authors: Baksmeier Christine , Blundell Pat , Steckel Julia , Schultz Verena , Gu Quan , Da Silva Filipe Ana , Kohl Alain , Linnington Chris , Lu Dongli , Dell Anne , Haslam Stuart , Wang Jiabin , Czajkowsky Dan , Goebels Norbert , Pleass Richard J. 
Published: April 2021

AbstractIntravenous immunoglobulin (IVIG) is an established treatment for numerous autoimmune conditions. Although Fc fragments derived from IVIG have shown efficacy in controlling immune thrombocytopenia in children, the mechanisms of action are unclear and controversial. The aim of this study was to dissect IVIG effector mechanisms using further adapted Fc fragments on demyelination in an ex vivo model of the central nervous system–immune interface. Using organotypic cerebellar slice cultures (OSCs) from transgenic mice, we induced extensive immune‐mediated demyelination and oligodendrocyte loss with an antibody specific for myelin oligodendrocyte glycoprotein (MOG) and complement. Protective effects of adapted Fc fragments were assessed by live imaging of green fluorescent protein expression, immunohistochemistry and confocal microscopy. Cysteine‐ and glycan‐adapted Fc fragments protected OSC from demyelination in a dose‐dependent manner where equimolar concentrations of either IVIG or control Fc were ineffective. The protective effects of the adapted Fc fragments are partly attributed to interference with complement‐mediated oligodendroglia damage. Transcriptome analysis ruled out signatures associated with inflammatory or innate immune responses. Taken together, our findings show that recombinant biomimetics can be made that are at least two hundred‐fold more effective than IVIG in controlling demyelination by anti‐MOG antibodies.
Effect of music therapy on improving sleep quality in older adults: A systematic review and meta‐analysis
Authors: Chen Chia‐Te , Tung Heng‐Hsin , Fang Ching‐Ju , Wang Jiun‐Ling , Ko Nai‐Ying , Chang Ying‐Ju , Chen Yen‐Chin 
Published: April 2021

AbstractObjectivesPoor sleep quality is a common issue among older adults; it can lead to a poor quality of life and impairments in cognitive function and physical health. This study aimed to conduct a systematic review and meta‐analysis of the effect of listening to music on sleep quality in older adults.DesignSystematic review and meta‐analyses.SettingFive databases, including Embase, Ovid Medline, Cochrane Library, Scopus, and the Index to Taiwan Periodical Literature System, were searched to identify studies assessing the efficacy of music therapy in older adults aged 60 years and older published through February 20, 2021.ParticipantsAdults aged 60 years and older.MeasurementsWe searched English‐ and Chinese‐language studies of randomized control trials. All studies were reviewed by two independent investigators. The primary sleep outcome was the Pittsburgh sleep quality index. The Cochrane Collaboration tool was used to assess the risk of bias, and Review Manager 5.3 software was used to conduct the meta‐analysis.ResultsFive randomized control trials were included in the meta‐analysis. Older adults who listened to music experienced significantly better sleep quality than those who did not listen to music [mean difference (MD): −1.96, 95% CI −2.23 to −1.73, P = 0.003]. The subgroup analysis revealed that older adults who listened to sedative music obtained a more effective improvement in sleep quality than those who listened to rhythm‐centered music (MD: −2.35, 95% CI –3.59 to −1.10, P = 0.0002). Furthermore, listening to music for longer than 4 weeks (MD: −2.61, 95% CI −4.72 to −0.50, P = 0.02) was to be effective at improving sleep quality.ConclusionsMusic therapy is safe and easy to administer and can effectively improve sleep quality among older adults, particularly those listening to more sedative music for at least a four‐week duration.