bluuebunny/crossref_metadata_2025_split huggingface dataset:
Evaluation of a Recessive Male Floret Color in Cultivated Northern Wild Rice (Zizania palustrisL.) for Pollen-Mediated Gene Flow Studies
Authors: Gietzel Clare , Duquette Jacques , McGilp Lillian , Kimball Jennifer 
Published: January 2021

AbstractNorthern wild rice (NWR;Zizania palustrisL.) is a wind-pollinated, annual, aquatic grass that grows naturally in the Great Lakes Region (GLR) of the United States and Canada, and is also cultivated in flooded paddies, predominantly in California and Minnesota. A better understanding of pollen-mediated gene flow is needed within the species for both conservation and breeding efforts as cultivation occurs within the species natural range and spatially-isolated, paddy structures are limited within breeding programs. Widely cited pollen travel research in NWR demonstrated that pollen could travel at least 3200m. However, a population segregating for male sterility was used as the pollen recipient in the study and was determined to not be adequate for NWR pollen travel studies. Here, we present the characterization of a recessive white male floret (WMF) population in contrast to the dominant, purple male floret (PMF) color of cultivated NWR along with estimates of pollen-mediated gene flow in a cultivated paddy setting. Studies conducted in 2018 and 2019 revealed that the primary amount of pollen-mediated gene flow occurred within the first 7m from the PMF donor source with no gene flow detected past 63m. These results suggest that the likelihood of pollen-mediated gene flow between cultivated NWR and natural stands remains low. We also identified a strong linkage between male floret, auricle, and culm color. This study demonstrates that the WMF trait is an excellent candidate for use in pollen-mediated gene flow studies in NWR.
STING agonism enhances anti-tumor immune responses and therapeutic efficacy of PARP inhibition inBRCA-associated breast cancer
Authors: Pantelidou Constantia , Jadhav Heta , Kothari Aditi , Liu Renyan , Guerriero Jennifer L. , Shapiro Geoffrey I. 
Published: January 2021

ABSTRACTPoly (ADP-ribose) polymerase (PARP) inhibitors exert their efficacy by inducing synthetic lethal effects, as well as cGAS/STING-mediated immune responses in BRCA- and other homologous recombination repair-deficient cancer cells. Here we investigated whether the immunologic and therapeutic effects of PARP inhibition in BRCA-deficient breast cancer models could be augmented by synthetic cyclic dinucleotide agonists of STING. Combined PARP inhibition and STING agonism induced a greater degree of STING pathway activation and proinflammatory cytokine production compared to monotherapies in BRCA1-deficient human and mouse triplenegative breast cancer cell lines. In a mouse model of BRCA1-deficient TNBC, the combination also induced an improved immune response compared to either monotherapy alone, evidenced by a greater degree of cytotoxic T cell recruitment and activation, and enhanced dendritic cell activation and antigen presentation. Nanostring mRNA analysis indicated that combinatorial effects were the result of augmented interferon signaling and antigen processing, as well as of heightened leukocyte and dendritic cell functions. Finally, the combination markedly improved anti-tumor efficacyin vivocompared to monotherapy treatment, with evidence of complete tumor clearance and prolongation of survival. These results support the development of combined PARP inhibition and STING agonism inBRCA-associated breast cancer.
Deep Directed Evolution of Solid Binding Peptides for Quantitative Big-data Generation
Authors: Yucesoy Deniz T. , Rath Siddharth S. , Rodriguez Jacob L. , Francis-Landau Jonathan , Nakano-Baker Oliver , Sarikaya Mehmet 
Published: January 2021

AbstractProteins have evolved over millions of years to mediate and carry-out biological processes efficiently. Directed evolution approaches have been used to genetically engineer proteins with desirable functions such as catalysis, mineralization, and target-specific binding. Next-generation sequencing technology offers the capability to discover a massive combinatorial sequence space that is costly to sample experimentally through traditional approaches. Since the permutation space of protein sequence is virtually infinite, and evolution dynamics are poorly understood, experimental verifications have been limited. Recently, machine-learning approaches have been introduced to guide the evolution process that facilitates a deeper and denser search of the sequence-space. Despite these developments, however, frequently used high-fidelity models depend on massive amounts of properly labeled quality data, which so far has been largely lacking in the literature. Here, we provide a preliminary high-throughput peptide-selection protocol with functional scoring to enhance the quality of the data. Solid binding dodecapeptides have been selected against molybdenum disulfide substrate, a two-dimensional atomically thick semiconductor solid. The survival rate of the phage-clones, upon successively stringent washes, quantifies the binding affinity of the peptides onto the solid material. The method suggested here provides a fast generation of preliminary data-pool with ∼2 million unique peptides with 12 amino-acids per sequence by avoiding amplification. Our results demonstrate the importance of data-cleaning and proper conditioning of massive datasets in guiding experiments iteratively. The established extensive groundwork here provides unique opportunities to further iterate and modify the technique to suit a wide variety of needs and generate various peptide and protein datasets. Prospective statistical models developed on the datasets to efficiently explore the sequence-function space will guide towards the intelligent design of proteins and peptides through deep directed evolution. Technological applications of the future based on the peptide-single layer solid based bio/nano soft interfaces, such as biosensors, bioelectronics, and logic devices, is expected to benefit from the solid binding peptide dataset alone. Furthermore, protocols described herein will also benefit efforts in medical applications, such as vaccine development, that could significantly accelerate a global response to future pandemics.
Evolutionary selection on synonymous codons in RNA G-quadruplex structural region
Authors: Xu Yuming , Qi Ting , Lu Zuhong , Zhou Tong , Gu Wanjun 
Published: January 2021

ABSTRACTIn addition to the amino acid sequence information, synonymous codons can encode multiple regulatory and structural signals in protein coding region. In this study, we investigated how synonymous codons have been adapted to the formation of RNA G-quadruplex (rG4) structure. We found a universal selective pressure acting on synonymous codons to facilitate rG4 formation in five eukaryotic organisms. WhileG-rich codons are preferred in rG4 structural region,C-rich codons are selectively unpreferred for rG4 structures. Gene’s codon usage bias, nucleotide composition and evolutionary rate can account for the selective variations on synonymous codons among rG4 structures within a species. Moreover, rG4 structures in translational initiation region showed significantly higher selective pressures than those in translational elongation region. These results bring us another dimension of evolutionary selection on synonymous codons for proper RNA structure and function.
Neutralization of SARS-CoV-2 spike 69/70 deletion, E484K, and N501Y variants by BNT162b2 vaccine-elicited sera
Authors: Xie Xuping , Liu Yang , Liu Jianying , Zhang Xianwen , Zou Jing , Fontes-Garfias Camila R. , Xia Hongjie , Swanson Kena A. , Cutler Mark , Cooper David , Menachery Vineet D. , Weaver Scott , Dormitzer Philip R. , Shi Pei-Yong 
Published: January 2021

AbstractWe engineered three SARS-CoV-2 viruses containing key spike mutations from the newly emerged United Kingdom (UK) and South African (SA) variants: N501Y from UK and SA; 69/70-deletion+N501Y+D614G from UK; and E484K+N501Y+D614G from SA. Neutralization geometric mean titers (GMTs) of twenty BTN162b2 vaccine-elicited human sera against the three mutant viruses were 0.81- to 1.46-fold of the GMTs against parental virus, indicating small effects of these mutations on neutralization by sera elicited by two BNT162b2 doses.
Lysosomal-Immune Axis Is Associated with COVID 19 Disease Severity: Insights from Patient Single Cell Data
Authors: Pande Rahul , Teeple Erin , Huang Weixiao , Klinger Katherine W. , Rajpal Deepak , Kumar Dinesh 
Published: January 2021

AbstractSARS-COV-2 has become a leading cause of illness, hospitalizations, and deaths worldwide yet heterogeneity in disease morbidity remains a conundrum. In this study, we analyzed publicly available single-cell RNA-seq data from 75076 cells sequenced from clinically staged COVID-19 patients using a network approach and identified lysosomal-immune axis as a factor significantly associated with disease severity. Our results suggest modulation of lysosomal-immune pathways may present a novel drug-targeting strategy to attenuate SARS-Cov-2 infections.
Key concepts for dietetic curriculum: An observational study of Australian dietitians' perceptions
Authors: Tweedie Judith , Wright Hattie H. , Palermo Claire , Pelly Fiona E. 
Published: January 2021

AbstractAimA concept‐based approach to dietetic curriculum design has been proposed to prevent content overload and promote critical thinking. Fifty‐six concepts were identified in a previous study. The aim of the present study was to investigate whether the dietetic profession views these concepts as representative of current practice and key for nutrition and dietetics education, and identify any new or emerging concepts.MethodsAccredited Practising Dietitians (APDs) were invited to participate in a self‐administered online survey that included scale responses on the relevance of the 56 concepts and open‐ended suggestions of additional concepts. Respondent characteristics were also collected.ResultsNinety‐eight APDs completed the survey. Greater than 65% of respondents agreed/strongly agreed that all 56 concepts were relevant. There was less agreement on the concepts of acid‐base balance; leadership; management; physical activity, exercise and health; quality assurance and improvement; risk; safety; stakeholder; standards; sustainability; systems and technology and health informatics. Respondents working in regional, rural and remote areas were less likely to agree that leadership was a key concept (χ2 = 4.45, P = .035). Respondents working in teaching and education were more likely to agree that sustainability was a key concept (χ2 = 7.02, P = .008). No new concepts were identified.ConclusionsThe existing 56 concepts were considered key for nutrition and dietetics education. Although the respondents to this survey view these concepts as relevant to current practice, this may not represent the entire profession. It is yet to be determined if the concepts will meet future priorities for the dietetic workforce.
Food acculturation experiences of new Iranian skilled migrant mothers in South Australia
Authors: Kavian Foorough , Coveney John , Matwiejczyk Louisa , Mehta Kaye 
Published: January 2021

AbstractAimThis research aimed to investigate the food acculturation experiences of Iranian mothers who have migrated to Australia.MethodsThe study used qualitative methodology to interview seven mothers with children aged 5 to 15 years, who: carried primary responsibility for family food provisioning; arrived in Australia within the last 5 years; and spoke reasonably fluent English.ResultsSeven mothers were interviewed, and the findings revealed three broad themes: (a) adjusting to foods/foodways in Australia (b) sociocultural identity and (c) children and intergenerational conflict. The study highlighted psychosocial and economic stresses associated with food acculturation for this immigrant group. The impact of food acculturation on immigrant health is intricately linked to the complex balance between maintaining traditional cultural identity and practices, while at the same time adapting to the food culture and practices of the new home.ConclusionsDietitians and healthcare professionals working with such immigrant groups need to consider food acculturation stress as a factor contributing to the health risks of new immigrants.
New model species for arctic‐alpine plant molecular ecology
Authors: Pyhäjärvi Tanja , Mattila Tiina M. 
Published: January 2021

Arctic and alpine, high latitude and high elevation environments are one of the most stressful environments for species to inhabit. This harshness manifests itself in lower species richness in comparison to more southern vegetation zones (Francis & Currie, 2003). Furthermore, the climatic oscillations—past and predicted—have the most dramatic effect on these ecosystems. For example, in regions of continental ice sheets—the northernmost part of Western Europe and North America—the Arctic species assemblages are no older than a few thousands of years, which is a relatively short period from an evolutionary perspective. Although similar environments may have existed further south during the Ice Age, allowing some preadaptation for the Arctic species, the current habitat is a unique combination of environmental factors such as the climate, soil, bedrock, and photoperiod. Hence, understanding the evolutionary forces shaping Arctic‐alpine species will be important for predicting these vulnerable environments’ population viability and adaptive potential in the future. In this issue of Molecular Ecology Resources, Nowak et al. (Molecular Ecology Resources) present extensive genome‐wide resources for an Arctic‐alpine plant Draba nivalis. This adds a valuable new member into the cabbage family models for evolutionary genetics and adaptation studies, to accompany e.g., Arabidopsis (Nature Genetics, 43, 476; Nature, 408, 796), Arabis (Nature Plants, 1, 14023) and Capsella (Nature Genetics, 45, 831). A whole new avenue will open up for molecular ecological studies not only for D. nivalis, but the whole large Draba genus with its diverse ecological and evolutionary characteristics.
Validated removal of nuclear pseudogenes and sequencing artefacts from mitochondrial metabarcode data
Authors: Andújar Carmelo , Creedy Thomas J. , Arribas Paula , López Heriberto , Salces‐Castellano Antonia , Pérez‐Delgado Antonio José , Vogler Alfried P. , Emerson Brent C. 
Published: January 2021

AbstractMetabarcoding of Metazoa using mitochondrial genes may be confounded by both the accumulation of PCR and sequencing artefacts and the co‐amplification of nuclear mitochondrial pseudogenes (NUMTs). The application of read abundance thresholds and denoising methods is efficient in reducing noise accompanying authentic mitochondrial amplicon sequence variants (ASVs). However, these procedures do not fully account for the complex nature of concomitant sequences and the highly variable DNA contribution of specimens in a metabarcoding sample. We propose, as a complement to denoising, the metabarcoding Multidimensional Abundance Threshold Evaluation (metaMATE) framework, a novel approach that allows comprehensive examination of multiple dimensions of abundance filtering and the evaluation of the prevalence of unwanted concomitant sequences in denoised metabarcoding datasets. metaMATE requires a denoised set of ASVs as input, and designates a subset of ASVs as being either authentic (mitochondrial DNA haplotypes) or nonauthentic ASVs (NUMTs and erroneous sequences) by comparison to external reference data and by analysing nucleotide substitution patterns. metaMATE (i) facilitates the application of read abundance filtering strategies, which are structured with regard to sequence library and phylogeny and applied for a range of increasing abundance threshold values, and (ii) evaluates their performance by quantifying the prevalence of nonauthentic ASVs and the collateral effects on the removal of authentic ASVs. The output from metaMATE facilitates decision‐making about required filtering stringency and can be used to improve the reliability of intraspecific genetic information derived from metabarcode data. The framework is implemented in the metaMATE software (available at https://github.com/tjcreedy/metamate).
Clinical outcomes and radiation pneumonitis after concurrent EGFR‐tyrosine kinase inhibitors and radiotherapy for unresectable stage III non‐small cell lung cancer
Authors: Xu Kunpeng , Liang Jun , Zhang Tao , Zhou Zongmei , Chen Dongfu , Feng Qinfu , Xiao Zefen , Hui Zhouguang , Lu Jima , Wang Xin , Deng Lei , Liu Wenyang , Wang Jianyang , Zhai Yirui , Wang Jie , Bi Nan , Wang Luhua 
Published: January 2021

AbstractBackgroundConcurrent epidermal growth factor receptor‐tyrosine kinase inhibitors (EGFR‐TKI) with radiotherapy in patients with EGFR‐mutant unresectable stage III non‐small cell lung cancer (NSCLC) might improve survival. However, both treatments carry a potential risk of pneumonitis.MethodsBetween May 2012 and December 2017, patients with unresectable stage III NSCLC treated with concurrent radiotherapy and EGFR‐TKI were enrolled in this retrospective study. The baseline characteristics were evaluated to determine correlations with toxicity development.ResultsAmong 45 eligible patients, 20 (44.4%) had an EGFR mutation and 44 (97.8%) received 50–66 Gy of radiotherapy. The median follow‐up was 62.7 months. The median progression free survival (PFS) and overall survival (OS) for patients with EGFR‐mutations were 27.9 (95% CI: 18.7–37.2) and 49.7 (95% CI: 27.7–71.8) months, and 13.8 (95% CI: 8.8–18.9) and 31.1 (95% CI: 9.8–52.4) months for EGFR wild‐type/unknown patients. A total of 17 patients (37.7%) developed radiation pneumonitis/pneumonitis (14 grade 2, 3 grade 3). In 16 patients, pneumonitis occurred within the radiation field and one patient had bilateral pneumonitis. The median time from the initial radiotherapy to pneumonitis was 74 days. Logistic regression analysis revealed a trend between the time of EGFR‐TKI and the development of G2+ pneumonitis. For late toxicity, only two patients had G2+ fibrosis. The daily dyspnea symptoms of patients with G2+ pneumonitis recovered significantly after the phase of pneumonitis (P = 0.007).ConclusionsCombined EGFR‐TKI and radiotherapy showed favorable survival in EGFR‐mutant patients with inoperable stage III NSCLC, with a 6.7% incidence of grade 3 radiation pneumonitis/pneumonitis, despite a higher incidence of mild‐to‐moderate radiation pneumonitis.Key pointsSignificant findings of the studyWe evaluated the outcomes and radiation pneumonitis after EGFR‐TKI during interval radiotherapy. EGFR‐TKI plus radiotherapy increased survival in patients with EGFR‐mutant inoperable stage III NSCLC. The mild‐to‐moderate radiation pneumonitis incidence increased but no grade 4–‐5 adverse events occurred.What this study addsThe combination of EGFR‐TKI and radiotherapy might carry a risk of pneumonitis; however, there are limited data concerning dose constraints. Our results showed a slightly higher incidence of mild or moderate radiation pneumonitis by strict dose limitation.
Weekend admission and mortality among patients with sepsis: A nationwide cohort study in South Korea
Authors: Oh Tak Kyu , Song In‐Ae 
Published: January 2021

BackgroundThis study aimed to investigate whether weekend admission was associated with a higher risk of 90‐day mortality in patients with sepsis.MethodsThis population‐based cohort study was based on health records from the National Health Insurance Service database in South Korea. All adult patients (age ≥ 18 years) admitted for sepsis (A40, A41) or septic shock (R65.2) as diagnosed according to the International Classification of Diseases, 10th revision codes, during 2010‐2018 were screened. Weekend admission was defined as admission for sepsis on weekends.ResultsIn all, 251 837 patients were enrolled, of which 43 327 (17.2%) were in the weekend admission group and 208 510 (82.8%) in the weekday admission group. After propensity score matching, 86 654 patients with sepsis (43 327 patients with sepsis in each group) were included in the analysis. The 90‐day mortality rates in the weekend admission and weekday admission groups were 44.3% (19 204/43 327) and 41.9% (18 157/43 327), respectively. On Cox regression analysis, the risk of 90‐day mortality in the weekend admission group was 1.09‐times higher than that in the weekday admission group (hazard ratio: 1.09, 95% confidence interval: 1.07‐1.12; P < .001).ConclusionUsing the national health claims database in South Korea, we showed that weekend admission for diagnosed sepsis was associated with an increased risk of 90‐day mortality, compared to that for weekday admission. This might be due to the higher severity of illness in patients with sepsis admitted during the weekend or relatively lesser hospital staff during the weekend.
Employee disclosures in the grocery industry before the COVID‐19 pandemic
Authors: Kent Pamela , McCormack Robyn , Zunker Tamara 
Published: January 2021

AbstractWe provide evidence on the consumer staples industry's commitment and accountability to employees prior to the COVID‐19 pandemic by analysing their employee‐related disclosures in annual reports. A high level of disclosure exists from 2004 to 2019 with 93 percent of the industry disclosing some information about employees. The highest categories of disclosure are remuneration, health and safety, and training and development. We find that total disclosure is significantly related to having employee share ownership, a Big 4 auditor, a larger board of directors, a majority independent board, independent chair, an audit and nomination committee and higher ROA.
Comparison of growth performance and biochemical components between parent and hybrid offspring in the oriental river prawn, Macrobrachium nipponense
Authors: Li Yiming , Jiang Qichen , Chen Qiang , Liu Zhiquan , Huang Yinying , Tian Jiangtao , Huang Youhui , Zhao Yunlong 
Published: January 2021

SummaryMacrobrachium nipponense, as one of the large‐yield farmed shrimp, is facing germplasm degradation. Genetic improvement through hybridization is one of the effective methods to solve this problem. In this study, using a three‐line hybrid strategy, two‐hybrid F1 populations were obtained using three local populations of M. nipponense as parents for crossbreeding. Five populations were then cultured for 3 months. Growth rate performance was measured by the hepatosomatic index, weight gain, body length growth rate and special growth rate. Biochemical components were also assessed. The results showed that the survival rate and growth performance of the hybrid progeny were better than those of the parents. The levels of triglycerides, total cholesterol, glycogen and lactic acid of the hybrid population were higher than those of the parents. This was consistent with variation in the activity of four digestive enzymes. Compared with the results of the fatty acid and amino acid analysis, it was found that the contents of polyunsaturated fatty acids such as eicosapentaenoic acid, docosapentaenoic acid and docosahexaenoic acid and eight essential amino acids in the hybrid populations were significantly higher than those of their parents, and the contents of flavor amino acids were higher. The expression level of molting genes related to the growth of the parent populations was lower than that of the hybrids. These results show that crossbreeding is effective for the genetic improvement of M. nipponense germplasm. Hybrids showed advantages in growth and nutrition and multigenerational breeding will be required to form a stable germplasm.