bluuebunny/crossref_metadata_2025_split huggingface dataset:
3’ untranslated regions of Marburg and Ebola virus mRNAs possess negative regulators of translation that are modulated by ADAR1 editing
Authors: Khadka Sudip , Williams Caroline G. , Sweeney-Gibbons Joyce , Basler Christopher F. 
Published: April 2021

AbstractThe filovirus family includes deadly pathogens such as Ebola virus (EBOV) and Marburg virus (MARV). A substantial portion of filovirus genomes encode 5’ and 3’ untranslated regions (UTRs) of viral mRNAs. Select viral genomic RNA sequences corresponding to 3’UTRs are prone to editing by ADAR1. A reporter mRNA approach, in which different 5’ or 3’UTRs were inserted into luciferase encoding mRNAs, demonstrates that MARV 3’UTRs yield different levels of reporter gene expression suggesting modulation of translation. The modulation occurs in cells unable to produce miRNAs and can be recapitulated in a minigenome assay. Deletion mutants identified negative regulatory regions at end of the MARV NP and L 3’UTRs. Apparent ADAR1 editing mutants were previously identified within the MARV NP 3’UTR. Introduction of these changes into the MARV nucleoprotein (NP) 3’UTR or deletion of the region targeted for editing enhances translation, as indicated by reporter assays and polysome analysis. In addition, the parental NP 3’UTR, but not the edited or deletion mutant NP 3’UTRs, induce a type I interferon (IFN) response upon transfection into cells. Because some EBOV isolates from the West Africa outbreak exhibited ADAR1 editing of the VP40 3’UTR, VP40 3’UTRs with parental and edited sequences were similarly assayed. The EBOV VP40 3’UTR edits also enhanced translation but neither the wildtype nor the edited 3’UTRs induced IFN. These findings implicate filoviral mRNA 3’UTRs as negative regulators of translation that can be inactivated by innate immune responses that induce ADAR1.ImportanceUTRs comprise a large percentage of filovirus genomes and are apparent targets of editing by ADAR1, an enzyme with pro- and antiviral activities. However, the functional significance of the UTRs and of ADAR1 editing have been uncertain. This study demonstrates that MARV and EBOV 3’UTRs can modulate translation, in some cases negatively. ADAR1 editing or deletion of select regions within the translation suppressing 3’UTRs, relieves the negative effects of the UTRs. These data indicate that filovirus 3’UTRs contain translation regulatory elements that are modulated by activation of ADAR1, suggesting a complex interplay between filovirus gene expression and innate immunity.
WzcandWcaJmutations in hypervirulentKlebsiella pneumoniaelead to phage resistance at the cost of reduced virulence
Authors: Song Lingjie , Yang Xianggui , Huang Jinwei , Zhu Xiaokui , Han Guohui , Wan Yan , Xu Ying , Luan Guangxin , Jia Xu 
Published: April 2021

AbstractHypervirulentKlebsiella pneumoniae(hvKp) is one of the major community-acquired pathogens, which can cause invasive infections such as liver abscess. In recent years, bacteriophages have been used in the treatment ofKlebsiella pneumoniae, but the characteristics of the phage resistant bacteria produced in the process of phage therapy need to be evaluated. In this study, two podoviridae phages, hvKpP1 and hvKpP2, were isolated and characterized. Invitroand invivoexperiments demonstrated that the virulence of the resistant bacteria was significantly reduced compared with that of the wild type. Comparative genomic analysis of monoclonal sequencing showed that nucleotide deletion mutations ofwzcandwcaJgenes led to phage resistance, and the electron microscopy and mucoviscosity results showed that mutations led to the loss of the capsule, meanwhile, animal assay indicated that loss of capsule reduced the virulence of hvKp. The findings can contribute to a better understanding of that bacteriophage therapy can not only kill bacteria directly, but also reduce the virulence of bacteria by phage screening.ImportanceBacteriophages are considered potential therapeutic alternative to antibiotics; however host-evolved phage resistance has accounted for the resurgences of pathogens, meaning further measures are need to improve the efficacy of phage therapy. This study showed two phages capable of infecting hypervirulentK. pneumoniaeand identified phage-resistant mutants whose virulence was significantly reduced. Gene sequencing analysis revealed that mutations ofwzcandwcaJgene, related to capsule synthesis, recovered phage resistance but reduced the virulence of hypervirulentK. pneumoniae.
Efficient prediction of a spatial transcriptomics profile better characterizes breast cancer tissue sections without costly experimentation
Authors: Monjo Taku , Koido Masaru , Nagasawa Satoi , Suzuki Yutaka , Kamatani Yoichiro 
Published: April 2021

AbstractSpatial transcriptomics is an emerging technology requiring costly reagents and considerable skills, limiting the identification of transcriptional markers related to histology. Here, we show that predicted spatial gene-expressions in unmeasured regions and tissues can enhance biologists’ histological interpretations. We developed theDeeplearning model forSpatial geneClusters andExpression, DeepSpaCE and confirmed its performance using the spatial-transcriptome profiles and immunohistochemistry images of consecutive human breast cancer tissue sections. For example, the predicted expression patterns ofSPARC, an invasion marker, highlighted a small tumor-invasion region that is difficult to identify using raw data of spatial transcriptome alone because of a lack of measurements. We further developed semi-supervised DeepSpaCE using unlabeled histology images and increased the imputation accuracy of consecutive sections, enhancing applicability for a small sample size. Our method enables users to derive hidden histological characters via spatial transcriptome and gene annotations, leading to accelerated biological discoveries without additional experiments.
Brain-Wide Inferiority and Equivalence Tests in fMRI Group Analyses: Selected Applications
Authors: Gerchen Martin Fungisai , Kirsch Peter , Feld Gordon Benedikt 
Published: April 2021

AbstractNull hypothesis significance testing is the major statistical procedure in the field of fMRI, but provides only a rather limited picture of the effects in a data set. When sample size and power is low relying only on strict significance testing may lead to a host of false negative findings. In contrast, with very large data sets virtually every voxel might become significant.It is thus desirable to complement significance testing with procedures like inferiority and equivalence tests that allow to formally compare effect sizes within and between data sets and offer novel approaches to obtain insight into fMRI data. The major component of these tests are estimates of standardized effect sizes and their confidence intervals. Here we show how Hedge’s g, the bias corrected version of Cohen’s d, and its confidence interval can be obtained from SPM t maps. We then demonstrate how these values can be used to evaluate whether non-significant effects are really statistically smaller than significant effects to obtain “regions of undecidability” within a data set, and to test for the replicability and lateralization of effects.This method allows the analysis of fMRI data beyond point estimates enabling researchers to take measurement uncertainty into account when interpreting their findings.
Genome-wide association uncovers the genetic architecture of tradeoff between flowering date and yield components in sesame
Authors: Sabag Idan , Morota Gota , Peleg Zvi 
Published: April 2021

AbstractUnrevealing the genetic makeup of crop morpho-agronomic traits is essential for improving yield quality and sustainability. Sesame (Sesamum indicumL.), one of the oldest oil-crops in the world, which despite its economical and agricultural importance, is an ‘orphan crop-plant’ that undergone limited modern selection, thus, preserving wide genetic diversity. Here we harnessed this natural variation in a newly developed sesame panel (SCHUJI) to perform genome-wide association studies for morpho-agronomic traits under the Mediterranean climate conditions. Field-based phenotyping of the SCHUJI panel across two seasons exposed wide phenotypic variation for all traits. Using 20,294 single-nucleotide polymorphism markers, we detected 50 genomic signals associated with these traits. Major genomic region on LG2 was associated with flowering date and yield-related traits, exemplified the key role of the flowering date on productivity. Our results shed light on the genetic architecture of flowering date and its interaction with yield components in sesame and may serve as a basis for future sesame breeding programs in the Mediterranean basin.
Prevalence and genotyping of Trichomonas gallinae in Riyadh, Saudi
Arabia
Authors: Albeshr Mohammed Fahad , Alrefaei Abdulwahed Fahad 
Published: April 2021

Abstract
Trichomonas gallinae is a single-celled protozoan
parasite and causative agent of trichomonosis. Trichomonosis is a disease with a
worldwide distribution, and has recently been highlighted as a pandemic threat
to several wild bird species. The aim of this study is to investigate the
prevalence and genotypic diversity of Trichomonas
gallinae in Riyadh, Saudi Arabia. A total of 273 oral swab
samples from birds were collected and tested for T.
gallinae infection, and the overall prevalence of
Trichomonas gallinae in these samples was 26.4%
(72 of 273). We compared the rates of infections with T.
gallinae between wild and domestic pigeons and found that the
infection was significantly higher in domestic pigeons; a finding which should
be considered by the Ministry of Environment, Water and Agriculture of Saudi
Arabia when evaluating the role of poultry markets in the transmission of
trichomonosis. Sequence analyses of the internal transcribed spacer (ITS) region
indicated genetic variation in these parasite strains, as found in the samples
collected. Among 48 sequences 15 different ribotypes were found, 12 of which
were novel, and 3 of which were previously-described ribotypes: ribotype A, C,
and II. This study demonstrates the diversity of T.
gallinae strains in Saudi Arabian birds for the first time,
and revealed that ribotypes A and C are predominant among Riyadh birds.
Financial innovation regulations and firm performance: Evidence from Chinese listed firms
Authors: Yang Minhua 
Published: April 2021

AbstractThis study investigates the impacts of financial innovation regulations on Chinese listed firms in the period of 2008 to 2020, which comes to the theoretical contribution of this paper. These regulations introduced in 2016 mainly focus on the peer‐to‐peer (P2P) lending platforms in this country and tend to be negatively associated with firm performance, especially for those firms investing in the P2P lending platforms, as a large amount of P2P lending platforms with unfavourable performance disappear in recent years, which may end up negatively affecting those firms investing in them. Survived P2P lending platforms tend to be stronger, then become a type of substitute of traditional banks and are able to carve up the market share of bank. The latter therefore has to increase credit supply to maximise profits, which leads to the access to more credits and therefore worse firm performance, especially for those firms with financial constraints in terms of the cash–cash flow sensitivity. The empirical results are robust to the potential endogeneity issue of financial constraints. Larger firms and state‐owned enterprises (SOEs) tend to have better performance, implying that authorities may take actions for smaller firms (non‐SOEs) to offset the negative impacts of financial innovation regulations they suffer and achieve better implementation of financial innovation regulations, which comes to the practical contribution of this paper.
Debiasing the Measurement of Conditional Conservatism
Authors: BADIA MARC , DURO MIGUEL , PENALVA FERNANDO , RYAN STEPHEN G. 
Published: April 2021

ABSTRACTBasu's [“The Conservatism Principle and the Asymmetric Timeliness of Earnings.” Journal of Accounting and Economics 24 (1997): 3–37] measurement of conditional conservatism as the asymmetric timeliness of earnings underlies hundreds of studies. However, many subsequent studies cast doubt on the extent to which Basu's measure captures conditional conservatism versus statistical biases or alternative constructs (collectively, “biases”), thereby questioning the validity of the inferences that empirical researchers draw from analyses using the measure. We modify Basu's measure in four simple ways to remove these biases. Our key modification is the inclusion of interactive controls for return variance, a volatility proxy that captures Patatoukas and Thomas’ [“More Evidence of Bias in Differential Timeliness Estimates of Conditional Conservatism.” The Accounting Review 86 (2011): 1765–1794] return variance effect and various sources of economic optionality and adjustment costs. This inclusion captures volatility‐related effects on both the level of earnings and the sensitivity of earnings to returns, and it allows the magnitudes of these effects to vary with the sign of returns. We conduct validation analyses using placebo‐dependent variables, synthetic returns, and nonconditionally conservative earnings components that show our modified Basu measure is largely free of known biases. We further show that our measure is associated with contracting and other economic variables as predicted by theory. Our findings suggest that researchers can rely on our modified Basu measure to identify the determinants and effects of conditional conservatism.
Health effects of dietary sulfated polysaccharides from seafoods and their interaction with gut microbiota
Authors: Zhu Zhenjun , Han Yanhui , Ding Yu , Zhu Beiwei , Song Shuang , Xiao Hang 
Published: April 2021

AbstractVarious dietary sulfated polysaccharides (SPs) have been isolated from seafoods, including edible seaweeds and marine animals, and their health effects such as antiobesity and anti‐inflammatory activities have attracted remarkable interest. Sulfate groups have been shown to play important roles in the bioactivities of these polysaccharides. Recent in vitro and in vivo studies have suggested that the biological effects of dietary SPs are associated with the modulation of the gut microbiota. Dietary SPs could regulate the gut microbiota structure and, accordingly, affect the production of bioactive microbial metabolites. Because of their differential chemical structures, dietary SPs may specifically affect the growth of certain gut microbiota and associated metabolite production, which may contribute to variable health effects. This review summarizes the latest findings on the types and structural characteristics of SPs, the effects of different processing techniques on the structural characteristics and health effects of SPs, and the current understanding of the role of gut microbiota in the health effects of SPs. These findings might help in better understanding the mechanism of the health effects of SPs and provide a scientific basis for their application as functional food.
Exo‐inulinase production from Aspergillus fumigatus NFCCI 2426: purification, characterization, and immobilization for continuous fructose production
Authors: Rawat Hemant Kumar , Soni Hemant , Suryawanshi Rahul Kumar , Choukade Ritumbhara , Prajapati Bhanu Pratap , Kango Naveen 
Published: April 2021

AbstractAspergillus fumigatus was found to produce thermostable exo‐inulinase (EC 3.8.1.80; 38 U/ml) on inulin‐rich infusions. Exo‐inulinase (14.6 U/mg) was immobilized on glutaraldehyde activated Ca‐alginate beads for continuous generation of fructose by hydrolyzing sucrose, chicory, and dandelion substrates. Immobilization of enzyme was confirmed by microscopic and spectroscopic techniques. The exo‐inulinase was purified using ion‐exchange (1.30‐folds) and size‐exclusion chromatography (2.71‐folds). The purified exo‐inulinase showed 64 kDa band on gel and was optimally active at 60 °C and pH 6.0. Kinetic constants, Km and Vmax of purified exo‐inulinase, were 5.88 mM and 1.66 µM/min, respectively, and its relative activity was found to be enhanced (125.8%) in the presence of calcium ion. Immobilized preparation was utilized for continuous generation of fructose from chicory juice (26 to 70%) and dandelion root extracts (16 to 24%) by recycling upto five cycles, respectively. In comparison to other sweeteners, such as sucrose, fructose is considered as a healthy alternative. The present study demonstrated the use of immobilized exo‐inulinase in continuous generation of fructose from some underutilized plant sources that can be used in food industry.Practical ApplicationThermostable exo‐inulinase produced by A. fumigatus was immobilized on calcium alginate matrix and was employed for continuous hydrolysis of chicory juice and dandelion root extract for generation of fructose syrup.
Effectiveness of ultrasound‐assisted immersion thawing on the thawing rate and physicochemical properties of chicken breast muscle
Authors: Zhang Chao , Sun Qinxiu , Chen Qian , Liu Qian , Kong Baohua 
Published: April 2021

AbstractThis study evaluated the effect of air thawing (AT), water thawing (WT), and ultrasound‐assisted immersion thawing (UT) at different power levels (200, 300, 400, and 500 W) on the thawing rate, physicochemical properties, and protein structure of chicken breast muscle (pectoralis), and the weight of each sample was approximately 106 ± 3 g. UT shortened the total thawing time and decreased the cutting force with increasing ultrasound power. Additionally, UT at 300 W (UT‐300) remarkably reduced the thawing and cooking losses of the samples compared to AT, WT, and other UT powers (p < 0.05). Low‐field nuclear magnetic resonance spectroscopy showed that the T21 and T22 of the UT‐300 samples were shorter than those of the AT and WT samples (p < 0.05), which revealed that UT‐300 reduced the mobility and losses of both immobilized and free water. Moreover, UT‐300 remarkably reduced the damage to the myofibrillar protein (MP) structure. Overall, with appropriate ultrasonic power, the thawing rate increased and changes in the MP structure were reduced.Practical ApplicationThis study found that compared to that of AT samples, the thawing time of the UT‐300 samples markedly decreased by 57%. In addition, UT‐300 could reduce the damage to the myofibrillar protein structure, which was very beneficial for further processing of frozen foods.
Shifts in behavioral allocation patterns as a natural recovery mechanism: Postresolution expenditure patterns
Authors: Tucker Jalie A. , Cheong JeeWon , Chandler Susan D. 
Published: April 2021

AbstractBackgroundBehavioral economics predicts that recovery from Alcohol Use Disorder involves shifts in resource allocation away from drinking, toward valuable nondrinking rewards that reinforce and stabilize recovery behavior patterns. Further, these shifts should distinguish nonproblem drinking (moderation) outcomes from outcomes involving abstinence or relapse. To evaluate these hypotheses, 5 prospective studies of recent natural recovery attempts were integrated to examine changes in monetary spending during the year following the initial cessation of heavy drinking as a function of 1‐year drinking outcomes.MethodsProblem drinkers from Southeastern U.S. communities (N = 493, 67% male, 65% white, mean age = 46.5 years) were enrolled soon after stopping heavy drinking without treatment and followed prospectively for a year. An expanded Timeline Followback interview assessed daily drinking and monetary spending on alcohol and nondrinking commodities during the year before and after recovery initiation.ResultsLongitudinal associations between postresolution drinking and spending were evaluated using MPlus v.8. Initial models evaluated whether changes in spending at 4‐month intervals predicted drinking outcomes at 1 year and showed significant associations in 6 commodity categories (alcohol, consumable goods, gifts, entertainment, financial/legal affairs, housing/durable goods/insurance; ps < 0.05). Cross‐lagged models showed that the moderation outcome group shifted spending mid‐year to obtain large rewards with enduring benefits (e.g., housing), whereas the abstinent and relapsed groups spent less overall and purchased smaller rewards (e.g., consumable goods, entertainment, and gifts) throughout the year.ConclusionsDynamic changes in monetary allocation occurred during the postresolution year. As hypothesized, compared to the groups who abstained or relapsed, the moderation group shifted spending in ways that, overall, yielded higher value alcohol‐free reinforcement that should reinforce recovery while they enjoyed some limited nonproblem drinking below heavy drinking thresholds. These findings add to evidence that moderation entails different behavioral regulation processes than abstinent and relapse outcomes, which were more similar to one another.
Estimation of risk of neuropsychiatric adverse events from varenicline, bupropion and nicotine patch versus placebo: secondary analysis of results from the EAGLES trial using Bayes factors
Authors: Beard Emma , Jackson Sarah E. , Anthenelli Robert M. , Benowitz Neal L. , Aubin Lisa St. , McRae Thomas , Lawrence David , Russ Cristina , Krishen Alok , Evins A. Eden , West Robert 
Published: April 2021

AbstractBackground and AimsAnalysed using classical frequentist hypothesis testing with alpha set to 0.05, the Evaluating Adverse Events in a Global Smoking Cessation Study (EAGLES) did not find enough evidence to reject the hypothesis of no difference in neuropsychiatric adverse events (NPSAEs) attributable to varenicline, bupropion, or nicotine patch compared with placebo. This might be because the null hypothesis was true or because the data were insensitive. The present study aimed to test the hypothesis more directly using Bayes factors.DesignEAGLES was a randomised, double‐blind, triple‐dummy, controlled trial.SettingGlobal (16 countries across five continents), between November 2011 and January 2015.ParticipantsParticipants were smokers with (n = 4116) and without (n = 4028) psychiatric disorders.InterventionsVarenicline (1 mg twice daily), bupropion (150 mg twice daily), nicotine patch (21 mg once daily with taper) and matched placebos.MeasurementsThe outcomes included: (i) a composite measure of moderate/severe NPSAEs; and (ii) a composite measure of severe NPSAEs. The relative evidence for there being no difference in NPSAEs versus data insensitivity for the medications was calculated in the full and sub‐samples using Bayes factors and corresponding robustness regions.FindingsFor all but two comparisons, Bayes factors were <1/3, indicating moderate to strong evidence for no difference in risk of NPSAEs between active medications and placebo (Bayes factor = 0.02–0.23). In the psychiatric cohort versus placebo, the data were suggestive, but not conclusive of no increase in NPSAEs with varenicline (Bayes factor = 0.52) and bupropion (Bayes factor = 0.71). Here, the robustness regions ruled out a ≥7% and ≥8% risk increase with varenicline and bupropion, respectively.ConclusionsSecondary analysis of the Evaluating Adverse Events in a Global Smoking Cessation Study trial using Bayes factors provides moderate to strong evidence that use of varenicline, bupropion or nicotine patches for smoking cessation does not increase the risk of neuropsychiatric adverse events relative to use of placebo in smokers without a history of psychiatric disorder. For smokers with a history of psychiatric disorder the evidence also points to no increased risk but with less confidence.