bluuebunny/crossref_metadata_2025_split huggingface dataset:
High nucleotide substitution rates associated with retrotransposon proliferation drive dynamic secretome evolution in smut pathogens
Authors: Depotter JRL , Ökmen B , Ebert MK , Beckers J , Jb Kruse , Thines M , Doehlemann G 
Published: April 2021

AbstractTransposable elements (TEs) play a pivotal role in shaping diversity in eukaryotic genomes. The covered smut pathogen on barley,Ustilago hordei, encountered a recent genome expansion. Using long reads, we assembled genomes of 6U. hordeistrains and 3 sister species, to study this genome expansion. We found that larger genome sizes can mainly be attributed to a higher genome fraction of long terminal repeat retrotransposons (LTR-RTs). In the studied smut genomes, LTR-RTs fractions are the largest inU. hordeiand are positively correlated to the mating-type locus sizes, which is up to ∼560 kb inU. hordei. Furthermore, LTR-RTs were found to be associated with higher nucleotide substitution levels, as these higher levels occur more clustered in smut species with a recent LTR-RT proliferation. Moreover, genes in genome regions with higher nucleotide substitution levels generally reside closer to LTR-RTs than other genome regions. Genome regions with many nucleotide substitutions encountered an especially high fraction of CG substitutions, which is not observed for LTR-RT sequences. The high nucleotide substitution levels particularly accelerate the evolution of secretome genes, as their more flexible nature results that substitutions often lead to amino acid alterations.ImportanceGenomic alteration can be generated through various means, in which transposable elements (TEs) can play a pivotal role. Their mobility causes mutagenesis in itself and can disrupt the function of the sequences they insert into. Indirectly, they also impact genome evolution as their repetitive nature facilitates non-homologous recombination. Furthermore, TEs have been linked to specific epigenetic genome organizations. We report a recent TE proliferation in the genome of the barley covered smut fungus,Ustilago hordei.This proliferation is associated with a distinct nucleotide substitution regime that has a higher rate and a higher fraction of CG substitutions. This different regime shapes the evolution of genes in subjected genome regions. Our findings highlight that TEs may influence the error-rate of DNA polymerase in a hitherto unknown fashion.
Full‐wave modelling of early‐time measurements in time‐domain electromagnetics: Consideration of coupling between Tx–Rx antennas and the ground
Authors: Finco Cécile , Schamper Cyril , Rejiba Fayçal , Cavalcante Fraga Luis H. 
Published: April 2021

ABSTRACTEarly‐time measurements of time‐domain electromagnetics carry information of the near surface, and therefore, the interpretation of such measurements is important, particularly when utilizing small‐loop acquisition devices. However, these early‐time gates are often distorted by responses from the acquisition system itself, primarily caused by self‐transients associated with the transmission link composed of the transmitter and receiver loops and with the investigated medium electrical properties. Estimating all such potential couplings is crucial for interpreting early‐time measurements and gathering information on the near surface. In this study, a receptor loop made of 20 turns was built for this purpose. Field results and simulations were then compared, which shows how full‐wave finite‐difference method in the time‐domain simulations can be used to accurately calculate the impedance characteristics of time‐domain electromagnetics systems. All simulations were performed using finite‐difference time‐domain software based on a fully explicit three‐dimensional solver. First and second sets of simulations, respectively, were carried out in free space to compare the results to an alternate simulation method with equivalent lumped electrical circuits and on a homogeneous half‐space with varying electrical resistivities. The results were then used to improve the inversion of field data acquired on a test site in Garchy, France.
How do soil microbes exert impact on soil respiration and its temperature sensitivity?
Authors: Tong Di , Li Zhongwu , Xiao Haibing , Nie Xiaodong , Liu Chun , Zhou Mi 
Published: April 2021

SummaryUnderstanding how soil microorganisms influence the direction and magnitude of soil carbon feedback to global warming is vital to predict future climate change. Although microbial activities are major contributors to soil respiration (RS) and its temperature sensitivity (Q10), the mechanisms underpinning microbial influence on RS and Q10 remain unclear. Coupling variation partitioning analysis (VPA), correlation analysis and multiple stepwise linear regression analysis, we illustrate that bacteria mainly affect RS and its temperature sensitivity (Q10) by shifting bacterial community composition (denoted by principal coordinates analysis). We also found that soil water content (SWC) and available nutrient (AN) were the factor key to changing bacterial community composition (P < 0.05). Co‐occurrence network demonstrated that Mod 0 ecological cluster composed of copiotrophic taxa groups was significantly associated with RS and Q10 (P < 0.01, R > 0.5), including Proteobacteria, Actinobacteria, and Bacteroidetes. Illuminating the mechanisms underpinning the influence of soil microbes on RS and Q10 values is fundamental to understanding mechanistic soil‐climate carbon cycles.
Need for speed: bacterial effector XopJ2 is associated with increased dispersal velocity of Xanthomonas perforans
Authors: Sharma Anuj , Timilsina Sujan , Abrahamian Peter , Minsavage Gerald V. , Colee James , Ojiambo Peter S. , Goss Erica M. , Vallad Gary E. , Jones Jeffrey B. 
Published: April 2021

SummaryBacterial spot caused by Xanthomonas perforans (Xp) is an economically important disease in tomato. Previous studies have shown that the recently isolated Xp strains have acquired and retained the effector gene, xopJ2, which has been reported to increase fitness of the pathogen in the field. To elucidate the fitness benefit of xopJ2, we quantified the effect of xopJ2 on the dispersal and evolution of Xp populations on tomato. We compared movement of two wild‐type Xp strains expressing xopJ2 to their respective xopJ2 mutants when co‐inoculated in the field. We developed a binary logistic model to predict the presence of Xp over spatial and temporal dimensions with or without xopJ2. Based on the model, wild‐type bacteria were dispersed approximately three times faster than the xopJ2 mutants. In a simulation experiment, the selective advantage due to increased dispersal velocity led to an increase in the frequency of xopJ2 gene in the Xp population and its apparent fixation within 10 to 12 cropping seasons of the tomato crop. Our results show that the presence of a single gene can affect the dispersal of a bacterial pathogen and significantly alter its population dynamics.
Fingermark ridge drift: Influencing factors of a not‐so‐rare aging phenomenon
Authors: De Alcaraz‐Fossoul Josep , Roberts Katherine A. , Johnson Cathy A. , Barrot Feixat Carme , Tully‐Doyle Ryan , Kammrath Brooke W. 
Published: April 2021

AbstractFingermark ridge drift is a random modification of (aged) fingermark patterns at a ridge scale. This phenomenon was previously proven to alter key elements used for identifications, such as the appearance of minutiae. Little is currently reported on the underlying factors contributing to its occurrence. The present study was designed to investigate further the variables of a previous study by including a total of 768 fingermarks from a male and female, two substrates (glazed ceramic tile and plastic), two distinct color powder developers (carbon black and titanium dioxide), three indoor lighting conditions (direct natural light, shade, and darkness), and two secretion types (sebaceous‐ and eccrine‐rich). Fingermarks were aged for 2–72 days, powdered, photographed, and drift detected by three independent observers. All aged fingermarks (672) were compared relative to fresh fingermarks (96), and ridge drift was observed in 42 of 672 (6%) fingermarks, while 168 (25%) were reported as indeterminate results. While ridge drift was detected in multiple fingermarks across all independent variables, statistical analysis using a multinomial logistics model showed that only powder type, secretion type, and the substrate indicated a significant correlation with increased incidences of this phenomenon. There was no significant correlation with the donor, time since deposition, or the environmental lighting conditions used. The highest incidence occurred when carbon black powder was used on a plastic substrate (>10%). The average observation of ridge drift is 6% of samples supporting that this phenomenon is not a rare event, particularly considering the conservative analysis approach implemented.
Balancing nutrients in a toxic environment: the challenge of eating
Authors: Wang Peng , Vassão Daniel G. , Raguschke Bettina , Furlong Michael J. , Zalucki Myron P. 
Published: April 2021

AbstractInsect herbivores can regulate their food intake by mixing food sources with different nutrient content, but face the resulting challenge of ingesting various plant secondary metabolites. How insects deal with toxins in a complex nutrient environment is unclear. Here we investigated the influence of a classic plant secondary metabolite, allyl glucosinolate (sinigrin), and its hydrolyzed product allyl isothiocyanate (AITC), on the development of Helicoverpa armigera (Hübner) (Lepidoptera: Noctuidae) when fed on diets with different protein‐to‐carbohydrate (p : c) ratios. We also examined the effects of these toxins on larval biochemistry, by chemically analyzing the frass produced by insects feeding on the different diets. As expected, AITC had a greater negative effect than sinigrin on H. armigera life‐history traits. However, AITC at low concentration appeared to have a positive effect on some traits. Both sinigrin and AITC‐induced detoxification activity in the gut, and the reaction was related to diet protein concentration. High‐protein diets can provide the required free amino acid, especially cysteine, needed for the detoxification process. The nutrient content of the diet influences how plant secondary metabolites are handled, and the use of artificial diets in experiments investigating the metabolic fate of plant secondary compounds needs to be carefully evaluated.
Random drug testing in prisons: Does a little testing go a long way?
Authors: Nguyen Holly , Midgette Greg , Loughran Thomas , Zhang Yiwen 
Published: April 2021

Research SummaryWe investigated whether higher rates of random drug testing lower substance use among people who are incarcerated and improve prison safety. To answer this question, we estimated linear panel two‐way fixed effects models using naturally varying monthly rates of random drug testing across all Pennsylvania state prisons over a 45‐month period during 2016–2019. Overall, we find that the testing rate is not related to any of the variables we consider, including our key measure of interest, positive drug tests.Policy ImplicationsOur analyses of historical monthly data find that higher levels of randomized testing did not yield more positive drug tests among incarcerated persons. Further and importantly, we did not find that lower testing rates was associated with negative consequences on other outcomes, suggesting that marginal increases in testing rates do not generate commensurate benefits. In this sense, our findings provide preliminary evidence that “a little testing goes a long way.” Replication and expansion of our study is required for stronger conclusions.
Evaluation of monitoring youth exposure to alcohol advertising on cable television, United States 2016–19
Authors: Ross Craig S. , Henehan Elizabeth R. , Alger Charlotte , White Laura F. 
Published: April 2021

AbstractBackground and aimsExposure to alcohol advertising is associated with underage drinking, which contributes to adolescent morbidity and mortality. Alcohol advertisements are regulated by the alcohol industry. Our research team has published reports monitoring alcohol advertisers’ compliance with industry guidelines. In this study, we estimated: (1) changes in youth and adult exposure to alcohol advertisements on cable television from 2016–19 and (2) changes in youth exposure to types of non‐compliant advertising highlighted in monitoring reports over the same period.DesignInterrupted time–series analysis using data from Nielsen US national television audience estimates, 2012–19.Measures and methodsOutcome was advertising impressions (the total number of times an alcohol advertisement was viewed by youth or adults) by month. Non‐compliant exposure was impressions from advertisements that did not meet guidelines. Covariates were advertising spending in multiple media categories. Seasonal autoregressive integrated moving average models estimated trends in exposure before the publication of monitoring reports (2012–15 reference period) and during the monitoring period (2016–19). We compared the modeled exposure trend during the monitoring period to the reference period projected trend.SettingUnited States.ParticipantsA total of 57 000 Nielsen panel householdsFindingsNon‐compliant exposure declined 6158 [95% confidence interval (CI) = −11 406 to −911] million impressions, or −77.3% during the monitoring period compared with the reference period trend. Total youth exposure declined by 20 995 (CI = −34 701 to −7288) million impressions (27.0%). Non‐compliant exposure on programs, network dayparts and brands highlighted in monitoring reports declined by −82.4, −79.0 and −82.2%—more than other programs (−52.7%), network dayparts (−71.0%) or brands (143%). Adult exposure declined by 9.3%.ConclusionsPublication of alcohol advertising monitoring reports appears to have been associated with a 27.0% decline in US youth exposure to alcohol advertising on cable television and a 77.3% decline in US youth exposure to non‐compliant alcohol advertising.
Prospective study of patient satisfaction with enhanced recovery after surgery (ERAS) protocol in the immediate post‐operative period in gynaecological oncology
Authors: Thangavel Dhivya , Gerges Bassem , Brand Alison 
Published: April 2021

BackgroundEnhanced recovery after surgery (ERAS) is a multimodal protocol which aims to facilitate faster discharge from hospital and recovery after surgery by minimising physiological and physical stress on the body before, during and after surgery.AimsThe aim of this study is to evaluate patient satisfaction while being managed with the ERAS pathway and to determine whether it is an acceptable model of care in this respect.Materials and MethodsThe study is an observational study of patient satisfaction in ERAS in gynaecological oncology. Patients who underwent laparoscopy or laparotomy for malignancy or suspected malignancy were asked to complete a validated questionnaire (EORTC IN‐PATSAT32) prior to discharge from hospital after surgery.ResultsThere were 113 (75.33%) patients recruited out of 150 patients who were approached. There were 68 cases of laparotomy and 45 cases of laparoscopy. There were no statistically significant differences between baseline characteristics of responders and non‐responders in both the laparotomy and the laparoscopy group. Patients reported high levels of satisfaction, with a mean score for general satisfaction of 92.2 (SD 11.44 ± 1.387) in the laparotomy group and 92.4 (SD 10.69 ± 1.594) for the laparoscopy group.ConclusionsThe results of our study reflect high levels of patient satisfaction in both the laparotomy and laparoscopy groups. This could be attributed to a strong focus on discharge planning through a multi‐disciplinary approach, specifically addressing key aspects to recovery from initial consultation. The study reflects the successful implementation of an ERAS protocol with gynaecological oncological surgery in this unit.
The effect of saline versus air for cuff inflation on the incidence of high intra‐cuff pressure in paediatric MicroCuff® tracheal tubes: a randomised controlled trial
Authors: Armstrong J. , Jenner P. , Poulose S. , Moppett I. K. 
Published: April 2021

SummaryThe use of cuffed tracheal tubes in paediatric anaesthesia is now common. The use of nitrous oxide in anaesthesia risks excessive tracheal tube cuff pressures, as nitrous oxide can diffuse into the cuff during the course of surgery. The aim of this single‐centre, prospective, randomised controlled trial was to compare the effect of saline versus air for the inflation of tracheal tube cuffs on the incidence of excessive intra‐operative cuff pressure in children undergoing balanced anaesthesia with nitrous oxide. Children (age ≤ 16 y) were randomly allocated to receive either saline (saline group) or air (air group) to inflate the cuff of their tracheal tube. The pressure in the tracheal tube cuff was measured during surgery and brought down to the initial inflation level if it breached a safe limit (25 cmH2O). Post‐extubation adverse respiratory events were noted. Data from 48 patients (24 in each group), aged 4 months to 16 y, were analysed. The requirement for reduction in intra‐cuff pressure occurred in 1/24 patients in the saline group, compared with 16/24 patients in the air group (p < 0.001). The incidence of extubation‐related adverse events was similar in the saline and air groups (15/24 vs. 13/24, respectively; p = 0.770). The use of saline to inflate the cuff of paediatric cuffed tubes reduces the incidence of high intra‐cuff pressures during anaesthesia. This may provide a pragmatic extra safety barrier to help reduce the incidence of excessive tracheal cuff pressure when nitrous oxide is used during paediatric anaesthesia.
Pharmacological inhibition of USP30 activates tissue‐specific mitophagy
Authors: Luo Hongke , Krigman Judith , Zhang Ruohan , Yang Mingchong , Sun Nuo 
Published: April 2021

AbstractAimMitophagy is the regulated process that targets damaged or dysfunctional mitochondria for lysosomal‐mediated removal. This process is an essential element of mitochondrial quality control, and dysregulation of mitophagy may contribute to a host of diseases, most notably neurodegenerative conditions such as Parkinson's disease. Mitochondria targeted for mitophagic destruction are molecularly marked by the ubiquitination of several outer mitochondrial membrane (OMM) proteins. This ubiquitination is positively regulated, in part, by the mitochondrial‐targeted kinase PINK1 and the E3 ubiquitin ligase Parkin. In contrast, the reverse phenomenon, deubiquitination, removes ubiquitin from Parkin substrates embedded in the OMM proteins, antagonizing mitophagy. Recent evidence suggests that the mitochondrial deubiquitinase USP30 negatively regulates Parkin‐mediated mitophagy, providing opportunities to identify USP30 inhibitors and test for their effects in augmenting mitophagy. Here we will characterize a USP30 inhibitor and demonstrate how the pharmacological inhibition of USP30 can augment stress‐induced mitophagic flux.MethodsWe have conducted mitophagy and mitochondrial analyses in cultured cells. We have determined the plasma pharmacokinetics of the USP30 inhibitor in mice and conducted analyses using the mt‐Keima mice to measure in vivo mitophagy directly.ResultsThe compound has minimal mitochondrial toxicity in cultured cells and is tolerated well in mice. Interestingly, we demonstrated tissue‐specific induction of mitophagy following USP30 pharmacological inhibition. In particular, pharmacological inhibition of USP30 induces a significant increase in cardiac mitophagy without detriment to cardiac function.ConclusionOur data support the evidence that USP30 inhibition may serve as a specific strategy to selectively increase mitophagic flux, allowing for the development of novel therapeutic approaches.
Finding meaning in unfair experiences: Using expressive writing to foster resilience and positive outcomes
Authors: Saldanha Maria Francisca , Barclay Laurie J. 
Published: April 2021

AbstractDecades of research have demonstrated that experiencing workplace unfairness can result in profound negative consequences for employees. Integrating conservation of resources theory with meaning‐finding perspectives, we argue that engaging in meaning‐finding in the aftermath of unfairness can foster state resilience and promote positive outcomes. To promote meaning‐finding, we develop and test a new expressive writing intervention (i.e. a guided writing technique that facilitates the processing of negative experiences). Results indicate that the meaning‐finding expressive writing intervention is associated with higher resilience than traditional expressive writing. Moreover, resilience mediates the relationship between meaning‐finding (vs. traditional) expressive writing and willingness to reconcile, positive relationships with others, and life satisfaction. Theoretically, our findings highlight that engaging in meaning‐finding can transform aversive experiences into opportunities to foster resilience and positive outcomes. Practically, meaning‐finding expressive writing provides an effective, simple, and cost‐effective tool that can be used by employees and counseling programs to promote recovery.
Learning by making: A framework to revisit practices in a constructionist learning environment
Authors: Morado María Florencia , Melo Ayelén Eva , Jarman Angela 
Published: April 2021

AbstractMakerspaces are collaborative workspaces where people construct their ideas using a variety of materials and tools ranging from no tech to high tech, where components can be moulded and transformed into different projects depending on each maker’s vision. Educational makerspaces allow educators to respond to the diverse interests of individual learners. This paper documents the learning of participants at an educational makerspace founded on constructionist principles. We analyse the characteristics of the Maker Movement and the features of an educational makerspace, identify learning dimensions, select a case, analyse field notes, photos and videos using an interpretivist paradigm and refine the practical framework guiding the facilitation of the case study discussed. Given that the investigators are also the facilitators of the activities, this framework allows an a posteriori analysis of the practices used to make learning visible.
Practitioner notesWhat is already known about this topic

Makerspaces promote learning in STEM, developing 21st century skills such as effective communication and problem solving.
Makerspaces accommodate diverse students and their interests.
Makerspaces encourage DIY practices and design thinking.
What this paper adds

New dimensions for analysing what has been learned in a constructionist educational makerspace.

New indicators that illustrate the different dimensions of learning, which permit in‐depth analysis of specific practices and promote reflection.

A framework which can be applied in the analysis of learning in similar environments.

Recognition that constructionist makerspaces can enhance learning in all disciplines, moving beyond the limits of STEM or STEAM.

Implications for practice and/or policy

New ways to plan and execute activities in an educational makerspace and any constructionist education centre.

A reference for identifying and making visible learning inside educational makerspaces and any constructionist education centre.

Assurance of the quality of learning developed in educational makerspaces and any constructionist education centre.