bluuebunny/crossref_metadata_2025_split huggingface dataset:
Limitations to photosynthesis in bryophytes: certainties and uncertainties regarding methodology
Authors: Perera-Castro Alicia V , Waterman Melinda J , Robinson Sharon A , Flexas Jaume 
Published: May 2022

Abstract
Bryophytes are the group of land plants with the lowest photosynthetic rates, which was considered to be a consequence of their higher anatomical CO2 diffusional limitation compared with tracheophytes. However, the most recent studies assessing limitations due to biochemistry and mesophyll conductance in bryophytes reveal discrepancies based on the methodology used. In this study, we compared data calculated from two different methodologies for estimating mesophyll conductance: variable J and the curve-fitting method. Although correlated, mesophyll conductance estimated by the curve-fitting method was on average 4-fold higher than the conductance obtained by the variable J method; a large enough difference to account for the scale of differences previously shown between the biochemical and diffusional limitations to photosynthesis. Biochemical limitations were predominant when the curve-fitting method was used. We also demonstrated that variations in bryophyte relative water content during measurements can also introduce errors in the estimation of mesophyll conductance, especially for samples which are overly desiccated. Furthermore, total chlorophyll concentration and soluble proteins were significantly lower in bryophytes than in tracheophytes, and the percentage of proteins quantified as Rubisco was also significantly lower in bryophytes (&lt;6.3% in all studied species) than in angiosperms (&gt;16% in all non-stressed cases). Photosynthetic rates normalized by Rubisco were not significantly different between bryophytes and angiosperms. Our data suggest that the biochemical limitation to photosynthesis in bryophytes is more relevant than so far assumed.
Post-translational regulation of metabolic checkpoints in plant tetrapyrrole biosynthesis
Authors: Wang Peng , Ji Shuiling , Grimm Bernhard 
Published: May 2022

AbstractTetrapyrrole biosynthesis produces metabolites that are essential for critical reactions in photosynthetic organisms, including chlorophylls, heme, siroheme, phytochromobilins, and their derivatives. Due to the paramount importance of tetrapyrroles, a better understanding of the complex regulation of tetrapyrrole biosynthesis promises to improve plant productivity in the context of global climate change. Tetrapyrrole biosynthesis is known to be controlled at multiple levels—transcriptional, translational and post-translational. This review addresses recent advances in our knowledge of the post-translational regulation of tetrapyrrole biosynthesis and summarizes the regulatory functions of the various auxiliary factors involved. Intriguingly, the post-translational network features three prominent metabolic checkpoints, located at the steps of (i) 5-aminolevulinic acid synthesis (the rate-limiting step in the pathway), (ii) the branchpoint between chlorophyll and heme synthesis, and (iii) the light-dependent enzyme protochlorophyllide oxidoreductase. The regulation of protein stability, enzymatic activity, and the spatial organization of the committed enzymes in these three steps ensures the appropriate flow of metabolites through the tetrapyrrole biosynthesis pathway during photoperiodic growth. In addition, we offer perspectives on currently open questions for future research on tetrapyrrole biosynthesis.
Searching for flaring star–planet interactions in AU Mic TESS observations
Authors: Ilin E , Poppenhaeger K 
Published: May 2022

ABSTRACT
Planets that closely orbit magnetically active stars are thought to be able to interact with their magnetic fields in a way that modulates stellar activity. This modulation in phase with the planetary orbit, such as enhanced X-ray activity, chromospheric spots, radio emission, or flares, is considered the clearest sign of magnetic star–planet interaction (SPI). However, the magnitude of this interaction is poorly constrained, and the intermittent nature of the interaction is a challenge for observers. AU Mic is an early M dwarf, and the most actively flaring planet host detected to date. Its innermost companion, AU Mic b, is a promising target for magnetic SPI observations. We used optical light curves of AU Mic obtained by the Transiting Exoplanet Survey Satellite to search for signs of flaring SPI with AU Mic b using a customized Anderson–Darling test. In the about 50 d of observations, the flare distributions with orbital, rotational, and synodic periods were generally consistent with intrinsic stellar flaring. We found the strongest deviation (p = 0.07, n = 71) from intrinsic flaring with the orbital period of AU Mic b, in the high-energy half of our sample (ED &gt; 1 s). If it reflects the true SPI signal from AU Mic b, extending the observing time by a factor of 2–3 will yield a &gt;3σ detection. Continued monitoring of AU Mic may therefore reveal flaring SPI with orbital phase, while rotational modulation will smear out due to the star’s strong differential rotation.
Radio masers on WX UMa: hints of a Neptune-sized planet, or magnetospheric reconnection?
Authors: Kavanagh Robert D , Vidotto Aline A , Vedantham Harish K , Jardine Moira M , Callingham Joe R , Morin Julien 
Published: May 2022

ABSTRACT
The nearby M dwarf WX UMa has recently been detected at radio wavelengths with LOFAR. The combination of its observed brightness temperature and circular polarization fraction suggests that the emission is generated via the electron–cyclotron maser instability. Two distinct mechanisms have been proposed to power such emission from low-mass stars: either a sub-Alfvénic interaction between the stellar magnetic field and an orbiting planet, or reconnection at the edge of the stellar magnetosphere. In this paper, we investigate the feasibility of both mechanisms, utilizing the information about the star’s surrounding plasma environment obtained from modelling its stellar wind. Using this information, we show that a Neptune-sized exoplanet with a magnetic field strength of 10–100 G orbiting at ∼0.034 au can accurately reproduce the observed radio emission from the star, with a corresponding orbital period of 7.4 d. Due to the stellar inclination, a planet in an equatorial orbit is unlikely to transit the star. While such a planet could induce radial velocity semi-amplitudes from 7 to 396 m s−1, it is unlikely that this signal could be detected with current techniques due to the activity of the host star. The application of our planet-induced radio emission model here illustrates its exciting potential as a new tool for identifying planet-hosting candidates from long-term radio monitoring. We also develop a model to investigate the reconnection-powered emission scenario. While this approach produces less favourable results than the planet-induced scenario, it nevertheless serves as a potential alternative emission mechanism which is worth exploring further.
Impact of radial truncation on global 2D hydrodynamic simulations for a Sun-like model
Authors: Vlaykov D G , Baraffe I , Constantino T , Goffrey T , Guillet T , Le Saux A , Morison A , Pratt J 
Published: May 2022

ABSTRACT
Stellar convection is a non-local process responsible for the transport of heat and chemical species. It can lead to enhanced mixing through convective overshooting and excitation of internal gravity waves (IGWs) at convective boundaries. The relationship between these processes is still not well understood and requires global hydrodynamic simulations to capture the important large-scale dynamics. The steep stratification in stellar interiors suggests that the radial extent of such simulations can affect the convection dynamics, the IGWs in the stably stratified radiative zone, and the depth of the overshooting layer. We investigate these effects using 2D global simulations performed with the fully compressible stellar hydrodynamics code music. We compare eight different radial truncations of the same solar-like stellar model evolved over approximately 400 convective turnover times. We find that the location of the inner boundary has an insignificant effect on the convection dynamics, the convective overshooting, and the travelling IGWs. We relate this to the background conditions at the lower convective boundary which are unaffected by the truncation, as long as a significantly deep radiative layer is included in the simulation domain. However, we find that extending the outer boundary by only a few per cent of the stellar radius significantly increases the velocity and temperature perturbations in the convection zone, the overshooting depth, the power and the spectral slope of the IGWs. The effect is related to the background conditions at the outer boundary, which are determined in essence by the hydrostatic stratification and the given luminosity.
The roles of ADAMDEC1 in trophoblast differentiation during normal pregnancy and preeclampsia
Authors: Li Zhuo-Hang , Li Xia , Li Fang-Fang , Wu Zhi-Hong , Xie You-Long , Zhang Shuang , Chen Xue-Mei , Wang Ying-Xiong , Ding Yu-Bin , Liu Tai-Hang 
Published: May 2022

Abstract
Human cytotrophoblast (CTB) differentiation into syncytiotrophoblast (STB) is essential for placental formation and function. Understanding the molecular mechanisms involved in trophoblast differentiation is necessary as it would help in the development of novel therapeutic agents to treat placentation-mediated pregnancy complications. In this study, we found a common upregulated gene, ADAM-like Decysin-1 (ADAMDEC1), from five published microarray and RNA-sequencing datasets. Interference to ADAMDEC1 impaired forskolin-induced BeWo cells differentiation, while ADAMDEC1 overexpression promoted BeWo cells and 3D JEG-3 spheroids differentiation. Interestingly, ADAMDEC1 may inhibit Thrombospondin 1 rather than E-cadherin to trigger the activation of the cAMP signal pathway during CTB differentiation into STB. More importantly, a decreasing in ADAMDEC1 might be involved in the development of preeclampsia. Therefore, ADAMDEC1 is expected to become a new target for prediction of and intervention in placenta-derived pregnancy diseases.
Novel eGZ-motif formed by regularly extruded guanine bases in a left-handed Z-DNA helix as a major motif behind CGG trinucleotide repeats
Authors: Fakharzadeh Ashkan , Zhang Jiahui , Roland Christopher , Sagui Celeste 
Published: May 2022

Abstract
The expansion of d(CGG) trinucleotide repeats (TRs) lies behind several important neurodegenerative diseases. Atypical DNA secondary structures have been shown to trigger TR expansion: their characterization is important for a molecular understanding of TR disease. CD spectroscopy experiments in the last decade have unequivocally demonstrated that CGG runs adopt a left-handed Z-DNA conformation, whose features remain uncertain because it entails accommodating GG mismatches. In order to find this missing motif, we have carried out molecular dynamics (MD) simulations to explore all the possible Z-DNA helices that potentially form after the transition from B- to Z-DNA. Such helices combine either CpG or GpC Watson-Crick steps in Z-DNA form with GG-mismatch conformations set as either intrahelical or extrahelical; and participating in BZ or ZZ junctions or in alternately extruded conformations. Characterization of the stability and structural features (especially overall left-handedness, higher-temperature and steered MD simulations) identified two novel Z-DNA helices: the most stable one displays alternately extruded Gs, and is followed by a helix with symmetrically extruded ZZ junctions. The G-extrusion favors a seamless stacking of the Watson-Crick base pairs; extruded Gs favor syn conformations and display hydrogen-bonding and stacking interactions. Such conformations could have the potential to hijack the MMR complex, thus triggering further expansion.
FABIAN-variant: predicting the effects of DNA variants on transcription factor binding
Authors: Steinhaus Robin , Robinson Peter N , Seelow Dominik 
Published: May 2022

AbstractWhile great advances in predicting the effects of coding variants have been made, the assessment of non-coding variants remains challenging. This is especially problematic for variants within promoter regions which can lead to over-expression of a gene or reduce or even abolish its expression. The binding of transcription factors to the DNA can be predicted using position weight matrices (PWMs). More recently, transcription factor flexible models (TFFMs) have been introduced and shown to be more accurate than PWMs. TFFMs are based on hidden Markov models and can account for complex positional dependencies. Our new web-based application FABIAN-variant uses 1224 TFFMs and 3790 PWMs to predict whether and to which degree DNA variants affect the binding of 1387 different human transcription factors. For each variant and transcription factor, the software combines the results of different models for a final prediction of the resulting binding-affinity change. The software is written in C++ for speed but variants can be entered through a web interface. Alternatively, a VCF file can be uploaded to assess variants identified by high-throughput sequencing. The search can be restricted to variants in the vicinity of candidate genes. FABIAN-variant is available freely at https://www.genecascade.org/fabian/.
PADLOC: a web server for the identification of antiviral defence systems in microbial genomes
Authors: Payne Leighton J , Meaden Sean , Mestre Mario R , Palmer Chris , Toro Nicolás , Fineran Peter C , Jackson Simon A 
Published: May 2022

Abstract
Most bacteria and archaea possess multiple antiviral defence systems that protect against infection by phages, archaeal viruses and mobile genetic elements. Our understanding of the diversity of defence systems has increased greatly in the last few years, and many more systems likely await discovery. To identify defence-related genes, we recently developed the Prokaryotic Antiviral Defence LOCator (PADLOC) bioinformatics tool. To increase the accessibility of PADLOC, we describe here the PADLOC web server (freely available at https://padloc.otago.ac.nz), allowing users to analyse whole genomes, metagenomic contigs, plasmids, phages and archaeal viruses. The web server includes a more than 5-fold increase in defence system types detected (since the first release) and expanded functionality enabling detection of CRISPR arrays and retron ncRNAs. Here, we provide user information such as input options, description of the multiple outputs, limitations and considerations for interpretation of the results, and guidance for subsequent analyses. The PADLOC web server also houses a precomputed database of the defence systems in &gt; 230,000 RefSeq genomes. These data reveal two taxa, Campylobacterota and Spriochaetota, with unusual defence system diversity and abundance. Overall, the PADLOC web server provides a convenient and accessible resource for the detection of antiviral defence systems.
8Media Theory
Authors: Enns Anthony 
Published: May 2022

AbstractMost countries experienced an extended period of lockdown during 2021 due to the rapid increase in the number of Covid-19 cases and the comparatively slow process of developing and distributing effective vaccines. It is therefore no surprise that the pandemic was often mentioned in the introductions to books on media theory, although these projects were clearly conceived and written long before the pandemic began, and many of them were directly responding to the social crisis that preceded our current one—namely, the rapid rise in participation in social media and the accompanying rise in online extremism, which had devastating political consequences in the US and around the world. While these books were released after the 6 January attack on the US Capitol and the end of Donald Trump’s term as president, many of them were attempting to examine how media technologies had contributed to the rise of authoritarianism and the decline of democratic values during his administration, and they often addressed similar concerns, such as the oppressive structures of digital media platforms, the potential threat that they pose to democracy, and how they might be used for political activism. The following review is divided into three sections that focus on each of these concerns: 1. Digital Media and Neoliberal Capitalism discusses how digital media introduced new forms of labour that were inherently linked to neoliberal capitalism; 2. Digital Media and Disinformation discusses the potential causes of and solutions to the problem of online disinformation; and 3. Digital Media and Political Change discusses the potential benefits and limitations of using digital media to promote positive political change, followed by 4. Conclusion. These books thus provide an insightful analysis of our current social, political, and economic situation, and they offer a wide range of suggestions on how our media technologies could be reconfigured in order to facilitate a more promising future.
Ralstonia Strains from Potato-Growing Regions of Kenya Reveal Two Phylotypes and Epidemic Clonality of Phylotype II Sequevar 1 Strains
Authors: Sharma Kalpana , Iruegas-Bocardo Fernanda , Abdurahman Abdulwahab , Alcalá-Briseño Ricardo I. , Garrett Karen A. , Goss Erica M. , Ngundo George , Kreuze Jan , Atieno Elly , Munguti Florence 
Published: May 2022

Bacterial wilt, caused by the Ralstonia solanacearum species complex (RSSC), is the most destructive potato disease in Kenya. Studies were conducted to (i) determine the molecular diversity of RSSC strains associated with bacterial wilt of potato in Kenya, (ii) generate an RSSC distribution map for epidemiological inference, and (iii) determine whether phylotype II sequevar 1 strains exhibit epidemic clonality. Surveys were conducted in 2018 and 2019, in which tubers from wilting potato plants and stem samples of potential alternative hosts were collected for pathogen isolation. The pathogen was phylotyped by multiplex PCR and 536 RSSC strains typed at a sequevar level. Two RSSC phylotypes were identified, phylotype II (98.4%, n = 506 [sequevar 1 ( n = 505) and sequevar 2 ( n = 1)]) and phylotype I (1.6%, n = 30 [sequevar 13 ( n = 9) and a new sequevar ( n = 21)]). The phylotype II sequevar 1 strains were haplotyped using multilocus tandem repeat sequence typing (TRST) schemes. The TRST scheme identified 51 TRST profiles within the phylotype II sequevar 1 strains with a modest diversity index (HGDI = 0.87), confirming the epidemic clonality of RSSC phylotype II sequevar 1 strains in Kenya. A minimum spanning tree and mapping of the TRST profiles revealed that TRST27 ‘8-5-12-7-5’ is the primary founder of the clonal complex of RSSC phylotype II sequevar 1 and is widely distributed via latently infected seed tubers. [Formula: see text] Copyright © 2022 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license .
Implicit Racial Bias in Pediatric Orthopaedic Surgery
Authors: Guzek Ryan , Goodbody Christine M. , Jia Lori , Sabatini Coleen S. , Sankar Wudbhav N. , Williams Brendan A. , Shah Apurva S. 
Published: May 2022

Introduction:
Racial and ethnic minority patients continue to experience disparities in health care. It is important to understand provider-level factors that may contribute to these inequities. This study aims to evaluate the presence of implicit racial bias among pediatric orthopaedic surgeons and determine the relationship between bias and clinical decision making.

Methods:
A web-based survey was distributed to 415 pediatric orthopaedic surgeons. One section measured for potential implicit racial bias using a child-race implicit association test (IAT). IAT scores were compared with US physicians and the US general population using publicly available data. Another section consisted of clinical vignettes with associated questions. For each vignette, surgeons were randomly assigned a single race-version, White or Black. Vignette questions were grouped into an opioid recommendation, management decision, or patient perception category for analysis based on subject tested. Vignette answers from surgeons with IAT scores that were concordant with their randomized vignette race-version (ie, surgeon with pro-White score assigned White vignette version) were compared with those that were discordant.

Results:
IAT results were obtained from 119 surveyed surgeons (29% response rate). Overall, respondents showed a minor pro-White implicit bias (P<0.001). Implicit bias of any strength toward either race was present among 103/119 (87%) surgeons. The proportion of pediatric orthopaedic surgeons with a strong pro-White implicit bias (29%) was greater than that of US physicians overall (21%, P=0.032) and the US general population (19%, P=0.004). No differences were found in overall opioid recommendations, management decisions, or patient perceptions between concordant and discordant groups.

Conclusion:
Most of the pediatric orthopaedic surgeons surveyed demonstrated implicit racial bias on IAT testing, with a large proportion demonstrating strong pro-White bias. Despite an association between implicit bias and clinical decision making in the literature, this study observed no evidence that implicit racial bias affected the management of pediatric fractures.

Level of Evidence:
Level IV.
Normative Values for Adolescent Quality of Life in Plastic Surgery: A Longitudinal, Cohort Study
Authors: Nuzzi Laura C. , Firriolo Joseph M. , McNamara Catherine T. , Malloy Shannon M. , Massey Gabrielle G. , DiVasta Amy D. , Labow Brian I. 
Published: May 2022

Background:
Adolescence is a challenging time, and an increasing number of young people are seeking plastic surgery. With the rise of health-related quality of life studies in plastic surgery, it is critical to understand the natural variation and changes in health-related quality of life for this population.

Methods:
In this longitudinal, cohort study validated surveys were administered to cisgender participants aged 12–21 years: Short-Form 36v2, Rosenberg Self-Esteem Scale, Breast-Related Symptoms Questionnaire, and Eating-Attitudes Test-26. Surveys were administered at baseline and up to 9 years follow-up. At the time of enrollment, participants were in a current state of good health with no considerable past or current medical, surgical, or psychological history.

Results:
A total of 149 female and 75 male participants were included, with a median (interquartile range) baseline age of 16.0 (4.4) years and follow-up time of 3.3 (4.1) years. Over the study period, girls who were not overweight or obese experienced significant declines in five SF-36 domains (general health, vitality, social functioning, role-emotional, and mental health) and on the Rosenberg Self-Esteem Scale, Breast-Related Symptoms Questionnaire, and Eating-Attitudes Test-26 (P < 0.05). In contrast, boys’ and overweight/obese girls’ health-related quality of life largely remained stable (P > 0.05).

Conclusions:
Adolescence is a challenging time, on which plastic surgery-related concerns are superimposed. Our findings suggest that girls may be more at risk for developing psychosocial deficits that worsen over adolescence and young adulthood. This observation is critical for the interpretation and contextualization of health-related quality of life in adolescent plastic surgery patients.