bluuebunny/crossref_metadata_2025_split huggingface dataset:
Gene family expansions underpin context-dependency of the oldest mycorrhizal symbiosis
Authors: Hernandez Damian J. , Pohlmann Gwendolyn B. , Afkhami Michelle E. 
Published: April 2024

AbstractAs environments worldwide change at unprecedented rates during the Anthropocene, understanding context-dependency – how species regulate interactions to match changing environments – is crucial. However, generalizable molecular mechanisms underpinning context-dependency remain elusive. Combining comparative genomics across 42 angiosperms with transcriptomics, genome-wide association mapping, and gene duplication origin analyses, we show for the first time that gene family expansions undergird context-dependent regulation of species interactions. Gene families expanded in mycorrhizal fungi-associating plants display up to 200% more context-dependent gene expression and double the genetic variation associated with mycorrhizal benefits to plant fitness. Moreover, we discover these gene family expansions arise primarily from tandem duplications with >2-times more tandem duplications genome-wide, indicating gene family expansions continuously supply genetic variation allowing fine-tuning of context-dependency in species interactions throughout plant evolution.One-Sentence SummaryGene family expansions arising from tandem duplications underpin genetic regulation and fitness effects of context-dependency
Widespread impact of nucleosome remodelers on transcription at cis-regulatory elements
Authors: Patty Benjamin J. , Hainer Sarah J. 
Published: April 2024

AbstractNucleosome remodeling complexes and other regulatory factors work in concert to build a chromatin environment that directs the expression of a distinct set of genes in each cell using cis-regulatory elements (CREs), such as promoters and enhancers, that drive transcription of both mRNAs and CRE-associated non-coding RNAs (ncRNAs). Two classes of CRE-associated ncRNAs include upstream antisense RNAs (uaRNAs), which are transcribed divergently from a shared mRNA promoter, and enhancer RNAs (eRNAs), which are transcribed bidirectionally from active enhancers. The complicated network of CRE regulation by nucleosome remodelers remains only partially explored, with a focus on a select, limited number of remodelers. We endeavored to elucidate a remodeler-based regulatory network governing CRE-associated transcription (mRNA, eRNA, and uaRNA) in murine embryonic stem (ES) cells to test the hypothesis that many SNF2-family nucleosome remodelers collaborate to regulate the coding and non-coding transcriptome via alteration of underlying nucleosome architecture. Using depletion followed by transient transcriptome sequencing (TT-seq), we identified thousands of misregulated mRNAs and CRE-associated ncRNAs across the remodelers examined, identifying novel contributions by understudied remodelers in the regulation of coding and non-coding transcription. Our findings suggest that mRNA and eRNA transcription are coordinately co-regulated, while mRNA and uaRNAs sharing a common promoter are independently regulated. Subsequent mechanistic studies suggest that while remodelers SRCAP and CHD8 modulate transcription through classical mechanisms such as transcription factors and histone variants, a broad set of remodelers including SMARCAL1 indirectly contribute to transcriptional regulation through maintenance of genomic stability and proper Integrator complex localization. This study systematically examines the contribution of SNF2-remodelers to the CRE-associated transcriptome, identifying at least two classes for remodeler action.
The chromatin-associated 53BP1 ortholog, HSR-9, regulates recombinational repair andXchromosome segregation in theCaenorhabditis elegansgerm line
Authors: Li Qianyan , Hariri Sara , Calidas Aashna , Kaur Arshdeep , Huey Erica , Engebrecht JoAnne 
Published: April 2024

ABSTRACT53BP1 plays a crucial role in regulating DNA damage repair pathway choice and checkpoint signaling in somatic cells; however, its role in meiosis has remained enigmatic. In this study, we demonstrate that theCaenorhabditis elegansortholog of 53BP1, HSR-9, associates with chromatin in both proliferating and meiotic germ cells. Notably, HSR-9 is enriched on theXchromosome pair in pachytene oogenic germ cells. HSR-9 is also present at kinetochores during both mitotic and meiotic divisions but does not appear to be essential for monitoring microtubule-kinetochore attachments or tension. Using cytological markers of different steps in recombinational repair, we found that HSR-9 influences the processing of a subset of meiotic double strand breaks into COSA-1-marked crossovers. Additionally, HSR-9 plays a role in meioticXchromosome segregation under conditions whereXchromosomes fail to pair, synapse, and recombine. Together, these results highlight that chromatin-associated HSR-9 has both conserved and unique functions in the regulation of meiotic chromosome behavior.Article SummaryWhile 53BP1 is known for its crucial role in DNA damage signaling and repair in somatic cells, its role in meiosis is not well understood. Li, Hariri, et al., show thatC. elegans53BP1 not only functions in meiotic recombination and checkpoint signaling but also regulates the transmission of sex chromosomes when meiosis is perturbed. These results highlight the importance of 53BP1 inC. elegansmeiosis and suggest that 53BP1 has both conserved and organism-specific functions.
foxg1ais required for hair cell development and regeneration in the zebrafish lateral line
Authors: Bell Jon M , Biesemeyer Cole , Turner Emily M , Vanderbeck Maddie M , McGraw Hillary F 
Published: April 2024

AbstractMechanosensory hair cells located in the inner ear mediate the sensations of hearing and balance. If damaged, mammalian inner ear hair cells are unable to regenerate, resulting in permanent sensory deficits. Aquatic vertebrates like zebrafish(Danio rerio)have a specialized class of mechanosensory hair cells found in the lateral line system, allowing them to sense changes in water current. Unlike mammalian inner ear hair cells, lateral line hair cells can robustly regenerate following damage. In mammalian models, the transcription factor Foxg1 functions to promote normal development of the inner ear. Foxg1a is expressed in lateral line sensory organs in zebrafish larvae, but its function during lateral line development and regeneration has not been investigated. We find that loss of Foxg1a function results in reduced hair cell development and regeneration, as well as decreased cellular proliferation in the lateral line system. These data suggest that Foxg1 may be a valuable target for investigation of clinical hair cell regeneration.Summary statementOur work demonstrates a role for Foxg1a in developing and regenerating new sensory cells through proliferation.
Release the Krakencoder: A unified brain connectome translation and fusion tool
Authors: Jamison Keith W. , Gu Zijin , Wang Qinxin , Tozlu Ceren , Sabuncu Mert R. , Kuceyeski Amy 
Published: April 2024

ABSTRACTBrain connectivity can be estimated in many ways, depending on modality and processing strategy. Here we present the Krakencoder, a joint connectome mapping tool that simultaneously, bidirectionally translates between structural (SC) and functional connectivity (FC), and across different atlases and processing choices via a common latent representation. These mappings demonstrate unprecedented accuracy and individual-level identifiability; the mapping between SC and FC has identifiability 42-54% higher than existing models. The Krakencoder combines all connectome flavors via a shared low-dimensional latent space. This “fusion” representation i) better reflects familial relatedness, ii) preserves age- and sex-relevant information and iii) enhances cognition-relevant information. The Krakencoder can be applied without retraining to new, out-of-age-distribution data while still preserving inter-individual differences in the connectome predictions and familial relationships in the latent representations. The Krakencoder is a significant leap forward in capturing the relationship between multi-modal brain connectomes in an individualized, behaviorally- and demographically-relevant way.
Attention and control of posture: the effects of light touch on the center-of-pressure time series regularity and simple reaction time task
Authors: Brachman Anna , Michalska Justyna , Bacik Bogdan 
Published: April 2024

AbstractThe stabilizing influence of a light touch on a postural sway has been consistently shown in the literature, however there is still no consensus in what way attentional resources are used when adopting additional tactile information during controlling an upright posture. To better elucidate the underlying mechanisms we introduced conditions of both sensory deprivation (closing the eyes), additional feedback (light touch), which seems to distracts from postural control and verified it by introducing dual task paradigm (i.e. measuring simple reaction time to an unpredictable auditory stimulus). Twenty five healthy students randomly performed eight postural tasks, four with (RT) and four without simple reaction task (NoRT). Center of pressure displacements were measured on a force plate in two visual conditions: eyes open (EO), eyes closed (EC) and two sensory conditions: with light touch (LT), without light touch (NoLT). Before each measurement participants were asked to consider the postural task as the primary task. Although simple reaction time did not differ between postural conditions (p>0.05), additional tactile information in anteroposterior direction caused decreased postural sway velocity (p<0.001, η2=0.86) and decreased standard deviation (p<0.001, η2=0.91) in both, reaction and visual conditions relative to NoLT conditions. Interestingly, simple reaction task modified subjects behavior in NoLT conditions and caused slower COP velocity (p<0.001, η2=0.53) without changes in signal regularity. Results also showed a significant increase in irregularity during standing with LT (p<0.001, η2=0.86) in both vision and reaction conditions, suggesting that the signal was more random. Although there were no significant changes between length of the reaction time between postural conditions but there was strong effect of light touch on COP regularity, we can conclude that light touch is attention demanding but changes of flow of attention are very subtle in this simple postural tasks. Furthermore COP regularity analysis is sensitive to even such subtle changes.
Trends and drivers of hypoxic thickness and volume in the Northern Gulf of Mexico: 1985-2018
Authors: Matli Venkata Rohith Reddy , Obenour Daniel 
Published: April 2024

AbstractHypoxia is a major environmental issue plaguing the commercially and ecologically important coastal waters of the Northern Gulf of Mexico. Several modeling studies have explored this phenomenon, but primarily focus on the areal extent of the mid-summer hypoxic zone. Research into the variability and drivers of hypoxic volume and thickness is also important in evaluating the seasonal progression of hypoxia and its impact on coastal resources. In this study, we compile data from multiple monitoring programs and develop a geospatial model capable of estimating hypoxic thickness and volume across the summer season. We adopt a space-time geostatistical framework and introduce a rank-based inverse normal transformation to simulate more realistic distributions of hypoxic layer thickness. Our findings indicate that, on average, there is a seasonal lag in peak hypoxic volume and thickness compared to hypoxic area. We assess long-term trends in different hypoxia metrics (area, thickness, and volume), and while most metrics did not exhibit significant trends, mid-summer hypoxic thickness is found to have increased at a rate of 5.9 cm/year (p<0.05) over the past three decades. In addition, spring nitrogen load is found to be the major driver of all hypoxia metrics, when considered along with other riverine inputs and meteorological factors in multiple regression models. Hypoxic volume, which was also often influenced by east-west wind velocities, was found to be more predictable than hypoxic thickness.
Why is usefulness rarely useful
Authors: Wang Fangyi , Feldmann Mitchell J. , Runcie Daniel E. 
Published: April 2024

ABSTRACTMate selection plays an important role in breeding programs. The usefulness criterion was proposed as a criterion for mate selection, combining information on both the mean and standard deviation of the potential offspring, particularly in clonally propagated outbred species where large family sizes are possible. Predicting mean values of offspring of a cross is generally easier than predicting the standard deviation, especially in outbred species where the linkage of alleles is often unknown and phasing is required. In this study, we developed a method for estimating phasing accuracy from unphased genotype data on possible parental lines and evaluated whether the accuracy was sufficient to predict family standard deviations of possible crosses using a set of simulations spanning a wide range of genetic architectures and genotypes from a real strawberry breeding population. We find that despite highly accurate computational phasing, predicting family standard deviations and using predicted values of the usefulness criterion per possible cross confers little benefit relative to simply selecting parents based on predicted family means. Therefore even in this species, which is clonally propagated, outbred, and produces large families, we find the usefulness criterion unlikely to be useful.
A Critical Analysis of UK Media Characterisations of Long Covid in Children and Young People
Authors: Connor Chloe , Kranert Michael , Mckelvie Sara , Clutterbuck Donna , Mcfarland Sammie , Alwan Nisreen A 
Published: April 2024

AbstractLong Covid is the continuation or development of symptoms related to a SARSCoV2 infection. Those with Long Covid may face epistemic injustice, where they are unjustifiably viewed as unreliable evaluators of their own illness experiences. Media articles both reflect and influence perception and subsequently how people regard children and young people (CYP) with Long Covid, and may contribute to epistemic injustice.We aimed to explore how the UK media characterises Long Covid in CYP through examining three key actor groups: parents, healthcare professionals, and CYP with Long Covid, through the lens of epistemic injustice. A systematic search strategy resulted in the inclusion of 103 UK media articles. We used an adapted corpus-assisted Critical Discourse Analysis in tandem with thematic analysis. Specifically, we utilised search terms to locate concordances of key actor groups.In the corpus, parents highlighted minimisation of Long Covid, barriers to care, and experiences of personal attacks. Mothers were presented as also having Long Covid. Fathers were not mentioned once. Healthcare professionals emphasised the rarity of Long Covid in CYP, avoided pathologizing Long Covid, and overemphasised psychological components. CYP rarely were consulted in media articles but were presented as formerly very able. Manifestations of Long Covid in CYP were validated or invalidated in relation to adults.Media characterisations contributed to epistemic injustice. The disempowering portrayal of parents promote stigma and barriers to care. Healthcare professionals’ narratives often contributed to negative healthcare experiences and enacted testimonial injustice, where CYP and parent’s credibility was diminished due to unfair identity prejudice, in their invalidation of Long Covid. Media characterisations reveal and maintain a lack of societal framework for understanding Long Covid in CYP. The findings of this study illustrate the discursive practices employed by journalists that contribute to experiences of epistemic injustice. Based on our findings, we propose recommendations for journalists.
A self-cooling self-humidifying mosquito carrier backpack for transporting live adult mosquitoes on foot over long distances under challenging field conditions
Authors: Kavishe Deogratius R , Msoffe Rogath V , Malika Goodluck Z , Walsh Katrina A , Duggan Lily M , Tarimo Lucia J , Butler Fidelma , Kaindoa Emmanuel W. , Ngowo Halfan S , Killeen Gerry F 
Published: April 2024

AbstractIt is often necessary to use motorized transport to move live mosquitoes from distant field collection points into a central insectary, so that their behavioural and/or physiological phenotypes can be assessed under carefully controlled conditions. However, a survey of heritable insecticide susceptibility traits among wild-caughtAnopheles arabiensismosquitoes, collected across an extensive study area composed largely of wilderness in southern Tanzania, necessitated that live mosquitoes were carried on foot over distances up to 25 km per day because most of the area was impassable by car, motorcycle or even bicycle during the rains. A self-cooling, self-humidifying carrier backpack was therefore developed that allows live adult mosquito specimens to be transported across rugged miombo woodland and floodplain terrain throughout the year. This wettable backpack was fabricated from stitched Tanzaniankitengecotton fabric and PVC-coated fiberglass netting that allows easy circulation of air in and out. An outer cover flap made of cotton towelling embedded inside a kitenge envelope overhangs the fiberglass netting upper body of the bag, to protect mosquitoes from direct sunlight, and can be soaked with water to maintain low temperature and high humidity inside. Mean survival of insectary-reared femaleAnopheles arabiensistransported through 9 different mobile camps inside the 509 km2Ifakara-Lupiro-Mang’ula Wildlife Management Area (ILUMA WMA), over up to 143km and 25 days, was indistinguishable from those left in the field insectary over the same period. Although considerable variance was observed between different batches of mosquitoes from the insectary and between individual cups of mosquitoes, the different levels and positions inside the backpack had no influence on survival. Temperature and humidity inside the backpack were maintained at standard insectary condition throughout, despite much more extreme conditions immediately outside. When the backpack was applied to collecting wildAn. arabiensisandAnopheles quadriannulatusacross a much larger study area of >4000 km2, encompassing the ILUMA WMA, some nearby villages and adjacent parts of Nyerere National Park (NNP), it achieved a mean survival rate of 58.2% [95% confidence interval 47.5 to 68.2]. Encouragingly, no difference in survival was observed between ILUMA WMA and NNP even though transport back from NNP involves much longer distances, sometimes involving lengthy journeys by car or boat. Overall, this mosquito carrier backpack prototype appears to represent a viable and effective method for transporting live wild-caught mosquitoes on foot across otherwise impassable terrain under challenging weather conditions with minimal detrimental impact on their survival.
REV-ERBβ Binding Pocket Dynamics with Implications for Rational Design of Small Molecule Modulators
Authors: Srivastava Shriyansh , Vishnu A.M. , Thakur Rakesh , Srivastava Ashutosh 
Published: April 2024

ABSTRACTREV-ERBβ is a nuclear receptor (NR) with heme as an endogenous ligand that regulates its transcriptional activity. With key role in cellular functions such as glucose metabolism, immune response, and dysregulation in pathologies such as Type-2 diabetes mellitus and obesity, small molecule agonists and antagonists targeting REV-ERBs have been discovered. However, due to lack of crystal structures in complex with these compounds, the structural and dynamical basis of these activities still remains elusive and hinders rational design of molecules targeting REV-ERB. Using molecular dynamics simulations and docking studies, we have characterized the dynamics of REV-ERBβ ligand-binding domain (LBD) in different conformational states. The presence of heme in the binding pocket within LBD was found to stabilize its dynamics as well as nuclear co-repressor (NCoR) peptide binding. We further show that the binding of antagonist destabilizes the NCoR peptide binding to LBD mediated by loss of interactions with residues at the NCoR-REV-ERBβ interface. These findings could be utilized to design molecular scaffolds with better activity and selectivity against REV-ERBβ.
Effect of Emoji on Autonomic Nervous System: Evidence from EDA and RSA studies
Authors: Patel Deeksha , Dixit Abhinav , Bhagat Om Lata 
Published: April 2024

AbstractBackgroundFacial expression, gesture, and posture play an important role in perceiving emotions during communication. In virtual communication platforms, users have devised and learned to use a variety of expressive emojis along with text messages to express certain emotions. The effect of emojis on human psychology and associated autonomic responses is still vague.MethodsA total of 100 healthy individuals (50 males and 50 females) aged between 18-40 years were recruited. Electrodermal activity (skin conductance level (SCL) and skin conductance response (SCR) amplitude) and Respiratory Sinus Arrhythmia (RSA) were assessed during the Emotional Stroop Task (EST). EST having expressive emojis superimposed with the congruent and incongruent words was used.ResultMean SCL and SCR amplitude was significantly increased during EST in incongruent and congruent blocks as compared to neutral block (respectively: 14.64 ± 6.73, 12.99 ± 6.26 vs. 7.75 ± 4.93 μS, p < 0.001 and 0.182 ± 0.168, 0.158 ± 0.134 vs. 0.021 ± 0.015 μS, p < 0.001). RSA was significantly decreased in incongruent and congruent blocks as compared to neutral blocks (respectively: 36.47 ± 10.53, 39.40 ± 10.15 vs. 48.66 ± 10.27 msec2, p < 0.001). We found an increased sympathetic activity and parasympathetic withdrawal while performing the task.ConclusionThe results of this study suggested that emojis are adequate stimuli to elicit autonomic responses and change both sympathetic (EDA) as well as parasympathetic responses (RSA). Males and females showed similar autonomic arousal for emoji but the baseline emotional status was different for both genders.
WITHDRAWN: Modified one-step conservative surgery for placenta accreta spectrum versus caesarean hysterectomy: The CMNT PAS prospective comparative Non-Randomized pilot study
Authors: Abouda Hassine S , Aloui Haithem , Marzouk Sofiene B , Frikha Hatem , Hammami Rami , Makdoud Khaoula , Minjli Sana , Chennoufi Badis , Karoui Abir , Maghrebi Hayen 
Published: April 2024

Withdrawal StatementThe authors have withdrawn their manuscript owing to [Since its posting, we have identified significant statistical errors resulting from a mix-up between data from the pilot study and the main study. Given these inaccuracies, we believe it is in the best interest of the scientific community to withdraw the manuscript. We have since corrected these errors in a revised version of the manuscript]. Therefore, the authors do not wish this work to be cited as reference for the project. If you have any questions, please contact the corresponding author.