bluuebunny/crossref_metadata_2025_split huggingface dataset:
Metagenomic signatures of balancing selection in the human gut
Authors: Moeller Andrew H. 
Published: April 2022

AbstractBacterial lineages that populate the human gut microbiota contend with spatial and temporal fluctuations in numerous environmental variables, including bouts of extreme selective agents such as antibiotics. Oscillations in the adaptive landscape can impose balancing selection on populations, leaving characteristic signatures in the sequence variation of functionally significant genomic loci. Despite their potential importance for gut bacterial adaptation, the metagenomic targets of balancing selection have not been identified. Here, I present population genetic evidence that balancing selection maintains allelic diversity in multidrug efflux pumps of multiple predominant gut bacterial species. Metagenome‐wide scans of 566,958 genes from 287 bacterial species represented by 118,617 metagenome‐assembled genomes indicated that most genes have been conserved by purifying selection. However, dozens of core open reading frames (CORFs) displayed positive Tajima's D values that deviated significantly from their species’ genomic backgrounds, indicating the action of balancing selection. Multidrug efflux pumps (MEPs) from a diversity of bacterial species were significantly enriched among the CORFs with Tajima's D values >3 in industrialized, but not nonindustrialized, human populations. The AcrB subunit of an MEP from Bacteroides dorei displayed the highest Tajima's D of any CORF. Divergent haplotypes of this CORF displayed evidence of positive selection and homology to an Escherichia coli AcrB subunit that binds tetracycline and macrolide antibiotics, suggesting functional significance and implicating medical antibiotics as an agent of selection acting on this locus. Other proteins identified as targets of balancing selection included peptidoglycan/LPS O‐acetylases and ion transporters. Intriguingly, the degree of balancing selection acting on gut bacterial species was associated with species abundance in the gut based on metagenomic data, further suggesting fitness benefits of the allelic variation identified.
Analysing diversification dynamics using barcoding data: The case of an obligate mycorrhizal symbiont
Authors: Perez‐Lamarque Benoît , Öpik Maarja , Maliet Odile , Afonso Silva Ana C. , Selosse Marc‐André , Martos Florent , Morlon Hélène 
Published: April 2022

AbstractAnalysing diversification dynamics is key to understanding the past evolutionary history of clades that led to present‐day biodiversity patterns. While such analyses are widespread in well‐characterized groups of species, they are much more challenging in groups for which diversity is mostly known through molecular techniques. Here, we use the largest global database on the small subunit (SSU) rRNA gene of Glomeromycotina, a subphylum of microscopic arbuscular mycorrhizal fungi that provide mineral nutrients to most land plants by forming one of the oldest terrestrial symbioses, to analyse the diversification dynamics of this clade in the past 500 million years. We perform a range of sensitivity analyses and simulations to control for potential biases linked to the nature of the data. We find that Glomeromycotina tend to have low speciation rates compared to other eukaryotes. After a peak of speciations between 200 and 100 million years ago, they experienced an important decline in speciation rates toward the present. Such a decline could be at least partially related to a shrinking of their mycorrhizal niches and to their limited ability to colonize new niches. Our analyses identify patterns of diversification in a group of obligate symbionts of major ecological and evolutionary importance and illustrate that short molecular markers combined with intensive sensitivity analyses can be useful for studying diversification dynamics in microbial groups.
Normothermic Machine Perfusion in pediatric liver transplantation: A survey of attitudes and barriers
Authors: Kadakia Yash , MacConmara Malcolm , Patel Madhukar S. , Shah Jigesh A. , de Gregorio Muniz Lucia , Desai Dev M. , Hanish Steven , Vagefi Parsia A. , Hwang Christine S. 
Published: April 2022

AbstractBackgroundNMP provides a superior strategy for the assessment and preservation of marginal donor livers and has demonstrated increased utilization and enhances organ quality when used in adult liver transplantation. We aimed to evaluate the interest of incorporating the use of NMP in pediatric liver transplantation.MethodsAn anonymous online survey was distributed to pediatric transplant surgeons and hepatologists across the United States. Respondent demographic information, attitudes toward NMP in pediatric liver transplantation, and barriers to utilization were examined.ResultsThirty‐two providers (18 transplant surgeons and 14 hepatologists) completed the survey, yielding a response rate of 64%. Half (50%) of respondents indicated prior exposure to NMP. Overall, 96% of respondents believed there was benefit to using NMP in pediatric liver transplantation. DCD (68%) and post–cross‐clamp (75%) grafts were the greatest opportunity for NMP use. A role in splitting livers ex vivo (71%) was also seen as a potential major opportunity. Cost was perceived as a barrier to implementation (36%), followed by institutional factors (32%). Cost tolerance was significantly greater in respondents residing in OPTN regions with greater than median wait times (63% vs. 11% in OPTN regions with greater vs. shorter wait times, p = .010).ConclusionsThere is significant interest within the pediatric liver transplant community for NMP to expand the donor pool. Interest appears particularly strong in regions where wait times for suitable pediatric donors are prolonged.
Metabolic and transcriptional responses to starvation are regulated by FOXO in the red flour beetle, Tribolium castaneum
Authors: Zhang Nan , Meng Xiangkun , Jiang Heng , Ge Huichen , Zheng Yang , Qian Kun , Wang Jianjun 
Published: April 2022

AbstractIntermittent food scarcity is commonly encountered in all organisms including insects. Although the forkhead box O (FOXO) transcription factor is a well‐known component of signalling cascades related to starvation stress, the detailed regulatory mechanisms during long‐term starvation remain poorly understood in insects. In the present study, using the red flour beetle, Tribolium castaneum, as a model organism, we showed that starvation treatment increased the expression of FOXO at both mRNA and protein levels and promoted its nuclear translocation to activate its transcriptional activity. Knockdown of FOXO leads to a significant reduction in the lifespan of T. castaneum accompanying reduced glycogen and triglyceride depletion as well as decreased glucose and trehalose accumulation under starvation conditions. Consistently, expression patterns of genes involved in gluconeogenesis, glycogenolysis and trehalose metabolism under starvation conditions were significantly affected in dsFOXO‐injected beetles. These results provided evidence that FOXO played an important role in the tolerance to prolonged starvation by regulating metabolic and transcriptional responses.
Designing and testing an ethnic‐ancestry question for Australian blood donors: Acceptability, feasibility, and understanding
Authors: Gahan Luke , Gemelli Carley N. , Kruse Sarah P. , Davison Tanya E. 
Published: April 2022

AbstractObjectivesWe aimed to evaluate the acceptability, feasibility, and understanding of a donor ethnic‐ancestry question with Australian blood donors.BackgroundEthnic‐ancestry assists blood collection agencies to meet the demand for rare blood‐types. However, there is no standard ethnicity question used by health/blood services around the world and we do not know how blood donors in Australia will respond to being asked for this information.Methods/MaterialsA survey and ethnic‐ancestry question was administered to a sample of donors (n = 506) to evaluate their views on being asked for their ethnic‐ancestry, test a comprehensive ethnic‐ancestry list, and determine the level of information required by donors.ResultsDonors reported being very comfortable providing their ethnic‐ancestry and the majority of donors found an ethnic‐ancestry option they were happy with (91.3%). Overall donors reported a high level of understanding of why ethnic‐ancestry was important to blood donation. However, when provided more information on why ethnic‐ancestry is required, donors reported increased understanding.ConclusionThe findings from this study demonstrated that it is acceptable and feasible to introduce a comprehensive ethnic‐ancestry question for Australian blood donors. We also found that a greater understanding is achieved when a more comprehensive explanation for inclusion of the question is provided.
Cell growth dynamics in two types of apical meristems in fern gametophytes
Authors: Wu Xiao , Yan An , Yang Xi , Banks Jo Ann , Zhang Shaoling , Zhou Yun 
Published: April 2022

SUMMARYIn contrast to seed plants, the gametophytes of seed‐free plants develop pluripotent meristems, which promote and sustain their independent growth and development. To date, the cellular basis of meristem development in gametophytes of seed‐free ferns remains largely unknown. In this study, we used Woodsia obtusa, the blunt‐lobe cliff fern, to quantitatively determine cell growth dynamics in two different types of apical meristems – the apical initial centered meristem and the multicellular apical meristem in gametophytes. Through confocal time‐lapse live imaging and computational image analysis and quantification, we determined unique patterns of cell division and growth that sustain or terminate apical initials, dictate the transition from apical initials to multicellular apical meristems, and drive proliferation of apical meristems in ferns. Quantitative results showed that small cells correlated to active cell division in fern gametophytes. The marginal cells of multicellular apical meristems in fern gametophytes undergo division in both anticlinal and periclinal orientations, not only increasing cell numbers but also playing a dominant role in increasing cell layers during gametophyte development. All these findings provide insights into the function and regulation of meristems in gametophytes of seed‐free vascular plants, suggesting both conserved and diversified mechanisms underlying meristem cell proliferation across land plants.
Cranial and vertebral osteosarcoma commonly has T2 signal heterogeneity, contrast enhancement, and osteolysis on MRI: A case series of 35 dogs
Authors: Tam Candace , Hecht Silke , Mai Wilfried , Nelson Nathan , Chen Annie V. , Griffin John F. 
Published: April 2022

AbstractMagnetic resonance imaging (MRI) is commonly used to evaluate the central nervous system (CNS) in dogs; however, published studies describing the MRI appearance of cranial and vertebral osteosarcoma are scarce. In this multicenter, retrospective, case series study, MRI studies of 35 dogs with cranial or vertebral osteosarcoma were prospectively scored by consensus of two veterinary radiologists. Recorded characteristics were location, signal intensity (compared to gray matter), homogeneity, contrast enhancement, margin delineation, local invasion, osteolysis, osteosclerosis, zone of transition, periosteal proliferation, pathological fracture, meningeal/CNS involvement, and presence of metastatic disease. Locations included the parietal bone (n = 1), occipital bone (n = 2), or cervical (n = 5), thoracic (n = 17), lumbar (n = 7), or sacral vertebrae (n = 3). Common features included signal heterogeneity in T2‐weighted (T2W) images (n = 35), contrast enhancement (in all 34 dogs with postcontrast MRI), osteolysis (n = 34), compression of the CNS or cauda equina (n = 33), an associated soft tissue mass (n = 33), a long zone of transition (n = 30), osteosclerosis (n = 28), signal isointensity to normal‐appearing gray matter in T1‐weighted images (T1W, n = 26), and T2W hyperintensity of adjacent brain or spinal cord (n = 23). Other findings included periosteal proliferation (n = 18), meningeal contrast enhancement (n = 17), T1W and T2W hypointense foci in the soft tissue mass (n = 14), invasion into adjacent bones (n = 10), pathological vertebral fractures (n = 7), regional lymphadenopathy (n = 6), skip metastases (n = 2), lung nodule (n = 1), diaphragmatic nodule (n = 1), and brain invasion (n = 1). Contrast enhancement was typically strong and heterogeneous. Magnetic resonance imaging features of cranial and vertebral osteosarcoma were analogous to those previously reported for other imaging modalities. Osteosarcoma should be a differential diagnosis for compressive, contrast‐enhancing, osteolytic lesions of the cranium or vertebrae.
Assessment of Heterogeneity in Lung Structure and Function During Mechanical Ventilation: A Review of Methodologies
Authors: Herrmann Jacob , Kollisch-Singule Michaela , Satalin Joshua , Nieman Gary , Kaczka David W. 
Published: April 2022

Abstract
The mammalian lung is characterized by heterogeneity in both its structure and function, by incorporating an asymmetric branching airway tree optimized for maintenance of efficient ventilation, perfusion, and gas exchange. Despite potential benefits of naturally occurring heterogeneity in the lungs, there may also be detrimental effects arising from pathologic processes, which may result in deficiencies in gas transport and exchange. Regardless of etiology, pathologic heterogeneity results in the maldistribution of regional ventilation and perfusion, impairments in gas exchange, and increased work of breathing. In extreme situations, heterogeneity may result in respiratory failure, necessitating support with a mechanical ventilator. This review will present a summary of measurement techniques for assessing and quantifying heterogeneity in respiratory system structure and function during mechanical ventilation. These methods have been grouped according to four broad categories: (1) inverse modeling of heterogeneous mechanical function; (2) capnography and washout techniques to measure heterogeneity of gas transport; (3) measurements of heterogeneous deformation on the surface of the lung; and finally (4) imaging techniques used to observe spatially-distributed ventilation or regional deformation. Each technique varies with regard to spatial and temporal resolution, degree of invasiveness, and risk posed to patients, as well as suitability for clinical implementation. Nonetheless, each technique can provide a unique perspective on the manifestations and consequences of mechanical heterogeneity in the diseased lung.
Evaluating the Normalized Coprime Factor-based Stability Metric for Rigid Systems
Authors: LiBretto Michael , Ueda Jun 
Published: April 2022

Abstract
The introduction of flexibility into rigid-body manipulator systems generally complicates the use of simple end-point feedback control. These flexibilities induce an unmodeled oscillation that cannot be necessarily compensated through end-point feedback control. The normalized coprime factor (NCF) based robustness metric ($\varepsilon_{max}$) has been well established in the realm of optimal control and can be applied to a rigid system with flexible modes in order to determine postures that will be robust to the flexibilities. This work illustrates that for rigid (double integrator) systems there is a fixed normalized coprime-factor robustness and, that for the special case of SISO systems, deviation from rigidity yields a similar change in NCF robustness.
Computational Fluid Dynamics Investigation of Flow in Scour Protection Around a Mono-Pile With the Volume-Averaged k-ω Model
Authors: Zhai Yanyan , Christensen Erik Damgaard 
Published: April 2022

Abstract
The study numerically investigates the flow behavior around a mono-pile with scour protection under steady and oscillatory flow conditions. A hydrodynamic model based on volume-averaged Reynolds-averaged Navier–Stokes (VARANS) equations with the volume-averaged k-ω turbulence closure is developed and implemented in openfoam. Three porosity transition types, i.e., constant, linear and parabolic, near the interface between stone cover and free flow are first evaluated in two-dimensional models. The simulated results, i.e., flow velocities, turbulence levels and bed shear stresses, are compared with previous experiments under steady and oscillatory flow conditions. The parabolic transition shows the best agreement with the measurements and is therefore used in the developed model. Under steady current, a three-dimensional model is validated against experimental measurements including flow features both inside and outside of the scour protection around a mono-pile, and it exhibits relatively good performance. Further, the volume-averaged k-ω model shows better agreement to experiments in porous medium compared to results from k-ω shear stress transport and volume-averaged k-ɛ models. The model is applied to investigate the flow patterns under the oscillatory flow condition. The results show that a horseshoe vortex is formed, and it penetrates the entire scour protection, which generates high flow velocities and bed shear stresses; erosion is most likely to occur at the area in the presence of vortex, which poses a threat to the pile stability. The simulations demonstrate the ability of the developed model to evaluate the flow behavior in scour protection.
Physiological and Sprint Kinetics Associated With the Yo-Yo Intermittent Recovery Test Level 1 Performances in Soccer Players
Authors: Kramer Mark , Sparks Martinique , Coetzee Ben 
Published: April 2022

Background: The Yo-Yo Intermittent Recovery Test Level 1 (YYIR1) is often utilized to indirectly assess the cardiorespiratory fitness of team-sport athletes due to its proposed association with match-play high-speed running performance and predicted maximal oxygen uptake. No previous research has investigated the relationships between YYIR1 performances, actual oxygen uptake recorded during the YYIR1, and true all-out sprint kinetics (eg, maximal sprint speed, maximal force capacity, and maximal power output), which therefore served as the primary objective of this study. Objectives: To assess the true physiological kinetics ( and heart-rate responses) during the YYIR1 and to evaluate the correlations between the physiological kinetics, sprint kinetics, and YYIR1 performance parameters. Methods: A total of 23 amateur male soccer players were recruited for the study (age 22.52 [2.86] y; height 1.75 [0.06] m; body mass 65.61 [8.43] kg). Each participant completed a YYIR1 and 2 all-out sprint tests. Results: Significant differences were observed between actual and predicted maximal oxygen-uptake values (Mdiff = 17.57 mL·kg−1·min−1, P < .001, r = .63). Shuttle distances showed statistically significant correlations with maximal sprint speed (r = .42, P = .044) and theoretic maximal speed (r = .44, P = .035). However, no other correlations with sprint kinetic parameters (eg, maximal force or power output) were observed. Conclusion: Practitioners should carefully consider the outcomes and utilities of the parameters derived from the YYIR1. The estimations of maximal oxygen uptake from shuttle performances as a proxy for cardiorespiratory fitness are not adequate. However, shuttle distances appear to be positively associated with all-out sprinting capacities.
A Retrospective Study on Students’ Perceived Experiences in Physical Education: Exploring Beliefs, Emotions, and Physical Activity Outcomes
Authors: Simonton Kelly L. , Washburn Nicholas , Prior Laura F. , Shiver Victoria N. , Fullerton Sean , Gaudreault Karen L. 
Published: April 2022

Purpose: This study utilized the control-value theory of achievement emotions to investigate relationships between retroactive physical education (PE) beliefs and emotions with adulthood physical activity (PA) attitudes and behaviors. Method: An exploratory structural equation model was employed to evaluate participants’ (N = 381) PE emotions, antecedents, and outcomes. Results: Control, intrinsic value, and extrinsic value antecedents predicted several emotions. PE enjoyment facilitated positive PA attitudes, whereas boredom and shame predicted negative PA attitudes. Shame predicted lower physical self-concept in students. Moderate to vigorous PA was traced positively with enjoyment and negatively from relief. Several indirect relationships were also observed that further support the control-value theory of achievement emotions. Conclusions: Emotions are a response to learning and finding value in PE, which clearly impacts PA-related beliefs and behaviors into adulthood. Considerations on the externally driven nature of PE outcomes (i.e., standards/performance) are needed given the juxtaposition for also targeting suggested goals like intrinsic value and enjoyment.
The influence of the Messinian Salinity Crisis on the tectonic evolution of the Northern Apennines
Authors: Bice David , Tavarnelli Enrico 
Published: April 2022

ABSTRACT
The Messinian Salinity Crisis (5.85–5.35 Ma) represents a nearly unprecedented unloading and loading event. During the Messinian Salinity Crisis, two important things happened in terms of surface load changes—the accumulation of thick evaporites represent a load addition, while the desiccation of the Mediterranean represents a load subtraction. The desiccation and evaporite deposition were followed by the rapid addition of water, refilling the Mediterranean during the Zanclean. The calculated flexural response to load changes imposed significant changes on the horizontal stresses in the upper crust of the Northern Apennines, an active orogenic system characterized by simultaneous zones of extension and compression that migrated eastward over time. We show that these flexural stresses (approaching ± 50 MPa), added to the preexisting stresses across the Northern Apennines, were large enough to have caused some areas in compressional stress regimes to flip to extensional regimes, and vice versa. Among other things, our model predicts that the Marches Apennines region, which was beginning to undergo compression at the leading edge of the orogen, should have experienced a brief interval of extensional deformation. Previous structural studies of this region have shown that there was, in fact, a brief period of extensional faulting near the onset of the Messinian Salinity Crisis, which was then followed by a return to compressional deformation, just as our model predicts. The hypothesis presented here provides a novel explanation for this extension occurring in an area that should have been undergoing compression, one in which the unique events of the Messinian Salinity Crisis generated significant flexural stresses that changed the deformational regime during the relatively brief time of the Messinian Salinity Crisis. We further suggest that this hypothesis may provide insight into similar unexpected tectonic episodes during this time period in other parts of the Apennines.