bluuebunny/crossref_metadata_2025_split huggingface dataset:
A new conceptual framework for the transformation of groundwater dissolved organic matter
Authors: McDonough Liza K. , Andersen Martin S. , Behnke Megan I. , Rutlidge Helen , Oudone Phetdala , Meredith Karina , O’Carroll Denis M. , Santos Isaac R. , Marjo Christopher E. , Spencer Robert G. M. , McKenna Amy M. , Baker Andy 
Published: April 2022

AbstractGroundwater comprises 95% of the liquid fresh water on Earth and contains a diverse mix of dissolved organic matter (DOM) molecules which play a significant role in the global carbon cycle. Currently, the storage times and degradation pathways of groundwater DOM are unclear, preventing an accurate estimate of groundwater carbon sources and sinks for global carbon budgets. Here we reveal the transformations of DOM in aging groundwater using ultra-high resolution mass spectrometry combined with radiocarbon dating. Long-term anoxia and a lack of photodegradation leads to the removal of oxidised DOM and a build-up of both reduced photodegradable formulae and aerobically biolabile formulae with a strong microbial signal. This contrasts with the degradation pathway of DOM in oxic marine, river, and lake systems. Our findings suggest that processes such as groundwater extraction and subterranean groundwater discharge to oceans could result in up to 13 Tg of highly photolabile and aerobically biolabile groundwater dissolved organic carbon released to surface environments per year, where it can be rapidly degraded. These findings highlight the importance of considering groundwater DOM in global carbon budgets.
Economic shocks predict increases in child wasting prevalence
Authors: Headey Derek D. , Ruel Marie T. 
Published: April 2022

AbstractIn low and middle income countries macroeconomic volatility is common, and severe negative economic shocks can substantially increase poverty and food insecurity. Less well understood are the implications of these contractions for child acute malnutrition (wasting), a major risk factor for under-5 mortality. This study explores the nutritional impacts of economic growth shocks over 1990–2018 by linking wasting outcomes collected for 1.256 million children from 52 countries to lagged annual changes in economic growth. Estimates suggest that a 10% annual decline in national income increases moderate/severe wasting prevalence by 14.4–17.8%. An exploration of possible mechanisms suggests negative economic shocks may increase risks of inadequate dietary diversity among children. Applying these results to the latest economic growth estimates for 2020 suggests that COVID-19 could put an additional 9.4 million preschoolers at risk of wasting, net of the effects of preventative policy actions.
TRMT6/61A-dependent base methylation of tRNA-derived fragments regulates gene-silencing activity and the unfolded protein response in bladder cancer
Authors: Su Zhangli , Monshaugen Ida , Wilson Briana , Wang Fengbin , Klungland Arne , Ougland Rune , Dutta Anindya 
Published: April 2022

AbstractRNA modifications are important regulatory elements of RNA functions. However, most genome-wide mapping of RNA modifications has focused on messenger RNAs and transfer RNAs, but such datasets have been lacking for small RNAs. Here we mapped N1-methyladenosine (m1A) in the cellular small RNA space. Benchmarked with synthetic m1A RNAs, our workflow identified specific groups of m1A-containing small RNAs, which are otherwise disproportionally under-represented. In particular, 22-nucleotides long 3′ tRNA-fragments are highly enriched for TRMT6/61A-dependent m1A located within the seed region. TRMT6/61A-dependent m1A negatively affects gene silencing by tRF-3s. In urothelial carcinoma of the bladder, where TRMT6/61A is over-expressed, higher m1A modification on tRFs is detected, correlated with a dysregulation of tRF targetome. Lastly, TRMT6/61A regulates tRF-3 targets involved in unfolded protein response. Together, our results reveal a mechanism of regulating gene expression via base modification of small RNA.
Metabolic plasticity can amplify ecosystem responses to global warming
Authors: Kordas Rebecca L. , Pawar Samraat , Kontopoulos Dimitrios-Georgios , Woodward Guy , O’Gorman Eoin J. 
Published: April 2022

AbstractOrganisms have the capacity to alter their physiological response to warming through acclimation or adaptation, but the consequence of this metabolic plasticity for energy flow through food webs is currently unknown, and a generalisable framework does not exist for modelling its ecosystem-level effects. Here, using temperature-controlled experiments on stream invertebrates from a natural thermal gradient, we show that the ability of organisms to raise their metabolic rate following chronic exposure to warming decreases with increasing body size. Chronic exposure to higher temperatures also increases the acute thermal sensitivity of whole-organismal metabolic rate, independent of body size. A mathematical model parameterised with these findings shows that metabolic plasticity could account for 60% higher ecosystem energy flux with just +2 °C of warming than a traditional model based on ecological metabolic theory. This could explain why long-term warming amplifies ecosystem respiration rates through time in recent mesocosm experiments, and highlights the need to embed metabolic plasticity in predictive models of global warming impacts on ecosystems.
Neutron-upscattering enhancement of the triple-alpha process
Authors: Bishop J. , Parker C. E. , Rogachev G. V. , Ahn S. , Koshchiy E. , Brandenburg K. , Brune C. R. , Charity R. J. , Derkin J. , Dronchi N. , Hamad G. , Jones-Alberty Y. , Kokalova Tz. , Massey T. N. , Meisel Z. , Ohstrom E. V. , Paneru S. N. , Pollacco E. C. , Saxena M. , Singh N. , Smith R. , Sobotka L. G. , Soltesz D. , Subedi S. K. , Voinov A. V. , Warren J. , Wheldon C. 
Published: April 2022

AbstractThe neutron inelastic scattering of carbon-12, populating the Hoyle state, is a reaction of interest for the triple-alpha process. The inverse process (neutron upscattering) can enhance the Hoyle state’s decay rate to the bound states of 12C, effectively increasing the overall triple-alpha reaction rate. The cross section of this reaction is impossible to measure experimentally but has been determined here at astrophysically-relevant energies using detailed balance. Using a highly-collimated monoenergetic beam, here we measure neutrons incident on the Texas Active Target Time Projection Chamber (TexAT TPC) filled with CO2 gas, we measure the 3α-particles (arising from the decay of the Hoyle state following inelastic scattering) and a cross section is extracted. Here we show the neutron-upscattering enhancement is observed to be much smaller than previously expected. The importance of the neutron-upscattering enhancement may therefore not be significant aside from in very particular astrophysical sites (e.g. neutron star mergers).
Vasa nucleates asymmetric translation along the mitotic spindle during unequal cell divisions
Authors: Fernandez-Nicolas Ana , Uchida Alicia , Poon Jessica , Yajima Mamiko 
Published: April 2022

AbstractmRNA translation on the spindle is hypothesized to be an essential strategy for the localized production of cell regulators. This mechanism may be important particularly in early embryonic cells, which have a large diffusion volume and that undergo rapid cell divisions. Evidence to test such a hypothesis has been, however, limited. Here, we use an embryo with both symmetric and asymmetric cell divisions and manipulate Vasa protein, an RNA-helicase, on the spindle in live sea urchin embryos. We learned that the spindle serves as a major site of translation and that protein synthesis within a single spindle can be unequal and help drive asymmetric cell divisions during embryogenesis. Recruiting Vasa to the ectopic sub-cellular region induced a new site of translation, disturbed asymmetric translation on the spindle, and changed the cell fate. Based on these observations, we conclude that Vasa functions in localized translation, which provides a spatiotemporal control in protein synthesis and is essential for rapidly developing embryonic cells.
RNA polymerase II pausing factor NELF in CD8+ T cells promotes antitumor immunity
Authors: Wu Bogang , Zhang Xiaowen , Chiang Huai-Chin , Pan Haihui , Yuan Bin , Mitra Payal , Qi Leilei , Simonyan Hayk , Young Colin N. , Yvon Eric , Hu Yanfen , Zhang Nu , Li Rong 
Published: April 2022

AbstractT cell factor 1 (TCF1) is required for memory and stem-like CD8+ T cell functions. How TCF1 partners with other transcription factors to regulate transcription remains unclear. Here we show that negative elongation factor (NELF), an RNA polymerase II (Pol II) pausing factor, cooperates with TCF1 in T cell responses to cancer. Deletion of mouse Nelfb, which encodes the NELFB subunit, in mature T lymphocytes impairs immune responses to both primary tumor challenge and tumor antigen-mediated vaccination. Nelfb deletion causes more exhausted and reduced memory T cell populations, whereas its ectopic expression boosts antitumor immunity and efficacy of chimeric antigen receptor T-cell immunotherapy. Mechanistically, NELF is associated with TCF1 and recruited preferentially to the enhancers and promoters of TCF1 target genes. Nelfb ablation reduces Pol II pausing and chromatin accessibility at these TCF1-associated loci. Our findings thus suggest an important and rate-limiting function of NELF in anti-tumor immunity.
Photoinduced evolution of lattice orthorhombicity and conceivably enhanced ferromagnetism in LaMnO3 membranes
Authors: Lu Qinwen , Cheng Yun , Wu Lijun , Guo Hongli , Qi Fengfeng , Zhang Haijuan , Yu Junxiao , Liu Qixin , Wang Qing , Liang Genhao , Chen Jie , Lu Yalin , Zhang Jie , Xiang Dao , Zhao Jin , Zhu Yimei , Zhai Xiaofang 
Published: April 2022

AbstractUltrashort laser pulses have been utilized to dynamically drive phase transitions in correlated quantum materials. Of particular interest is whether phases not achievable in thermal equilibrium can be induced in complex oxides with intricately coupled lattice, electron and spin degrees of freedom. Here, we tracked atomic motions in LaMnO3 following photoexcitation with MeV ultrafast electron diffraction (MeV-UED) technique. We found that the light excited state exhibits numerous signatures different from thermal equilibrium ones, including nearly conserved Bragg intensities, strongly suppressed La cation and oxygen anion displacements, and the long-range lattice orthorhombicity evolution. Furthermore, using first-principles calculations, we predict that the ferromagnetic ordering and conductivity are both enhanced upon laser excitation due to the reduction of the lattice orthorhombicity. This work benefits from recent advance in fabrication of membrane films with high epitaxial quality and in MeV-UED with large momentum space access and high temporal resolution.
Neural activation during emotional interference corresponds to emotion dysregulation in stressed teachers
Authors: Fynes-Clinton Samuel , Sherwell Chase , Ziaei Maryam , York Ashley , O’Connor Emma Sanders , Forrest Kylee , Flynn Libby , Bower Julie , Reutens David , Carroll Annemaree 
Published: April 2022

AbstractTeacher stress and burnout has been associated with low job satisfaction, reduced emotional wellbeing, and poor student learning outcomes. Prolonged stress is associated with emotion dysregulation and has thus become a focus of stress interventions. This study examines emotional interference effects in a group of teachers suffering from high stress and to explore how individual differences in cognitive control, emotion dysregulation, and emotion recognition related to patterns of neural activation. Forty-nine teachers suffering moderate-high stress participated in an emotional counting Stroop task while their brain activity was imaged using functional magnetic resonance imaging. Participants viewed general or teacher specific words of either negative or neutral valence and were required to count the number of words on screen. Behavioural and neuroimaging results suggest that teachersareable to control emotional responses to negative stimuli, as no evidence of emotional interference was detected. However, patterns of neural activation revealed early shared engagement of regions involved in cognitive reappraisal during negative task conditions and unique late engagement of the hippocampus only while counting teacher-specific negative words. Further, we identified that greater emotion dysregulation was associated with increased activation of regions involved in cognitive control processes during neutral word trials. Teachers who showed slower emotion recognition performance were also found to have greater activation in regions associated with visual and word processing, specifically during the teacher specific negative word condition of the task. Future research should explore emotion regulation strategy use in teachers and utilise temporally sensitive neuroimaging techniques to further understand these findings.
Intron-mediated induction of phenotypic heterogeneity
Authors: Lukačišin Martin , Espinosa-Cantú Adriana , Bollenbach Tobias 
Published: April 2022

AbstractIntragenic regions that are removed during maturation of the RNA transcript—introns—are universally present in the nuclear genomes of eukaryotes1. The budding yeast, an otherwise intron-poor species, preserves two sets of ribosomal protein genes that differ primarily in their introns2,3. Although studies have shed light on the role of ribosomal protein introns under stress and starvation4–6, understanding the contribution of introns to ribosome regulation remains challenging. Here, by combining isogrowth profiling7with single-cell protein measurements8, we show that introns can mediate inducible phenotypic heterogeneity that confers a clear fitness advantage. Osmotic stress leads to bimodal expression of the small ribosomal subunit protein Rps22B, which is mediated by an intron in the 5′ untranslated region of its transcript. The two resulting yeast subpopulations differ in their ability to cope with starvation. Low levels of Rps22B protein result in prolonged survival under sustained starvation, whereas high levels of Rps22B enable cells to grow faster after transient starvation. Furthermore, yeasts growing at high concentrations of sugar, similar to those in ripe grapes, exhibit bimodal expression of Rps22B when approaching the stationary phase. Differential intron-mediated regulation of ribosomal protein genes thus provides a way to diversify the population when starvation threatens in natural environments. Our findings reveal a role for introns in inducing phenotypic heterogeneity in changing environments, and suggest that duplicated ribosomal protein genes in yeast contribute to resolving the evolutionary conflict between precise expression control and environmental responsiveness9.
Opening of glutamate receptor channel to subconductance levels
Authors: Yelshanskaya Maria V. , Patel Dhilon S. , Kottke Christopher M. , Kurnikova Maria G. , Sobolevsky Alexander I. 
Published: April 2022

AbstractIonotropic glutamate receptors (iGluRs) are tetrameric ligand-gated ion channels that open their pores in response to binding of the agonist glutamate1–3. An ionic current through a single iGluR channel shows up to four discrete conductance levels (O1–O4)4–6. Higher conductance levels have been associated with an increased number of agonist molecules bound to four individual ligand-binding domains (LBDs)6–10. Here we determine structures of a synaptic complex of AMPA-subtype iGluR and the auxiliary subunit γ2 in non-desensitizing conditions with various occupancy of the LBDs by glutamate. We show that glutamate binds to LBDs of subunits B and D only after it is already bound to at least the same number of LBDs that belong to subunits A and C. Our structures combined with single-channel recordings, molecular dynamics simulations and machine-learning analysis suggest that channel opening requires agonist binding to at least two LBDs. Conversely, agonist binding to all four LBDs does not guarantee maximal channel conductance and favours subconductance states O1 and O2, with O3 and O4 being rare and not captured structurally. The lack of subunit independence and low efficiency coupling of glutamate binding to channel opening underlie the gating of synaptic complexes to submaximal conductance levels, which provide a potential for upregulation of synaptic activity.
Modeling of lophotrichous bacteria reveals key factors for swimming reorientation
Authors: Park Jeungeun , Kim Yongsam , Lee Wanho , Lim Sookkyung 
Published: April 2022

AbstractLophotrichous bacteria swim through fluid by rotating their flagellar bundle extended collectively from one pole of the cell body. Cells experience modes of motility such as push, pull, and wrapping, accompanied by pauses of motor rotation in between. We present a mathematical model of a lophotrichous bacterium and investigate the hydrodynamic interaction of cells to understand their swimming mechanism. We classify the swimming modes which vary depending on the bending modulus of the hook and the magnitude of applied torques on the motor. Given the hook’s bending modulus, we find that there exist corresponding critical thresholds of the magnitude of applied torques that separate wrapping from pull in CW motor rotation, and overwhirling from push in CCW motor rotation, respectively. We also investigate reoriented directions of cells in three-dimensional perspectives as the cell experiences different series of swimming modes. Our simulations show that the transition from a wrapping mode to a push mode and pauses in between are key factors to determine a new path and that the reoriented direction depends upon the start time and duration of the pauses. It is also shown that the wrapping mode may help a cell to escape from the region where the cell is trapped near a wall.
Genomic evaluation of hybridization in historic and modern North American Bison (Bison bison)
Authors: Stroupe Sam , Forgacs David , Harris Andrew , Derr James N. , Davis Brian W. 
Published: April 2022

AbstractDuring the late nineteenth century North American bison underwent a significant population bottleneck resulting in a reduction in population size of over 99% and a species-level near-extinction event. Factors responsible for this destruction included indiscriminate killing, loss of access to suitable habitat, and diseases. At the nadir of this population crash, very few wild plains bison survived and were restricted to Yellowstone National Park, USA and a small number of wild wood bison remained in Wood Buffalo National Park, Canada. However, most surviving bison in the late 1800’s were maintained by cattle ranchers in private herds where hybridization between bison with various breeds of domestic cattle was often encouraged. Over the last 20 years, the legacy of this introgression has been identified using mitochondrial DNA and limited nuclear microsatellite analyses. However, no genome-wide assessment has been performed, and some herds were believed to be free of introgression based on current genetic testing strategies. Herein, we report detailed analyses using whole genome sequencing from nineteen modern and six historical bison, chosen to represent the major lineages of bison, to identify and quantitate signatures of nuclear introgression in their recent (within 200 years) history. Both low and high coverage genomes provided evidence for recent introgression, including animals from Yellowstone, Wind Cave, and Elk Island National Parks which were previously thought to be free from hybridization with domestic cattle. We employed multiple approaches, including one developed for this work, to identify putative cattle haplotypes in each bison genome. These regions vary greatly in size and frequency by sample and herd, though we detected domestic cattle introgression in all bison genomes tested. Since our sampling strategy spanned across the diversity of modern bison populations, these finding are best explained by multiple historical hybridization events between these two species with significant genetic recombination over the last 200 years. Our results demonstrate that whole genome sequencing approaches are required to accurately quantitate cattle introgression in bison.
The protein folding rate and the geometry and topology of the native state
Authors: Wang Jason , Panagiotou Eleni 
Published: April 2022

AbstractProteins fold in 3-dimensional conformations which are important for their function. Characterizing the global conformation of proteins rigorously and separating secondary structure effects from topological effects is a challenge. New developments in applied knot theory allow to characterize the topological characteristics of proteins (knotted or not). By analyzing a small set of two-state and multi-state proteins with no knots or slipknots, our results show that 95.4% of the analyzed proteins have non-trivial topological characteristics, as reflected by the second Vassiliev measure, and that the logarithm of the experimental protein folding rate depends on both the local geometry and the topology of the protein’s native state.
Night work, chronotype and cortisol at awakening in female hospital employees
Authors: Burek Katarzyna , Rabstein Sylvia , Kantermann Thomas , Vetter Céline , Rotter Markus , Wang-Sattler Rui , Lehnert Martin , Pallapies Dirk , Jöckel Karl-Heinz , Brüning Thomas , Behrens Thomas 
Published: April 2022

AbstractTo examine the effect of night shift on salivary cortisol at awakening (C1), 30 min later (C2), and on the cortisol awakening response (CAR, the difference between C2 and C1). We compared shift and non-shift workers with a focus on the impact of worker chronotype. Our study included 66 shift-working females (mean age = 37.3 years, SD = 10.2) and 21 non-shift working females (mean age = 47.0 years, SD = 8.9). The shift workers collected their saliva samples at C1 and C2 on each two consecutive day shifts and night shifts. Non-shift workers collected their samples on two consecutive day shifts. We applied linear mixed-effects models (LMM) to determine the effect of night shift on CAR and log-transformed C1 and C2 levels. LMMs were stratified by chronotype group. Compared to non-shift workers, shift workers before day shifts (i.e. after night sleep) showed lower cortisol at C1 (exp $$(\widehat{\beta })$$

(

β
^

)

=0.58, 95% CI 0.42, 0.81) but not at C2. In shift workers, the CARs after night shifts (i.e. after day sleep) were lower compared to CARs before day shifts ($$\widehat{\beta }$$

β
^

= − 11.07, 95% CI − 15.64, − 6.50). This effect was most pronounced in early chronotypes (early: $$\widehat{\beta }$$

β
^

= − 16.61, 95% CI − 27.87, − 5.35; intermediate: $$\widehat{\beta }$$

β
^

= − 11.82, 95% CI − 18.35, − 5.29; late: $$\widehat{\beta }$$

β
^

= − 6.27, 95% CI − 14.28, 1.74). Chronotype did not modify the association between night shift and CAR. In our population of shift workers, there was a mismatch between time of waking up and their natural cortisol peak at waking up (CAR) both during day and night shift duties.