bluuebunny/crossref_metadata_2025_split huggingface dataset:
Causes and consequences of telomere lengthening in a wild vertebrate population
Authors: Brown Thomas J. , Spurgin Lewis G. , Dugdale Hannah L. , Komdeur Jan , Burke Terry , Richardson David S. 
Published: July 2021

AbstractTelomeres have been advocated to be important markers of biological age in evolutionary and ecological studies. Telomeres usually shorten with age and shortening is frequently associated with environmental stressors and increased subsequent mortality. Telomere lengthening – an apparent increase in telomere length between repeated samples from the same individual – also occurs. However, the exact circumstances, and consequences, of telomere lengthening are poorly understood. Using longitudinal data from the Seychelles warbler (Acrocephalus sechellensis), we tested whether telomere lengthening – which occurs in adults of this species – is associated with specific stressors (reproductive effort, food availability, malarial infection and cooperative breeding) and predicts subsequent survival. In females, telomere shortening was observed under greater stress (i.e., low food availability, malaria infection), while telomere lengthening was observed in females experiencing lower stress (i.e., high food availability, assisted by helpers, without malaria). The telomere dynamics of males were not associated with the key stressors tested. These results indicate that, at least for females, telomere lengthening occurs in circumstances more conducive to self‐maintenance. Importantly, both females and males with lengthened telomeres had improved subsequent survival relative to individuals that displayed unchanged, or shortened, telomeres – indicating that telomere lengthening is associated with individual fitness. These results demonstrate that telomere dynamics are bidirectionally responsive to the level of stress that an individual faces, but may poorly reflect the accumulation of stress over an individuals lifetime.
A Bayesian smoothing for input‐state estimation of structural systems
Authors: Ebrahimzadeh Hassanabadi Mohsen , Heidarpour Amin , Eftekhar Azam Saeed , Arashpour Mehrdad 
Published: July 2021

AbstractInstantaneous output‐only inversion of a system with delayed appearance of input influences on the measured outputs via filtering methods suffer from intensive amplification of the observation noise in the estimated quantities due to the ill‐conditionedness. To remedy this issue, in this paper, a new unbiased recursive Bayesian smoothing method is developed for input‐state estimation of linear systems without direct feedthrough to reduce estimation uncertainty through an extended observation equation. By minimizing input and state estimation error variance, the optimal smoothing input and state gain matrices are derived. Moreover, a new efficient method is proposed for the recursive calculation of correlation of state estimation error with modeling and observation noise vectors.
The association between Hfq and RNase E in long‐term nitrogen‐starved Escherichia coli
Authors: McQuail Josh , Carpousis Agamemnon J. , Wigneshweraraj Sivaramesh 
Published: July 2021

AbstractUnder conditions of nutrient adversity, bacteria adjust metabolism to minimize cellular energy usage. This is often achieved by controlling the synthesis and degradation of RNA. In Escherichia coli, RNase E is the central enzyme involved in RNA degradation and serves as a scaffold for the assembly of the multiprotein complex known as the RNA degradosome. The activity of RNase E against specific mRNAs can also be regulated by the action of small RNAs (sRNA). In this case, the ubiquitous bacterial chaperone Hfq bound to sRNAs can interact with the RNA degradosome for the sRNA guided degradation of target RNAs. The RNA degradosome and Hfq have never been visualized together in live bacteria. We now show that in long‐term nitrogen starved E. coli, both RNase E and Hfq co‐localize in a single, large focus. This subcellular assembly, which we refer to as the H‐body, forms by a liquid‐liquid phase separation type mechanism and includes components of the RNA degradosome, namely, the helicase RhlB and the exoribonuclease polynucleotide phosphorylase. The results support the existence of a hitherto unreported subcellular compartmentalization of a process(s) associated with RNA management in stressed bacteria.
Plasticity of rosette size in response to nitrogen availability is controlled by an RCC1‐family protein
Authors: Duarte Gustavo Turqueto , Pandey Prashant K. , Vaid Neha , Alseekh Saleh , Fernie Alisdair R. , Nikoloski Zoran , Laitinen Roosa A. E. 
Published: July 2021

AbstractNitrogen (N) is fundamental to plant growth, development and yield. Genes underlying N utilization and assimilation are well‐characterized, but mechanisms underpinning plasticity of different phenotypes in response to N remain elusive. Here, using Arabidopsis thaliana accessions, we dissected the genetic architecture of plasticity in early and late rosette diameter, flowering time and yield, in response to three levels of N in the soil. Furthermore, we found that the plasticity in levels of primary metabolites were related with the plasticities of the studied traits. Genome‐wide association analysis identified three significant associations for phenotypic plasticity, one for early rosette diameter and two for flowering time. We confirmed that the gene At1g19880, hereafter named as PLASTICITY OF ROSETTE TO NITROGEN 1 (PROTON1), encoding for a regulator of chromatin condensation 1 (RCC1) family protein, conferred plasticity of rosette diameter in response to N. Treatment of PROTON1 T‐DNA line with salt implied that the reduced plasticity of early rosette diameter was not a general growth response to stress. We further showed that plasticities of growth and flowering‐related traits differed between environmental cues, indicating decoupled genetic programs regulating these traits. Our findings provide a prospective to identify genes that stabilize performance under fluctuating environments.
Estimation of Singlet Oxygen Quantum Yield Using Novel Green‐Absorbing Baird‐type Aromatic Photosensitizers†
Authors: Morgan Jayla , Yun Young Ju , Ayitou A. Jean‐Luc 
Published: July 2021

AbstractWe report two new organic green‐absorbing singlet oxygen (1O2) photosensitizers: Quinoidal naphthyl thioamide (QDM) and bis‐iodol‐dipyrrolonaphthyridine‐dione (I2–DPND), with triplet energies of 40.8 and 47.5 kcal mol−1(at 77 K in a glassy matrix) , respectively. The UV–vis absorption and emission characteristics of QDM and I2–DPND are similar to other commercially available organic 1O2 photosensitizers such as Rose Bengal, which was used as standard/reference to estimate the 1O2 quantum yield (Φ∆) of the chromophores under study. Using 9,10‐diphenylanthracene (DPA) as an 1O2 quencher, we estimated the Φ∆ ≈ 67–85% for QDM and Φ∆ ≈ 25–32% for I2–DPND. The discrepancy in the Φ∆ values could be explained by the apparent photo‐decomposition of the later dye. Nevertheless, the high Φ∆ value for QDM is unprecedented, as this chromophore exhibits relatively low structural complexity and could further be derivatized to create novel photodynamic agents.
Environmental and anthropogenic factors affecting natural regeneration of degraded dry Afromontane forest
Authors: Hishe Hadgu , Giday Kidane , Fremout Tobias , Negussie Aklilu , Aerts Raf , Muys Bart 
Published: July 2021

Natural regeneration of trees may provide a cost‐effective way to restore degraded tropical dry forests, but the factors predominantly affecting natural regeneration success are poorly understood. We performed a multifactor analysis of natural regeneration in an Afromontane forest in Northern Ethiopia. Inventory plots of 400 m2, each with a nested 9 m2 subplot, were systematically established. All trees larger than 5 cm DBH and natural regeneration were identified and recorded in the plots and subplots, respectively. Variables describing climate, topography, soil, vegetation, and indications of local human degradation were collected. Determinants of regeneration presence and abundance were analyzed using Hurdle negative binomial regressions. Sixty‐nine woody species were represented in the regeneration, with an average regeneration density (SE) of 14,700 (51) ha−1. The presence of regeneration was positively associated with canopy cover (p < 0.001), distance to the road network (p = 0.04), precipitation (p = 0.003) and tree species diversity (p = 0.03), and negatively with Northing (p = 0.003). The regeneration abundance was positively associated with soil quality (p = 0.001), canopy cover (p = 0.04), and precipitation (p = 0.01). Including the abundance of dominant species in the tree canopy and regeneration layers in the regression model did not affect the presence of natural regeneration, but it clearly affected regeneration abundance. In such a model, the regeneration abundance was positively associated with Euclea racemosa seedlings abundance and negatively associated with the basal area of Dodonaea angustifolia (p = 0.02) and Rhus natalensis (p = 0.04). In this model, forest degradation (p = 0.01) negatively affected the late‐successional species regeneration but not the regeneration of the drought‐resistant light‐demanding species. The low representation of late‐successional trees species in the natural regeneration calls for active restoration intervention.
Growing up in the Iran–Iraq war and preferences for strong defense
Authors: Farzanegan Mohammad Reza , Gholipour Hassan F. 
Published: July 2021

AbstractThe purpose of this study is to examine the relationship between individuals’ experiences of the Iran–Iraq war (1980–1988) during early adulthood (18–25 years) and their preference for strong national defense forces and their willingness to fight for Iran (in the event of another war). Using the World Values Survey data, we provide evidence that Iranians who experienced the war during their early adulthood give top priority to strong defense forces. However, we find that there is no significant association between individuals’ experiences of the war during early adulthood and their willingness to fight for Iran. The results are robust to controlling for a set of individuals’ socioeconomic and political characteristics as well as different age cohorts. Finally, we show that our results are not influenced by age cohort effect.
Capillary‐gravity solitary waves on water of finite depth interacting with a linear shear current
Authors: Gao T. , Milewski P. A. , Wang Z. 
Published: July 2021

AbstractThe problem of two‐dimensional capillary‐gravity waves on an inviscid fluid of finite depth interacting with a linear shear current is considered. The shear current breaks the symmetry of the irrotational problem and supports simultaneously counter‐propagating waves of different types: Korteweg de‐Vries (KdV)‐type long solitary waves and wave‐packet solitary waves whose envelopes are associated with the nonlinear Schrödinger equation. A simple intuition for the broken symmetry is that the current modifies the Bond number differently for left‐ and right‐propagating waves. Weakly nonlinear theories are developed in general and for two particular resonant cases: the case of second harmonic resonance and long‐wave/short‐wave interaction. Traveling‐wave solutions and their dynamics in the full Euler equations are computed numerically using a time‐dependent conformal mapping technique, and compared to some weakly nonlinear solutions. Additional attention is paid to branches of elevation generalized solitary waves of KdV type: although true embedded solitary waves are not detected on these branches, it is found that periodic wavetrains on their tails can be arbitrarily small as the vorticity increases. Excitation of waves by moving pressure distributions and modulational instabilities of the periodic waves in the resonant cases described above are also examined by the fully nonlinear computations.
No association between maternal exercise during pregnancy and the child’s weight status at age 7 years: The MoBa study
Authors: Andreassen Silje Malen , Ekelund Ulf , Bernhardsen Guro Pauck 
Published: July 2021

IntroductionMaternal lifestyle during pregnancy may affect the development of overweight and obesity in the child. We examined whether maternal exercise during pregnancy is associated with offspring overweight and obesity in childhood. A secondary aim was to examine whether the association is affected by the child's physical activity level.Materials and methodsThis study is based on data from the Norwegian Mother, Father and Child Cohort Study (MoBa), including 44 352 pregnancies and children (n = 32 304 in week 17 and n = 32 419 in week 30 in the final adjusted model). Maternal exercise during pregnancy was self‐reported in gestational weeks 17 and 30. We conducted linear and logistic regression separately for girls and boys, and outcomes were the child's body mass index (BMI) and weight status (overweight/obese) at age 7 years. We further examined the additive joint association between maternal exercise during pregnancy and the child's leisure time physical activity on weight status at age 7 years.ResultsIn total, 12.4% of the children were classified as overweight or obese, and 1.7% as obese. The results suggest no association between maternal exercise in both gestational weeks 17 and 30 and the weight status of the child at age 7 years. The association between maternal exercise and the child's weight status at age 7 years appears not to be affected by the child's physical activity level.ConclusionMaternal exercise level during pregnancy does not appear to be associated with the child's BMI or odds of being overweight or obese in childhood.
Validation of skeletal muscle mass estimation equations in active young adults: A preliminary study
Authors: Sagayama Hiroyuki , Yamada Yosuke , Tanabe Yoko , Kondo Emi , Ohnishi Takahiro , Takahashi Hideyuki 
Published: July 2021

We analyzed the validity of the estimation equations for skeletal muscle mass (SMM) using mass of appendicular lean soft tissue (ALST), evaluated by dual‐energy X‐ray absorptiometry (DXA), in healthy young males undergoing training, and compared it with the results obtained using whole‐body magnetic resonance imaging (MRI). We hypothesized that a novel variable, that is, trunk and trunk‐to‐appendicular ratio of lean soft tissues (trunk/ALST), would be useful in reducing estimation errors in athletes or physically active participants. We analyzed the data of 30 participants (mean age 19.9 ± 1.8 years). SMM was measured using whole‐body MRI, while mass of trunk and ALST was assessed using DXA. Three previously utilized estimation equations were retrieved from the literature and used for comparison. The estimated SMM values using previous equations highly correlated with measured SMM, which was determined by MRI, but the mean estimated SMM values were significantly lower than the measured‐SMM values. Stepwise regression analysis revealed that mass of ALST, trunk/ALST ratio, and percent body fat were significant predictors of SMM and were incorporated as the new suggested variables. This equation accounted for 90.3% of the variance in SMM. While the previous equations’ estimated SMM correlated with measured‐SMM in participants with trunk/ALST ratios ≤1.05, they underestimated SMMs in those with trunk/ALST ratios >1.05. The present study confirms that the previously used equations underestimate the actual SMM, particularly in participants with high trunk/ALST ratios (>1.05). The current equation may be used in healthy and active young males, including athletes, as a preliminary tool.
The racialized patterns of police violence: The critical importance of research as praxis
Authors: Durán Robert J. , Shroulote‐Durán Charlene M. 
Published: July 2021

AbstractThe tragic killing of George Floyd at the hands of the police resulted in hundreds of thousands of protestors marching in the streets demanding change. The call for change criticized the killing of Blacks by law enforcement and challenged White supremacy as an institution of social control and racial violence. A key component of the marches and protests was a message to the residents of the United States: “Black Lives Matter.” As society grapples with a reckoning, researchers studying police violence for the past 6 decades have been empirically and theoretically debating the reasons why use of force by law enforcement continues to have a higher proportion of Black and Brown victims compared to Whites. Although the research on fatal police killings was studied by only a small number of individuals prior to 2014, after the killing of Michael Brown in Ferguson, Missouri the research in different areas of the country increased rapidly as did the forms of analysis and research disciplines making their own contributions. TheWashington PostandGuardiannews agencies established that deaths at the hands of the police were occurring for at least 900 to 1100 individual deaths per year for which firearms resulted in the greatest cause of death. As US government agencies failed to produce a national data source on police involved killings, the media took a leading role in providing greater national understanding. The authors examine what role academic researchers contribute to the discussion for solutions, particularly those from marginalized backgrounds. As protestors march, lawyers sue and defend, and politicians create new forms of legislation, researchers need to play a more important role initiating critical studies, making sense of the data, and providing a theoretical framework for which police violence can be understood. This article will provide an overview of the literature on racialized police violence, point out key patterns involving racial and ethnic disparities, and emphasize how researchers can play a more important role in advocating for change.
Neurocysticercosis and HIV/AIDS co‐infection: A scoping review
Authors: Jewell Paul D. , Abraham Annette , Schmidt Veronika , Buell Kevin G. , Bustos Javier A. , Garcia Hector H. , Dixon Matthew A. , Walker Martin , Ngowi Bernard J. , Basáñez Maria‐Gloria , Winkler Andrea S. 
Published: July 2021

AbstractObjectivesNeurocysticercosis (NCC) and human immunodeficiency virus (HIV) have a high disease burden and are prevalent in overlapping low‐ and middle‐income areas. Yet, treatment guidance for people living with HIV/AIDS (PLWH/A) co‐infected with NCC is currently lacking. This study aims to scope the available literature on HIV/AIDS and NCC co‐infection, focusing on epidemiology, clinical characteristics, diagnostics and treatment outcomes.MethodsThe scoping literature review methodological framework, and the Preferred Reporting Items for Systematic Reviews and Meta‐Analyses guidelines were followed. A total of 16,969 records identified through database searching, and 45 additional records from other sources were reduced to 52 included studies after a standardised selection process.ResultsTwo experimental studies, ten observational studies, 23 case series/case reports and 17 reviews or letters were identified. Observational studies demonstrated similar NCC seroprevalence in PLWH/A and their HIV‐negative counterparts. Of 29 PLWH/A and NCC co‐infection, 17 (59%) suffered from epileptic seizures, 15 (52%) from headaches and 15 (52%) had focal neurological deficits. Eighteen (62%) had viable vesicular cysts, and six (21%) had calcified cysts. Fifteen (52%) were treated with albendazole, of which 11 (73%) responded well to treatment. Five individuals potentially demonstrated an immune‐reconstitution inflammatory syndrome after commencing antiretroviral therapy, although this was in the absence of immunological and neuroimaging confirmation.ConclusionsThere is a paucity of evidence to guide treatment of PLWH/A and NCC co‐infection. There is a pressing need for high‐quality studies in this patient group to appropriately inform diagnostic and management guidelines for HIV‐positive patients with NCC.
Spatial distribution of proteins and metabolites in developing wheat grain and their differential regulatory response during the grain filling process
Authors: Zhang Shuang , Ghatak Arindam , Bazargani Mitra Mohammadi , Bajaj Prasad , Varshney Rajeev K. , Chaturvedi Palak , Jiang Dong , Weckwerth Wolfram 
Published: July 2021

SUMMARYGrain filling and grain development are essential biological processes in the plant’s life cycle, eventually contributing to the final seed yield and quality in all cereal crops. Studies of how the different wheat (Triticum aestivum L.) grain components contribute to the overall development of the seed are very scarce. We performed a proteomics and metabolomics analysis in four different developing components of the wheat grain (seed coat, embryo, endosperm, and cavity fluid) to characterize molecular processes during early and late grain development. In‐gel shotgun proteomics analysis at 12, 15, 20, and 26 days after anthesis (DAA) revealed 15 484 identified and quantified proteins, out of which 410 differentially expressed proteins were identified in the seed coat, 815 in the embryo, 372 in the endosperm, and 492 in the cavity fluid. The abundance of selected protein candidates revealed spatially and temporally resolved protein functions associated with development and grain filling. Multiple wheat protein isoforms involved in starch synthesis such as sucrose synthases, starch phosphorylase, granule‐bound and soluble starch synthase, pyruvate phosphate dikinase, 14‐3‐3 proteins as well as sugar precursors undergo a major tissue‐dependent change in abundance during wheat grain development suggesting an intimate interplay of starch biosynthesis control. Different isoforms of the protein disulfide isomerase family as well as glutamine levels, both involved in the glutenin macropolymer pattern, showed distinct spatial and temporal abundance, revealing their specific role as indicators of wheat gluten quality. Proteins binned into the functional category of cell growth/division and protein synthesis/degradation were more abundant in the early stages (12 and 15 DAA). At the metabolome level all tissues and especially the cavity fluid showed highly distinct metabolite profiles. The tissue‐specific data are integrated with biochemical networks to generate a comprehensive map of molecular processes during grain filling and developmental processes.
Genome‐wide analysis of genomic imprinting in the endosperm and allelic variation in flax
Authors: Jiang Haixia , Guo Dongliang , Ye Jiali , Gao Yanfang , Liu Huiqing , Wang Yue , Xue Min , Yan Qingcheng , Chen Jiaxun , Duan Lepeng , Li Gongze , Li Xiao , Xie Liqiong 
Published: July 2021

SummaryGenomic imprinting is an epigenetic phenomenon that causes biased expression of maternally and paternally inherited alleles. In flowering plants, genomic imprinting predominantly occurs in the triploid endosperm and plays a vital role in seed development. In this study, we identified 248 candidate imprinted genes including 114 maternally expressed imprinted genes (MEGs) and 134 paternally expressed imprinted genes (PEGs) in flax (Linum usitatissimum L.) endosperm using deep RNA sequencing. These imprinted genes were neither clustered in specific chromosomal regions nor well conserved among flax and other plant species. MEGs tended to be expressed specifically in the endosperm, whereas the expression of PEGs was not tissue‐specific. Imprinted single nucleotide polymorphisms differentiated 200 flax cultivars into the oil flax, oil‐fiber dual purpose flax and fiber flax subgroups, suggesting that genomic imprinting contributed to intraspecific variation in flax. The nucleotide diversity of imprinted genes in the oil flax subgroup was significantly higher than that in the fiber flax subgroup, indicating that some imprinted genes underwent positive selection during flax domestication from oil flax to fiber flax. Moreover, imprinted genes that underwent positive selection were related to flax functions. Thirteen imprinted genes related to flax seed size and weight were identified using a candidate gene‐based association study. Therefore, our study provides information for further exploration of the function and genomic variation of imprinted genes in the flax population.