bluuebunny/crossref_metadata_2025_split huggingface dataset:
Long coleoptile genotype and soil texture interactions determine establishment success and early growth parameters of wheat sown at depth
Authors: Stummer B E , Flohr B M , Rebetzke G J , Meiklejohn R , Ware A , Haskins B , Whitworth R , McBeath T 
Published: June 2023

Abstract
Long coleoptile (LC) - wheat genotypes sown deeper (> 10 cm) than current practice (< 5 cm) enables earlier deep sowing into subsurface soil moisture. The LC genotype shows promise to broaden sowing windows and remove reliance on the shifting seasonal break for crop establishment. The suitability of this sowing strategy to the highly variable soils of the southern Australian wheatbelt warrants investigation to identify suitable environments for potential establishment benefits. We conducted controlled environment room (CER) and field experiments using pairs of near-isogenic-lines (NILs) that differed genetically only for coleoptile length. The experiments investigated the suitability of deep sown (12 cm) LC wheats in soils with different texture (sand versus loam). The CER experiment identified that LC genotypes exhibited greater emergence and early seedling growth, producing greater shoot and root biomass, when deep sown (12 cm) in loam. While LC and short coleoptile (SC) genotypes produced similar shoot growth when sown at depth in sand, LC produced greater root biomass reflected in more seminal roots. In the field on sand, LC and SC had similar emergence and early shoot growth characteristics at all sowing depths (5, 8 and 10 cm). However, the heavy-textured, loam soil reduced seedling emergence and restricted leaf growth with deep sowing (12 cm) in the SC. Our results indicate that the LC trait was more critical for plant emergence and early growth parameters (shoot and root biomass) from depth in a heavier textured loam compared with a sand. By identifying environments that will likely benefit most from deep sown LC, we are one step closer to adapting crop production to shifting rainfall patterns in southern Australia.
Phenotyping heart failure by cardiac magnetic resonance imaging of cardiac macro- and microscopic structure: state of the art review
Authors: Pan Jiliu , Ng Sher May , Neubauer Stefan , Rider Oliver J 
Published: June 2023

Abstract
Heart failure demographics have evolved in past decades with the development of improved diagnostics, therapies, and prevention. Cardiac magnetic resonance (CMR) has developed in a similar timeframe to become the gold-standard non-invasive imaging modality for characterizing diseases causing heart failure.
CMR techniques to assess cardiac morphology and function have progressed since their first use in the 1980s. Increasingly efficient acquisition protocols generate high spatial and temporal resolution images in less time. This has enabled new methods of characterizing cardiac systolic and diastolic function such as strain analysis, exercise real-time cine imaging and four-dimensional flow.
A key strength of CMR is its ability to non-invasively interrogate the myocardial tissue composition. Gadolinium contrast agents revolutionized non-invasive cardiac imaging with the late gadolinium enhancement technique. Further advances enabled quantitative parametric mapping to increase sensitivity at detecting diffuse pathology. Novel methods such as diffusion tensor imaging and artificial intelligence-enhanced image generation are on the horizon.
Magnetic resonance spectroscopy (MRS) provides a window into the molecular environment of the myocardium. Phosphorus (31P) spectroscopy can inform the status of cardiac energetics in health and disease. Proton (1H) spectroscopy complements this by measuring creatine and intramyocardial lipids. Hyperpolarized carbon (13C) spectroscopy is a novel method that could further our understanding of dynamic cardiac metabolism.
CMR of other organs such as the lungs may add further depth into phenotypes of heart failure. The vast capabilities of CMR should be deployed and interpreted in context of current heart failure challenges.
Using Twitter to Understand COVID-19 Vaccine-Related Ageism During the Pandemic
Authors: Bacsu Juanita-Dawne R , Andrew Melissa K , Azizi Mehrnoosh , Berger Corinne , Cammer Allison , Chasteen Alison L , Fraser Sarah Anne , Grewal Karl S , Green Shoshana , Gowda-Sookochoff Rory , Mah Jasmine Cassy , McGilton Katherine S , Middleton Laura , Nanson Kate , Spiteri Raymond J , Tang Yikai , O’Connell Megan E 
Published: June 2023

AbstractBackground and ObjectivesDuring the rollout of coronavirus 2019 (COVID-19) vaccines, older adults in high-income countries were often prioritized for inoculation in efforts to reduce COVID-19-related mortality. However, this prioritization may have contributed to intergenerational tensions and ageism, particularly with the limited supply of COVID-19 vaccines. This study examines Twitter discourse to understand vaccine-related ageism during the COVID-19 pandemic to inform future vaccination policies and practices to reduce ageism.Research Design and MethodsWe collected 1,369 relevant tweets on Twitter using the Twint application in Python from December 8, 2020, to December 31, 2021. Tweets were analyzed using thematic analysis, and steps were taken to ensure rigor.ResultsOur research identified four main themes including (a) blame and hostility: “It’s all their fault”; (b) incompetence and misinformation: “clueless boomer”; (c) ageist political slander; and (d) combatting ageism: advocacy and accessibility.Discussion and ImplicationsOur findings exposed issues of victim-blaming, hate speech, pejorative content, and ageist political slander that is deepening the divide of intergenerational conflict. Although a subset of tweets countered negative outcomes and demonstrated intergenerational solidarity, our findings suggest that ageism may have contributed to COVID-19 vaccine hesitancy among older adults. Consequently, urgent action is needed to counter vaccine misinformation, prohibit aggressive messaging, and promote intergenerational unity during the COVID-19 pandemic and beyond.
Malaysian conceptions of international order: paradoxes of small-state pragmatism
Authors: Kuik Cheng-Chwee 
Published: June 2023

Abstract
Why do weaker states perceive the liberal international order (LIO) with ambivalence? This article argues that in the case of small states like Malaysia, historical memories, structural realities and domestic imperatives combine to explain their conceptions of and responses to the LIO. The article traces the features and unpacks the factors underpinning the paradoxes of small-state pragmatism vis-à-vis international order: a) rejecting power hierarchy but recognizing (and leveraging) power asymmetry; b) acknowledging its smallness but actively punching above its weight whenever possible; and c) promoting co-existence through principled contradictions. Such paradoxical pragmatism is quintessentially an act of hedging aimed at mitigating and off-setting multiple risks amid increasing uncertainties. This article makes three contributions. First, it contributes to the literature on international order by presenting a small-state perspective on the LIO, highlighting that small-state responses are more about ‘struggle for survival’, rather than ‘struggle for power’. Second, the notion of ‘paradoxical pragmatism’ engages the ongoing debate on ‘hedging’ in international relations. Third, the article's findings suggest that, theoretically, hedging and its dualistic elements are attributable to both structural and domestic-level factors. While structural conditions drive states to hedge, domestic factors determine the extent and manner in which states hedge.
Using science to respond to public exposures from chemical hazards during emergencies in England
Authors: Urquhart Graham J , Symington Matthew , Foxall Kerry , Harrison Henrietta , Sepai Ovnair 
Published: June 2023

Abstract
This paper describes how toxicological considerations are an essential component of acute chemical incident response, and how the UK Health Security Agency (UKHSA), as Category 1 responders under the Civil Contingencies Act (2004), provide that expert, authoritative, and timely advice to protect people from exposure to harmful substances. Background information about the general response to emergencies is provided, which gives context to how scientific advice has a positive impact. The importance of chemical identification and speciation, local, and systemic effects, and exposure characteristics are described. The public health risk assessment is considered in conjunction with mixtures, mass casualties, recovery, and psychological impacts. A brief summary of the type of incidents that the UKHSA are notified about is also provided.
Is Damage Control Surgery Better than Traditional Surgery in Multiple Trauma: A Meta Analysis
Authors: Zeng Siyao , Ma Lei , Yang Lishan , Hu Xiaodong , Guo Xinxin , Li Yi , Zhang Yao , Lei Jing , Ma Like , Ma Xia , Luo Qingpeng 
Published: June 2023

ABSTRACT

Background:
The concept of damage control surgery (DCS) has been proposed and used for many years. In this study, we investigated whether the DCS is more effective than traditional surgery (TS) for treating multiple traumas.

Methods:
After formulating the retrieval strategy, we searched 12 databases and two clinical trial centers. Data from eligible studies were included and extracted based on the inclusion and exclusion criteria. To analyze the results, we used the risk ratio (RR), weighted mean difference (WMD), and 95% confidence interval (95% CI). The Cochrane Collaboration tool was used to assess the risk of bias in all the included studies. RevMan (version 5.3) and Stata (version 14 and 17) were used for data analysis.

Results:
First, the mortality rate of DCS group was reduced (RR = 0.27, 95% CI: 0.22 to 0.34, P < 0.001), and the success rate of rescue was improved (RR = 1.36, 95% CI: 1.29 to 1.44, P < 0.001). Second, the DCS group had shorter in-hospital length of stay (WMD = −5.58, 95% CI: −6.83 to −4.32, P < 0.001) and intensive care unit (ICU) length of stay (WMD = −3.54, 95% CI: −4.57 to −2.51, P < 0.001), and significantly reduced the incidence of complications (RR = 0.36, 95% CI: 0.31 to 0.43, P < 0.001), especially disseminated intravascular coagulation (DIC) (RR = 0.27, 95% CI: 0.20 to 0.36, P < 0.001), multiple organ dysfunction syndrome (MODS) (RR = 0.44, 95% CI: 0.31 to 0.61, P < 0.001), and shock (RR = 0.38, 95% CI: 0.25 to 0.56, P < 0.001). Then, the recovery time of body temperature (WMD = −7.68, 95% CI: −9.39 to −5.97, P < 0.001), clearance time of lactic acid (WMD = −17.58, 95% CI: −21.05 to −14.12, P < 0.001), the recovery time of prothrombin time (PT) (WMD = −11.79, 95% CI: −13.67 to −9.91, P < 0.001), activated partial thromboplastin time (APTT) (WMD = −12.69, 95% CI: −14.53 to −10.85, P < 0.001) and base excess (BE) (WMD = −16.07, 95% CI: −16.58 to −15.55, P < 0.001) of DCS group decreased. Finally, the DCS group showed reduced intraoperative blood loss (WMD = −421.53, 95% CI: −494.44 to −348.62, P < 0.001), operation time (WMD = −24.65, 95% CI: −35.50 to −13.80, P = 0.007), and red blood cell transfusion volume (WMD = −5.95, 95% CI: −7.01 to −4.89, P < 0.001).

Conclusion:
Our research shows that for patients who have suffered multiple trauma, DCS is more efficient than TS for patients who have experienced multiple traumas. In the future, more detailed, large-scale, multicenter, randomized controlled trials are required to verify our findings.
Defined synthetic microbial communities colonize and benefit field-grown sorghum
Authors: Fonseca-García Citlali , Wilson Andrew , Elmore Joshua , Pettinga Dean , McClure Ryan , Atim Jackie , Pedraza Julie , Hutmacher Robert , Egbert Robert , Coleman-Derr Devin 
Published: June 2023

ABSTRACTThe rhizosphere represents a dynamic and complex interface between plant hosts and the microbial community found in the surrounding soil. While it is recognized that manipulating the rhizosphere has the potential to improve plant fitness and health, engineering the rhizosphere microbiome through inoculation has often proved challenging. This is in large part due to the competitive microbial ecosystem in which the added microbes must survive, and lack of adaptation of these added microbes to the specific metabolic and environmental pressures of the rhizosphere. Here, we constructed an inoculation formula using a defined synthetic community (dSynCom) approach that we hypothesized would improve engraftment efficiency and potentially the relationship with the host plant,Sorghum bicolor. The dSynCom was assembled from bacterial isolates that were either: 1) identified to potentially play a role in community cohesion through network analysis, or 2) identified to benefit from host-specific exudate compounds. Growth of the dSynCom was first evaluatedin vitroon solid media, secondlyin plantaunder gnotobiotic laboratory conditions, and finally using sorghum plants grown in the field. We demonstrate that the dSynCom performs best in terms of maintaining diversity when grown in the presence of the plant host in lab conditions, and that many lineages are lost from the community when grown eitherin vitroor in a native field setting. Finally, we demonstrate that the dSynCom is able to promote growth of above- and below-ground plant phenotypes compared to uninoculated controls, both in the lab and when applied to plants grown in the field. These results demonstrate the potential utility of SynComs for supporting crop performance even in the absence of persistence, and the need for a deeper mechanistic understanding of community control of host fitness in agricultural contexts.
Alterations in RNA editing in skeletal muscle following exercise training in individuals with Parkinson’s disease
Authors: Mercer Heather Milliken , Nair Aiswarya Mukundan , Ridgel Angela , Piontkivska Helen 
Published: June 2023

AbstractParkinson’s Disease (PD) is the second most common neurodegenerative disease behind Alzheimer’s Disease, currently affecting more than 10 million people worldwide and 1.5 times more males than females. The progression of PD results in the loss of function due to neurodegeneration and neuroinflammation. The etiology of PD is multifactorial, including both genetic and environmental origins. Here we explored changes in RNA editing, specifically editing through the actions of the Adenosine Deaminases Acting on RNA (ADARs), in the progression of PD. Analysis of ADAR editing of skeletal muscle transcriptomes from PD patients and controls, including those that engaged in a rehabilitative exercise training program revealed significant differences in ADAR editing patterns based on age, disease status, and following rehabilitative exercise. Further, deleterious editing events in protein coding regions were identified in multiple genes with known associations to PD pathogenesis. Our findings of differential ADAR editing complement findings of changes in transcriptional network identified by a recent Lavin et al. (2020) study and offer insights into dynamic ADAR editing changes associated with PD pathogenesis.
A Bayesian approach to Mendelian randomization using summary statistics in the univariable and multivariable settings with correlated pleiotropy
Authors: Grant Andrew J. , Burgess Stephen 
Published: June 2023

AbstractMendelian randomization uses genetic variants as instrumental variables to make causal inferences on the effect of an exposure on an outcome. Due to the recent abundance of high-powered genome-wide association studies, many putative causal exposures of interest have large numbers of independent genetic variants with which they associate, each representing a potential instrument for use in a Mendelian randomization analysis. Such polygenic analyses increase the power of the study design to detect causal effects, however they also increase the potential for bias due to instrument invalidity. Recent attention has been given to dealing with bias caused by correlated pleiotropy, which results from violation of the Instrument Strength independent of Direct Effect assumption. Although methods have been proposed which can account for this bias, a number of restrictive conditions remain in many commonly used techniques. In this paper, we propose a novel Bayesian framework for Mendelian randomization which provides valid causal inference under very general settings. We propose the methods MR-Horse and MVMR-Horse, which can be performed without access to individual-level data, using only summary statistics of the type commonly published by genome-wide association studies, and can account for both correlated and uncorrelated pleiotropy. In simulation studies, we show that the approach retains type I error rates below nominal levels even in high pleiotropy scenarios. We consider an applied example looking at the causal relationship between combinations of four exposures (LDL-cholesterol, triglycerides, fasting glucose and birth weight) and three outcomes (coronary artery disease, type 2 diabetes and asthma).
Coherent feedback leads to robust background compensation in oscillatory and non-oscillatory homeostats
Authors: Nygård Melissa , Ruoff Peter 
Published: June 2023

AbstractWhen in an integral feedback controller a step perturbation is applied at a constant background, the controlled variable (described here asA) will in general respond with decreased response amplitudes ΔAas backgrounds increase. The controller variableEwill at the same time provide the necessary compensatory flux to moveAback to its set-point. A typical example of decreased response amplitudes at increased backgrounds is found in retinal light adaptation. Due to remarks in the literature that retinal light adaptation would also involve a compensation of backgrounds we became interested in conditions how background compensation could occur. In this paper we describe how background influences can be robustly eliminated. When such a background compensation is active, oscillatory controllers will respond to a defined perturbation with always the same (damped or undamped) frequency profile, or in the non-oscillatory case, with the same response amplitude ΔA, irrespective of the background level. To achieve background compensation we found that two conditions need to apply: (i) an additional set of integral controllers (here described asI1andI2) have to be employed to keep the manipulated variableEat a defined set-point, and (ii),I1andI2need to feed back to theA-Esignaling axis directly through the controlled variableA. In analogy to a similar feedback applied in quantum control theory, we term these feedback conditions as ‘coherent feedback’. When analyzing retinal light adaptations in more detail, we find no evidence in the presence of background compensation mechanisms. Although robust background compensation, as described theoretically here, appears to be an interesting regulatory property, relevant biological or biochemical examples still need to be identified.
pOPARA: Vectors for Golden Gate assembly of expression constructs containing the araBAD promoter
Authors: Milnes Lesley , Youles Mark , Maidment Josephine H. R. 
Published: June 2023

AbstractHeterologous protein production is often required to investigate the structural, biochemical, and biophysical properties of a protein of interest. Frequently, optimisation of expression conditions is required to obtain soluble protein and maximise yield. Trialling a variety of solubility and purification tags, as well as constructs containing different regulatory elements, is desirable. Golden Gate cloning allows modular assembly of different constructs using Type IIS restriction enzymes. The pOPIN vector suite, which utilises the T7 expression system, has been adapted to be compatible with Golden Gate assembly. Here, we present the pOPARA vectors. Expression from pOPARA vectors is driven by the araBAD promoter (pBAD) and is induced by addition of arabinose to the culture medium. pOPARA allows modular assembly of expression constructs using Golden Gate cloning with the CDS of interest and an optional C-terminal tag. pOPARA1 contains a carbenicillin resistance cassette flanked by restriction sites to allow exchange of the selectable markers. In pOPARA2, the carbenicillin resistance cassette has been exchanged for a spectinomycin resistance cassette. We demonstrate that both vectors can be used to express and produce a control protein.
Metagenomic Profiles of Archaea and Bacteria within Thermal and Geochemical Gradients of the Guaymas Basin Deep Subsurface
Authors: Geller-McGrath David , Mara Paraskevi , Edgcomb Virginia , Beaudoin David , Morono Yuki , Teske Andreas 
Published: June 2023

AbstractWhile the temperature gradients of Earth’s crust and sediments are thought to delineate the downward extent and ultimate limits of the subsurface biosphere, the actual course of consecutively changing microbial communities and activities, from cool surficial sediments towards the deep, hot biosphere, remains to be charted. We used metagenomic and metatranscriptomic analyses of the hydrothermally heated, massive sediment layers of Guaymas Basin (Gulf of California, Mexico) to examine the environmental distribution and activity patterns of bacteria and archaea along thermal, geochemical and cell count gradients. Composition and distribution of MAGs, dominated by Chloroflexota and Thermoproteota, were shaped by biogeochemical parameters as long as temperatures remained moderate, but downcore increasing temperatures overrode other factors beyond ca. 45°C. Consistently, MAG genome size and diversity decreased with increasing temperature, indicating a conspicuous downcore winnowing of the subsurface biosphere. In contrast, specific archaeal MAGs within the Thermoproteota and Hadarchaeota increased in relative abundance and in recruitment of transcriptome reads towards deeper, hotter sediments, and mark the transition towards a distinct deep, hot biosphere.
Integrative Multiscale Biochemical Mapping of the Brain via Deep-Learning-Enhanced High-Throughput Mass Spectrometry
Authors: Xie Yuxuan Richard , Castro Daniel C. , Rubakhin Stanislav S. , Trinklein Timothy J. , Sweedler Jonathan V. , Lam Fan 
Published: June 2023

AbstractElucidating the spatial-biochemical organization of the brain across different scales produces invaluable insight into the molecular intricacy of the brain. While mass spectrometry imaging (MSI) provides spatial localization of compounds, comprehensive chemical profiling at a brain-wide scale in three dimensions by MSI with single-cell resolution has not been achieved. We demonstrate complementary brain-wide and single-cell biochemical mapping via MEISTER, an integrative experimental and computational mass spectrometry framework. MEISTER integrates a deep-learning-based reconstruction that accelerates high-mass-resolving MS by 15-fold, multimodal registration creating 3D molecular distributions, and a data integration method fitting cell-specific mass spectra to 3D data sets. We imaged detailed lipid profiles in tissues with data sets containing millions of pixels, and in large single-cell populations acquired from the rat brain. We identified region-specific lipid contents, and cell-specific localizations of lipids depending on both cell subpopulations and anatomical origins of the cells. Our workflow establishes a blueprint for future developments of multiscale technologies for biochemical characterization of the brain.