bluuebunny/crossref_metadata_2025 huggingface dataset:
A new approach to the design of surface subsystems of polymeric insulators for HV and MV apparatus under AC voltage
Authors: Montanari Gian Carlo , Nath Debasish , Cambareri Pasquale
Published: June 2023

The design of high voltage and medium voltage AC and DC standoff insulators, and, in general, of insulation systems where surface and interface properties are predominant factors, is based on specifications and standards that rely upon long‐term experiences and lab testing. Surface insulating properties depend on electrical and thermal stresses, besides environmental factors, and the inception of extrinsic ageing phenomena, such as partial discharges, can be already a cause of reduced reliability and premature failure (for organic insulating materials). An innovative approach, based on field simulation, discharge modelling, and partial discharge inception measurements is presented by the authors, which can establish a solid basis to optimise insulation design for any type of supply voltage waveform. This method, the three‐leg approach, is applied here to a cable system under AC sinusoidal voltage, but it can work for any type of insulation system, such as bushings, switch gears, transformers, rotating machines, and power electronics boards.
Dynamic optimal power flow for multi‐operator renewable energy‐based virtual power plants
Authors: Basu Mousumi , Jena Chitralekha , Khan Baseem
Published: June 2023

Recently, infiltration of distributed energy resources (DERs) is augmented considerably to upsurge network flexibility, better economic indicator, and reduced power loss. But integration of different DERs may cause challenges in power grid. To overwhelmed these challenges and obtain maximum advantage of DERs, virtual power plant's concept has been emerged. Virtual power plants (VPPs) has the capacity to partake in electricity market and rivalry of VPPs to achieve more profit, deregulated multi‐operator markets are developed. This paper suggests dynamic optimum power flow (DOPF) for multi‐operator VPPs considering demand side management (DSM) and uncertainty of renewable energy sources. VPPs with different proprietorships are interconnected with each other by tie lines. Each VPP has small hydro power plants (SHPPs), solar PV plants (SPVPs), wind turbine generators (WTGs), bioenergy power plant (BPPs), and plug‐in electric vehicles (PEVs). VPP 1 comprises IEEE 33‐bus system, VPP 2 comprises 15‐bus system, and VPP 3 comprises IEEE 69‐bus system. Bottlenose dolphin optimizer (BDO), HPSO‐TVAC, and GWO have been applied to solve DOPF problem and maximize the net profit of multi‐operator VPPs.
Influence of non‐ideal line‐reflect‐match calibration standards on vector network analyzer S‐parameter measurements
Authors: Zhao Wei , Cheng Chunyue , Yang Chao , Xiao Jiankang , Wang Yibang , Huo Ye
Published: June 2023

In this paper, an improved two‐step method is presented for the sensitivity analysis of vector network analyzer (VNA) S‐parameter measurements due to the non‐ideal line‐reflect‐match (LRM) calibration standards. This improved method is based on the indirect uncertainty propagation mechanism, which is especially suitable for the S‐parameter measurements applying the self‐calibration technique. To further simplify the formula derivation, the deviation matrices [δA] and [δB] are newly defined to represent the uncertainties of the T‐matrices of error boxes. With this definition, formulas for the deviations of device under test (DUT) S‐parameters can be concluded as functions of [δA] and [δB] in a concise form. Eventually, by solving only three linear combinations of the elements from [δA] and [δB], the sensitivity coefficients of DUT S‐parameters due to non‐ideal LRM can be conveniently deduced in an analytical form. Finally, experiments are performed to verify the proposed method.
Financing the orderly transition to a low carbon economy in the EU: the regulatory framework for the banking channel
Authors: Nieto María J. , Papathanassiou Chryssa
Published: June 2023

Among the largest economies of the world, the EU not only has set the most ambitious and legally binding objectives for the reduction of the GHG emissions but also it has accompanied these objectives with a “state of the art” regulatory framework in the realms of investor protection and safety and soundness. Our paper focuses on the bank financing channel and highlights regulatory areas for improvement. To mobilize the necessary funds worldwide, a degree of interoperability of regional taxonomies is required, which calls for international cross-pollination and coordination to mitigate financial risks and the risk of harmful market fragmentation (BCBS 2022, FSB 2022). Also, the full interoperability between the international and the EU corporate reporting standards is a desirable objective. A building bloc methodological approach would make such interoperability easier having the sustainability impact perspective of the “double materiality objective” as an additional layer of the international requirements well understood to all investors in EU undertakings. As per the inclusion of climate risks in prudential regulation, it is completed for Pillar 3 disclosures relating effectively with the EU Taxonomy. Climate risk’s long-term horizon still needs to be implemented in Pillar 2 by linking bank transition plans with stress testing based on climate risk scenario analysis covering both transition and physical risk. The inclusion of climate risks in Pillar 1 faces challenges similar to those of supervisors internationally. Fostering global ambition is an explicit objective of the EU. Its leadership on the realms of investor protection and prudential regulation of climate risks should ideally inform international cooperation and impregnate international standards. This will secure that investments for the fulfillment of the EU climate objectives will flow from in and outside the EU.
The assessment of the quality of campus public spaces as key parts of the learning landscape: experience from a crowdsensing study on the Third Campus of Jagiellonian University, Krakow, Poland
Authors: Działek Jarosław , Homiński Bartłomiej , Miśkowiec Magdalena , Świgost-Kapocsi Agnieszka , Gwosdz Krzysztof
Published: June 2023

The learning landscape concept reflects shifts in the methods of learning and conducting research in universities. Public spaces within university campuses should constitute an essential component of the learning landscape as arenas of planned and serendipitous encounters, which may foster creativity and trans-disciplinary networking. However, their spatial configurations remain an under-researched topic. This paper assesses the quality of public spaces on campus based on the results of a crowdsensing survey. The Third Campus of Jagiellonian University in Krakow was selected as a case study; this is one of the largest projects of this kind carried out in Poland since the political and economic transformation of 1989. The behaviour of users provides evidence of the generally low quality of the public spaces despite the advantages of the urban layout of the campus. The paper proposes recommendations that may bring the spatial organisation of the campus closer to a fully fledged learning landscape.
Wicked problems in a post-truth political economy: a dilemma for knowledge translation
Authors: Tieu Matthew , Lawless Michael , Hunter Sarah C. , Pinero de Plaza Maria Alejandra , Darko Francis , Mudd Alexandra , Yadav Lalit , Kitson Alison
Published: June 2023

The discipline of knowledge translation (KT) emerged as a way of systematically understanding and addressing the challenges of applying health and medical research in practice. In light of ongoing and emerging critique of KT from the medical humanities and social sciences disciplines, KT researchers have become increasingly aware of the complexity of the translational process, particularly the significance of culture, tradition and values in how scientific evidence is understood and received, and thus increasingly receptive to pluralistic notions of knowledge. Hence, there is now an emerging view of KT as a highly complex, dynamic, and integrated sociological phenomenon, which neither assumes nor creates knowledge hierarchies and neither prescribes nor privileges scientific evidence. Such a view, however, does not guarantee that scientific evidence will be applied in practice and thus poses a significant dilemma for KT regarding its status as a scientific and practice-oriented discipline, particularly within the current sociopolitical climate. Therefore, in response to the ongoing and emerging critique of KT, we argue that KT must provide scope for relevant scientific evidence to occupy an appropriate position of epistemic primacy in public discourse. Such a view is not intended to uphold the privileged status of science nor affirm the “scientific logos” per se. It is proffered as a counterbalance to powerful social, cultural, political and market forces that are able to challenge scientific evidence and promote disinformation to the detriment of democratic outcomes and the public good.
Development of an atmospheric fluorocarbon plasma jet generated by pulse modulated microwave discharge
Authors: CHEN Sile , REN Xinliu , CHEN Zhaoquan , XU Xiaojuan , CHENG Tao , LI Ping , ZHANG Guanjun , LU Xinpei
Published: June 2023

Atmospheric fluorocarbon plasma plays an important role in the surface modification of insulating materials like polymers. The existing fluorocarbon plasma is usually generated by dielectric barrier discharge, which has a low concentration of reactive species and may cause insufficient surface fluorination. This work attempts to develop an atmospheric fluorocarbon plasma jet using a coaxial transmission line resonator by microwave discharge with locally enhanced electric field and high density. The gas temperature is reduced by pulse modulation technology. Three kinds of working gases, pure CF4, Ar/CF4 and He/CF4, are utilized to generate the atmospheric microwave fluorocarbon plasma jet. The discharge images, optical emission spectra, electron densities and gas temperatures are studied experimentally. The results show that the Ar/CF4 plasma jet has the best comprehensive performance, such as strong discharge intensity and controllable gas temperature. The electron density of the Ar/CF4 plasma jet has a magnitude of 1020 m−3, indicating a higher density than that of the frequently used dielectric barrier discharge. With the other conditions unchanged, the gas temperature at the end of the Ar/CF4 plasma jet can be reduced from 410.2 to 347.3 K by decreasing the duty cycle of the modulated pulse from 0.5 to 0.1. Thence, the microwave Ar/CF4 plasma jet is considered to be a promising fluorocarbon plasma source for surface fluorination of polymers.
Ionization wave propagation and cathode sheath formation due to surface dielectric-barrier discharge sustained in pulsed mode
Authors: GIOTIS Konstantinos , SVARNAS Panagiotis , AMANATIDES Eleftherios , GAZELI Kristaq , LOMBARDI Guillaume , PAPADOPOULOS Polykarpos K
Published: June 2023

This work deals with the experimental study of a surface dielectric-barrier discharge, as a part of the ongoing interest in the control of plasma induced electro-fluid dynamic effects (e.g. plasma actuators). The discharge is generated using a plasma reactor consisting of a fused silica plate which is sandwiched between two printed circuit boards where the electrodes are developed. The reactor is driven by narrow high voltage square pulses of asymmetric rising (25 ns) and falling (2.5 μs) parts, while the discharge evolution is considered in a temporarily and spatially resolved manner over these pulses. That is, conventional electrical and optical emission analyzes are combined with high resolution optical emission spectroscopy and ns-resolved imaging, unveiling main characteristics of the discharge with a special focus on its propagation along the dielectric-barrier surface. The voltage rising part leads to cathode-directed ionization waves, which propagate with a speed up to 105 m s−1. The voltage falling part leads to cathode sheath formation on the driven electrode. Τhe polarization of the dielectric barrier appears critical for the discharge dynamics.
Enhanced surface-insulating performance of EP composites by doping plasma-fluorinated ZnO nanofiller
Authors: DUAN Qijun , SONG Yanze , SHAO Shuai , YIN Guohua , RUAN Haoou , XIE Qing
Published: June 2023

The surface flashover of epoxy resin (EP) composites is a pivotal problem in the field of high-voltage insulation. The regulation of the interface between the filler and matrix is an effective means to suppress flashover. In this work, nano ZnO was fluorinated and grafted using low-temperature plasma technology, and the fluorinated filler was doped into EP to study the DC surface flashover performance of the composite. The results show that plasma fluorination can effectively inhibit the agglomeration by grafting –CF
x
groups onto the surface of nano-ZnO particles. The fluorine-containing groups at the interface provide higher charge binding traps and enhance the insulation strength at the interface. At the same time, the interface bond cooperation caused by plasma treatment also promoted the accelerating effect of nano ZnO on charge dissipation. The two effects synergistically improve the surface flashover performance of epoxy composites. When the concentration of fluorinated ZnO filler is 20%, the flashover voltage has the highest increase, which is 31.52% higher than that of pure EP. In addition, fluorinated ZnO can effectively reduce the dielectric constant and dielectric loss of epoxy composites. The interface interaction mechanism was further analyzed using molecular dynamics simulation and density functional theory simulation.
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

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

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

Background and Objectives

During 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 Methods

We 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.

Results

Our 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 Implications

Our 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

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

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

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.
Direct-print three-dimensional electrodes for large-scale, high-density, and customizable neural interfaces
Authors: Wang Pingyu , Wu Eric G. , Uluşan Hasan , Phillips A.J. , Hays Madeline Rose , Kling Alexandra , Zhao Eric T. , Madugula Sasidhar , Vilkhu Ramandeep S. , Vasireddy Praful Krishna , Hierlemann Andreas , Hong Guosong , Chichilnisky E.J. , Melosh Nicholas A.
Published: June 2023

Silicon-based planar microelectronics is a powerful tool for scalably recording and modulating neural activity at high spatiotemporal resolution, but it remains challenging to target neural structures in three dimensions (3D). We present a method for directly fabricating 3D arrays of tissue-penetrating microelectrodes onto silicon microelectronics. Leveraging a high-resolution 3D printing technology based on 2-photon polymerization and scalable microfabrication processes, we fabricated arrays of 6,600 microelectrodes 10-130 µm tall and at 35-μm pitch onto a planar silicon-based microelectrode array. The process enables customizable electrode shape, height and positioning for precise targeting of neuron populations distributed in 3D. As a proof of concept, we addressed the challenge of specifically targeting retinal ganglion cell (RGC) somas when interfacing with the retina. The array was customized for insertion into the retina and recording from somas while avoiding the axon layer. We verified locations of the microelectrodes with confocal microscopy and recorded high-resolution spontaneous RGC activity at cellular resolution. This revealed strong somatic and dendritic components with little axon contribution, unlike recordings with planar microelectrode arrays. The technology could be a versatile solution for interfacing silicon microelectronics with neural structures and modulating neural activity at large scale with single-cell resolution.
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

The 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

Parkinson’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

Mendelian 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

When 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

Heterologous 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

While 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

Elucidating 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.
A Microfluidic Transistor for Liquid Signal Processing
Authors: Gopinathan Kaustav A. , Mishra Avanish , Mutlu Baris R. , Edd Jon F. , Toner Mehmet
Published: June 2023

Abstract/Summary

Microfluidics have enabled significant advances in molecular biology1–3, synthetic chemistry4,5, diagnostics6,7, and tissue engineering8. However, there has long been a critical need in the field to manipulate fluids and suspended matter with the precision, modularity, and scalability of electronic circuits9–11. Just as the electronic transistor enabled unprecedented advances in the control of electricity on an electronic chip, a microfluidic analogue to the transistor could enable improvements in the complex, scalable control of reagents, droplets, and single cells on an autonomous microfluidic chip. Prior works on creating a microfluidic analogue to the electronic transistor12–14could not replicate the transistor’s saturation behavior, which is crucial to perform analog amplification15and is fundamental to modern circuit design16. Here we exploit the fluidic phenomenon offlow-limitation17to develop a microfluidic element with flow-pressure characteristics completely analogous to the current-voltage characteristics of the electronic transistor. As this microfluidic transistor successfully replicates all of the key operating regimes of the electronic transistor (linear, cut-off and saturation), we are able to directly translate a variety of fundamental electronic circuit designs into the fluidic domain, including the amplifier, regulator, level shifter, logic gate, and latch. Finally, we demonstrate a “smart” particle dispenser that senses single suspended particles, performs liquid signal processing, and accordingly controls the movement of said particles in a purely fluidic system without electronics. By leveraging the vast repertoire of electronic circuit design, microfluidic transistor-based circuits are easy to integrate at scale, eliminate the need for external flow control, and enable uniquely complex liquid signal processing and single-particle manipulation for the next generation of chemical, biological, and clinical platforms.
Enhancing gene co-expression network inference for the malaria parasitePlasmodium falciparum
Authors: Li Qi , Button-Simons Katrina A , Sievert Mackenzie AC , Chahoud Elias , Foster Gabriel F , Meis Kaitlynn , Ferdig Michael T , Milenković Tijana
Published: June 2023

Background

Malaria results in more than 550,000 deaths each year due to drug resistance in the most lethalPlasmodium(P.) speciesP. falciparum. A fullP. falciparumgenome was published in 2002, yet 44.6% of its genes have unknown functions. Improving functional annotation of genes is important for identifying drug targets and understanding the evolution of drug resistance.

Results

Genes function by interacting with one another. So, analyzing gene co-expression networks can enhance functional annotations and prioritize genes for wet lab validation. Earlier efforts to build gene co-expression networks inP. falciparumhave been limited to a single network inference method or gaining biological understanding for only a single gene and its interacting partners. Here, we explore multiple inference methods and aim to systematically predict functional annotations for allP. falciparumgenes. We evaluate each inferred network based on how well it predicts existing gene-Gene Ontology (GO) term annotations using network clustering and leave-one-out cross-validation. We assess overlaps of the different networks’ edges (gene co-expression relationships) as well as predicted functional knowledge. The networks’ edges are overall complementary: 47%-85% of all edges are unique to each network. In terms of accuracy of predicting gene functional annotations, all networks yield relatively high precision (as high as 87% for the network inferred using mutual information), but the highest recall reached is below 15%. All networks having low recall means that none of them capture a large amount of all existing gene-GO term annotations. In fact, their annotation predictions are highly complementary, with the largest pairwise overlap of only 27%. We provide ranked lists of inferred gene-gene interactions and predicted gene-GO term annotations for future use and wet lab validation by the malaria community.

Conclusions

The different networks seem to capture different aspects of theP. falciparumbiology in terms of both inferred interactions and predicted gene functional annotations. Thus, relying on a single network inference method should be avoided when possible.

Supplementary data

Attached.

Availability and implementation

All data and code are available athttps://nd.edu/~cone/pfalGCEN/.

Contact

tmilenko@nd.edu
Interactions Between the Histone Variant H2Av and the Suppressor of Hairy wing Insulator Influence the DNA Damage Response and Lymph Gland Development inDrosophila
Authors: Simmons James Ryan , Kemp Justin D. J. , Labrador Mariano
Published: June 2023

Genome architecture is regulated by chromatin insulator proteins, and misregulation of insulator function is associated with genome instability and transcriptional regulatory defects in both vertebrates andDrosophila. Indeed, mutations of the sole insulator protein in humans, CTCF, are carcinogenic and mutations in theDrosophilainsulator proteinSuppressor of Hairy wing[Su(Hw)] lead to chromosomal rearrangements. However, the mechanism that links the DNA damage response and the regulation of transcription with insulator function is not yet understood. Here we show that enrichment of Su(Hw) insulator proteins at insulator sites increases after DNA damage. Additionally, Su(Hw) is necessary for phosphorylation of the histone variant H2Av in response to both UV treatment and X-ray irradiation. The requirement of Su(Hw) for H2Av phosphorylation appears to be tissue-specific, since H2Av is phosphorylated in response to DNA damage also in neurons, where Su(Hw) is not normally expressed. Similarly, we provide evidence that Su(Hw) and H2Av work together to ensure proper development of the lymph gland inDrosophilalarvae. We show that H2Av regulates formation of the larval lymph gland, and mutation of H2Av causes formation of large melanotic tumors that are rescued by mutation ofsu(Hw)in theHis2Av810mutant background. Double mutants ofsu(Hw)-andHis2Av810also form supernumerary lymph gland lobes that are larger than in wild type. Our findings support a role for the Su(Hw) in the DNA damage response through the regulation of H2Av phosphorylation and suggest that Su(Hw) and H2Av also work together to ensure proper development of the lymph gland.
WITHDRAWN: Prevalence of coronary artery disease among COVID-19 patients: a systematic review and meta-analysis
Authors: Akhtar Naushaba , Padhi Bijaya Kumar , Shamim Muhammad Aaqib , Gandhi Nandhni Chiruganam , Satapathy Prakisini , Pati Sanghamitra , Nowrouzi-Kia Behdin , Chattu Vijay Kumar
Published: June 2023

Withdrawal Statement

The authors have withdrawn their manuscript owing to a complete change in methods and results. Therefore, the authors do not wish this work to be cited as reference for the project. If you have any questions, please contact the first author.
A novel family of sugar-specific phosphodiesterases that remove zwitterionic modifications ofN-acetylglucosamine
Authors: Fossa Samantha L. , Anton Brian P. , Kneller Daniel W. , Petralia Laudine M.C. , Boisvert Madison L. , Ganatra Mehul B. , Vainauskas Saulius , Chan S. Hong , Hokke Cornelis H. , Foster Jeremy M. , Taron Christopher H.
Published: June 2023

The zwitterions phosphorylcholine (PC) and phosphoethanolamine (PE) are often found esterified to certain sugars in polysaccharides and glycoconjugates in a wide range of biological species. One such modification involves PC attachment to the 6-carbon ofN-acetylglucosamine (GlcNAc-6-PC) in N-glycans and glycosphingolipids (GSLs) of parasitic nematodes, a modification that helps the parasite evade host immunity. Knowledge of enzymes involved in the synthesis and degradation of PC and PE modifications is limited. More detailed studies on such enzymes would contribute to a better understanding of the function of PC modifications and have potential application in the structural analysis of zwitterion-modified glycans. In this study, we used functional metagenomic screening to identify phosphodiesterases encoded in a human fecal DNA fosmid library that remove PC from GlcNAc-6-PC. A novel bacterial phosphodiesterase was identified and biochemically characterized. This enzyme (termed GlcNAc-PDase) shows remarkable substrate preference for GlcNAc-6-PC and GlcNAc-6-PE, with little or no activity on other zwitterion-modified hexoses. The identified GlcNAc-PDase protein sequence is a member of the large endonuclease/exonuclease/phosphatase (EEP) superfamily where it defines a distinct subfamily of related sequences of previously unknown function, mostly fromClostridiumbacteria species. Finally, we demonstrate use of GlcNAc-PDase to confirm the presence of GlcNAc-6-PC in N-glycans and GSLs of the parasitic nematodeBrugia malayiin a glycoanalytical workflow.