bluuebunny/crossref_metadata_2025_split huggingface dataset:
The genome of Gynandropsis gynandra provides insights into whole-genome duplications and the evolution of C4 photosynthesis in Cleomaceae
Authors: Hoang Nam V. , Sogbohossou E. O. Deedi , Xiong Wei , Simpson Conor J. C. , Singh Pallavi , van den Bergh Erik , Zhu Xin-Guang , Brautigam Andrea , Weber Andreas P. M. , van Haarst Jan C. , Schijlen Elio G. W. M. , Hendre Prasad S. , Deynze Allen Van , Achigan-Dako Enoch G. , Hibberd Julian M. , Schranz M. Eric 
Published: July 2022

ABSTRACTGynandropsis gynandra (Cleomaceae) is a cosmopolitan leafy vegetable and medicinal plant, which has also been used as a model to study C4 photosynthesis due to its evolutionary proximity to Arabidopsis. Here, we present a high-quality genome sequence of G. gynandra, anchored onto 17 main super- scaffolds with a total length of 740 Mb, an N50 of 42 Mb and 30,933 well-supported gene models. The G. gynandra genome and previously released genomes of C3 relatives in the Cleomaceae and Brassicaceae make an excellent model for studying the role of genome evolution in the transition from C3 to C4 photosynthesis. We revealed that G. gynandra and its C3 relative Tarenaya hassleriana shared a whole-genome duplication event (Gg-α), then an addition of a third genome (Th-α, +1x) took place in T. hassleriana but not in G. gynandra. Analysis of syntenic copy number of C4 photosynthesis-related gene families indicates that G. gynandra generally retained more duplicated copies of these genes than C3 T. hassleriana, and also that the G. gynandra C4 genes might have been under positive selection pressure. Both whole-genome and single-gene duplication were found to contribute to the expansion of the aforementioned gene families in G. gynandra. Collectively, this study enhances our understanding of the impact of gene duplication and gene retention on the evolution of C4 photosynthesis in Cleomaceae.
Neuromechanical Coupling is Reflected in the Spatial Organization of the Spinal Motoneuron Pools
Authors: Taitano Rachel I. , Yakovenko Sergiy , Gritsenko Valeriya 
Published: July 2022

AbstractRecent advances in neuroprosthetics have shown that activating the surviving spinal circuitry below the level of spinal damage can produce complex movements and restore function. This is because the spinal cord circuitry plays an important role in the control of complex movements by integrating descending execution-related signals with feedback sensory signals. To generate efficient movements through muscle contractions, the nervous system embeds the anatomical and dynamical properties of the controlled body parts, a concept termed neuromechanical tuning. The motoneurons innervating the skeletal muscles of the body form complex spatial structures that span multiple segments. The goal of this study is to determine if these structures can support neuromechanical tuning. We performed a comparative analysis of the spatial organization of the motoneuron pools and the functional organization of the muscles they innervate. We developed a three-dimensional model of the spatial organization of motoneuron pools innervating upper limb muscles in the macaque and quantified their relative distances. We then utilized a musculoskeletal model of the macaque upper extremity to characterize the functional relationship between the muscles innervated by the motoneuron pools. We found that the distances between motoneuron pools mimicked the agonistic or antagonistic actions of muscles they innervate. This shows that the spatial organization of the motoneuron pools embeds the functional musculoskeletal anatomy evolved to support the large repertoire of upper limb movements in primates. This spinal anatomy may play an important role in the neuromechanical tuning and simplify the sensorimotor control of the arm.
Signal Alignment Enables Analysis of DIA Proteomics Data from Multisite Experiments
Authors: Gupta Shubham , Sing Justin C. , Röst Hannes L. 
Published: July 2022

AbstractDIA has become a mainstream method for quantitative proteomics, however consistent quantification across multiple LC-MS/MS instruments remains a bottleneck in parallelizing the data-acquisition. To produce a highly consistent and quantitatively accurate data matrix, we have developed DIAlignR which uses raw fragment-ion chromatograms for cross-run alignment. Its performance on a gold standard annotated dataset, demonstrates a threefold reduction in the identification error-rate when compared to standard non-aligned DIA results. A similar performance is achieved for a dataset of 229 runs acquired using 11 different LC-MS/MS setups. Finally, the analysis of 949 plasma runs with DIAlignR increased the number of statistically significant proteins by 43% and 62% for insulin resistant (IR) and respiratory viral infection (RVI), respectively compared to prior analysis without it. Hence, DIAlignR fills a gap in analyzing DIA runs acquired in-parallel using different LC-MS/MS instrumentation.
Targeting Acid Ceramidase Ameliorates Fibrosis in Mouse Models of Nonalcoholic Steatohepatitis
Authors: Yu Amy , Cable Carson , Shihan Mahbubul H. , Sharma Sachin , Mattis Aras N. , Mileva Izolda , Hannun Yusuf A. , Duwaerts Caroline C. , Chen Jennifer Y. 
Published: July 2022

1)ABSTRACTNonalcoholic fatty liver disease (NAFLD) is a common cause of liver disease worldwide, and is characterized by the accumulation of fat in the liver. Nonalcoholic steatohepatitis (NASH), an advanced form of NAFLD, is a leading cause of liver transplantation. Fibrosis is the histologic feature most associated with liver-related morbidity and mortality in patients with NASH, and treatment options remain limited. In previous studies, we discovered that acid ceramidase (aCDase) is a potent antifibrotic target using human hepatic stellate cells (HSCs) and models of hepatic fibrogenesis. Using two dietary mouse models, we demonstrate that depletion of aCDase in HSC reduces fibrosis without worsening metabolic features of NASH, including steatosis, inflammation, and insulin resistance. Consistently, pharmacologic inhibition of aCDase ameliorates fibrosis but does not alter metabolic parameters. The findings suggest that targeting aCDase is a viable therapeutic option to reduce fibrosis in patients with NASH.
Tumor subclones, where are you?
Authors: Su Xianbin , Bai Shihao , Xie Gangcai , Shi Yi , Zhao Linan , Yang Guoliang , Tian Futong , He Kun-Yan , Wang Lan , Li Xiaolin , Long Qi , Han Ze-Guang 
Published: July 2022

AbstractIntroductionTumor clonal structure is closely related to future progression, which has been mainly investigated via mutation abundance clustering in bulk sample. With limited studies at single-cell resolution, a systematic comparison of the two approaches is still lacking.MethodsHere, using bulk and single-cell mutational data from liver and colorectal cancers, we would like to check the possibility of obtaining accurate tumor clonal structures from bulk-level analysis. We checked whether co-mutations determined by single-cell analysis had corresponding bulk variant allele frequency (VAF) peaks. We examined VAF ranges for different groups of co-mutations, and also the possibility of discriminating them.ResultsWhile bulk analysis suggested absence of subclonal peaks and possibly neutral evolution in some cases, single-cell analysis identified co-existing subclones. The overlaps of bulk VAF ranges for co-mutations from different subclones made it difficult to separate them, even with other parameter introduced. The difference between mutation cluster and tumor subclone is accountable for the challenge in bulk clonal deconvolution, especially in case of branched evolution as shown in colorectal cancer.ConclusionComplex subclonal structures and dynamic evolution are hidden under the seemingly clonal neutral pattern at bulk level, suggesting single-cell analysis will be needed to avoid under-estimation of tumor heterogeneity.Research HighlightsBulk-level mutation abundance clusters are not equal to tumor subclones.Different groups of co-mutations could not be discriminated at bulk-level.Single-cell mutational analysis can identify rather than infer tumor subclones.Co-existing tumor subclones may have clonal neutral appearance at bulk-level.Lay summarySystematic comparison of tumor clonal structure differences between bulk and single-cell mutational analysis is lacking. Here we performed such as study and found that complex subclonal structures and dynamic evolution are hidden under clonal neutral appearance at bulk level in liver and colorectal cancers, suggesting single-cell analysis will be needed to avoid under-estimation of tumor heterogeneity.
Longitudinal Urine Metabolic Profiling and Gestational Age Prediction in Pregnancy
Authors: Chen Songjie , Shen Xiaotao , Liang Liang , Avina Monika , Zackriah Hanyah , Jelliffe-Pawlowski Laura , Rand Larry , Snyder Michael 
Published: July 2022

AbstractPregnancy is a critical time that has long-term impacts on both maternal and fetal health. During pregnancy, the maternal metabolome undergoes dramatic systemic changes, although correlating longitudinal changes in maternal urine remain largely unexplored. We applied an LCMS-based untargeted metabolomics profiling approach to analyze 346 longitudinal maternal urine samples collected throughout pregnancy for 36 women from diverse ethnic backgrounds with differing clinical characteristics. We detected 20,314 metabolic peaks and annotated 875 metabolites. Altered metabolites include a broad panel of glucocorticoids, lipids, and amino acid derivatives, which revealed systematic pathway alterations during pregnancy. We also developed a machine-learning model to precisely predict gestational age (GA) at time of sampling using urine metabolites that provides a non-invasive method for pregnancy dating. This longitudinal maternal urine study demonstrates the clinical utility of using untargeted metabolomics in obstetric settings.One Sentence SummaryMachine-learning based gestational age and due date using longitudinal urine samples of pregnancy.
Phosphorylation of light-harvesting complex II controls excitation energy spillover between photosystems
Authors: Tokutsu Ryutaro , Kim Eunchul , Akimoto Seiji , Yokono Makio , Fujimura-Kamada Konomi , Ohnishi Norikazu , Ueno Yoshifumi , Minagawa Jun 
Published: July 2022

AbstractLand plants and microalgae convert solar energy into electrochemical energy by using cooperative two photosystems (PSI and PSII). To maintain optimal photosynthetic rates under variable light conditions in nature, phosphorylation of light-harvesting complex for PSII (LHCII) balances the excitation energy distribution between the two photosystems. Here, we investigated the mechanism of this balancing in a green alga. We show that phospho-LHCIIs physically bind to both photosystems. The energy transfer from the LHCIIs to the PSII core complexes becomes less efficient, whereas the excitation level of PSI increases. The time-resolved fluorescence spectra showed an increase in delayed PSI fluorescence, which represents energetical spillover from PSII to PSI. In addition, the spillover is likely mediated by phospho-LHCIIs and PSI antennas. We hypothesize that the spillover explains the larger extent of phospho-LHCIIs dependent energy balancing in the green alga than land plants, which is important for the short-term photoadaptaion in the algal habitat.
Adaptive dynamic surface output feedback control for a class of quadrotor aircraft with actuator faults
Authors: Zhu Guoqiang , Li He , Zhang Huan , Wang Sen , Zhang Xiuyu 
Published: July 2022

Purpose
The purpose of this study is to propose an adaptive fault-tolerant control approach based on output feedback for a class of quadrotor unmanned aerial vehicles system. In the event of a controlled actuator failure, a stable flying of the aircraft can be achieved by selecting an appropriate sliding mode surface.

Design/methodology/approach
Aiming at the actuator failure of quadrotor aircraft during flight in the controllable range, a dynamic surface sliding mode passive fault-tolerant controller based on output feedback is designed based on the strong robustness of sliding mode method. Due to the unknown nonlinearity dynamics and parameter uncertainties in the system, a nonlinear observer is used to estimate them online.

Findings
The stability of the suggested algorithm is established using appropriate Lyapunov functions, and the performance of the proposed control approach is demonstrated using hardware-in-the-loop simulation.

Originality/value
An error performance function is introduced into the controller to ensure the convergence speed and accuracy of errors are within the predetermined range. By using the norm estimation method, there is only one parameter that needs to be updated in each step of the control process, which considerably minimizes the calculation burden. Finally, the validity of the proposed control scheme is verified on the hardware-in-the-loop simulation, and the results show that the proposed control method has achieved the desired results.
The drivers and challenges of adopting the Malaysia industrialised building system for sustainable infrastructure development
Authors: Ismail Sushilawati , Hon Carol K.H. , Crowther Philip , Skitmore Martin , Lamari Fiona 
Published: July 2022

Purpose
Malaysia’s industrialised building system (IBS) has been increasingly adopted for sustainable development by the country’s construction industry. However, although it has been used for commercial building projects, its application to sustainable infrastructure development has been limited to date. This study aims to examine the drivers and challenges involved.

Design/methodology/approach
A preliminary conceptual framework was initially developed based on a systematic literature review. Semi-structured interviews involving 20 participants were undertaken to gain insightful thoughts from the construction practitioners to discover the perception towards IBS application in the construction industry, the applicability of IBS, particularly in infrastructure projects, the strategies of IBS delivery and the sustainable potential of its application. A two-round Delphi study was conducted with 15 experienced and knowledgeable panellists to further identify, verify and prioritise factors developed from the literature review and interview findings. Then, the results were synthesised and triangulated to demonstrate a holistic insight.

Findings
The results show the main drivers to be better productivity, quality, environmental, safety and health, constructability design and cost, policy and requirements, with the main challenges being project planning and cost-related issues, inexperience and industry capacity.

Originality/value
The study’s main contribution is in systematically determining the practical implications involved in applying the IBS to sustainable infrastructure developments in Malaysia and other similar developing countries.
Government support, talent, coupling of innovation chain and capital chain: empirical analysis in integrated circuit enterprises
Authors: Chen Qiuling , Wang Tianchi 
Published: July 2022

Purpose
This study aims to investigate the impact of government support on the coupling coordination degree of innovation chain and capital chain in integrated circuit (IC) enterprises and to explore the mechanism for considering talent in the influence path.

Design/methodology/approach
This paper uses coupling coordination degree model to estimate the coupling of two chains, and applies dynamic panel system generalized method of moments (system-GMM) to analyze the impact of government support on coupling of two chains and conducts dynamic panel threshold regression to explore the threshold effect of talent in the influence of government support on coupling coordination degree.

Findings
Serious imbalance in the coupling of two chains is a major obstacle in IC enterprises. Government support significantly reduces the coupling coordination degree. The talent in IC enterprises has a significant threshold effect. When the number of talent is lower than the threshold value, government support has a negative impact. Once the number of talent reaches a certain level, government support can significantly enhance the coupling of two chains. Compared with state-owned enterprises, government support has a greater negative impact on the coupling of the two chains in non-state-owned enterprises. The former needs more talent to take advantage of government support.

Originality/value
This paper applies the concept of coupling into enterprises and deeply studies the coupling coordination degree of two chains. The influence mechanism of government support and talent on the coupling of two chains is explored, which reveals that government support cannot achieve the expected incentive effect without the support of talent. We also discuss the heterogeneous effect of government support and of talent in enterprises of different ownership types.
Supporting students' employability through structured, event-based engagement with employers
Authors: Mason Claire M. , Burns Shanae M. , Bester Elinor A. 
Published: July 2022

PurposeThe authors proposed that participation in large-scale, structured events designed to match students to employers' internship opportunities could support students' employability by focussing students' career goals, strengthening students' career self-efficacy and growing students' social capital.Design/methodology/approachInterviews were carried out with 49 students both before and after the students took part in the event to assess whether students career goals, self-efficacy or social capital changed after taking part in the events. In the second interview, the authors also asked students what outcomes students gained from the event and how the event process had contributed to these outcomes.FindingsStudents' descriptions of their outcomes from the event aligned with social capital theory and self-efficacy theory. The students valued the information, connections, skills and experience they developed through taking part in the interviews and connecting with employers and students. The longitudinal analyses revealed that most students career goals did not change, but students' career self-efficacy improved and students could identify more actions for achieving their career goals after taking part in the event. Importantly, these actions were often explicitly connected with information or connections that students gained from the event.Originality/valueThe interviews illustrate that students can build social capital from short, one-on-one engagement with employers that then enable them to identify ways of furthering students' career goals. The authors' findings suggest that structured, event-based engagement with employers can provide an efficient and equitable means of enhancing students' social capital and career self-efficacy.
AQI revisioned: a critical realism approach to transforming air pollution
Authors: Boonmavichit Thasanawan 
Published: July 2022

Purpose
This paper aims to present the case for critical realism (CR) as a framework in steering the anticipatory and participatory activities an appropriate analysis of complex problems, aiming toward a transformative change.

Design/methodology/approach
Through observation, interview and facilitation for Circular Design Lab and Thai Clean Air Network, this paper unpacks their foresight activities, their key findings and subsequently connects to the Morphogenesis analysis based on an alternative foresight epistemology of CR.

Findings
Foresight based on CR philosophy provides a deeper understanding of the complexity and invisibility of air pollution issues in Thailand. Acknowledging the transitive reality beyond this study’s perception, the activity design applies the iceberg models to investigate problem framing and illustrate the stratified reality in three domains: the empirical based on emission reports and legislative regulations; the actual based on patterns of farmers practice and industrial development, activated by causal mechanisms; the real based on structural and mental models, driven by cultural and belief systems in Thailand. At the bottom layer of the iceberg, the real lies the generative mechanisms of pre-existing structural and cultures that constrain Thai citizen from acting on social change.

Research limitations/implications
CR’s emancipatory theory provides an immanent critique towards social improvement by illustrating comprehensive causal explanations of complex problems such as air pollution; while morphogenesis theory elaborates on the unconscious domination of the existing social structures, agencies, and cultures. Thus, the ethical inquiry of CR research is committed to the emancipation of false beliefs and creating conditions for “human prosperity”. However, this non-neutral value commitment is debated in the futures studies field.

Practical implications
The anticipatory activities on air pollution in Thailand bring to light the reality of power and oppression beyond human perception and illustrate the connection to the belief systems and its consequential action or lack thereof in dealing with the issues. The insight to power relationship provides an unconventional way to empower citizens in creating transformative change.

Originality/value
Modern foresight practice has developed under western cultures and societies. Recent efforts are made to investigate the epistemology underlying this field, for the future issues are ever more complex and interrelated across multiple sectors. This requires this study’s consideration of the meaning of knowledge and knowing, influencing the research paradigm. This paper proposes CR as a suitable foresight approach to emancipate this study from the widely accepted epistemologies and examine this study’s presupposition about social reality by a philosophical explanation based on the elements of ontology, causation, structure and persons.
Awakening the unconscious imagination and igniting ethical aspirations: the case of Hiraya Foresight via the engaged foresight approach
Authors: Cruz Shermon Ortega , Kahn-Parreño Nicole Anne 
Published: July 2022

Purpose
This paper aims to introduce, unpack, explore, make sense and share Hiraya Foresight via the Engaged Foresight approach as a futures concept, framework and methodology to reconceptualize foresight and reframe anticipatory processes to enable the self and communities to reimagine visions of the future. This indigenous foresight process offers to strip the husk and break the shell of conscious, colonial anticipation and reveal and liberate unconscious imagination that enables ethical aspirations to emerge.

Design/methodology/approach
This paper introduces and examines the context, purpose and process of the four waves of the Hiraya Foresight Framework via the Engaged Foresight approach. These were constructed through the use of the Engaged Foresight approach, through workshops, a literature review and an action–learning approach. The first wave, lawak, looks into the breadth of foresight. The second wave, lalim, looks into the depth of foresight. Tayog, the third wave, looks into the peak of foresight. Finally, the fourth wave of foresight kababaang-loob contemplates the nature, values and wisdom of foresight.

Findings
This paper shares the processes, experiences and impacts through five case studies where the Hiraya Foresight Framework via the Engaged Foresight approach was applied. This paper shares the impacts of Hiraya Foresight in democratizing and indigenizing futures literacy.

Originality/value
This paper describes and offers Hiraya Foresight via the Engaged Foresight approach as an indigenous approach to decolonize futures studies and foresight practice.