bluuebunny/crossref_metadata_2025_split huggingface dataset:
Assessing flower-visiting arthropod diversity in apple orchards through environmental DNA flower metabarcoding and visual census
Authors: Gomez Nerea Gamonal , Sørensen Didde Hedegaard , Shi Chua Physilia Ying , Sigsgaard Lene 
Published: January 2022

AbstractArthropods are essential to maintaining healthy and productive agricultural systems. Apples are cultivated worldwide and rely on pollination. Honey bees are used for pollination but wild bees and other arthropods also contribute to pollination. Flower visitors can also be natural enemies or herbivores. In some cases, such as Syrphids, a group can have more than one role, adults being pollinators and the larvae being natural enemies of pests. In the present study, we assessed the biodiversity of arthropod flower visitors in four Danish apple orchards and compared the use of molecular and non-molecular techniques to study arthropod communities in agricultural ecosystems. Arthropod DNA collected from apple flowers was analysed by metabarcoding and pollinators were recorded through visual assessment in the orchards. These techniques resulted in two complementary lists of arthropods detected. Non-bee arthropods constituted a big part of the community of apple flower visitors by both methods. Metabarcoding detected 14 taxa and had 72% species resolution while visual census identified 7 different taxa with 14% species resolution. This study showed the importance of using different sampling methodologies to obtain a more accurate picture of fauna present. It also revealed the high presence of non-bee arthropods visiting flowers in apple orchards. The outcome of our study provides information regarding the effects of management practices on arthropod biodiversity, which can contribute to informing on suitable management practices to increase crop yield and maintain healthy agricultural systems.
Forecasted trends of the new COVID-19 epidemic due to the Omicron variant in Thailand, 2022
Authors: Suphanchaimat Rapeepong , Teekasap Pard , Nittayasoot Natthaprang , Phaiyarom Mathudara , Cetthakrikul Nisachol 
Published: January 2022

AbstractBackgroundThe introduction of the Omicron variant is of significant concern to the Thai Government due to the possibility of a new wave of the COVID-19 epidemic, which may cause a huge strain to the country’s health system. This study aims to forecast the trends of COVID-19 cases and deaths given the advent of the Omicron variant in Thailand.MethodsWe used a compartmental susceptible-exposed-infectious-recovered model in combination with a system dynamics model. We developed four scenarios according to differing values of the production number (R) and varying vaccination rates.ResultsThe findings indicated that in the most pessimistic scenario (R = 7.5 and base vaccination rate), the number of incident cases reached a peak of 49,523 (95% CI: 20,599 to 99,362) by day 73 and the peak daily deaths enlarged to 270 by day 50 (95% CI: 124 to 520). The predicted cumulative cases and deaths at the end of the wave (day 120) were approximately 3.7 million and 22,000 respectively. In the most optimistic assumption (with R = 4.5 and a speedy vaccination rate [tripled the base rate]), the peak of the incident cases was about one third of the most pessimistic assumption (15,650, 95% CI: 12,688 to 17,603). The corresponding daily fatalities were 72 (95% CI: 54 to 84) and the prevalent intubated cases numbered 572 (95% CI: 429 to 675).ConclusionsIn the coming months, Thailand may face a new wave of the COVID-19 epidemic due to the Omicron variant. The case toll due to the Omicron wave is likely to outnumber the earlier Delta wave, but the death toll is proportionately lower. Despite the immune-escape characteristic of the Omicron variant, the vaccination campaign for the booster dose should be expedited as an effective way of preventing severe illness and death.
Reactive Oxygen Species-induced Protein Carbonylation Promotes Deterioration of Physiological Activity of Wheat Seeds
Authors: Li Bang-Bang , Zhang Shuai-Bing , Lv Yang-Yong , Wei Shan , Hu Yuan-Sen 
Published: January 2022

AbstractDuring the seed aging process, reactive oxygen species (ROS) can induce the carbonylation of proteins, which changes their functional properties and affects seed vigor. However, the impact and regulatory mechanisms of protein carbonylation on wheat seed vigor are still unclear. In this study, we investigated the changes in wheat seed vigor, carbonyl protein content, ROS content and embryo cell structure during an artificial aging process, and we analyzed the correlation between protein carbonylation and seed vigor. During the artificial wheat-seed aging process, the activity levels of antioxidant enzymes and the contents of non-enzyme antioxidants decreased, leading to the accumulation of ROS and an increase in the carbonyl protein content, which ultimately led to a decrease in seed vigor, and there was a significant negative correlation between seed vigor and carbonyl protein content. Moreover, transmission electron microscopy showed that the contents of protein bodies in the embryo cells decreased remarkably. We postulate that during the wheat seed aging process, an imbalance in ROS production and elimination in embryo cells leads to the carbonylation of proteins, which plays a negative role in wheat seed vigor.
The m6A writer FIONA1 methylates the 3’UTR of FLC and controls flowering in Arabidopsis
Authors: Sun Bin , Bhati Kaushal Kumar , Edwards Ashleigh , Petri Louise , Kruusvee Valdeko , Blaakmeer Anko , Dolde Ulla , Rodrigues Vandasue , Straub Daniel , Wenkel Stephan 
Published: January 2022

ABSTRACTAdenosine bases of RNA can be transiently modified by the deposition of a methyl-group to form N6-methyladenosine (m6A). This adenosine-methylation is an ancient process and the enzymes involved are evolutionary highly conserved. A genetic screen designed to identified suppressors of late flowering transgenic Arabidopsis plants overexpressing the miP1a microProtein yielded a new allele of the FIONA1 (FIO1) m6A-methyltransferase. To characterize the early flowering phenotype of fio1 mutant plants we employed an integrative approach of mRNA-seq, Nanopore direct RNA-sequencing and meRIP-seq to identify differentially expressed transcripts as well as differentially methylated mRNAs. We provide evidence that FIO1 is the elusive methylase responsible for the 3’-end methylation of the FLOWERING LOCUS C (FLC) transcript. Furthermore, our genetic and biochemical data suggest that 3’-methylation stabilizes FLC mRNAs and non-methylated FLC is a target for rapid degradation.
Morphological analysis of human and mouse dendritic spines reveals a morphological continuum and differences across ages and species
Authors: Ofer Netanel , Benavides-Piccione Ruth , DeFelipe Javier , Yuste Rafael 
Published: January 2022

ABSTRACTDendritic spines have diverse morphologies, with a wide range of head and neck sizes, and these morphological differences likely generate different synaptic and functional properties. To explore how this morphological diversity differs across species we analyzed 3D confocal reconstructions of ~8,000 human spines and ~1,700 mouse spines, labeled by intracellular injections in fixed tissue. Using unsupervised machine-learning algorithms, we computationally separated spine heads and necks and systematically measured morphological features of spines in apical and basal dendrites from cortical pyramidal cells. Human spines had unimodal distributions of parameters, without any evidence of morphological subtypes. Their spine necks were longer and thinner in apical than in basal spines, and spine head volumes of an 85-years-old individual were larger than those of a 40-years-old individual. Human spines overall had longer and thicker necks and bigger head volumes than mouse spines. Our results indicate that human spines form part of a morphological continuum, are larger and longer than those of mice, and become larger with increasing adult age. These morphological differences in spines across species could generate functional differences in biochemical and electrical spine compartmentalization, or in synaptic properties, across species and ages.
Increased parasite load is associated with reduced metabolic rates and escape responsiveness in pumpkinseed sunfish host
Authors: Guitard Joëlle , Chrétien Emmanuelle , De Bonville Jérémy , Roche Dominique G. , Boisclair Daniel , Binning Sandra A. 
Published: January 2022

AbstractWild animals have parasites that can compromise their physiological and/or behavioural performance. Yet, the extent to which parasite load is related to intraspecific variation in performance traits within wild populations remains relatively unexplored. We used pumpkinseed sunfish (Lepomis gibbosus) and their endoparasites as a model system to explore the effects of infection load on host aerobic metabolism and escape performance. Metabolic traits (standard and maximum metabolic rates, aerobic scope) and fast-start escape responses following a simulated aerial attack by a predator (responsiveness, response latency, and escape distance) were measured in fish from across a gradient of visible (i.e. trematodes causing black spot disease counted on fish surfaces) and non-visible (i.e. cestodes in fish abdominal cavity counted post-mortem) endoparasite infection. We found that a higher infection load of non-visible endoparasites was related to lower standard and maximum metabolic rates, but not aerobic scope in fish. Non-visible endoparasite infection load was also related to decreased responsiveness of the host to a simulated aerial attack. Visible endoparasites were not related to changes in metabolic traits nor fast-start escape responses. Our results suggest that infection with parasites that are inconspicuous to researchers can result in intraspecific variation in physiological and behavioral performance in wild populations, highlighting the need to more explicitly acknowledge and account for the role played by natural infections in studies of wild animal performance.
Theoretical Principles of Enhancer-Promoter Communication in Transcriptional Bursting
Authors: Wang Zihao , Zhang Zhenquan , Luo Songhao , Zhou Tianshou , Zhang Jiajun 
Published: January 2022

AbstractTranscriptional regulation occurs through genomic contacts between enhancers and their cognate promoters, and most genes are transcribed in a bursty fashion. To understand the relationship between these two phenomena, we develop a general modeling framework in terms of the information transmission from upstream genomic organization to downstream transcriptional bursting. Importantly, we uncover fundamental theoretical principles of enhancer-promoter (E-P) spatial communication in the modulation of transcriptional burst size (BS) and burst frequency (BF). First, BS and BF obey their respective power-law dependences on the E-P communication strength and distinct scaling exponents. Second, the E-P spatial distance follows a Maxwell-Boltzmann distribution rather than the previously assumed Gauss distribution. Third, the E-P genomic distance affects transcriptional outcomes biphasically (i.e., in an exponential decay for small E-P genomic distances but insensitively to large E-P genomic distances). Fourth, the E-P communication mainly modulates BF rather than BS. Finally, the mutual information between BS (or BF) and E-P spatial distance further reveals essential characteristics of the information transfer from the upstream to the downstream. Our predictions are experimentally verifiable, e.g., confirmed by experimental data on Drosophila. The overall analysis provides insights into the role of the E-P communication in the control of transcriptional bursting.SignificanceMeasurement technologies of chromatin conformations and genome-wide occupancy data of architectural proteins have revealed that genome topology is tightly intertwined with gene transcription. However, a long-standing question in transcriptional regulation is how the enhancer-promoter (E-P) spatial communication impacts transcriptional bursting kinetics. To address this issue, we develop a multiscale model that couples upstream chromatin dynamics to downstream transcriptional bursting. This model not only reveals fundamental principles of E-P communication in transcriptional bursting kinetics (e.g., burst size and frequency follow their own power-law behaviors) but also provides a general modeling framework toward the 4D nucleome project.
Structure of ATP synthase under strain during catalysis
Authors: Guo Hui , Rubinstein John L. 
Published: January 2022

AbstractATP synthases are macromolecular machines consisting of an ATP-hydrolysis-driven F1 motor and a proton-translocation-driven FO motor. The F1 and FO motors oppose each other’s action on a shared rotor subcomplex and are held stationary relative to each other by a peripheral stalk. Structures of resting mitochondrial ATP synthases revealed a left-handed curvature of the peripheral stalk even though rotation of the rotor, driven by either ATP hydrolysis in F1 or proton translocation through FO, would apply a right-handed bending force to the stalk. We used cryoEM to image yeast mitochondrial ATP synthase under strain during ATP-hydrolysis-driven rotary catalysis, revealing a large deformation of the peripheral stalk. The structures show how the peripheral stalk opposes the bending force and suggests that proton translocation during ATP synthesis causes accumulation of strain in the stalk, which relaxes by driving the relative rotation of the rotor through six sub-steps within F1, leading to catalysis.
Economic complexity and the dynamics of regional competitiveness a systematic review
Authors: Bahrami Farideh , Shahmoradi Behrooz , Noori Javad , Turkina Ekaterina , Bahrami Hassan 
Published: January 2022

Purpose
This study aims to systematically review the economic complexity literature to advance the knowledge on its contribution to building regional competitiveness.

Design/methodology/approach
In this study, we did a systematic review of 111 relevant papers. In this regard, we did a thematic analysis on all the collected papers, which led to a two-level processed approach. In the first level, the contributions of the reviewed articles have been classified into three main streams. In the second level, the findings under each contribution category are analyzed and explained. This approach led to a thematic network demonstrating economic complexity and the dynamics of regional competitiveness and a set of managerial and policy implications. We followed a multiple processed approach for the systematic review of 95 papers that reveals considerable contributions in three categories, including measurement techniques, criticisms and exploratory studies.

Findings
Despite some critiques and the undertaken evolution in measurement techniques of complexity, economic complexity has become a well-known method mainly for regions' competitiveness dynamics. Our review demonstrates a nested network of economic complexity dynamics that drives policy advice concerning countries' status in their development path. The provided set of policies includes guidelines for underdeveloped and developing countries and general policy implications, applicable for all regional contexts for building competitiveness dynamics.

Originality/value
This research contributes to the literature on competitiveness from the window of economic complexity. The study allows a deep understanding of regions' productive structure role in their development and competitiveness. A set of policies for building regional competitiveness is provided concerning the study's findings. The literature gaps are identified, and future research ideas are provided for using economic complexity methodologically and logically to boost regional competitiveness.
“System aisa hi hai” – exploring local researchers' perspective on barriers toward conducting locally relevant disaster research
Authors: Das Manomita 
Published: January 2022

PurposeThe paper explores why local disaster scholars often fail to put the needs of local people at the centre of their research. Specifically, it explores two questions: (1) why local concerns are often not reflected in the research agenda? And (2) why we are falling behind in generating locally applicable disaster knowledge? The paper engages with the experiences of local disaster researchers to answer the research questions.Design/methodology/approachA qualitative approach was undertaken to conduct the study. In total, 15 in-depth interviews were conducted with practitioners and academics working in the domain of disaster studies in different regions of India. Criterion sampling was employed to recruit the participants. An interview guide with open ended questions was used to conduct the interviews. The data were thematically analysed utilizing qualitative data analysis software to arrive at the findings.FindingsThe participants identified three potential reasons behind the lack of locally relevant disaster research. First, the existing concepts and terminologies which guide disaster research are often inadequate to represent the local reality. Second, “foreign” funders and policymakers often influence the agenda and emphasis of the research which creates barriers in developing research agenda relevant to the local needs. The time-bound project format of research is often problematic. It resembles looking at the community through a peephole which hardly gives the whole picture. Third, resource constraints also create substantial hindrances in conducting locally relevant research.Research limitations/implicationsThe sample only included participants who believed that disaster research is often not relevant locally in India. Participants having different standpoints on the issue were not included which remains as a limitation of the study. Practical implicationsThe research highlights the challenges that local researchers face while conducting locally relevant research and how they can be overcome. The author expects that the findings of the research will help in challenging and transforming established practices in disaster studies and bridging the gap between disaster research and vulnerable people.Originality/valueThis paper is valuable because it documents the perspectives of local researchers on the barriers that need to be overcome to produce locally relevant disaster research.
Diverging influences of usability in online authentication system: the role of culture (US vs Korea)
Authors: Jang Jung Min , Kim Heejin 
Published: January 2022

PurposeAlthough the use of online authentication systems in banking services is expanding globally, little is known about cultural differences in forming consumers' responses to these services. This paper examines how the usability of an online security service and culture impact consumers' behaviour.Design/methodology/approachThe authors conduct a 2 (usability: high vs low) × 2 (culture: US vs Korea) between-subjects, full factorial design.FindingsThe results indicate a differential influence of the usability of a security system by culture. In particular, US consumers exhibit greater behavioural intention in a high (vs low) usability condition, whereas Korean consumers showed more favourable responses in a low-usability condition. Moreover, perceived effort is confirmed as a crucial mediator that explains the psychological mechanism of the proposed effect.Practical implicationsThis research contributes to the literature on online banking where security is an important determinant of success. Especially for managers involved in international banking services, the findings of cultural differences offer insights about the importance of local understanding and differentiation of bank services for specific target markets which can enhance consumers' response towards an online security service.Originality/valueThe current study is one of a very few attempts to examine the role of usability of an online security system in forming consumers' behavioural intention. More importantly, this study integrates the concept of culture to explain how usability influences positive or negative behavioural intention in an international market.
The Internet search engines as an additional tool in public health research in the context of disease outbreaks
Authors: Batrimenko Andrey Valerievich , Denisova Svetlana , Lisovskii Dmitrii , Orlov Sergey , Soshnikov Sergey 
Published: January 2022

PurposeThe study aims to help epidemiologists identify new patterns and trends in spreading infections on the example of the current coronavirus disease 2019 (COVID-19) pandemic using data from search engines. The study identified the types of thematic search of Russian Internet users and queries that have a mathematically confirmed correlation with public health indicators: mortality and morbidity from COVID-19. The study aims to determine digital epidemiology search trends to the current COVID-19 pandemic. The study identified the types of thematic search of RuNet users and queries that have a mathematically confirmed correlation with public health indicators: mortality and morbidity from COVID-19.Design/methodology/approachThe authors explored two types of data: (1) the monthly datasets of keywords relevant to COVID-19 extracted from the Yandex search engine and (2) officially published statistics data. Alongside, the authors searched for associations between all variables in this dataset. The Benjamin–Hochberg correction for multiple hypothesis testing was applied to the obtained results to improve the reliability of the results. The authors built a unique website with opportunities to update datasets and designed dashboards to visualize the research outcomes using PHP and Python.FindingsThe research results show the number of significant relationships that the authors interpreted in epidemiology as a new instrument in Public Health research. There are 132 data combinations with a correlation higher than 75%, making it possible to determine a mathematically reliable relationship between search statistics trends and mortality/morbidity indicators. The most statistically significant effects identified in bundles “query” – “query”, “query” – “morbidity”, “query” – “mortality”.Originality/valueThe authors developed a new approach in analyzing outbreaks of infections and their consequences based on a comprehensive analysis of epidemiological and infodemic data. The research results are relevant to public health as other decision-making and situational analysis tools for citizens and specialists who want to receive additional confirmation for the indicators of the official statistics of the headquarters for control and monitoring of the situation with coronavirus and others infections.