bluuebunny/crossref_metadata_2025_split huggingface dataset:
Differential effect of climate on structural and biochemical plant traits
Authors: Thakur Dinesh , Hadincová Věroslava , Schnablová Renáta , Synková Helena , Haisel Daniel , Wilhelmová Nada , Dostálek Tomáš , Münzbergová Zuzana 
Published: July 2022

ABSTRACTExploring patterns and causes of intraspecific trait variation is crucial for a better understanding of the effects of climate change on plant populations and ecosystems. However, our current understanding of the intraspecific trait variation is mainly based on structural (morphological) traits, and we have limited knowledge on patterns and causes of variation in biochemical traits (e.g., leaf pigments), which are also crucial for plant adaptation. As a result, we also do not know how similar the climatic effects on structural versus biochemical traits are.Using plant traits from 110 genotypes representing 11Festuca rubrapopulations grown in 4 different climates, we studied trait covariation among structural traits (linked to fitness, resource use, gas exchange, and reproduction) and biochemical traits (linked to photosynthesis, photoprotection, and oxidative stress). We also disentangled the relative role of the climate of origin and the climate of cultivation in the structural versus biochemical traits and tested for adaptive plasticity in the traits.We found that 1) biochemical traits did not covary with structural traits and represent independent‘photoharvesting – photoprotection’strategy dimension of functional variation; 2) interactive effects of climate of origin and cultivation were more pronounced for biochemical than structural traits. 3) Trait plasticity was affected by the climate of origin (precipitation and temperature as well as their interaction); 4)F. rubrashowed both adaptive and mal-adaptive plasticity, and adaptiveness depended upon trait type, cultivation climate, and climate of origin.Overall, our results suggest that structural and biochemical plant traits respond differentially to climate and thus the response of one group of traits cannot be predicted from the other. Responses are also strongly determined by interactions between the climate of origin and cultivation. Thus, more studies on variation in biochemical traits, their correspondence to other traits, and their variation with climate are needed.
A virus-induced circular RNA maintains latent infection of Kaposi sarcoma herpesvirus
Authors: Tagawa Takanobu , Oh Daniel , Dremel Sarah , Mahesh Guruswamy , Koparde Vishal N. , Duncan Gerard , Andresson Thorkell , Ziegelbauer Joseph M. 
Published: July 2022

ABSTRACTNon-coding RNAs (ncRNAs) play important roles in host-pathogen interactions; oncogenic viruses like Kaposi sarcoma herpesvirus (KSHV) employ ncRNAs to establish a latent reservoir and persist for the life of the host. We previously reported that KSHV infection alters a novel class of RNA, circular RNAs (circRNAs). CircRNAs are alternative splicing isoforms and regulate gene expression but, their importance in infection is largely unknown. Here, we showed that a human circRNA, hsa_circ_0001400, is induced by various pathogenic viruses, namely KSHV, Epstein-Barr virus, and human cytomegalovirus. The induction of circRNAs including circ_0001400 by KSHV is co-transcriptionally regulated, likely at splicing. Consistently, screening for circ_0001400-interacting proteins identified a splicing factor, PNISR. Functional studies using infected primary endothelial cells revealed that circ_0001400 inhibits KSHV lytic transcription and virus production. Simultaneously, the circRNA promoted cell cycle, inhibited apoptosis, and induced immune genes. RNA-pulldown assays identified transcripts interacting with circ_0001400, including TTI1, which is a component of the pro-growth mTOR complexes. We thus identified a circRNA that is pro-growth and anti-lytic replication. These results support a model in which KSHV induces circ_0001400 expression to maintain latency. Since circ_0001400 is induced by multiple viruses, this novel viral strategy may be widely employed by other viruses.AUTHOR SUMMARYCircular RNAs (circRNAs) are single-stranded, closed-circular RNAs. They coincide with linear mRNAs as alternative splice isoforms. CircRNAs binds to other RNAs or proteins to regulate their abundance or functions. We previously showed that specific human circRNAs are differentials regulated upon infection with an oncogenic DNA virus, Kaposi’s sarcoma herpesvirus (KSHV). Functions of such circRNAs for virus infections were largely elusive. Here, we identified that one of circRNAs, hsa_circ_0001400 controls both viral and human gene expression so that infected human cells have less virus production but better cell growth. KSHV, like other herpesviruses, has two phases: latent and lytic cycle. The functions of circ_0001400 suggest it biases the cells to latent cycle during which, unlike lytic phase, viruses express only limited number of genes to survive and new viruses are not produced. Since oncogenic viruses like KSHV mainly stay at latent phase for the life of the host, our results suggest that the virus utilized circRNAs to switch to latent phase after the infection. Infection of other pathogenic viruses like Epstein-Barr virus and human cytomegalovirus were also found to induce circ_0001400. The circRNA may be thus controlling infection of various viruses.
ASOs are an effective treatment for disease-associated oligodendrocyte signatures in premanifest and symptomatic SCA3 mice
Authors: Schuster Kristen H. , Zalon Annie J. , DiFranco Danielle M. , Putka Alexandra F. , Stec Nicholas R. , Jarrah Sabrina I. , Naeem Arsal , Haque Zaid , Zhang Hanrui , Guan Yuanfang , McLoughlin Hayley S. 
Published: July 2022

ABSTRACTSpinocerebellar ataxia type 3 (SCA3) is the most common dominantly inherited ataxia. Currently, no preventative or disease-modifying treatments exist for this progressive neurodegenerative disorder, although efforts using gene silencing approaches are under clinical trial investigation. The disease is caused by a CAG repeat expansion in the mutant gene,ATXN3, producing an enlarged polyglutamine tract in the mutant protein. Similar to other paradigmatic neurodegenerative diseases, studies evaluating the pathogenic mechanism focus primarily on neuronal implications. Consequently, therapeutic interventions often overlook non-neuronal contributions to disease. Our lab recently reported that oligodendrocytes display some of the earliest and most progressive dysfunction in SCA3 mice. Evidence of disease-associated oligodendrocyte signatures has also been reported in other neurodegenerative diseases, including Alzheimer’s disease, ALS, Parkinson’s disease, and Huntington’s disease. Here, we assess the effects of anti-ATXN3antisense oligonucleotide (ASO) treatment on oligodendrocyte dysfunction in premanifest and symptomatic SCA3 mice. We report a severe, but modifiable, deficit in oligodendrocyte maturation caused by the toxic gain-of-function of mutant ATXN3 early in SCA3 disease that is transcriptionally, biochemically, and functionally rescued with anti-ATXN3ASO. Our results highlight the promising use of an ASO therapy across neurodegenerative diseases that requires glial targeting in addition to affected neuronal populations.
Complexes of tubulin oligomers and tau form an intervening network cross-bridging microtubules into bundles
Authors: Kohl Phillip , Song Chaeyeon , Fletcher Bretton , Best Rebecca L. , Tchounwou Christine , Arceo Ximena Garcia , Chung Peter J. , Miller Herbert P. , Wilson Leslie , Choi Myung Chul , Li Youli , Feinstein Stuart C. , Safinya Cyrus R. 
Published: July 2022

AbstractThe axon-initial-segment (AIS) of mature neurons contains microtubule (MT) fascicles (linear bundles) that are implicated as retrograde diffusion barriers in the retention of MT-associated protein (MAP) tau inside axons. While the role of tau in MT bundling is poorly understood, tau dysfunction and leakage outside of the axon is associated with neurodegeneration. We report on the structure of steady-state MT bundles in response to varying concentrations of divalent cations (Mg2+or Ca2+) in dissipative reaction mixtures containing αβ-tubulin, full-length tau, and GTP at 37°C. A concentration-time kinetic phase diagram generated by synchrotron small-angle X-ray scattering (SAXS) reveals a wide-spacing MT bundle phase (Bws), a transient intermediate MT bundle phase (Bint), and a tubulin ring phase. Remarkably, SAXS analysis combined with TEM of plastic embedded samples provides direct evidence of an intervening network (IN) of complexes of tubulin oligomers and tau (≈5 nm wide filaments), which stabilize MT bundles. In this model, αβ-tubulin oligomers in the IN are crosslinked by tau’s MT binding repeats, which also link αβ-tubulin oligomers to αβ-tubulin within the MT lattice. The finding of a new role for tubulin revises current dogma where cross-bridging of MTs is attributed entirely to interactions between MAPs. The tubulin-tau complexes of the IN should enhance the barrier properties of MT fascicles in preventing tau missorting to the somatodendritic compartment as happens during neurodegeneration. Furthermore, tubulin-tau complexes in the IN or bound to isolated MTs are potential sites for enzymatic modification of tau promoting nucleation and growth of tau fibrils in tauopathies.Significance StatementA cell free model of microtubule (MT) bundles of the axon-initial-segment (known as MT fascicles) was studied in physiologically relevant buffer conditions. MT fascicles have a role in retaining neuronal protein tau, a key protein stabilizing MTs, in the axon. X-ray scattering and electron microscopy led to the discovery of complexes of tubulin oligomers and tau as building blocks of an intervening network that cross-bridge MTs into stable bundles with precisely the same linear geometry observedin-vivoin neurons. Significantly, changes to the chemical structure of tau because of abnormal interactions with cellular enzymes, would be predicted to disrupt the intervening tubulin-tau network and the MT-fascicle’s barrier function, promoting leakage of tau to the somatodendritic compartment and neuron degradation.
Genomic mapping of the modifiers of teosinte crossing barrier 1 (Tcb1)
Authors: Maharjan Namrata , Khaipho-Burch Merritt , Awale Prameela , Gyawali Abiskar , Shrestha Vivek , Wu Yajun , Auger Donald L. 
Published: July 2022

AbstractPollen cross-contamination has been a major problem for maize breeders. Mechanical methods applied to avoid cross-contamination are largely ineffective and time-consuming. Cross incompatibility barriers are genetic factors involved in maize fertilization that can be used as an effective method to prevent pollen cross-contamination. Teosinte crossing barrier 1 (Tcb1) is a cross-incompatibility system in which silks possessing dominant Tcb1-s reject pollen possessing the recessive allele (tcb1). However, successful fertilization occurs when Tcb1-s pollen falls upon tcb1 silks or under self-fertilization of Tcb1-s pollen on Tcb1-s silks. Previous studies have shown that the efficacy of dominant Tcb1-s was reduced when repeatedly backcrossing with maize inbred lines suggesting the presence of modifiers to Tcb1-s. To find those modifiers, we conducted a QTL mapping experiment using the Intermated B73 x Mo17 (IBM) recombinant inbred lines (RILs) for two consecutive years. Two significant and stable QTL were identified on chromosomes 4L and 5S explained 16% and 17.6% of the total phenotypic variation (R2), and both had negative additive effects. Further investigation of these QTL regions identified twelve candidate genes that could modify Tcb1-s activity. The introgression of the Tcb1-s genetic system, and its appropriate modifying factors, could be a novel and reliable solution for cultivar isolation in maize breeding.
Culturomics of Andropogon gerardii rhizobiome revealed nitrogen transforming capabilities of stress-tolerant Pseudomonas under drought conditions
Authors: Sarkar Soumyadev , Kamke Abigail , Ward Kaitlyn , Hartung Eli , Ran Qinghong , Feehan Brandi , Galliart Matthew , Jumpponen Ari , Johnson Loretta , Lee Sonny T.M. 
Published: July 2022

AbstractBackgroundClimate change will result in more frequent droughts that impact soil-inhabiting microbiomes in the agriculturally vital North American perennial grasslands. In this study, we used the combination of culturomics and high-resolution genomic sequencing of microbial consortia isolated from the rhizosphere of a tallgrass prairie foundation grass, Andropogon gerardii. We cultivated the plant host-associated microbes under artificial drought-induced conditions and identified the microbe(s) that might play a significant role in the rhizobiome of Andropogon gerardii under drought conditions.ResultsPhylogenetic analysis of the non-redundant metagenome-assembled genomes (MAGs) identified the bacterial population of interest – MAG-Pseudomonas. Further metabolic pathway and pangenome analyses detected genes and pathways related to nitrogen transformation and stress responses in MAG-Pseudomonas.ConclusionsOur data indicate that the metagenome-assembled MAG-Pseudomonas has the functional potential to contribute to the plant host’s growth during stressful conditions. This study provided insights into optimizing plant productivity under drought conditions.
Intrinsic BMP inhibitor Gremlin regulates lung alveolar progenitor cell proliferation and differentiation
Authors: Yanagihara Toyoshi , Zhou Quan , Tsubouchi Kazuya , Revill Spencer , Ayoub Anmar , Chong Sy Giin , Dvorkin-Gheva Anna , Ask Kjetil , Shi Wei , Kolb Martin RJ 
Published: July 2022

AbstractType 1 alveolar epithelial cells (AT1s) and type 2 alveolar epithelial cells (AT2s) regulate the structural integrity and function of alveoli. AT1s mediate gas exchange, whereas AT2s serve multiple functions, including surfactant secretion and alveolar repair through proliferation and differentiation into AT1s as progenitors. However, mechanisms regulating AT2 proliferation and differentiation remain unclear. Here we demonstrate that Gremlin, an intrinsic inhibitor of bone morphogenetic protein (BMP), induces AT2 proliferation and differentiation. Transient overexpression of Gremlin in rat lungs by adenovirus vector delivery suppressed BMP signaling, induced proliferation of AT2s and the production of Bmp2, which in turn led to the recovery of BMP signaling and induced AT2 differentiation into AT1s. Gremlin was upregulated in a bleomycin-induced lung injury model. TGF-β and IL-1β induced Gremlin expression in fibroblasts. Taken together, our findings implicate that Gremlin expression during lung injury leads to precisely timed inhibition of BMP signaling and activates AT2s, leading to alveolar repair.
The First Geographic Identification by Country of Sustainable Mutations of SARS-COV2 Sequence Samples: Worldwide Natural Selection Trends
Authors: Mahmanzar Mohammadamin , Houseini Seyed Taleb , Rahimian Karim , Namini Arsham Mikaeili , Gholamzad Amir , Tokhanbigli Samaneh , Sisakht Mahsa Mollapour , Farhadi Amin , Kuehu Donna Lee , Deng Youping 
Published: July 2022

ABSTRACTThe high mutation rates of RNA viruses, coupled with short generation times and large population sizes, allow viruses to evolve rapidly and adapt to the host environment. The rapidity of viral mutation also causes problems in developing successful vaccines and antiviral drugs. With the spread of SARS-CoV-2 worldwide, thousands of mutations have been identified, some of which have relatively high incidences, but their potential impacts on virus characteristics remain unknown. The present study analyzed mutation patterns, SARS-CoV-2 AASs retrieved from the GISAID database containing 10,500,000 samples. Python 3.8.0 programming language was utilized to pre-process FASTA data, align to the reference sequence, and analyze the sequences. Upon completion, all mutations discovered were categorized based on geographical regions and dates. The most stable mutations were found in nsp1(8% S135R), nsp12(99.3% P323L), nsp16 (1.2% R216C), envelope (30.6% T9I), spike (97.6% D614G), and Orf8 (3.5% S24L), and were identified in the United States on April 3, 2020, and England, Gibraltar, and, New Zealand, on January 1, 2020, respectively. The study of mutations is the key to improving understanding of the function of the SARS-CoV-2, and recent information on mutations helps provide strategic planning for the prevention and treatment of this disease. Viral mutation studies could improve the development of vaccines, antiviral drugs, and diagnostic assays designed with high accuracy, specifically useful during pandemics. This knowledge helps to be one step ahead of new emergence variants.IMPORTANCEMore than two years into the global COVID-19 pandemic, the focus of attention is shifted to the emergence and spread of the SARS-CoV-2 variants that cause the evolutionary trend.Here, we analyzed and compared about 10.5 million sequences of SARS-CoV-2 to extract the stable mutations, frequencies and the substitute amino acid that changed with the wild-type one in the evolutionary trend.Also, developing and designing accurate vaccines could prepare long-term immunization against different local variants. In addition, according to the false negative results of the COVID-19 PCR test report in the diagnosis of new strains, investigating local mutation patterns could help to design local primer and vaccine.
Influence of dynamic content on visual attention during video advertisements
Authors: Wooley Brooke , Bellman Steven , Hartnett Nicole , Rask Amy , Varan Duane 
Published: July 2022

PurposeDynamic advertising, including television and online video ads, demands new theory and tools developed to understand attention to moving stimuli. The purpose of this study is to empirically test the predictions of a new dynamic attention theory, Dynamic Human-Centred Communication Systems Theory, versus the predictions of salience theory.Design/methodology/approachAn eye-tracking study used a sample of consumers to measure visual attention to potential areas of interest (AOIs) in a random selection of unfamiliar video ads. An eye-tracking software feature called intelligent bounding boxes (IBBs) was used to track attention to moving AOIs. AOIs were coded for the presence of static salience variables (size, brightness, colour and clutter) and dynamic attention theory dimensions (imminence, motivational relevance, task relevance and stability).FindingsStatic salience variables contributed 90% of explained variance in fixation and 57% in fixation duration. However, the data further supported the three-way interaction uniquely predicted by dynamic attention theory: between imminence (central vs peripheral), relevance (motivational or task relevant vs not) and stability (fleeting vs stable). The findings of this study indicate that viewers treat dynamic stimuli like real life, paying less attention to central, relevant and stable AOIs, which are available across time and space in the environment and so do not need to be memorised.Research limitations/implicationsDespite the limitations of small samples of consumers and video ads, the results of this study demonstrate the potential of two relatively recent innovations, which have received limited emphasis in the marketing literature: dynamic attention theory and IBBs.Practical implicationsThis study documents what does and does not attract attention to video advertising. What gets attention according to salience theory (e.g. central location) may not always get attention in dynamic advertising because of the effects of relevance and stability. To better understand how to execute video advertising to direct and retain attention to important AOIs, advertisers and advertising researchers are encouraged to use IBBs.Originality/valueThis study makes two original contributions: to marketing theory, by showing how dynamic attention theory can predict attention to video advertising better than salience theory, and to marketing research, showing the utility of tracking visual attention to moving objects in video advertising with IBBs, which appear underutilised in advertising research.
Proceedings of the annual meetings of the association for information science and technology: analysis of two decades of published research
Authors: Islam Md. Anwarul , Agarwal Naresh Kumar 
Published: July 2022

Purpose
The purpose of this study is to investigate the research and publication trends in the articles published in the conference proceedings of the Association for Information Science & Technology (ASIS&T) since the year 2000.

Design/methodology/approach
We analyzed two decades of ASIS&T proceedings to uncover bibliometric patterns. This study uses two bibliometric procedures applied to the publications in the ASIS&T conference proceedings – a bibliometrics analysis using three data sources (Scopus, ASIS&T proceedings website and Scimago journal ranking) and a scientific mapping analysis using VOSViewer.

Findings
We found 3,129 publications from 2000 to 2020, with more than three-quarters jointly authored. Most authors are from the United States, Canada and China. Social media and information behavior are the top-researched areas. The top-cited journals are the Journal of the Association for Information Science & Technology, Information Processing and Management and Library and Information Science Research.

Research limitations/implications
The study will help information professionals understand patterns in recent research, which should help guide them in their future research directions.

Practical implications
The findings affirm ASIS&T’s move to an international association and point to the growing importance of collaborative work and social media.

Originality/value
ASIS&T has been holding annual meetings since the 1950s. While there have been various bibliometric studies analyzing publication trends in different journals in the field of information science, none of these studies have analyzed the ASIS&T conference proceedings.
Lean implementation: analysis of individual-level factors in a biopharmaceutical organisation
Authors: Duggan Jeff , Cormican Kathryn , McDermott Olivia 
Published: July 2022

Purpose
An understanding of the motivation of individual employees to adopt lean practices is fundamental to successful lean implementation. This study aims to investigate the adoption of lean practices and provides an analysis of the individual-level factors necessary for lean implementation. This study presents a method for assessing the impact of individual-level factors in a company deploying lean within a biopharmaceutical manufacturing subsidiary.

Design/methodology/approach
The case study explores the attitudes of individuals within a functionally structured organisation undergoing a lean implementation initiative. A quantitative data collection approach was used to capture data from employees in a medical device manufacturing organisation.

Findings
The study found that personality and affective organisational commitment positively affects an individual’s intention to adopt lean practices. Employees with greater levels of affective commitment are more likely to partake in lean-related practices. Individuals in functions that directly support the production process, as opposed to those in functions that indirectly support production, are more likely to participate in lean practices. Finally, individuals in supervisory roles are more likely to adopt lean practices than those in non-supervisory roles, and management should involve top performers in lean.

Originality/value
There is a paucity of case study research in the area of individual-level factors for lean practice adoption. The findings of this study offer practical guidance on individual-level factors for lean practice adoption and illuminate new avenues for future research. This analysis also makes a practical contribution to the literature. From a managerial perspective, understanding why certain employees are more willing to adopt lean practices contributes to an overall lean organisational readiness and implementation framework. This insight enables the development of carefully tailored communication and training programs for managing employee motivation for and receptivity to lean.