bluuebunny/crossref_metadata_2025_split huggingface dataset:
The genetic interaction of REVOLUTA and WRKY53 links plant development, senescence, and immune responses
Authors: Bresson Justine , Doll Jasmin , Vasseur François , Stahl Mark , von Roepenack-Lahaye Edda , Kilian Joachim , Stadelhofer Bettina , Kremer James M. , Kolb Dagmar , Wenkel Stephan , Zentgraf Ulrike 
Published: July 2021

AbstractIn annual plants, tight coordination of successive developmental events is of primary importance to optimize performance under fluctuating environmental conditions. The recent finding of the genetic interaction of WRKY53, a key senescence-related gene with REVOLUTA, a master regulator of early leaf patterning, raises the question of how early and late developmental events are connected. Here, we investigated the developmental and metabolic consequences of an alteration of the REVOLUTA and WRKY53 gene expression, from seedling to fruiting. Our results show that REVOLUTA critically controls late developmental phases and reproduction while inversely WRKY53 determines vegetative growth at early developmental stages. We further show that these regulators of distinct developmental phases frequently, but not continuously, interact throughout ontogeny and demonstrated that their genetic interaction is mediated by the salicylic acid (SA). Moreover, we showed that REVOLUTA and WRKY53 are keys regulatory nodes of development and plant immunity thought their role in SA metabolic pathways, which also highlights the role of REV in pathogen defence. Together, our findings demonstrate how late and early developmental events are tightly intertwined by molecular hubs. These hubs interact with each other throughout ontogeny, and participate to the interplay between plant development and immunity.
Selection and evaluation of qPCR reference genes for expression analysis in the tiny egg parasitoid wasp,Trichogramma dendrolimiMatsumura (Hymenoptera: Trichogrammatidae)
Authors: Huo Liang-xiao , Bai Xue-ping , Che Wu-nan , Ning Su-fang , Lv Lin , Zhang Li-sheng , Zhou Jin-cheng , Dong Hui 
Published: July 2021

AbstractThe egg parasitoidTrichogrammaspp. is an important biological control agent used against multiple species of Lepidopteran pest in forestry and agriculture. Due to the importance ofTrichogrammaspp. in biocontrol programs, its biological characteristics have been studied in detail, and current investigations should focus on the molecular biology of these tiny parasitoids. Real-time quantitative PCR (qPCR) is considered as the standard method for quantifying the gene expression of organisms. Surprisingly, the appropriate reference genes to ensure robust qPCR have not been documented at all for theTrichogrammagenus. This study aimed to identify suitable reference genes for use in qPCR procedure ofTrichogramma dendrolimi. Nine candidate housekeeping genes, namely glyceraldehyde-3-phosphate dehydrogenase (GAPDH), forkhead box O (FOXO), superoxide dismutase (SOD), beta-actin (ACTIN), ribosomal protein L10a (RPL10a), L18 (RPL18), L28 (RPL28), S13 (RPS13), and S15 (RPS15), were tested for their suitability as reference genes for developmental stage (3rd, 4th, 5th, 6th, 7th, 8th, 9th, and 10thday after parasitization), tissue (head, thorax, and abdomen of adults), sex of adults (male and female), and temperature (17 °C, 25 °C, and 32 °C). According to the GeNorm analysis, robust analysis should involve using an appropriate combination of reference genes, namely, at least three genes for different development stages, two genes for different tissues, two genes for different sex, and two genes for different temperature, respectively. According to the RelFinder method and by assessing the integrated values from using the ΔCt method, GeNorm, NormFinder, and BestKeeper, we identified the developmental stage-specific reference genesSOD, GAPDH, andACTIN; tissue-specific reference genesRPL18andRPS15; sex-specific reference genesSODandRPL18; and temperature-specific reference genesRPL18andRPL10. When testing the use of stable vs. unstable reference genes, the substantial differences were observed in the estimation expression of a hypothetical target gene,HSP90, in response to temperature. The present study provides a robust method for the measurement of gene expression inT. dendrolimiand will be helpful for future biological control programs usingTrichogrammawasps.
spatialGE: Quantification and visualization of the tumor microenvironment heterogeneity using spatial transcriptomics
Authors: Ospina Oscar E. , Wilson Christopher M. , Soupir Alex C. , Berglund Anders , Smalley Inna , Tsai Kenneth Y. , Fridley Brooke L. 
Published: July 2021

AbstractSummarySpatially-resolved transcriptomics promises to increase our understanding of the tumor microenvironment and improve cancer prognosis and therapies. Nonetheless, analytical methods to explore associations between the spatial heterogeneity of the tumor and clinical data are not available. Hence, we have developed spatialGE, a software that provides visualizations and quantification of the tumor microenvironment heterogeneity through gene expression surfaces, spatial heterogeneity statistics (SThet) that can be compared against clinical information, spot-level cell deconvolution, and spatially-informed clustering (STclust), all using a new data object to store data and resulting analyses simultaneously.Availability and implementationThe R package and tutorial/vignette are available at https://github.com/FridleyLab/spatialGE. A script to reproduce the analyses in this manuscript is available in Supplementary information.ContactFridley.Lab@Moffitt.org or Brooke.Fridley@Moffitt.orgSupplementary informationAvailable at Bioinformatics online.Abstract FigureGraphical abstractOverview of spatialGE features. A. The STList data object from spatialGE can be creared from several sources, including comma- or tab-separated files containing gene counts and spatial coordinates. The object can also be created directly from Visium outputs, Seurat objects, or GeoMx outputs. B. Users can optionally provide a metadata file, containing information associated with each sample (one row per sample, or per ROI if GeoMx data). C. Methods for quality control of data are provided by spatialGE, including visualizations of counts and genes per spot, as well as filtering of spots or genes within user-determined thresholds. D. A novel method (STclust) performs spatially informed clustering of spots and tissue domain identification. E. spatialGE provides different types of data visualization, including gene expression at each spot (“quilt plots”), as well as adaptation of spatial interpolation (“kriging”) to spatial transcriptomics data (transcriptomic surface). F. spatialGE also leverages spatial statistics (Moran’s I, Geary’s C, Getis-Ord Gi) to quantitatively describe heterogeneity within the tumor microenvironment and to explore associations between spatial heterogeneity and clinical oucomes. G. Gene expression deconvolution can also be applied to each spot to detect immune cell types (xCell) and classification of spots as tumor or stroma (ESTIMATE).
Water Nanoconfined in a Hydrophobic Pore: MD Simulations and Water Models
Authors: Lynch Charlotte I. , Klesse Gianni , Rao Shanlin , Tucker Stephen J. , Sansom Mark S. P. 
Published: July 2021

AbstractWater molecules within biological ion channels are in a nano-confined environment and therefore exhibit novel behaviours which differ from that of bulk water. Here, we investigate the phenomenon of hydrophobic gating, the process by which a nanopore may spontaneously de-wet to form a ‘vapour lock’ if the pore is sufficiently hydrophobic and/or narrow. Notably, this occurs without steric occlusion of the pore. Using molecular dynamics simulations with both additive and polarisable (AMOEBA) force fields, we investigate this wetting/de-wetting behaviour in the TMEM175 ion channel. We examine how a range of rigid fixed-charge (i.e. additive) and polarisable water models affect wetting/de-wetting in both the wild-type structure and in mutants chosen to cover a range of nanopore radii and pore-lining hydrophobicities. Crucially, we find that the rigid fixed-charge water models lead to similar wetting/de-wetting behaviours, but that the polarisable water model resulted in an increased wettability of the hydrophobic gating region of the pore. This has significant implications for molecular simulations of nano-confined water, as it implies that polarisability may need to be included if we are to gain detailed mechanistic insights into wetting/de-wetting processes. These findings are of importance for the design of functionalised biomimetic nanopores (for e.g. sensing or desalination), as well as for furthering our understanding of the mechanistic processes underlying biological ion channel function.
CRISPR-Cas Controls Cryptic Prophages
Authors: Song Sooyeon , Semenova Ekaterina , Severinov Konstantin , Fernández-García Laura , Benedik Michael J. , Maeda Toshinari , Wood Thomas K. 
Published: July 2021

AbstractThe bacterial archetypal adaptive immune system, CRISPR-Cas, is thought to be repressed in the best-studied bacterium,Escherichia coliK-12. We show here that theE. coliCRISPR-Cas system is active and serves to inhibit its nine defective (i.e., cryptic) prophages. Specifically, compared to the wild-type strain, reducing the amounts of specific interfering RNAs (crRNA) decreases growth by 40%, increases cell death by 700%, and prevents persister cell resuscitation. Similar results were obtained by inactivating CRISPR-Cas by deleting the entire 13 spacer region (CRISPR array); hence, CRISPR-Cas serves to inhibit the remaining deleterious effects of these cryptic prophages, most likely through CRISPR array-derived crRNA binding to cryptic prophage mRNA, rather than through cleavage of cryptic prophage DNA; i.e., self-targeting. Consistently, four of the 13E. colispacers contain complementary regions to the mRNA sequences of seven cryptic prophages, and inactivation of CRISPR-Cas increases the level of mRNA for lysis protein YdfD of cryptic prophage Qin and lysis protein RzoD of cryptic prophage DLP-12. Also, lysis is clearly seen via transmission electron microscopy when the whole CRISPR-Cas array is deleted, and eliminating spacer #12, which encodes crRNA with complementary regions for DLP-12 (includingrzoD), Rac, Qin (includingydfD), and CP4-57 cryptic prophages, also results in growth inhibition and cell lysis. Therefore, we report the novel results that (i) CRISPR-Cas is active inE. coliand (ii) CRISPR-Cas is used to tame cryptic prophages, likely through RNAi; i.e., unlike with active lysogens, active CRISPR-Cas and cryptic prophages may stably co-exist.
miR-17∼92 exerts stage-specific effects in adult V-SVZ neural stem cell lineages
Authors: Favaloro Fabrizio , DeLeo Annina , Delgado Ana C. , Doetsch Fiona 
Published: July 2021

SummaryIn the adult mouse brain, neural stem cells (NSCs) in the ventricular-subventricular zone (V-SVZ) generate neurons and glia throughout life. microRNAs are important regulators of cell states, frequently acting in a stage- or context-dependent manner. Here, miRNA profiling of FACS-purified populations identified miR-17∼92 as highly upregulated in activated NSCs and transit amplifying cells (TACs) in comparison to quiescent NSCs. Conditional deletion of miR-17∼92 in NSCs reduced stem cell proliferation both in vitro and in vivo. In contrast, in TACs, miR-17∼92 deletion caused a selective shift from neurogenic DLX2+ TACs towards oligodendrogenic OLIG2+ TACs, resulting in increased oligodendrogenesis to the corpus callosum. miR-17∼92 deletion also decreased proliferation and maturation of intraventricular oligodendrocyte progenitor cells. Together, these findings reveal stage- and cell-type-specific functions of the miR-17∼92 cluster within adult V-SVZ neural stem cell lineages.
Unravelling the effects of disease-associated mutations in TDP-43 protein via molecular dynamics simulation and machine learning
Authors: Sharma Abhibhav , Dey Pinki 
Published: July 2021

AbstractOver the last two decades, the pathogenic aggregation of TAR DNA-binding protein 43 (TDP-43) is found to be strongly associated with several fatal neurodegenerative diseases such as amyotrophic lateral sclerosis (ALS) and frontotemporal lobar degeneration (FTD), etc. While the mutations and truncation in TDP-43 protein have been suggested to be responsible for TDP-43 pathogenesis by accelerating the aggregation process, the effects of these mutations on the bio-mechanism of pathologic TDP-43 protein remained poorly understood. Investigating this at the molecular level, we formulized an integrated workflow of molecular dynamic simulation and machine learning models (MD-ML). By performing an extensive structural analysis of three disease-related mutations (i.e. I168A, D169G, and I168A-D169G) in the conserved RNA recognition motifs (RRMs) of TDP-43 and we observed that the I168A-D169G double mutant delineates the highest packing of the protein inner core as compared to the other mutations, which may indicate more stability and higher chances of pathogenesis. Moreover, through our MD-ML workflow, we identified the biological descriptors of TDP-43 which includes the interacting residue pairs and individual protein residues that influence the stability of the protein and could be experimentally evaluated to develop potential therapeutic strategies.
Nuclear-cytoplasmic compartmentalization promotes robust timing of mitotic events by cyclin B1-Cdk1
Authors: Maryu Gembu , Yang Qiong 
Published: July 2021

SummaryStudies applying well-mixed cytosolic extracts found the mitotic network centered on cyclin-dependent kinase (Cdk1) performs robust relaxation oscillations with tunable frequency [1–6]. However, recent work also highlighted the importance of cyclin B1-Cdk1 nuclear translocation in mitotic timing [7, 8]. How nuclear compartmentalization affects the oscillator properties and the accurate ordering of mitotic events, especially in embryos lacking checkpoints, remains elusive. Here we developed a Förster resonance energy transfer (FRET) biosensor for analyzing Cdk1 spatiotemporal dynamics in synthetic cells containing nuclei compared to those without. We found cellular compartmentalization significantly impacts clock behaviors. While the amplitude-frequency dependency measured in the homogeneous cytoplasm showed highly tunable frequency for a fixed amplitude, confirming predictions by non-spatial models [4], the frequency remains constant against cyclin variations when nuclei are present, suggesting a possible buffering mechanism of nuclear compartments to ensure robust timing. We also found all cyclin degrades within similar mitotic durations despite variable interphase cyclin expression. This scalable degradation of cyclin may further promote the precise mitotic duration. Simultaneous measurements revealed Cdk1 and cyclin B1 cycle rigorously out of phase, producing a wide orbit on their phase plane, essential for robust oscillations. We further mapped mitotic events on the phase-plane orbits. Unlike cytoplasmic-only cells showing delayed Cdk1 activation, nucleus-containing cells exhibit steady cyclin B1-Cdk1 nuclear accumulation until nuclear envelope breakdown (NEB) followed by an abrupt cyclin-independent activation to trigger anaphase. Thus, both biphasic activation and subcellular localization of Cdk1 ensure accurate ordering of substrates.
Estimation of the income and price elasticity of pharmaceutical import demand in Iran
Authors: Otobideh Seyed Alireza , Moeeni Shahram , Mohammadzadeh Yousef , Rahimi Bahlol , Shabaninejad Hosein , Yusefzadeh Hasan 
Published: July 2021

Purpose
Investigating the import of pharmaceutical products, as one of the essential goods of the country to improve health and medical conditions, is important in accelerating the economic growth and enhancing the welfare of the community. This paper aims to estimate the income and price elasticity of pharmaceutical import demand in Iran.

Design/methodology/approach
In this research, the function of Iran's pharmaceutical import demand was estimated and calculated using the co-integration method and error correction techniques with the seasonal data of 2005–2016 to identify factors related to import, as well as relevant price, and income elasticity.

Findings
The research results showed that the price elasticity of Iran's long-term pharmaceutical import demand was 0.04; that is, the rate of pharmaceutical import demanded by Iran was not sensitive to change in relative price. Additionally, the long-term income elasticity of Iran's pharmaceutical demand was 0.69, meaning that an increase in Iran's income did not have a highly positive impact on the volume of Iran's pharmaceutical import.

Originality/value
Estimating the function of the demand for pharmaceutical import may pave the way to adopt appropriate economic policies. Furthermore, estimating this function and calculating income and price elasticity is a step toward minimizing government expenditures and can be a great contribution in designing trade policies.
An empirical analysis of self-service technologies: mediating role ofcustomer powerlessness
Authors: Cao Zhongpeng , Xiao Qian , Zhuang Weiling , Wang Lina 
Published: July 2021

PurposeAs self-service technologies (SSTs) become more prevalent, service providers are actively encouraging customers’ involvement with these technologies, sometimes even forcing their customers to use SSTs. This paper aims to examine the influence of the SST-only (vs full-service) mode on customers’ negative attitude toward SST providers through the mediating mechanism of powerlessness and explores how SST familiarity and SST anthropomorphism moderate the impacts of the SST-only mode on powerlessness.Design/methodology/approachThree experiments were performed, study 1 tested the main and mediating effect and studies 2 and 3 verified the moderating effects.FindingsThe results suggest that customer perceived powerlessness mediates the relationship between SST-only (vs full-service) mode and negative attitude toward SST providers. When the levels of SST familiarity and SST anthropomorphism are high, the impacts of SST-only on powerlessness are attenuated. Alternative mediating mechanism of powerlessness is examined and ruled out.Research limitations/implicationsFuture research should investigate other moderators that may reduce the impacts of SST on customer powerlessness. These moderators could be service-operating procedures, SST interface design, types of service situations and customer characteristics. In addition, other consequences of powerlessness, other than the negative attitude toward SST providers and intention to switch investigated here, should be investigated as well.Practical implicationsThis research provides guidelines helping service providers to improve their customers’ SST usage experience by showing both SST familiarity and SST anthropomorphism may alleviate the negative effects of SST-only mode on customer perceived powerlessness more effectively.Originality/valueThis research examines the role of customers’ psychological reactions toward the SST-only mode, particularly from the perspective of power and control.
Bringing social marketing closer to the disability field
Authors: Gil Guzman Jose Manuel , Hernandez-Fernandez Asuncion , Canales-Ronda Pedro 
Published: July 2021

Purpose
This paper aims to show the advantages that social marketing training programs for disability professionals can play in improving the approach to the problems faced by people with disabilities, offering a necessary mutual understanding between both sectors. So, describing what are the training needs in social marketing expressed by disability professionals and providing an initial shared theoretical framework of both fields that could contribute to implementing social marketing strategies in the field of disability as an inducer of quality of life.

Design/methodology/approach
This is a mixed-method approach combining: a quantitative analysis with a web-based self-administered questionnaire completed in six European countries and a qualitative analysis: interviews to experts pre and post questionnaire.

Findings
Quantitative data has identified that: front-line professionals working directly with people with disabilities have high social marketing training needs; these needs are mostly related to the assessment and modification of clients’ behavior and the development of interventions according to the concept of value co-creation. Qualitative data has shown that: both fields share some similar theoretical frameworks. Therefore, it is stated that social marketing has the potential to be better implemented in the disability field.

Research limitations/implications
Considering public policy; stigma and discrimination; regulations; other models and improving the sampling method.

Originality/value
Sharing theoretical framework of both fields, social marketing strategies into the disability field as an inductor for quality of life. No research has analyzed the needs of disability professionals when they have to face a problem and find a solution that social marketing strategies could offer into the disability field.
Non‐tariff measures and productivity of Ukrainian food‐processing firms
Authors: Shepotylo Oleksandr , Vakhitov Volodymyr , Movchan Veronika , Panga Mariia 
Published: July 2021

AbstractUsing detailed data on veterinary, ecological, sanitary, phytosanitary and mandatory certification measures, this paper studies the effect of non‐tariff measures (NTMs) on firm productivity in the food‐processing industry through forward and backward linkages. Using quantity and value of output at product level, we calculate and compare quantity‐ and revenue‐based measures of total factor productivity (TFP). Exploiting the episode of NTM liberalisation in Ukraine in 2008–2012, we find that NTMs on intermediate inputs have a negative effect on quantity‐based TFP. Other trade policy variables, including input tariffs and output NTMs also negatively influence productivity. The effect on the revenue‐based TFP is weaker due to price and quality adjustments. Interacting changes in input NTMs with import intensity prior to trade liberalisation, we find that firms that used imported inputs more intensively tend to have lower long‐run TFP growth.
Large‐scale reanalysis of refrigerated antemortem blood samples for ethanol content at random intervals
Authors: Kosecki Patrick Allan , Abbott Lori Ann , Raines Melinda Evonne 
Published: July 2021

AbstractEthanol stability in antemortem blood stored under various conditions has been widely studied. Most such studies have somewhat limited sample size (<50) and limited variation in the length of time between the blood draw and the first analysis and between the first analysis and the reanalysis. In the work presented here, the antemortem blood drawn for forensic purposes and stored refrigerated (~4°C) in 371 cases was analyzed for ethanol concentration using headspace gas chromatography at various times after the blood draw based on routine case flow and then also analyzed at various times within approximately 1 year after the first analysis. This methodology is intended to provide insight into the range of differences expected when cases are analyzed in the normal flow of casework and then reanalyzed at random times afterwards as occurs when reanalysis is performed by the defense or by the laboratory if the original analyst is unavailable to testify. In 22 cases, the same blood tube from the case was reanalyzed. The previously unopened blood tube from the case was analyzed in 349 cases. The 25 cases in which the blood was ethanol‐negative based on the first analysis remained ethanol‐negative when reanalyzed. The average difference in ethanol concentration between tests for the ethanol‐positive cases was −0.004 g/dL. This decrease was statistically significant at the 0.05 level of significance. The range of differences was −0.0197 to 0.0103 g/dL. The difference measured in 85% of the ethanol‐positive cases was in in the range of −0.008 to −0.001 g/dL.