bluuebunny/crossref_metadata_2025_split huggingface dataset:
Transcription Factor Dynamics in Cross-Regulation of Plant Hormone Signaling Pathways
Authors: Yin Lingling , Zander Mark , Huang Shao-shan Carol , Xie Mingtang , Song Liang , Guzmán J. Paola Saldierna , Hann Elizabeth , Shanbhag Bhuvana K. , Ng Sophia , Jain Siddhartha , Janssen Bart J. , Clark Natalie M. , Walley Justin W. , Beddoe Travis , Bar-Joseph Ziv , Lewsey Mathew G. , Ecker Joseph R. 
Published: March 2023

AbstractCross-regulation between hormone signaling pathways is indispensable for plant growth and development. However, the molecular mechanisms by which multiple hormones interact and co-ordinate activity need to be understood. Here, we generated a cross-regulation network explaining how hormone signals are integrated from multiple pathways in etiolated Arabidopsis (Arabidopsis thaliana) seedlings. To do so we comprehensively characterized transcription factor activity during plant hormone responses and reconstructed dynamic transcriptional regulatory models for six hormones; abscisic acid, brassinosteroid, ethylene, jasmonic acid, salicylic acid and strigolactone/karrikin. These models incorporated target data for hundreds of transcription factors and thousands of protein-protein interactions. Each hormone recruited different combinations of transcription factors, a subset of which were shared between hormones. Hub target genes existed within hormone transcriptional networks, exhibiting transcription factor activity themselves. In addition, a group of MITOGEN-ACTIVATED PROTEIN KINASES (MPKs) were identified as potential key points of cross-regulation between multiple hormones. Accordingly, the loss of function of one of these (MPK6) disrupted the global proteome, phosphoproteome and transcriptome during hormone responses. Lastly, we determined that all hormones drive substantial alternative splicing that has distinct effects on the transcriptome compared with differential gene expression, acting in early hormone responses. These results provide a comprehensive understanding of the common features of plant transcriptional regulatory pathways and how cross-regulation between hormones acts upon gene expression.
Modeling the role of the thalamus in resting-state functional connectivity: nature or structure
Authors: Cabrera-Álvarez Jesús , Doorn Nina , Maestú Fernando , Susi Gianluca 
Published: March 2023

AbstractThe thalamus is a central brain structure that serves as a relay station for sensory inputs from the periphery to the cortex and regulates cortical arousal. Traditionally, it has been regarded as a passive relay that transmits information between brain regions. However, recent studies have suggested that the thalamus may also play a role in shaping functional connectivity (FC) in a task-based context. Based on this idea, we hypothesized that due to its centrality in the network and its involvement in cortical activation, the thalamus may also contribute to resting-state FC, a key neurological biomarker widely used to characterize brain function in health and disease. To investigate this hypothesis, we constructed ten in-silico brain network models based on neuroimaging data (MEG, MRI, and dwMRI), and simulated them including and excluding the thalamus. and raising the noise into thalamus to represent the afferences related to the reticular activating system (RAS) and the relay of peripheral sensory inputs. We simulated brain activity and compared the resulting FC to their empirical MEG counterparts to evaluate model’s performance. Results showed that a parceled version of the thalamus with higher noise, able to drive damped cortical oscillators, enhanced the match to empirical FC. However, with an already active self-oscillatory cortex, no impact on the dynamics was observed when introducing the thalamus. We also demonstrated that the enhanced performance was not related to the structural connectivity of the thalamus, but to its higher noisy inputs. Additionally, we highlighted the relevance of a balanced signal-to-noise ratio in thalamus to allow it to propagate its own dynamics. In conclusion, our study sheds light on the role of the thalamus in shaping brain dynamics and FC in resting-state and allowed us to discuss the general role of criticality in the brain at the mesoscale level.Author summarySynchrony between brain regions is an essential aspect of coordinated brain function and serves as a biomarker of health and disease. The thalamus, due to its centrality and widespread connectivity with the cortex, is a crucial structure that may contribute to this synchrony by allowing distant brain regions to work together. In this study, we used computational models to investigate the thalamus’s role in generating brain synchrony at rest. Our findings suggest that the structural connectivity of the thalamus is not its primary contribution to brain synchrony. Instead, we found that the thalamus plays a critical role in driving cortical activity, and when it is not driving this activity, its impact on brain synchrony is null. Our study provides valuable insights into the thalamocortical network’s role in shaping brain dynamics and FC in resting state, laying the groundwork for further research in this area.
Transcript-specific induction of stop codon readthrough using CRISPR-dCas13 system
Authors: Manjunath Lekha E. , Singh Anumeha , Kar Debaleena , Sellamuthu Karthi , Eswarappa Sandeep M. 
Published: March 2023

AbstractStop codon readthrough (SCR) is the process where translation continues beyond a stop codon on an mRNA. Here, we describe a strategy to enhance or induce SCR in a transcript-selective manner using CRISPR-dCas13 system. Using specific guide RNAs, we targeted dCas13 to the downstream region of the canonical stop codons of mammalianAGO1andVEGFA,which are known to exhibit natural SCR. Results of readthrough assays revealed the enhancement of SCR of these mRNAs (both exogenous and endogenous) caused by dCas13. This effect was associated with ribosomal pausing, which has been reported in several SCR events. Furthermore, our results show that CRISPR-dCas13 can induce SCR across premature termination codons (PTC) in the mRNAs of green fluorescent protein andTP53. Finally, we demonstrate the utility of this strategy in the induction of readthrough across the thalassemia-causing PTC inHBBmRNA. Thus, CRISPR-dCas13 can be programmed to enhance or induce SCR in a transcript-selective and stop codon-specific manner.
Analysis of histone antibody specificity directly in sequencing data using siQ-ChIP
Authors: Kupai Ariana , Vaughan Robert M. , Rothbart Scott B. , Dickson Bradley M. 
Published: March 2023

ABSTRACTWe previously developed sans spike-in quantitative chromatin immunoprecipitation sequencing (siQ-ChIP), a technique that introduces an absolute quantitative scale to ChIP-seq data without reliance on spike-in normalization approaches. The physical model of siQ-ChIP predicted that the IP step of ChIP would produce a classical binding isotherm when antibody or epitope was titrated. Here, we define experimental conditions in which this titration is observable for antibodies that recognize modified states of histone proteins. We show that minimally sequenced points along an isotherm can reveal differential binding specificities that are associated with on- and off-target epitope interactions. This work demonstrates that the interpretation of histone post-translational modification distribution from ChIP-seq data has a dependence on antibody concentration. Collectively, these studies introduce a simplified and reproducible experimental method to generate quantitative ChIP-seq data without spike-in normalization and demonstrate that histone antibody specificity can be analyzed directly in ChIP-seq experiments.
Top-down, auditory pallial regulation of the social behavior network
Authors: Spool Jeremy A. , Lally Anna P. , Remage-Healey Luke 
Published: March 2023

AbstractSocial encounters rely on sensory cues that carry nuanced information to guide social decision-making. While high-level features of social signals are processed in the telencephalic pallium, nuclei controlling social behaviors, called the social behavior network (SBN), reside mainly in the diencephalon. Although it is well known how mammalian olfactory pallium interfaces with the SBN, there is little information for how pallial processing of other sensory modalities can modulate SBN circuits. This is surprising given the importance of complex vocalizations, for example, for social behavior in many vertebrate taxa such as humans and birds. Using gregarious and highly vocal songbirds, female Zebra finches, we asked to what extent auditory pallial circuits provide consequential input to the SBN as it processes social sensory cues. We transiently inactivated auditory pallium of female Zebra finches during song playback and examined song-induced activation in SBN nuclei. Auditory pallial inactivation impaired responses to song specifically within the lateral ventromedial nucleus of the hypothalamus (VMHl), providing the first evidence in vertebrates of a connection between auditory pallium and the SBN. This same treatment elevated feeding behavior, which also correlated with VMHl activation. This suggests that signals from auditory pallium to VMHl can tune the balance between social attention and feeding drive. A descending influence of sensory pallium on hypothalamic circuits could therefore provide a functional connection for the integration of social stimuli with internal state to influence social decision-making.SignificanceSensory cues such as vocalizations contain important social information. These social signals can be substantially nuanced, containing information about vocalizer identity, prior experience, valence, and emotional state. Processing these features of vocalizations necessitates processing the fast, complex sound streams in song or speech, which depends on circuits in pallial cortex. But whether and how this information is then transferred to social circuits in limbic and hypothalamic regions remains a mystery. Here, we identify a top-down influence of the songbird auditory pallium on one specific node of the social behavior network within the hypothalamus. Descending functional connections such as these may be critical for the wide range of vertebrate species that rely on intricate sensory communication signals to guide social decision-making.
The CGG triplet repeat binding protein 1 counteracts DNA secondary structure-induced transcription-replication conflicts
Authors: Ummethum Henning , Lalonde Maxime , Werner Marcel , Trauner Manuel , Chanou Anna , Weiβ Matthias , Lee Clare S. K. , Kruse Elisabeth , Ettinger Andreas , Hamperl Stephan 
Published: March 2023

SummaryShort tracts of trinucleotide repeats with less than 10 repeats are found frequently throughout the genome without any apparent negative impact on DNA replication fork progression or transcription elongation. CGG binding protein 1 (CGGBP1) binds to CGG triplet repeats and has been implicated in multiple cellular processes such as transcription, replication and DNA damage. Here, we show that CGGBP1 binds to human gene promoter sites prone to G-quadruplex and R-loop secondary structure formation. Altering CGGBP1 levels results in the accumulation of R-loops and causes a defect in transcriptional elongation by RNA polymerase II, which subsequently leads to replication fork stalling and transcription-replication conflicts. Together, our work shows that short trinucleotide repeats are a source of genome-destabilizing secondary structures and cells rely on specific DNA-binding factors to maintain proper transcription and replication progression at short trinucleotide repeats.
Intragroup conflict dynamics and their linkages with horizontal power disparity configurations, upper management conflicts and coworker support
Authors: Tremblay Michel 
Published: March 2023

Purpose
This study aims to examine how changes in power disparity shape in-groups and upper-level management conflict are associated with intragroup relationship and task conflict variations. It also examines how workplace conflicts relate to focal employees’ perceptions of coworker support.

Design/methodology/approach
Data were collected from 3,343 respondents for nine years, comprising measurements taken on six occasions in 47 departments and stores of a Canadian retailer. The relationships between, within and across levels were tested using multilevel structural equation modeling.

Findings
The results showed that higher levels of power concentration vested by a few members or a single person are associated wih higher levels of intragroup conflict than usual. Furthermore, higher levels of task and relationship conflicts at upper management levels are associated with higher-than-usual task and relationship conflicts between nonhierarchical employees. Additionally, a higher-than-usual intragroup task conflict level was associated with lower-than-usual coworker support, supporting the proposed multilevel dynamic model.

Research limitations/implications
An important limitation of this study is that all variables are self-reported despite using the six-wave repeated measurements, thereby increasing the possibility of inflating some observed relationships. Future research should examine the emergence of a larger spectrum of power dispersion configurations and their role on process conflict.

Practical implications
Retail managers should legitimize why a high-power concentration occurs when the equal distribution of power is not possible and find ways to minimize the trickle-down effects of conflicts at upper levels on their subordinates.

Originality/value
This study examines the effect of variability on power configurations and conflict in upper management ranks on conflict dynamic. The findings show that a high-power concentration elicits increasing conflicts, and that there is no empirical evidence that intragroup conflict is associated with positive outcomes.
Education Briefing Property capitalisation rates –benchmarking the property market
Authors: Camilleri Denis 
Published: March 2023

PurposeThe aim of this Education Briefing is to comment upon the construction and role of the capitalisation rate in the valuation of property assets and how the implicit assumptions of growth are market derived and may be considered more robust than the use of growth explicit discounted cash flow (DCF) models where explicit growth assumptions can be questioned.Design/methodology/approachThis Education Briefing will look at the role of analysing initial yields to derive market capitalisation rates, and it will look at component parts of the yield to isolate growth assumptions and compare property returns to the government bond market.FindingsLooking at the Maltese market, the briefing shows that the valuer needs to be aware of the advantages and disadvantages of implicit and explicit valuation models.Practical implicationsThe choice of valuation model is dependent upon the availability of suitable comparable information and the appropriateness of the model for the market in question. More transparent markets can benefit from the use of explicit models but where information is less available, such as the Maltese market, implicit models may be considered more robust at estimating market value.Originality/valueThis is an Education Briefing discussing the construction and applicability of implicit valuation models using a market capitalisation rate.
Predicting long‐run risk factors of stock returns: Evidence from Australia
Authors: Banerjee Rajabrata , Cavoli Tony , McIver Ron , Meng Shannon , Wilson John K. 
Published: March 2023

AbstractThis study utilises the stock market data provided by the Australian Equity Database to analyse the long‐run relationship between Australian stock returns and key macroeconomic variables over the period 1926–2017. To measure the diverse risk factors in the stock market, we examine the possible determinants in four main categories: real, financial, domestic and international. Our results reveal that historical stock returns are strongly connected to financial and international factors as compared to real and domestic factors. Both the 1973–1974 OPEC Oil Price Crisis and 2007–2008 Global Financial Crisis had dampening effects on stock returns. There is a positive association between the US and Australian stock markets in the long‐run. These findings on stock market dynamics and their linkages with domestic and international macroeconomic policy changes in the long‐run have important implications for traders and practitioners.
Beyond Performance: Does Assessed Potential Matter to Employees’ Voluntary Departure Decisions?
Authors: DELLER CAROLYN 
Published: March 2023

ABSTRACTFirms are increasingly implementing performance–potential assessment systems, whereby supervisors evaluate employees’ current performance and future‐oriented potential (i.e., promotion prospects). Whether retention is greatest for high performance–high potential (HiPo) employees under such a system is an empirical question—while the “promise” of a promotion may aid retention, these employees likely face attractive outside options. Using data from a multinational firm, I find that HiPos generally depart at a lower rate than lower performing non‐HiPos. Among shorter tenured employees, I find the strongest evidence that potential matters to departures, above and beyond performance. In several instances, the rate of departure is lower when assessed potential is higher, holding performance constant. This is the case both among higher performers, where high potential leads to HiPo status, and among lower performers where high potential affords no such status. My findings suggest that HiPo status and potential ratings may help in facilitating employees’ early sorting decisions.
Effect of ticagrelor on the function of tunneled cuffed catheter in maintenance hemodialysis patients
Authors: Shen Jianming , Deng Yanyan , Wang Liping , Zha Fei 
Published: March 2023

AbstractObjectiveTo observe the effect of ticagrelor on the function of a tunneled cuffed catheter (TCC) in maintenance hemodialysis (MHD) patients.MethodsEighty MHD patients (control group: 39 cases, observation group: 41 cases) using TCC as vascular access were enrolled from January 2019 to October 2020 in this prospective study. Patients in the control group were routinely treated with aspirin for antiplatelet therapy, while patients in the observation group were treated with ticagrelor. The catheter life time, catheter dysfunction, coagulation function, and antiplatelet drug‐related adverse events of the two groups were recorded.ResultsThe median life time of TCC in the control group was significantly higher than that in the observation group. Moreover, the log rank test showed that the difference was statistically significant (p < 0.001).ConclusionTicagrelor may reduce the incidence of catheter dysfunction and prolong the life time of the catheter by preventing and reducing the thrombosis of TCC in MHD patients, without obvious side effects.
Longer leukocyte telomere length increases cardiovascular mortality in type 2 diabetes patients
Authors: Chen Ziwei , Shen Yao , He Jing , Shen Yang , Zhu Weida , Wu Xiaohui , Xiao Mingbing 
Published: March 2023

AbstractAimsLeukocyte telomere length (LTL), as a biomarker of biological aging, is associated with the prevalence and complications of diabetes. This study aims to investigate the associations between LTL and all‐cause and cause‐specific mortality in patients with type 2 diabetes.MethodsAll participants with baseline LTL records were included from the National Health and Nutrition Examination Survey 1999–2002. Death status and its causes were ascertained for National Death Index based on International Classification of Diseases, Tenth Revision code. Cox proportional hazards regression models were established to estimate the hazard ratios (HRs) of LTL associating with all‐cause and cause‐specific mortality.ResultsThe study enrolled 804 diabetic patients with the mean follow‐up of 14.9 ± 2.59 years. There were 367 (45.6%) all‐cause deaths, 80 (10.0%) cardiovascular deaths, and 42 (5.2%) cancer‐related deaths. Longer LTL was associated with reduced all‐cause mortality, whereas this association disappeared after adjusting for other variables. Compared with the lowest tertiles of LTL, the multivariable‐adjusted hazard ratio of cardiovascular mortality was 2.11 (95% confidence interval [CI] 1.31–3.39; p < .05) in the highest tertiles. In terms of cancer mortality, the highest tertile was negatively correlated with the risk of cancer mortality (HR 0.58 [95% CI 0.37, 0.91], p < .05).ConclusionIn conclusion, LTL was independently associated with the risk of cardiovascular mortality in patients with type 2 diabetes and was negatively correlated with the risk of cancer mortality. Telomere length may be a predictor of cardiovascular mortality in diabetes.
Mortality and prognostic factors in connective tissue disease‐associated pulmonary arterial hypertension patients complicated with right heart failure
Authors: Deng Xiaoyue , Jiang Nan , Huang Can , Zhou Shuang , Peng Linyi , Zhang Li , Liu Jinjing , Wang Li , Zhou Jiaxin , Wang Qian , Weng Li , Peng Jinmin , Zhao Jiuliang , Li Mengtao , Zeng Xiaofeng 
Published: March 2023

AbstractObjectiveTo identify predictive factors associated with mortality in connective tissue disease‐associated pulmonary arterial hypertension (CTD‐PAH) patients who were complicated with right heart failure (RHF).MethodsIn this single‐center retrospective study, baseline demographics, clinical features, laboratory results, and hemodynamic assessments were collected. Kaplan–Meier analysis was applied to analyze all‐cause mortality. Univariate and forward stepwise multivariate Cox proportional regression analyses were performed to identify independent predictors of mortality.ResultsA total of 51 right heart catheterization‐confirmed CTD‐PAH patients complicated with RHF were consecutively enrolled in this study from 2012 to 2022. Forty‐eight (94%) enrolled patients were female and the mean age was 36.0 ± 11.8 years. Thirty‐two (61.5%) were systemic lupus erythematosus‐PAH and 33%/67% showed World Health Organization functional class III/IV, respectively. Twenty‐five (49%) of those patients died and Kaplan–Meier analysis showed the overall 1‐, 3‐, and 5‐week survival rates from the time of hospitalization as 86.28%, 60.78%, and 56.86%, respectively. RHF in CTD‐PAH patients mainly resulted from progression of PAH (n = 19) and infection (n = 5), which also contributed to the leading causes of death. Statistical analysis between survivors and non‐survivors showed that death from RHF was associated with higher levels of urea (9.66 vs 6.34 mmol/L, P = 0.002), lactate (cLac: 2.65 vs 1.9 mmol/L, P = 0.006), total bilirubin (23.1 vs 16.9 μmol/L, P = 0.018) and direct bilirubin (10.5 vs 6.5 μmol/L, P = 0.004), but with lower levels of hematocrit (33.7 vs 39, P = 0.004), cNa+ (131 vs 136 mmol/L, P = 0.003). Univariate and forward stepwise multivariate Cox proportional regression analyses indicated that the level of cLac (hazards ratio:1.297; 95% CI: 1.076–1.564; P = 0.006) was an independent risk factor for mortality.ConclusionThe short‐term prognosis of CTD‐PAH complicated with RHF was very poor, and hyperlactic acidemia (cLac > 2.85 mmoL/L) was an independent predicting factor for mortality of CTD‐PAH patients complicated with RHF.