bluuebunny/crossref_metadata_2025_split huggingface dataset:
Determinants of transcription initiation efficiency and start site selection by RNA polymerase I
Authors: Parilova Olena , Bartos Piia , Malinen Anssi M. 
Published: October 2024

ABSTRACTRNA polymerase I (Pol I) synthesizes pre-ribosomal RNA, which is essential for ribosome biogenesis. Increased Pol I activity supports rapid cell growth, a key characteristic of cancer cells. Consequently, drugs targeting Pol I in cancer are being actively investigated. The first step in pre-rRNA synthesis involves the assembly of the Pol I transcription initiation complex on the rRNA gene promoter, yet the quantitative and dynamic parameters of this process remain inadequately defined. We combined biochemical, biophysical, and molecular dynamics simulation analyses to enhance molecular models illustrating how Pol I apparatus isolatedSaccharomyces cerevisiaerecognizes the promoter and the transcription start site (TSS). Time-resolved binding data shows that CF relies on a two-step mechanism, consisting of the binding and isomerization steps, to recognize its binding site on the promoter. The next step, CF-mediated recruitment of the Pol I– Rrn3 complex to the promoter, was inefficient, leading to the rapid dissociation of Pol I. The selection of the TSS by Pol I is influenced by the distance to CF and the properties of downstream DNA, such as bendability. The dynamics revealed in the Pol I transcription apparatus establish a framework for comparing the functions and mechanisms of Pol I activators and inhibitors.
Multiscale excitation-inhibition balance dynamics: integrating metabolite kinetics with time-varying executive networks
Authors: Saviola Francesca , Tambalo Stefano , Beghini Laura , Ferrari Asia , Cassone Barbara , Van De Ville Dimitri , Jovicich Jorge 
Published: October 2024

AbstractThe balance between neural excitation and inhibition (EIB) is an essential mechanism supporting cognitive processes. Yet, little is understood about how EIB shifts with cognitive load and its impact on functional connectivity dynamics. In this study, we investigate temporal profiles of the reciprocal modulation between EIB and functional network dynamics during working memory tasks, revealing that EIB prefrontal kinetics scale with increasing cognitive load. Notably, prefrontal EIB kinetics correlated with cognitive load, impacting stability of networks crucial for cognitive function. On one hand, brain dynamics adapt to meet increasing cognitive challenges with a shift towards more focused and sustained neural activity patterns in terms of connectivity. On the other, imbalances favouring excitation may hinder cognitive adaptability. Importantly, this experimental approach demonstrates a link between EIB kinetics, brain network dynamics and cognitive performance, defining the groundwork for exploring healthy and aberrant cognitive states.TeaserHighly focused or less responsive? Chemical signalling and network dynamics are coupled to produce persistent cognitive states.
Working Memory Bridges Cognition, Emotion, and Brain Structure: A Multilayer Network Analysis of the Human Connectome Project-Young Adult
Authors: Firman-Sadler Lyndon , Singh Mervyn , Domínguez D Juan F. , Simpson-Kent Ivan L. , Caeyenberghs Karen 
Published: October 2024

AbstractMultilayer network analyses allow for the exploration of complex relationships across different modalities. Specifically, this study employed a novel method that integrates psychometric networks with structural covariance networks to explore the relationships between cognition, emotion and the brain. Psychological (NIH Toolbox Cognition Battery and NIH Toolbox Emotion Battery) and anatomical MRI (cortical volume) data were extracted from the Human Connectome Project Young Adult dataset (n=1113). Partial correlation networks with graphical lasso regularisation and extended Bayesian information criterion tuning were used to model a psychometric bi-layer network consisting of seven cognitive nodes and four emotion nodes, as well as a neuro-psychometric tri-layer network consisting of these same nodes in addition to 24 brain nodes from the central executive and salience networks. Bridge strength centrality was used to identify nodes that bridged between layers. For the bi-layer network, it was found that stress was the most central bridge node. For the tri-layer network, it was found that working memory was the most central bridge node and that the right inferior parietal gyrus was the most central brain bridge node. The findings demonstrate the utility of multilayer networks in integrating multiple modalities of data for the potential identification of targets to improve psychological wellbeing.
WTools: a MATLAB-based toolbox for time-frequency analysis
Authors: Ferrari Ambra , Filippin Luca , Buiatti Marco , Parise Eugenio 
Published: October 2024

AbstractElectroencephalography (EEG) is an established method for investigating neurocognitive functions during human development. In cognitive neuroscience, time-frequency analysis of the EEG is a widely used analytical approach. This paper introduces WTools, a new MATLAB-based toolbox capable of performing time-frequency analysis of EEG signals using complex wavelet transformation. WTools features an intuitive GUI that guides users through the analysis steps, focusing on essential parameters. Being free and open-source, it can be integrated and expanded with new features, making it a handy tool that is growing its popularity in developmental cognitive neuroscience. Here, we provide a detailed description of the WTools algorithm for wavelet transformation and we compare it with state-of-the-art methods implemented in EEGLAB. Alongside the official tool release, we also offer a comprehensive illustrated tutorial to enhance accessibility and promote the transparent and reproducible usage of WTools by the scientific community.HighlightsWTools is a new MATLAB-based toolbox for time-frequency analysis of the EEG signalIt uses wavelet transformation and the algorithm is fully describedIt is designed to be very user friendly through its simple GUIIt is open source and flexible as the code is freely availableWe provide a step-by-step tutorial and an example dataset to learn the toolbox
Pupil dilation offers a time-window on prediction error
Authors: Colizoli Olympia , van Leeuwen Tessa , Rutar Danaja , Bekkering Harold 
Published: October 2024

AbstractTask-evoked pupil dilation has been linked to many cognitive variables, perhaps most notably unexpected events. Zénon (2019) proposed a unifying framework stating that pupil dilation related to cognition should be considered from an information-theory perspective. In the current study, we investigated whether the pupil’s response to decision outcome in the context of associative learning reflects a prediction error defined formally as information gain, while also exploring the time course of this prediction error signal. To do so, we adapted a simple model of trial-by-trial learning of stimulus probabilities based on information theory from previous literature. We analyzed two data sets in which participants performed perceptual decision-making tasks that required associative learning while pupil dilation was recorded. Our findings consistently showed that a significant proportion of variability in the post-feedback pupil response during decision-making can be explained by a formal quantification of information gain shortly after feedback presentation in both task contexts. In the later time window, the relationship between information-theoretic variables and the post-feedback pupil response differed per task. For the first time, we present evidence that whether the pupil dilates or constricts along with information gain seems to be context dependent, specifically related to increasing or decreasing average uncertainty (entropy) across trials. This study offers empirical evidence showcasing how the pupil’s response can offer valuable insights into the process of model updating during learning, highlighting the promising utility of this readily accessible physiological indicator for investigating internal belief states.
Managerial insight on triple bottom line reporting – an analysis of the Indian banking sector
Authors: Munjal Parul , Sharma Deergha 
Published: October 2024

Purpose
Reporting on triple bottom line (TBL) practices has emerged as an essential aspect in banking sector due to evolving social and environmental concerns. Engaging in social and environmental activities is a strategic means to uphold dynamic alliances with stakeholders and eventually attain sustainable development. Furthermore, perception towards social and environmental practices is strategic to satisfy stakeholders’ interests. This paper aims to examine managers’ perception about reporting on social-environmental performance and its impact on financial performance (FP) in Indian banking sector. Research further assesses moderating effect of gender and experience in influencing the relationship between the constructs and also determines importance and performance of the constructs.

Design/methodology/approach
A well-structured questionnaire was distributed to 400 bank managers across India’s public, private, regional-rural, foreign and cooperative banks. The collected data were analysed through Smart PLS structural equation modelling. The moderating effect of demographics of bank managers in influencing the relationship was assessed using PLS-multi-group analysis (MGA). Besides, importance performance map analysis (IPMA) was used to understand the importance and performance of the constructs.

Findings
Findings indicate that bank managers believe that social and environmental activities strengthen relations between banks and stakeholders, resulting in better FP, thereby endorsing the stakeholder theory. Results of MGA suggest that gender and experience of bank managers are not effectual moderators in determining relationship between the constructs. Using IPMA, findings advocate that managers perceive environmental performance as a relatively high performance and a more important construct in influencing FP than social performance.

Social implications
Research would pave the way for banks to effectively communicate their commitment to sustainable development goals, engage stakeholders and demonstrate their commitment to creating positive social and environmental impacts. Furthermore, managerial perceptions can have a marked effect on customers’ understanding of social and environmental practices. This may influence customer satisfaction, conviction, commitment and constancy. Besides, a better understanding of the performance on social and environmental aspects over and above the FP of banks would facilitate the investors to make more informed and effectual decisions.

Originality/value
Considering the paucity of studies on the managerial perception of social and environmental activities and determining how the perception affects financial success, this study makes significant contribution to the literature. It would facilitate banks to design appropriate strategies and legislations to incorporate reporting on TBL practices for improved performance analysis. This would eventually ensure profitability along with sustainability in the Indian banking sector.
Profit-oriented balancing of two-sided disassembly lines with resource-dependent task times
Authors: Degirmencioglu Demiralay Yuksel , Kara Yakup 
Published: October 2024

Purpose
As a result of environmentally conscious production requirements in the world, the concept of disassembly has been a focus of interest by researchers and practitioners over the last two decades. Disassembly is an important process in circular economy to recover and reuse of parts and materials. End-of-life and large-sized products such as minibuses and trucks may be disassembled on two-sided lines. The ability of using both right and left sides of two-sided lines may increase line efficiency and reduce space requirements across the line. This paper aims to address a two-sided disassembly line balancing problem (TSDLBP), which deals with assigning disassembly tasks, various equipments and assistants to the workstations to maximize total net recovery profit of the line.

Design/methodology/approach
A detailed explanation of the TSDLBP is first presented in the paper. A new 0–1 integer linear programming model is then proposed for the TSDLBP, aiming at maximizing total net recovery profit from disassembly of products. A set of test problems is generated, and an experimental analysis is conducted to make a comparison between traditional one-sided disassembly lines (TOSDL) and two-sided disassembly lines by means of performance improvement rate.

Findings
Optimal results are obtained in 132 (81.48%) out of 162 the TOSDL balancing problems, while 92 (56.79%) out of 162 the TSDLBP using the proposed model. Total net recovery profits are compared on 88 problems for which optimal solutions are obtained in both the TOSDL and the TSDLBP. Results showed that implementing two-sided disassembly lines provides 29.18% increment in total net recovery profit compared to the TOSDL. Furthermore, the effects of different parameter levels on the net recovery profit are analyzed using two-way analysis of variance. According to the results, implementing two-sided disassembly line configuration increases total net recovery profit of the line significantly compared to traditional disassembly line configuration.

Originality/value
The use of disassembly lines has become essential because of increasing consumption that results in a huge number of end-of-life products in the world. Two-sided disassembly lines may be preferred for dismantling large-sized products due to their high disassembly capacity and fewer space requirements. This paper proposes a new mathematical model for disassembly line balancing problem. The proposed model differs from the existing models by means of efficiently assigning limited disassembly resources as well as assigning disassembly tasks to the workstations to maximize total net recovery profit of the production system. The model allows decision-makers to consider several resource limitations when balancing their disassembly lines. The paper also provides a comprehensive experimental study to compare traditional and two-sided disassembly lines by means of profitability of disassembly processes.
GLP‐1 receptor agonist liraglutide alleviates kidney injury by regulating nuclear translocation of NRF2 in diabetic nephropathy
Authors: Lin Tingting , Zhang Yuze , Wei Qifeng , Huang Zugui 
Published: October 2024

AbstractDiabetic nephropathy (DN) is a severe renal disorder that arises as a complication of diabetes. Liraglutide, an analogue of a glucagon‐like peptide 1 (GLP‐1) receptor agonist, has been shown to decrease diabetes‐caused renal damage. Nevertheless, the complete understanding of the roles and mechanism remains unclear. In our study, diabetic rat models were created through a single intraperitoneal injection of streptozotocin (STZ). The level of fasting blood glucose, 24‐h urine protein, serum creatinine (Scr) and blood urea nitrogen (BUN) were assessed. Periodic acid‐Schiff (PAS) staining was applied to examine the pathological changes in renal tissues. Reactive oxygen species (ROS) formation was measured via dichloro‐dihydro‐fluorescein diacetate (DCFH‐DA) probes. Western blot was conducted to examine the levels of oxidative stress‐related and extracellular matrix (ECM)‐associated proteins. The nuclear translocation of NRF2 was investigated through immunofluorescence and Western blot assays. We demonstrated that liraglutide attenuated DN‐induced oxidative stress and ECM deposition in vitro and in vivo. Liraglutide exerted a reno‐protective effect by promoting nuclear translocation of NRF2 in mesangial cells. ML385, an NRF2 inhibitor, counteracted the beneficial impact of liraglutide.
Irrigation rates and turfgrass evapotranspiration in cities with contrasting water availability
Authors: Wilfong Matthew , Litvak Elizaveta , Grijseels Noortje H. , Hamilton Kristin , Kucera Dion , Welsh Lisa , Endter‐Wada Joanna , Jenerette G. Darrel , Pataki Diane E. 
Published: October 2024

AbstractAs water scarcity is worsened by drought and climate change, there is more interest in efficient management of urban irrigation, requiring understanding of the drivers of evapotranspiration (ET) and the role of irrigation inputs. We developed and validated a method to accurately measure ET of turfgrass lawns in contrasting climates using portable static chambers. We made in situ measurements of ET and irrigation inputs in lawns across three metropolitan areas in the United States with varying climatic conditions, water availability, and water conservation policies: Salt Lake Valley, Utah; San Fernando Valley, California; and Tallahassee, Florida. In full sun, mean daily ET estimates (ETsun) were 0.7 ± 0.4 mm day−1 in Tallahassee, 1.6 ± 0.8 mm day−1 in Los Angeles, and 3.3 ± 1.1 mm day−1 in Salt Lake Valley. In the shade, daily ET estimates (ETshade) were two to three times lower. In all three regions, ET was primarily driven by solar radiation (I0) and atmospheric vapor pressure deficit (D). Across the cities, irrigation rates were a key driver of ET, along with I0 and D. Daily irrigation ranged from 0 mm day−1 in Tallahassee (most were unirrigated) to 1.9 ± 1.2 mm day−1 in Los Angeles and 5.1 ± 2.9 mm day−1 in Salt Lake Valley. ET increased linearly with irrigation up to ~3 mm day−1, after which ET remained relatively constant despite irrigation increases. Our results highlight the importance of accounting for nonlinear responses and shading effects on ET in developing accurate irrigation recommendations.
Osteoinductively Functionalized 3D‐Printed Scaffold for Vertical Bone Augmentation in Beagle Dogs
Authors: Wang Ting , Xu Gaoli , Zhang Chuankai , Forouzanfar Tymour , Liang Junwei , Pan Yulei , Shen Chenxi , Wu Gang , Lin Haiyan 
Published: October 2024

ABSTRACTObjectiveTo evaluate the efficacy of 3D‐printed scaffolds that were osteoinductively functionalized with a bone morphogenetic protein 2 (BMP‐2)‐incorporated biomimetic calcium phosphate particles (BMP‐2‐inc. BpNcCaP)/hyaluronic acid (HA) composite gel in vertical bone augmentation in beagle dogs.Materials and MethodsFour Beagle dogs were used in this study. Three months after the extraction of 1st, 2nd, 3rd, and 4th premolars at both sides of the lower jaws of Beagle dogs, one or two critical‐size vertical bone defects (4 mm vertical bone defect without buccal and lingual bone) on each side were surgically created. The defects were randomly subjected to the following groups: (1) Control (without bone‐defect‐filling materials); (2) 3D scaffold; (3) BMP2‐inc. BpNcCaP/HA‐functionalized 3D scaffold. Six weeks post‐surgery, samples were harvested and subjected to micro‐CT and histomorphometric analyses.ResultsThe struts of the BMP2‐inc. BpNcCaP/HA‐func. 3D scaffold were covered by a thick layer of cemented irregular particles with an average pore size at 327 ± 27 μm. The BpNcCaP/HA‐func. 3D scaffold group bore significantly higher bone volume, bone volume fraction, trabecular number, trabecular thickness, bone mineral density, connectivity density, and bone volumes in three directions (mesiodistal, buccolingual, and apicocoronal) when compared with the groups of Control and 3D scaffold. Moreover, the BMP2‐inc. BpNcCaP/HA‐func. 3D scaffold group bore significantly lower trabecular separation and exhibited significantly higher bone‐to‐scaffold contact percentage and newly formed bone area percentage within pores in comparison with 3D scaffold.ConclusionsBMP2‐inc. BpNcCaP/HA‐func. 3D scaffold dramatically enhanced vertical alveolar bone augmentation, which suggests a promising application potential of BMP2‐inc. BpNcCaP/HA‐func. 3D scaffold in dental clinic.
Cerebrospinal fluid red blood cells and total protein are associated with clinical outcome in spontaneous subarachnoid hemorrhage
Authors: Berek Klaus , Lindner Anna , Kindl Philipp , Di Pauli Franziska , Schiefecker Alois J. , Pfausler Bettina , Helbok Raimund , Deisenhammer Florian , Beer Ronny , Rass Verena , Hegen Harald 
Published: October 2024

AbstractBackground and PurposePrognostication in patients with spontaneous subarachnoid hemorrhage (SAH) can be challenging. The aim of this study was to assess whether cerebrospinal fluid (CSF) red blood cell (RBC) count and total protein (TP) concentration are associated with SAH prognosis.MethodsPatients with SAH treated at the neurological intensive care unit (ICU) in Innsbruck were included in this real‐world, observational study. Longitudinal CSF samples were collected as part of routine diagnostics. RBC count and CSF TP at the time of admission (RBCfirst, TPfirst), in Week 1 (RBCDays1–7, TPDays1–7), Week 2 (RBCDays8–14, TPDays8–14), and Week 3 or thereafter (RBCDay>14, TPDay>14), the highest detected value (RBChighest, TPhighest), as well as the RBC count adjusted for disease duration (RBCadjusted) were assessed. Primary outcomes were good functional outcome after 3 months, defined as modified Rankin scale score ≤2 and ICU survival.ResultsA total of 183 SAH patients with a female predominance (69%), a median (interquartile range [IQR]) age of 60 (50–70) years and median (IQR) Hunt and Hess score of 4 (3–5) were included. Multivariable analyses revealed that lower values of RBCfirst, RBCadjusted, RBChighest, TPfirst and TPhighest were associated with good functional outcome and hospital survival. Lower TP concentrations in Weeks 1, 2 and 3 were associated with good functional outcome, and in Weeks 1 and 2 with ICU survival. Early RBC measurements (Week 1) were associated with good functional outcome and ICU survival.ConclusionsLow CSF RBC counts and TP concentrations were associated with good functional outcome and ICU survival in a real‐world cohort of SAH patients requiring external ventricular drainage.
Impact of SCB Specimen Size, Temperature, Loading Rate, and Loading Mode on Fracture Behavior of Asphalt Mixture Using Response Surface Method
Authors: Vaseghi Zahra , Pirmohammad Sadjad , Momeni Ramin 
Published: October 2024

ABSTRACTThis study aimed to investigate the influence of semicircular bend (SCB) specimen size (R), loading mode (Me), and loading rate (Lr) on fracture resistance indicators, namely, fracture work (Wf), fracture energy (Gf), and fracture strength (Kf), of asphalt concrete at three different temperatures (−30°C, −20°C, and 10°C). Using Minitab software, response surface methodology (RSM) under central composite design (CCD) was employed to design experiments and develop predictive models for Wf, Gf, and Kf in terms of R, Me, and Lr at each temperature. The results demonstrated that the RSM models accurately predicted the fracture test data for all temperatures. The analysis of variance (ANOVA) revealed that R, Me, and Lr significantly influenced Wf, Gf, and Kf at each temperature, whereas the square terms R2, Me2, and Lr2 were not significant. The significance of two‐way interaction terms varied across different responses and temperatures. Overall, the experiments conducted at −30°C, −20°C, and 10°C indicated that varying R, Lr, and Me had notable effects on Wf, Gf, and Kf. Increasing R and Me while decreasing Lr resulted in an increase in Wf and Gf. Furthermore, Kf exhibited a direct relationship with R and Lr but an inverse relationship with Me.