bluuebunny/crossref_metadata_2025_split huggingface dataset:
Use of stacked proportional bar graphs (“Grotta bars”) to visualize functional outcome distributions in observational neurology research
Authors: Forrest Meghan R. , Weissgerber Tracey L. , Lieske Emma S. , Tamayo Cuartero Elena , Fischer Elena , Jones Lydia , Piccininni Marco , Rohmann Jessica L. 
Published: July 2024

AbstractBackground and ObjectivesStacked proportional bar graphs (nicknamed “Grotta bars”) are commonly used to visualize functional outcome scales in stroke research and are also used in other domains of neurological research. In observational studies that present adjusted effect estimates, Grotta bars can mislead readers if they show unadjusted, confounded comparisons. In a sample of recent observational neurology studies with confounding-adjusted effect estimates, we aimed to determine the frequency with which Grotta bars were used to visualize functional outcomes and how often unadjusted Grotta bars were presented without an accompanying adjusted version. We also assessed the methods used to generate adjusted Grotta bars.MethodsIn this meta-research study, we systematically examined all observational studies published in the top 15 Clinical Neurology journals between 2020-2021 with an ordinal functional outcome and confounding-adjusted effect estimate. We determined whether at least one comparison using Grotta bars was present, whether the visualized comparisons were adjusted, and which adjustment strategies were applied to generate these graphs.Results250 studies met all inclusion criteria. Of these, 93 (37.2%) used Grotta bars to depict functional outcome scale distributions, with 73 (81.7%) presenting only Grotta bars without model-based adjustment. Amongst the 17 studies that presented Grotta bars adjusted using a model, the adjustment strategies included propensity score matching (n=10; 58.8%), regression (n=6; 35.3%), and inverse probability weighting (n=1; 5.9%). Most studies with Grotta bars (n=87; 87.9%) were stroke studies.DiscussionGrotta bars were most often used in stroke research within our sample. Papers that present adjusted associations for functional outcomes commonly showed only unadjusted Grotta bars, which alone may be misleading for causal questions. In observational research, Grotta bars are most informative if an adjusted version, aligning with adjusted effect estimates, is presented directly alongside the unadjusted version. Based on our findings, we offer recommendations to help authors generate informative Grotta bars and facilitate correct interpretation for readers.
Tom1p ubiquitin ligase structure, interaction with Spt6p, and function in maintaining normal transcript levels and the stability of chromatin in promoters
Authors: Madrigal Jennifer , Schubert Heidi L. , Sdano Matthew A. , McCullough Laura , Connell Zaily , Formosa Tim , Hill Christopher P. 
Published: July 2024

ABSTRACTPhosphorylation-dependent binding of theS. cerevisiaeSpt6p tSH2 domain (Spt6ptSH2) to the Rbp1p subunit of RNA polymerase II supports efficient transcription. Here, we report that Spt6ptSH2also binds the HECT-family E3 ubiquitin ligase Tom1p, a homolog of human HUWE1. Tom1p/HUWE1 have been implicated in targeting many small basic proteins for degradation, including excess ribosomal subunits and histones, although the mechanism of substrate recognition is not known. Our cryo-EM data revealed that Tom1p can adopt a compact α-solenoidal “basket” similar to the previously described structure of HUWE1, with the central cavity partially occupied by a disordered acidic domain. Sub-regions of this acidic domain supported binding to Spt6p or histones/nucleosomesin vitro, and the histone-binding region was important for Tom1p functionin vivo. We also visualized Tom1p in more extended forms, and speculate that transitions among these forms could be important for substrate selection and ubiquitylation. Genomic analyses provided additional support for the previously observed role for Tom1p in maintaining ribosomal protein pools, and also demonstrated a role in maintaining chromatin structure near genes. This suggests that the interaction with Spt6ptSH2affects substrate specificity by anchoring Tom1p to localized environments where histone ubiquitylation alters chromatin architecture.
Comparative vitreous proteomic profiling of proliferative diabetic retinopathy and diabetic with no-retinopathy subjects implicates impaired autophagy in DR pathogenesis
Authors: Sharma Sarmeela , Hameed Shahna Shahul , Vishwakarma Sushma , Chhablani Jay , Tyagi Mudit , Narayanan Raja , Pappuru Rajeev R , Swarup Ghanshyam , Chakrabharti Subhabrata , Kaur Inderjeet 
Published: July 2024

AbstractPurposeDiabetic retinopathy (DR) is a neurovascular complication of diabetes (DM) causing the loss of neurons (ganglion cells) in the retina. The disease etiology and potential pathogenic mechanisms in this disease remains unclear. In the present study, we aimed to further understand the key and novel pathogenic mechanisms involved in DR pathogenesis by taking cues from our global proteomics data.MethodologyThe study was approved by the institutional review board (IRB) of LVPEI, Hyderabad, India. Vitreous humour samples (PDR; n=3, DM; n=3, Control; n=3) were collected from patients undergoing vitrectomy and subjected to LC-MS-MS analysis. The acquired raw data were searched against the human vitreous proteome and was further analysed by various bioinformatic and proteomic tools. Western blotting and IHC was performed to validate crucial pathways. Blood samples from patients (DM, PDR & NPDR) and controls (n=50); cadaveric retinas from diabetic and non-diabetic donors (n=10) and epiretinal membranes (ERM, n=10) from DR cases and controls were collected and RNA was isolated. Quantitative expression of genes involved in autophagy were performed. ɅɅCT was compared across different categories and significance estimated using a student t-test.ResultA total of 1079 proteins were identified with 16 completely novel proteins in eye proteome. Top pathways identified were autophagy, inflammation, LXR/RXR activation (lipid metabolism), ROS generation by macrophages, apoptosis and protein degradation. Regulatory proteins identified were associated with cell death, phagocytic activation, angiogenesis and apoptosis. Autophagy inducers such as ROS was found to be accumulated in the DR vitreous. TREM2, microglial receptor was identified as a novel protein in PDR vitreous. The expression ofTREM2, anautophagy-associated gene was significantly (p-value = 0.05) upregulated in all categories as compared to control (NDM and/or NDM/No-DR). TREM2 protein also seemed to colocalise with microglial marker F4/80 in retinal tissues and intense expression was observed near the blood vessels in case of PDR retina. Other autophagy-associated markers were also differentially regulated in DR as compared to controls.ConclusionThis study emphasises on the strong role of autophagy pathways and its associated genes in the development of DR.
A cost-effective and scalable approach for DNA extraction from FFPE tissues
Authors: Geisenberger Christoph , Chimal Edgar , Jurmeister Philipp , Klauschen Frederick 
Published: July 2024

AbstractGenomic profiling of cancer plays an increasingly vital role for diagnosis and therapy planning. In addition, research of novel diagnostic applications such as DNA methylation profiling requires large training and validation cohorts. Currently, most diagnostic cases processed in pathology departments are stored as formalin-fixed and paraffin embedded tissue blocks (FFPE). Consequently, there is a growing demand for high-throughput extraction of nucleic acids from FFPE tissue samples. While proprietary kits are available, they are expensive and offer little flexibility. Here, we present ht-HiTE, a high-throughput implementation of a recently published and highly efficient DNA extraction protocol. This approach enables manual and automated processing of 96-well plates with a liquid handler, offers two options for purification and utilizes off-the-shelf reagents. Finally, we show that methylation profiles obtained from DNA processed with ht-HiTE are of equivalent quality as compared to a manual, kit-based approach.
Jasmonic acid signalling is targeted by a smut fungal Tin2-fold effector
Authors: Gul Summia , Mendoza-Rojas Gabriel , Heßler Natascha , Galle Stefanie , Smits Sander H.J. , Altegoer Florian , Göhre Vera 
Published: July 2024

AbstractIn plants, jasmonate signaling is a hub integrating environmental cues with growth and development. Due to its role in balancing defense responses against pathogens, it is a target of effector proteins from various pathogens. Here, we characterized the fungal effector protein Tue1 from the Brassicaceae smut fungusThecaphora thlaspeos.T. thlaspeosnaturally infectsArabis hirsutabut can also colonize the non-hostArabidopsis thaliana. In planta, the fungal protein Tue1 hijacks the plant importin-α dependent nuclear transporter to reach the plant nucleus. It interacts with jasmonate ZIM domain 10 (JAZ10) proteins of bothA. thalianaandAr. hirsuta. Structure-guided analysis of Tue1 suggests that it binds the Jas motif of JAZ10 indicating a role in stabilization or binding competition with proteins like MYC3 and COI1. A subset of jasmonate-responsive genes is differentially regulated duringT. thlaspeosinfection, proposing a link of the Tue1 function to infection. Tue1 share structural similarity to the Tin2-fold family recently described in the corn smutUstilago maydis. Our study therefore suggests that this structural effector family is expanded across fungal pathogens, although future studies have to reveal whether targeting JAZ-repressors is a conserved mechanism or specifically acquired as an adaptation to its perennial host.
Chromatin endogenous cleavage provides a global view of yeast RNA polymerase II transcription kinetics
Authors: VanBelzen Jake , Sakelaris Bennet , Brickner Donna Garvey , Marcou Nikita , Riecke Hermann , Mangan Niall , Brickner Jason H. 
Published: July 2024

AbstractChromatin immunoprecipitation (ChIP-seq) is the most common approach to observe global binding of proteins to DNAin vivo. The occupancy of transcription factors (TFs) from ChIP-seq agrees well with an alternative method, chromatin endogenous cleavage (ChEC-seq2). However, ChIP-seq and ChEC-seq2 reveal strikingly different patterns of enrichment of yeast RNA polymerase II. We hypothesized that this reflects distinct populations of RNAPII, some of which are captured by ChIP-seq and some of which are captured by ChEC-seq2. RNAPII association with enhancers and promoters - predicted from biochemical studies - is detected well by ChEC-seq2 but not by ChIP-seq. Enhancer/promoter bound RNAPII correlates with transcription levels and matches predicted occupancy based on published rates of enhancer recruitment, preinitiation assembly, initiation, elongation and termination. The occupancy from ChEC-seq2 allowed us to develop a stochastic model for global kinetics of RNAPII transcription which captured both the ChEC-seq2 data and changes upon chemical-genetic perturbations to transcription. Finally, RNAPII ChEC-seq2 and kinetic modeling suggests that a mutation in the Gcn4 transcription factor that blocks interaction with the NPC destabilizes promoter-associated RNAPII without altering its recruitment to the enhancer.
Default Mode Network activation at task switches reflects mental task-set structure
Authors: Zhou Ashley X. , Duncan John , Mitchell Daniel J. 
Published: July 2024

AbstractRecent findings challenge traditional views of the Default Mode Network (DMN) as purely task-negative or self-oriented, showing increased DMN activity during demanding switches between externally-focused tasks (Crittenden et al., 2015; Smith et al., 2018; Zhou et al., 2024). However, it is unclear what modulates the DMN at switches, with transitions within a stimulus domain activating DMN regions in some studies but not others. Differences in the number of tasks suggest that complexity or structure of the set of tasks may be important. In this fMRI study, we examined whether the DMN’s response to task switches depends on the complexity of the active set of tasks, manipulated by the number of tasks in a run, or abstract task groupings based on instructional order. Core DMN activation at task switches was unaffected by the number of currently relevant tasks. Instead, it depended on the order in which groups of tasks had been learnt. Multivariate decoding revealed that Core DMN hierarchically represents individual tasks, task domains, and higher-order task groupings based on instruction order. We suggest that, as the complexity of instructions increases, rules are increasingly organized into higher-level chunks, and Core DMN activity is highest at switches between chunks.
Innovative strategic multicriteria decision-making selection model of infrastructures projects delivery systems using multiobjective optimization, case of Egypt
Authors: Nouh Meshref Ahmed , Elkasaby Elsayed , Wageh Omnia 
Published: July 2024

Purpose
To help decision-makers choose appropriate infrastructure project delivery systems (IPDS) and keep up with the construction industry’s rapid growth, this study aims to develop a goal optimization technique.This looks into team integration, large production and optimum sustainability. The suggested approach for meeting several infrastructure project objectives is flexible and expandable. This research overcomes the significant discrepancy between the construction industry’s progress and the rate at which project delivery methods evolve.

Design/methodology/approach
This study examined pertinent literature to choose an appropriate project delivery method and gave information on several elements that affect that decision. After optimization using a genetic algorithm (GA), a Pareto front of solutions has been found. The three construction goals of sustainability, mass production and team integration are all met by the chosen best solution. The four most popular possibilities for studying the suggested approach are five primary categories, each of which has 22 variables, and the weight of each variable was established using Simo’s procedure. This is optimized, demonstrating the accuracy of the optimization model.

Findings
Sustainability, mass production and team integration are the major goals of selecting the finest IPDS. The Pareto-optimal solutions discovered through analysis demonstrated that the created GA is reliable and generates solid outcomes. In fact, it enables decisions that were based on a single criterion to be overturned. The process has therefore demonstrated its efficacy in identifying the ideal answer. First integrated project delivery (IPD), second design-build (DB), third design-bid-build (DBB) and last construction manager at risk (CMR) are the best options. The weight of the aims function has found these rankings to be satisfactory.

Practical implications
The findings demonstrate that the suggested strategy can lead to optimization, providing the government with a wide range of options for attaining certain project objectives. The ability of this study to evaluate the combined effects of three objectives in choosing the best IPDS, the production of optimal selection solutions (IPDS), which can help with better decision-making when many objectives are present, and the flexibility and extendibility of the suggested approach for achieving priorities in infrastructure projects are what make it unique. This approach was able to select IPDS to meet developments in the construction project.

Originality/value
To confirm the validity of the GA, the factor of error was calculated, which is equal to 1.7599e-08.
Research visualization trends in research data management (RDM): a bibliometric analysis
Authors: Shah Naimat Ullah , Ali Nusrat , Hamid Aamir , Khan Muhammad Ajmal 
Published: July 2024

Purpose
This study aims to examine research visualization trends in research data management (RDM), analyzing factors such as contributions, publications, document types, authors and research areas, emphasizing the dynamic nature of RDM research in the scholarly landscape.

Design/methodology/approach
The study analyzed citation histories for 1,401 publications from 2001 to 2021 in the Web of Science database, extracting no restrictions on document type or language. Literature visualization tools such as Biblioshiny, VOSviewer, ScientoPy and MS Excel were used. The researchers explored institutional collaborations, data-centric trends and RDM frontiers.

Findings
The majority of RDM research is conducted by librarians and information scientists. Research on RDM has increased over the past 21 years, peaking in 2019. Among universities, Sheffield and Pittsburgh have the most productivity in RDM research, and the USA is the most productive country. Most productive authors are Aleixandre-Benavent-R and Da Silva Jr. RDM; however, improvement is still needed, especially at academic universities.

Originality/value
This study provides valuable insights into the published literature on RDM and identifies patterns of collaboration among researchers in RDM.
Short-term rentals and residential rents: evidence from a regulation in Santa Monica
Authors: Chaves Fonseca Cayrua 
Published: July 2024

Purpose
This study aims to investigate the relationship between Airbnb and long-term residential rents, using Santa Monica, California, as a case study. In 2015, Santa Monica adopted the home sharing ordinance (HSO), a stringent regulation aimed at restricting short-term rentals (STR). This research examines the implications of this ordinance on the local housing market.

Design/methodology/approach
The synthetic control method (SCM) is applied to a panel data set comprising Airbnb listings and residential rents from multiple cities in Los Angeles County. This approach is used to estimate the causal effects of Santa Monica’s HSO on two outcomes: Airbnb listings and residential rents.

Findings
The empirical results show a 60% reduction in Airbnb listings in Santa Monica within two years of implementing the ordinance. Despite this significant decrease, the effect of the regulation on rents was not significant. Suggestive evidence indicates that the ordinance’s ineffectiveness in increasing the number of houses allocated to long-term tenants may have contributed to its negligible impact on rental rates.

Originality/value
To the best of the author’s knowledge, this research is the first to use the SCM for evaluating the impact of STR regulations. It offers crucial insights to policymakers on regulating platforms like Airbnb. The study reveals a scenario where a marked decrease in Airbnb activity did not lower residential rents, highlighting the need for context-specific evaluations in understanding the housing market’s dynamics. Additionally, these findings are valuable for investors considering the implications of regulatory changes in the STR sector.
Export Potential Index for Textile Industry (EPIT) model proposal with structural equation modelling and application
Authors: Kırkın Metin , Aktepe Adnan , Toklu Bilal 
Published: July 2024

PurposeThe aim of this study is to develop a new multidimensional index to measure export potential of textile firms by using firm-level data.Design/methodology/approachAfter a conceptual model, a structural equation model is developed with five dimensions and 27 observed variables based on resource-based view theory. The measurement model is solved by Linear Structural Relations (LISREL) with maximum likelihood algorithm by using data collected from 454 textile firms in Türkiye.FindingsIn this study, a new multidimensional index that measures export potential of textile firms is developed. With the proposed model, the export potential of textile firms can be calculated numerically with the five dimensions: Resources, Dynamism, Knowledge, Innovation and Sustainability. The comparison of the output of the proposed model with the control variable, firm’s actual export values, shows a significantly high success ratio of 90.76%.Research limitations/implicationsThe model is applicable for textile firms at different export levels, regions and sub-sectors. The Export Potential Index for Textile Industry model is verified by using Turkish textile industry data. The robustness of the model may be increased by verifying the model by using some other countries data. This model can be implemented to other industrial sectors with some modification of the dimensions and variables.Practical implicationsThe proposed model will contribute to the firms by calculating their export potential in five dimensions with their own variables numerically. The model will help firms to develop strategies to increase their export potential and to the governmental and industrial organizations to develop incentives policies.Originality/valueThis paper fills the gap in the literature by proposing a multidimensional index that determines a firm’s export potential numerically by using firm-level data.
Directional connectedness between the electricity prices and natural gas prices: evidence from Alberta’s electricity market
Authors: Oviedo-Gómez Andrés , Londoño-Hernández Sandra Milena , Manotas-Duque Diego Fernando 
Published: July 2024

Purpose
This study aims to assess volatility spillovers and directional connectedness between electricity (EPs) and natural gas prices (GPs) in the Canadian electricity market, based on a hydrothermal power generation market strongly dependent on exogenous variables such as fossil fuel prices and climatology factors.

Design/methodology/approach
The methodology is divided into two stages. First, a quantile vector autoregression model is used to evaluate the direction and magnitude of the influence between natural gas and electricity prices through different quantiles of their distributions. Second, a cross-quantilogram is estimated to measure the directional predictability between these prices. The data set consists of daily electricity and natural gas prices between January 2015 and December 2023.

Findings
The main finding shows that electricity prices are pure shock receivers of volatility from natural gas prices for the different quantiles. In this way, natural gas price fluctuations explain 0.20%, 0.98% and 22.72% of electricity price volatility for the 10th, 50th and 90th quantiles, respectively. On the other hand, a significant and positive correlation is observed in the high quantiles of the electricity prices for any natural gas price value.

Originality/value
The study described the risk to the electricity market caused by nonrenewable source price fluctuations and provided evidence for designing regulatory policies to reduce its exposure in Alberta, Canada. It also allows us to understand the importance of natural gas in the energy transition process and define it as the fundamental determinant of the electricity market dynamic.