bluuebunny/crossref_metadata_2025_split huggingface dataset:
PTFSpot: Deep co-learning on transcription factors and their binding regions attains impeccable universality in plants
Authors: Gupta Sagar , Kesarwani Veerbhan , Bhati Umesh , Jyoti  , Shankar Ravi 
Published: November 2023

AbstractUnlike animals, variability in transcription factors (TF) and their binding regions (TFBR) across the plants species is a major problem which most of the existing TFBR finding software fail to tackle, rendering them hardly of any use. This limitation has resulted into underdevelopment of plant regulatory research and rampant use ofArabidopsislike model species, generating misleading results. Here we report a revolutionary transformers based deep-learning approach, PTFSpot, which learns from TF structures and their binding regions co-variability to bring a universal TF-DNA interaction model to detect TFBR with complete freedom from TF and species specific models’ limitations. During a series of extensive benchmarking studies over multiple experimentally validated data, it not only outperformed the existing software by >30% lead, but also delivered consistently >90% accuracy even for those species and TF families which were never encountered during model building process. PTFSpot makes it possible now to accurately annotate TFBRs across any plant genome even in the total lack of any TF information, completely free from the bottlenecks of species and TF specific models.
Public Health Response to Pan-ResistantPseudomonas aeruginosaSequence Type 309 with Tandem Guiana Extended Spectrum β-Lactamases – Genetic Characterization andIn VivoEfficacy Assessment using Translational Murine Model
Authors: Lloyd Tyler , Gill Christian M. , Herrera Jade Aquino , Heaton Dustin , Shemsu Munira , Trivedi Kavita K. , Gorzalski Andrew , Bender Monica , Pandori Mark , Varghese Vici , Nicolau David P. 
Published: November 2023

AbstractThrough phenotypic and genetic profiling, we identified the first pan resistantPseudomonas aeruginosahigh-risk sequence type 309 (ST-309) with Guiana Extended Spectrum β-Lactamase (GES) in California, prior to a national outbreak of VIM-GESPseudomonas aeruginosa(1). Our findings highlight detection and use of the translational murine model provide treatment implications for this emergingPseudomonas aeruginosa.
Association with TFIIIC limits MYCN localization in hubs of active promoters and chromatin accumulation of non-phosphorylated RNA Polymerase II
Authors: Vidal Raphael , Leen Eoin , Herold Steffi , Müller Mareike , Fleischhauer Daniel , Schülein-Völk Christina , Papadopoulos Dimitrios , Röschert Isabelle , Uhl Leonie , Ade Carsten P. , Gallant Peter , Bayliss Richard , Eilers Martin , Büchel Gabriele 
Published: November 2023

SummaryMYC family oncoproteins regulate the expression of a large number of genes and broadly stimulate elongation by RNA polymerase II. While the factors that control the chromatin association of MYC proteins are well understood, much less is known about how interacting proteins mediate MYC’s effects on transcription. Here we show that TFIIIC, an architectural protein complex that controls the three-dimensional chromatin organization at its target sites, binds directly to the amino-terminal transcriptional regulatory domain of MYCN. Surprisingly, TFIIIC has no discernible role in MYCN-dependent gene expression and transcription elongation. Instead, MYCN and TFIIIC preferentially bind to promoters with paused RNAPII and globally limit the accumulation of non-phosphorylated RNAPII at promoters. Consistent with its ubiquitous role in transcription, MYCN broadly participates in hubs of active promoters. Depletion of TFIIIC further increases MYCN localization to these hubs. This increase correlates with a failure of the nuclear exosome and BRCA1, both of which are involved in nascent RNA degradation, to localize to active promoters. Our data suggest that MYCN and TFIIIC exert an censoring function in early transcription that limits promoter accumulation of inactive RNAPII and facilitates promoter-proximal degradation of nascent RNA.
Improving Diagnostic Sensitivity for Imbalanced Musculoskeletal Disorder Data: A Sensitivity-Based Multi-Sampling Technique for Osteoarthritis Prediction
Authors: Kim Jun-hee 
Published: November 2023

ABSTRACTBackgroundMedical datasets containing musculoskeletal disorders may have data imbalances due to the incidence of the disease, which may limit the predictive ability, such as the sensitivity, of musculoskeletal diagnostic prediction models built from these data. This study aimed to increase the sensitivity performance of osteoarthritis (OA) prediction when building a model by adjusting an OA imbalanced dataset using a sensitivity-based multi-sampling (SMS) technique.MethodsOA Data were obtained from the Korea National Health and Nutrition Examination Survey (KNHANES). SMS technique combining oversampling and undersampling was applied to the imbalanced OA data, and the RandomForest algorithm was used for machine learning modeling. Model performance was evaluated based on accuracy, sensitivity, and specificity and compared with other hybrid sampling techniques.ResultIn the SMS technique, ADASYN, Borderline-SMOTE, SMOTE oversampling and ENN undersampling techniques were combined and applied. The OA prediction model using the SMS technique showed the highest sensitivity (82.20) but the lowest specificity (82.26) and accuracy (82.26) compared to other hybrid models.ConclusionSMS technique offers a potential solution for improving sensitivity performance for prediction models built on medical data imbalances due to low-incidence diseases. Nonetheless, caution is warranted due to the concern that while improving sensitivity, it may decrease specificity with a trade-off.
Development of an EngineeredMycobacterium tuberculosisStrain for a Safe and Effective Tuberculosis Human Challenge Model
Authors: Wang Xin , Su Hongwei , Wallach Joshua B. , Wagner Jeffrey C. , Braunecker Benjamin , Gardner Michelle , Guinn Kristine M. , Klevorn Thais , Lin Kan , Liu Yue J. , Liu Yao , Mugahid Douaa , Rodgers Mark , Sixsmith Jaimie , Wakabayashi Shoko , Zhu Junhao , Zimmerman Matthew , Dartois Véronique , Flynn JoAnne L. , Lin Philana Ling , Ehrt Sabine , Fortune Sarah M. , Rubin Eric J. , Schnappinger Dirk 
Published: November 2023

AbstractHuman challenge experiments could greatly accelerate the development of a tuberculosis (TB) vaccine. Human challenge for tuberculosis requires a strain that can both replicate in the host and be reliably cleared. To accomplish this, we designedMycobacterium tuberculosis(Mtb) strains featuring up to three orthogonal kill switches, tightly regulated by exogenous tetracyclines and trimethoprim. The resultant strains displayed immunogenicity and antibiotic susceptibility similar to wild-type Mtb under permissive conditions. In the absence of supplementary exogenous compounds, the strains were rapidly killed in axenic culture, mice and nonhuman primates. Notably, the strain that contained three kill switches had an escape rate of less than 10-10per genome per generation and displayed no relapse in a SCID mouse model. Collectively, these findings suggest that this engineered Mtb strain could be a safe and effective candidate for a human challenge model.
Targeted deletion of Pf prophages from diversePseudomonas aeruginosaisolates impacts quorum sensing and virulence traits
Authors: Schmidt Amelia K. , Schwartzkopf Caleb M. , Pourtois Julie D. , Burgener Elizabeth , Faith Dominick R. , Joyce Alex , Lamma Tyrza , Kumar Geetha , Bollyky Paul L. , Secor Patrick R. 
Published: November 2023

AbstractPseudomonas aeruginosais an opportunistic bacterial pathogen that commonly causes medical hardware, wound, and respiratory infections. Temperate filamentous Pf phages that infectP. aeruginosaimpact numerous bacterial virulence phenotypes. Most work on Pf phages has focused on strain Pf4 and its hostP. aeruginosaPAO1. Expanding from Pf4 and PAO1, this study explores diverse Pf strains infectingP. aeruginosaclinical isolates. We describe a simple technique targeting the Pf lysogeny maintenance gene,pflM(PA0718), that enables the effective elimination of Pf prophages from diverseP. aeruginosahosts. This study also assesses the effects different Pf phages have on host quorum sensing, biofilm formation, virulence factor production, and virulence. Collectively, this research not only introduces a valuable tool for Pf prophage elimination from diverseP. aeruginosaisolates, but also advances our understanding of the complex relationship betweenP. aeruginosaand filamentous Pf phages.ImportancePseudomonas aeruginosais an opportunistic bacterial pathogen that is frequently infected by filamentous Pf phages (viruses) that integrate into its chromosome, affecting behavior. While prior work has focused on Pf4 and PAO1, this study investigates diverse Pf strains in clinical isolates. A simple method targeting the deletion of the Pf lysogeny maintenance genepflM(PA0718) effectively eliminates Pf prophages from clinical isolates. The research evaluates the impact Pf prophages have on bacterial quorum sensing, biofilm formation, and virulence phenotypes. This work introduces a valuable tool to eliminate Pf prophages from clinical isolates and advances our understanding ofP. aeruginosaand filamentous Pf phage interactions.
Challenges in estimating species age from phylogenetic trees
Authors: Calderón del Cid Carlos , Hauffe Torsten , Carrillo Juan D. , Warnock Rachel C. M. , Silvestro Daniele 
Published: November 2023

AbstractAimSpecies age, the elapsed time since origination, can give an insight into how species longevity might influence eco-evolutionary dynamics and has been hypothesized to influence extinction risk. Traditionally, species ages have been measured in the fossil record. However, recently, numerous studies have attempted to estimate the ages of extant species from the branch lengths of time-calibrated phylogenies. This approach poses problems because phylogenetic trees contain direct information about species identity only at the tips and not along the branches. Here, we show that incomplete taxon sampling, extinction, and different assumptions about speciation modes can significantly alter the relationship between true species age and phylogenetic branch lengths, leading to high error rates. We found that these biases can lead to erroneous interpretations of eco-evolutionary patterns derived from the comparison between phylogenetic age and other traits, such as extinction risk.InnovationFor bifurcating speciation, which is the default assumption in most analyses, we propose a probabilistic approach to improve the estimation of species ages, based on the properties of a birth-death process. We show that our model can reduce the error by one order of magnitude under cases of high extinction and high percentage of unsampled extant species.Main conclusionOur results call for caution in interpreting the relationship between phylogenetic ages and eco-evolutionary traits, as this can lead to biased and erroneous conclusions. We show that, under the assumption of bifurcate, it is possible to obtain better approximations of species age by combining information from branch lengths with the expectations of a birth-death process.
Statistical Analysis Plan for the INTIMET study (Insulin Resistance in Type 1 Diabetes Managed with Metformin)
Authors: Snaith Jennifer R , Olsen Nick , Greenfield Jerry R 
Published: November 2023

AbstractThis document provides the full statistical analysis plan (SAP) for the INTIMET study (Insulin Resistance in Type 1 Diabetes Managed with Metformin), a randomised double-blinded placebo-controlled trial, designed to evaluate the effect of metformin on insulin resistance and cardiometabolic health in type 1 diabetes. This trial was prospectively registered within the Australian and New Zealand Clinical Trials Registry (ACTRN12619001440112). The study protocol has previously been published (Snaith JR et al, Diabetic Medicine 2021).
The overlooked first intercostal ligament: Does it help to stabilize the Weberian apparatus?
Authors: Leyhr Jake , Haitina Tatjana , Bird Nathan C. 
Published: November 2023

ABSTRACTThe Weberian apparatus is a novel hearing adaptation that facilitates increased hearing sensitivity in otophysan fishes. The apparatus is a complex system composed of modifications to anterior vertebral elements, the inner ear, and the swim bladder. A critical piece of the system that often receives minor attention are the various ligaments that bridge these three regions. Most famous of the ligaments is the interossicular ligament, which connects the weberian ossicle chain (scaphium-intercalarium-tripus). Several other ligaments are present, including the suspensor (tripus to parapophysis 4) and the triple ligament (tripus-os suspensorium-tunica externa). Here, by combining diffusible iodine-based contrast enhancement (DICE) and propagation phase-contrast synchrotron radiation micro-computed tomography (PPC-SRμCT) with classic histological methods we shine new light on the first intercostal ligament (ICL1) and discuss its potential function in relation to the Weberian apparatus. ICL1 is nearly absent from the cypriniform literature, typically only mentioned in a general discussion together with other intercostal ligaments. This study examines the development and structure of ICL1 comparatively with the other definitive Weberian ligaments in the zebrafish (Danio rerio). We provide a comprehensive view of development, three-dimensional shape, and composition to generate hypotheses regarding potential functions of ICL1 within the greater Weberian apparatus. Given new detail presented herein regarding the structure of ICL1, modifications to rib 5 and parapophysis 4 for ICL1 attachment, and the alignment of ICL1 with the os suspensorium, we propose a supportive (anchoring) role of ICL1 to aid in minimizing non-optimal movement of the structures of the fourth vertebra, thereby allowing the focus of vibrations anteriorly to the ossicle chain with minimal signal loss in zebrafish and other species with similar Weberian apparatus morphologies. We conclude that ICL1 should be included in future analyses of Weberian apparatus function where ligaments are addressed.
Microcephaly with a disproportionate hippocampal reduction, stem cell loss and neuronal lipid droplet symptoms inTrappc9KO mice
Authors: Aljuraysi Sultan , Platt Mark , Pulix Michela , Poptani Harish , Plagge Antonius 
Published: November 2023

AbstractMutations of the humanTRAFFICKING PROTEIN PARTICLE COMPLEX SUBUNIT 9(TRAPPC9) cause a neurodevelopmental disorder characterised by microcephaly and intellectual disability. Trappc9 constitutes a subunit specific to the intracellular membrane-associated TrappII complex. The TrappII complex interacts with Rab11 and Rab18, the latter being specifically associated with lipid droplets (LDs). Here we used non-invasive imaging to characteriseTrappc9knock-out (KO) mice as a model of the human hereditary disorder. KOs developed postnatal microcephaly with many grey and white matter regions being affected.In vivoMRI identified a disproportionately stronger volume reduction in the hippocampus, which was associated with a significant loss of Sox2-positive neural stem and progenitor cells. Diffusion Tensor imaging indicated a reduced organisation or integrity of white matter areas.Trappc9KOs displayed behavioural abnormalities in several tests related to exploration, learning and memory. Trappc9-deficient primary hippocampal neurons accumulated a larger LD volume per cell following Oleic Acid stimulation, and the coating of LDs by Perilipin-2 was much reduced. Additionally,Trappc9KOs developed obesity, which was significantly more severe in females than in males. Our findings indicate that, beyond previously reported Rab11-related vesicle transport defects, dysfunctions in LD homeostasis might contribute to the neurobiological symptoms of Trappc9 deficiency.
Analytic hierarchy process (AHP) assessment of Kuwait mega construction projects' complexity
Authors: AlKheder Sharaf , Al Otaibi Hajar , Al Baghli Zahra , Al Ajmi Shaikhah , Alkhedher Mohammad 
Published: November 2023

PurposeMegaproject's construction is essential for the development and economic growth of any country, especially in the developing world. In Kuwait, megaprojects are facing many restrictions that discourage their execution causing a significant delay in bidding, design, construction and operation phases with the execution quality being affected. The objective of this study is to develop a complexity measurement model using analytic hierarchy process (AHP) for megaprojects in Kuwait, with a focus on the New Kuwait University multi-billion campus Shadadiyah (College of Social Science, Sharia and Law (CSSL)) as a case study.Design/methodology/approachThe study applies a hybrid fuzzy analytic hierarchy process (FAHP) method to compare the results with those obtained using the conventional AHP method. This can facilitate the project management activities during the different stages of construction. Data were collected based on the results of a two-round Delphi questionnaire completed by seniors and experts of the selected project.FindingsIt was found that project modeling methodology was responsible for complexity. It was grouped under several categories that include technological, goal, organizational, environmental and cultural complexities. The study compares complexity degrees assessed by AHP and FAHP methods. “Technological Complexity” scores highest in both methods, with FAHP reaching 7.46. “Goal Complexity” follows closely behind, with FAHP. “Cultural Complexity” ranks third, differing between methods, while “Organizational” and “Environmental Complexity” consistently score lower, with FAHP values slightly higher. These results show varying complexity levels across dimensions. Assessing and understanding such complexities were essential toward the completion of such megaprojects.Originality/valueThe contribution of this study is on providing the empirical evidential knowledge for the priority over construction complexities in a developing country (Kuwait) in the Middle East.
Understanding how ethical claims in advertising affect subjective ambivalence toward buying ethical products
Authors: Toti Jean-François , Sánchez Romero Andrea Milena 
Published: November 2023

Purpose
The purpose of this paper is to examine the effect of subjective ambivalence on ethical consumption behaviors and the role of ethical claims in reducing feelings of ambivalence toward buying ethical products.

Design/methodology/approach
The authors conducted two studies. In study 1, the authors carried out an online survey with a sample of 230 French consumers. The authors applied structural equation modeling with Amos to test the relationships among skepticism, ambivalence and ethical consumption behaviors. Study 2 is an experimental design in which the authors manipulated ethical claims (low – few ethical arguments vs. high – many ethical arguments) in advertising (176 French panelists). The authors tested the relationships among consumer ethical sensitivity, perceived brand ethicality, skepticism, ambivalence and intention to purchase an ethical product, depending on ethical claims in advertising.

Findings
Study 1 shows that skepticism toward advertising of ethical products amplifies feelings of ambivalence and that ambivalence reduces consumers’ willingness to adopt ethical consumption behaviors. Study 2 shows that strong claims in advertising of ethical products reduce skepticism toward advertising of ethical products and feelings of ambivalence toward buying an ethical product through perceived brand ethicality, with consumers’ ethical sensitivity positively moderating these relationships.

Research limitations/implications
The two studies explore only one form of ambivalence (i.e. subjective), and the experimental study focuses on a single category of products.

Practical implications
The findings highlight the difficulties in promoting ethical products. Consumers need to know if a product is “really” ethical, as they may feel ambivalent toward that product. This paper shows that strong ethical claims in advertising ethical products significantly help to overcome this barrier.

Originality/value
Based on attribution theory and persuasion models, this research reveals how ethical claims in advertising affect feelings of ambivalence, which negatively influence consumers’ willingness to adopt ethical consumption. In addition, it follows a holistic approach to ethical consumption behaviors to explore consumers’ ambivalence.
Social representations of retirement: a study with professors from public higher education institutions
Authors: Vasconcelos da Nóbrega Cléverson , Helal Diogo Henrique 
Published: November 2023

PurposeThe article aims at analyzing the social representations of retirement in two different groups of professors – pre-retired and retired – from a public higher education institution. The goal is to explore the experiences, reflections, beliefs, and attitudes originated from the transition to retirement.Design/methodology/approachThe research, of exploratory and descriptive nature, was guided by the Social Representation Theory (SRT) and took a qualitative approach. 16 professors were interviewed, 8 in each group (pre-retired and retired professors), using semi-structured interviews that followed a script designed to discover the main aspects of the transition to retirement.FindingsThree figurative cores were raised – the financial aspect, the centrality of work, and the will to continue contributing, and the unpreparedness for retirement – and testimonies have shown heterogeneous representations. The study observed that although relevant, the bonus for continued services is not the main determinant for professors to continue working in the university.Originality/valueThe results of this study indicate the need to treat retirement as a complex and multidimensional process, offering a fresh perspective on the social representations of retirement in the academic context. The use of the Social Representation Theory to explore these perspectives adds to the originality of the approach, highlighting the multifaceted nature of the retirement process in this specific professional group.
Budgeting changes and success: abandonment, reform or stability in Finnish manufacturing firms?
Authors: Kihn Lili-Anne 
Published: November 2023

Purpose
The need to change budgeting has been frequently debated. Drawing on the literature on management accounting and budgeting change, this study aims to explore changes in budgeting and whether experienced success of budgeting varied with time and budget type. Changes in the use of the following budget types were investigated: fixed, revised, rolling, flexible and hybrid budgets.

Design/methodology/approach
This study uses a mixed research methodology. Survey data was collected from the same business units of large Finnish manufacturing firms in 2004 (Time 1) and 2016/2017 (Time 2) (N = 28). In addition, some of the respondents of the latter survey were interviewed in 2023 (Time 3).

Findings
Almost all business units were found to have remained loyal to budgeting. However, changes in budget types were not uncommon and varied considerably. Overall, the use of fixed budgets continued strongly, the use of revised and hybrid budgets declined, and the use of rolling budgets increased over time. Moreover, the joint use of budgets declined. The perceived success of budgetary processes was, initially, weakened by the use of fixed budgets and, later, by the use of revised budgets. The interview data further illustrates some of the patterns of, and reasons behind, the changes.

Originality/value
Longitudinal analysis of change in the same business units was useful in revealing the patterns of change in budgeting and on relationships between the variables analysed over time. Further research could be carried out using more extensive case studies in companies or sector-focused surveys longitudinally.