bluuebunny/crossref_metadata_2025_split huggingface dataset:
Biochemical Impact of p300-Mediated Acetylation of Replication Protein A: Implications for DNA Metabolic Pathway Choice
Authors: Ononye Onyekachi , Surendran Sneha , Howald Olivia K. , Kantartzis-Petrides Athena , Jordan Matthew R. , Ainembabazi Diana , Wold Marc S. , Turchi John J. , Balakrishnan Lata 
Published: April 2024

ABSTRACTReplication Protein A (RPA), a single-stranded DNA (ssDNA) binding protein, is vital for various aspects of genome maintenance such as replication, recombination, repair and cell cycle checkpoint activation. Binding of RPA to ssDNA protects it from degradation by cellular nucleases, prevents secondary structure formation and illegitimate recombination. In our current study, we identified the acetyltransferase p300 to be capable of acetylating the 70kDa subunit of RPA in vitro and within cells. The acetylation status of RPA was increased specifically during the G1/S phase of the cell cycle and also following exposure to UV-induced damage. Furthermore, we were able to specifically identify RPA directly associated with the replication fork during the S phase and UV damage to be acetylated. Based on these observations, we evaluated the impact of lysine acetylation on the biochemical properties of RPA. Investigation of binding properties of RPA revealed that acetylation of RPA increased its binding affinity to ssDNA compared to unmodified RPA. The improvement in binding efficiency was a function of DNA length with the greatest increases observed on shorter length ssDNA oligomers. Furthermore, the mechanism of acetylated RPAs’ increased affinity for ssDNA was shown to be a function of a slower rate of dissociation compared to the unmodified form of the RPA. Our findings demonstrate that p300-dependent, site-specific acetylation enhances RPA’s DNA binding properties, potentially regulating its function during various DNA transactions.
Remote Neuroinflammation in Newly Diagnosed Glioblastoma Correlates with Unfavorable Clinical Outcome
Authors: Bartos Laura M , Quach Stefanie , Zenatti Valerio , Kirchleitner Sabrina V , Blobner Jens , Wind-Mark Karin , Kolabas Zeynep Ilgin , Ulukaya Selin , Holzgreve Adrien , Ruf Viktoria C , Kunze Lea H , Kunte Sebastian T , Hoermann Leonie , Härtel Marlies , Park Ha Eun , Groß Mattes , Franzmeier Nicolai , Zatcepin Artem , Zounek Adrian , Kaiser Lena , Riemenschneider Markus J , Perneczky Robert , Rauchmann Boris-Stephan , Stöcklein Sophia , Ziegler Sibylle , Herms Jochen , Ertürk Ali , Tonn Joerg C , Thon Niklas , von Baumgarten Louisa , Prestel Matthias , Tahirovic Sabina , Albert Nathalie L , Brendel Matthias 
Published: April 2024

AbstractLocal therapy strategies still provide only limited success in the treatment of glioblastoma, the most frequent primary brain tumor in adults, indicating global involvement of the brain in this fatal disease. To study the impact of neuroinflammation distant of the primary tumor site on the clinical course of patients with glioblastoma, we performed translocator protein (TSPO)-PET in patients with newly diagnosed glioblastoma, glioma WHO 2 and healthy controls and compared signals of the non-lesion (i.e. contralateral) hemisphere. Back-translation in syngeneic glioblastoma mice was used to characterize PET alterations on a cellular level. Ultimately, multiplex gene expression analyses served to profile immune cells in remote brain. Our study revealed elevated TSPO-PET signals in contralateral hemispheres of patients with newly diagnosed glioblastoma compared to healthy controls. Contralateral TSPO was associated with persisting epilepsy and short survival independent of the tumor phenotype. Back-translation pinpointed myeloid cells as the source of TSPO-PET signal increases and revealed a complex immune signature comprised of joint myeloid cell activation and immunosuppression in distant brain regions. In brief, neuroinflammation within the contralateral hemisphere is associated with poor outcome in patients with newly diagnosed glioblastoma. TSPO-PET serves to detect patients with global neuroinflammation who may benefit from immunomodulatory strategies.
Defining the multiplex probe panel for detecting mutating viruses with high clinical sensitivity
Authors: Kozlowski Hannah N. , Lekuti Ayokunle A. , Zahoor Muhammad Atif , Feld Jordan J. , Chan Warren C. W. 
Published: April 2024

ABSTRACTNucleic acid technology has emerged as an important diagnostic for infectious diseases, cancer, cardiovascular diseases, and other diseases. However, mismatches between the probes and targets can lead to misdiagnosis. Here we determine how many mismatches between the probe and target lead to poor clinical performance and respond by developing a rationale multiplex strategy to overcome this detection problem. We found that the probe-target mismatches of greater than 20% yielded clinical sensitivity of 22% or less, rendering the diagnostic test useless. We designed probe panels to improve the clinical sensitivity. We tested our multiplex probe strategy using hepatitis C virus as the model pathogen because this virus has high mutation rates. We showed that we can improve the clinical sensitivity for detecting hepatitis C virus from 31 to 89% when we designed and applied a four-probe panel to the diagnostic test instead of a single probe system. Interestingly, increasing beyond four probes did not significantly increase the clinical sensitivity. We present a strategy to overcome the poor clinical sensitivity of nucleic acid tests for mutating genetic targets. Incorporating this panel design strategy can lead to improved diagnostic test performance, fewer false negatives and more accurate treatment planning for patients.
PRC2 Promotes Canalisation During Endodermal Differentiation
Authors: Hölzenspies Jurriaan J. , Sengupta Dipta , Bickmore Wendy A. , Brickman Joshua M. , Illingworth Robert S. 
Published: April 2024

AbstractThe genetic circuitry that encodes the developmental programme of mammals is regulated by transcription factors and chromatin modifiers. During early gestation, the three embryonic germ layers are established in a process termed gastrulation. The impact of deleterious mutations in chromatin modifiers such as the polycomb proteins manifests during gastrulation, leading to early developmental failure and lethality in mouse models. Embryonic stem cells have provided key insights into the molecular function of polycomb proteins, but it is impossible to fully appreciate the role of these epigenetic factors in development, or how development is perturbed due to their deficiency, in the steady-state. To address this, we have employed a tractable embryonic stem cell differentiation system to model primitive streak formation and early gastrulation. Using this approach, we find that loss of the repressive polycomb mark H3K27me3 is delayed relative to transcriptional activation, indicating a subordinate rather than instructive role in gene repression. Despite this, chemical inhibition of polycomb enhanced endodermal differentiation efficiency, but did so at the cost of lineage fidelity. These findings highlight the importance of the polycomb system in stabilising the developmental transcriptional response and, in so doing, in shoring up cellular specification.
Capsular Polysaccharide Restrains Type VI Secretion inAcinetobacter baumannii
Authors: Flaugnatti Nicolas , Bader Loriane , Croisier-Coeytaux Mary , Blokesch Melanie 
Published: April 2024

AbstractThe type VI secretion system (T6SS) is a sophisticated, contact-dependent nanomachine involved in interbacterial competition. To function effectively, the T6SS must penetrate the membranes of both attacker and target bacteria. Structures associated with the cell envelope, like polysaccharides chains, can therefore introduce spatial separation and steric hindrance, potentially affecting the efficacy of the T6SS. In this study, we examined how the capsular polysaccharide (CPS) ofAcinetobacter baumanniiaffects T6SS’s antibacterial function. Our findings show that the CPS confers resistance against T6SS-mediated assaults from rival bacteria. Notably, under typical growth conditions, the presence of the surface-bound capsule also reduces the efficacy of the bacterium’s own T6SS. This T6SS impairment is further enhanced when CPS is overproduced due to genetic modifications or antibiotic treatment. Furthermore, we demonstrate that the bacterium adjusts the level of the T6SS inner tube protein Hcp according to its secretion capacity, by initiating a degradation process involving the ClpXP protease. Collectively, our findings contribute to a better understanding of the dynamic relationship between T6SS and CPS and how they respond swiftly to environmental challenges.
Beyond A and B Compartments: how major nuclear locales define nuclear genome organization and function
Authors: Gholamalamdari Omid , van Schaik Tom , Wang Yuchuan , Kumar Pradeep , Zhang Liguo , Zhang Yang , Gonzalez Gabriela A. Hernandez , Vouzas Athanasios E. , Zhao Peiyao A. , Gilbert David M. , Ma Jian , van Steensel Bas , Belmont Andrew S. 
Published: April 2024

AbstractModels of nuclear genome organization often propose a binary division into active versus inactive compartments yet typically overlook nuclear bodies. Here we integrated analysis of sequencing and image-based data to compare genome organization in four human cell types relative to three different nuclear locales: the nuclear lamina, nuclear speckles, and nucleoli. Whereas gene expression correlates mostly with nuclear speckle proximity, DNA replication timing correlates with proximity to multiple nuclear locales. Speckle attachment regions emerge as DNA replication initiation zones whose replication timing and gene composition vary with their attachment frequency. Most facultative LADs retain a partially repressed state as iLADs, despite their positioning in the nuclear interior. Knock out of two lamina proteins, Lamin A and LBR, causes a shift of H3K9me3-enriched LADs from lamina to nucleolus, and a reciprocal relocation of H3K27me3-enriched partially repressed iLADs from nucleolus to lamina. Thus, these partially repressed iLADs appear to compete with LADs for nuclear lamina attachment with consequences for replication timing. The nuclear organization in adherent cells is polarized with nuclear bodies and genomic regions segregating both radially and relative to the equatorial plane. Together, our results underscore the importance of considering genome organization relative to nuclear locales for a more complete understanding of the spatial and functional organization of the human genome.
Distinguishing Quasiparticle-Phonon Interactions by Ultrahigh-Resolution Lifetime Measurements
Authors: Liu Boyao , Allison William , Peng Bo , Avidor Nadav , Monserrat Bartomeu , Jardine Andrew P. 
Published: April 2024

We present a determination of quasiparticle-phonon interaction strengths at surfaces through measurements of phonon spectra with ultrahigh energy resolution. The lifetimes of low energy surface phonons on a pristine Ru(0001) surface were determined over a wide range of temperatures and an analysis of the temperature dependence enables us to attribute separate contributions from electron-phonon interactions, phonon-phonon interactions, and defect-phonon interactions. Strong electron-phonon interactions are evident at all temperatures and we show they dominate over phonon-phonon interactions below 400 K.

Published by the American Physical Society
2024
Structural insights into the molecular mechanism of phytoplasma immunodominant membrane protein
Authors: Liu Chang-Yi , Cheng Han-Pin , Lin Chan-Pin , Liao Yi-Ting , Ko Tzu-Ping , Lin Shin-Jen , Lin Shih-Shun , Wang Hao-Ching 
Published: April 2024

Immunodominant membrane protein (IMP) is a prevalent membrane protein in phytoplasma and has been confirmed to be an F-actin-binding protein. However, the intricate molecular mechanisms that govern the function of IMP require further elucidation. In this study, the X-ray crystallographic structure of IMP was determined and insights into its interaction with plant actin are provided. A comparative analysis with other proteins demonstrates that IMP shares structural homology with talin rod domain-containing protein 1 (TLNRD1), which also functions as an F-actin-binding protein. Subsequent molecular-docking studies of IMP and F-actin reveal that they possess complementary surfaces, suggesting a stable interaction. The low potential energy and high confidence score of the IMP–F-actin binding model indicate stable binding. Additionally, by employing immunoprecipitation and mass spectrometry, it was discovered that IMP serves as an interaction partner for the phytoplasmal effector causing phyllody 1 (PHYL1). It was then shown that both IMP and PHYL1 are highly expressed in the S2 stage of peanut witches' broom phytoplasma-infected Catharanthus roseus. The association between IMP and PHYL1 is substantiated through in vivo immunoprecipitation, an in vitro cross-linking assay and molecular-docking analysis. Collectively, these findings expand the current understanding of IMP interactions and enhance the comprehension of the interaction of IMP with plant F-actin. They also unveil a novel interaction pathway that may influence phytoplasma pathogenicity and host plant responses related to PHYL1. This discovery could pave the way for the development of new strategies to overcome phytoplasma-related plant diseases.
The inhibitor effect of migrating corrosion inhibitors on Q235 steel in high alkaline environment under cathodic polarization
Authors: Jia Hang , Gao Zhiming , Wu Shixiong , Liu Jia Liang , Hu Wenbin 
Published: April 2024

Purpose
This study aims to investigate the corrosion inhibitor effect of migrating corrosion inhibitor (MCI) on Q235 steel in high alkaline environment under cathodic polarization.

Design/methodology/approach
This study investigated the electrochemical characteristics of Q235 steel with and without MCI by polarization curve and electrochemical impedance spectroscopy. Besides, the surface composition of Q235 steel under different environments was analyzed by X-ray photoelectron spectroscopy. In addition, the migration characteristic of MCI and the adsorption behavior of MCI under cathodic polarization were studied using Raman spectroscopy.

Findings
Diethanolamine (DEA) and N, N-dimethylethanolamine (DMEA) can inhibit the increase of Fe(II) in the oxide film of Q235 steel under cathodic polarization. The adsorption stability of DMEA film was higher under cathodic polarization potential, showing a higher corrosion inhibition ability. The corrosion inhibition mechanism of DEA and DMEA under cathodic polarization potential was proposed.

Originality/value
The MCI has a broad application prospect in the repair of damaged reinforced concrete due to its unique migratory characteristics. The interaction between MCIs, rebar and concrete with different compositions has been studied, but the passivation behavior of the steel interface in the presence of both the migrating electric field and corrosion inhibitors has been neglected. And it was investigated in this paper.
An empirical investigation of the impact of marketing analytics capability on SME performance: a resource-based view approach
Authors: Abrokwah-Larbi Kwabena 
Published: April 2024

PurposeThe aim of this study is to empirically investigate the impact of marketing analytics capability on business performance from the perspective of RBV theory.Design/methodology/approachThis study used a survey method to gather information from 225 food processing SMEs registered with the Ghana Enterprise Agency (GEA) in Ghana’s eastern region. A structural equation modeling (SEM) path analysis was used to assess the impact of marketing analytics capability (MAC) on the performance of SMEs.FindingsThe results of the study show that MAC significantly and positively affect the financial performance (FP), customer performance (CF), internal business process performance (IBPP) and learning and growth performance (LGP) of Ghanaian SMEs. The findings of this study also illustrated the significance of MAC determinants, including marketing analytics skills (MAS), data resource management (DRM) and data processing capabilities (DPC), in achieving SME success in Ghana.Originality/valueThe research’s conclusions give RBV theory strong credence. The results of this study also provide credence to previous research finding that SMEs should view MAC and its determinants (i.e. DRM, DPC, MAS) as a crucial strategic capability to improve their performance (i.e. FP, CF, IBPP, LGP). With regard to its contribution, this study broadens the body of knowledge on MAC and SME performance, particularly in the context of an emerging economy.
Challenges in the quantification of household food waste: the need for consistent methodologies
Authors: Wunderlich Shahla M. , Feldman Charles H. 
Published: April 2024

Purpose The purpose of this short communication is to shed light on the accuracy of quantification methods of household food waste (HFW).Design/methodology/approach Thirty-seven recently published studies in HFW were surveyed for this commentary. Exemplary methods and findings of these studies were compared.Findings It is challenging to draw conclusions on the amount of the HFW per person/town/country due to the inconsistent and heterogeneous methodologies used. We recommend using direct measurements or triangulation of methods to help ensure valid findings. Governments should incentivize consumers to deliver their food waste to designated locations where weights could accurately be assessed. Monetary or tax incentives could help stimulate an accurate accounting of waste and encourage reductions. Food waste measurements should be consistently reported as kg/person/week.Social implications Food and water security must be provided for all. It is estimated that one-third of edible food for humans is currently lost or wasted globally. According to the World Food Program (WFP), this is about 1.3 billion tons of food per year and at the same time this wasted food could be sufficient to feed two billion people.Originality/value The aim of this paper is to fill a gap in the literature about the magnitude and significance of HFW and its impact on the environment and social welfare. Currently, there are no generally accepted uniform methods of food waste quantification at the household level. This original communication brings the importance and challenges of the quantification of HFW to light.
Predicting ground vibrations from railway tunnels using an improved 2.5D FEM-PML model with soil spatial variability
Authors: Di H.G. , Xu Pingbao , Gong Quanmei , Guo Huiji , Su Guangbei 
Published: April 2024

PurposeThis study establishes a method for predicting ground vibrations caused by railway tunnels in unsaturated soils with spatial variability.Design/methodology/approachFirst, an improved 2.5D finite-element-method-perfect-matching-layer (FEM-PML) model is proposed. The Galerkin method is used to derive the finite element expression in the ub-pl-pg format for unsaturated soil. Unlike the ub-v-w format, which has nine degrees of freedom per node, the ub-pl-pg format has only five degrees of freedom per node; this significantly enhances the calculation efficiency. The stretching function of the PML is adopted to handle the unlimited boundary domain. Additionally, the 2.5D FEM-PML model couples the tunnel, vehicle and track structures. Next, the spatial variability of the soil parameters is simulated by random fields using the Monte Carlo method. By incorporating random fields of soil parameters into the 2.5D FEM-PML model, the effect of soil spatial variability on ground vibrations is demonstrated using a case study.FindingsThe spatial variability of the soil parameters primarily affected the vibration acceleration amplitude but had a minor effect on its spatial distribution and attenuation over time. In addition, ground vibration acceleration was more affected by the spatial variability of the soil bulk modulus of compressibility than by that of saturation.Originality/valueUsing the 2.5D FEM-PML model in the ub-pl-pg format of unsaturated soil enhances the computational efficiency. On this basis, with the random fields established by Monte Carlo simulation, the model can calculate the reliability of soil dynamics, which was rarely considered by previous models.
Experimental and numerical analysis of the behavior of rehabilitated aluminum structures using chopped strand mat GFRP composite patches
Authors: Althahban Sultan Mohammed , Nowier Mostafa , El-Sagheer Islam , Abd-Elhady Amr , Sallam Hossam , Reda Ramy 
Published: April 2024

PurposeThis paper comprehensively addresses the influence of chopped strand mat glass fiber-reinforced polymer (GFRP) patch configurations such as geometry, dimensions, position and the number of layers of patches, whether a single or double patch is used and how well debonding the area under the patch improves the strength of the cracked aluminum plates with different crack lengths.Design/methodology/approachSingle-edge cracked aluminum specimens of 150 mm in length and 50 mm in width were tested using the tensile test. The cracked aluminum specimens were then repaired using GFRP patches with various configurations. A three-dimensional (3D) finite element method (FEM) was adopted to simulate the repaired cracked aluminum plates using composite patches to obtain the stress intensity factor (SIF). The numerical modeling and validation of ABAQUS software and the contour integral method for SIF calculations provide a valuable tool for further investigation and design optimization.FindingsThe width of the GFRP patches affected the efficiency of the rehabilitated cracked aluminum plate. Increasing patch width WP from 5 mm to 15 mm increases the peak load by 9.7 and 17.5%, respectively, if compared with the specimen without the patch. The efficiency of the GFRP patch in reducing the SIF increased as the number of layers increased, i.e. the maximum load was enhanced by 5%.Originality/valueThis study assessed repairing metallic structures using the chopped strand mat GFRP. Furthermore, it demonstrated the superiority of rectangular patches over semicircular ones, along with the benefit of using double patches for out-of-plane bending prevention and it emphasizes the detrimental effect of defects in the bonding area between the patch and the cracked component. This underlines the importance of proper surface preparation and bonding techniques for successful repair.Graphical abstract