bluuebunny/crossref_metadata_2025_split huggingface dataset:
The dual nature of DNA damage response in obesity and bariatric surgery-induced weight loss
Authors: Escobar Marcillo David Israel , Guglielmi Valeria , Privitera Grete Francesca , Signore Michele , Simonelli Valeria , Manganello Federico , Dell’Orso Ambra , Laterza Serena , Parlanti Eleonora , Pulvirenti Alfredo , Marcon Francesca , Siniscalchi Ester , Fertitta Veronica , Iorio Egidio , Varì Rosaria , Nisticò Lorenza , Valverde Mahara , Sbraccia Paolo , Dogliotti Eugenia , Fortini Paola 
Published: September 2024

AbstractThis novel study applies targeted functional proteomics to examine tissues and cells obtained from a cohort of individuals with severe obesity who underwent bariatric surgery (BS), using a Reverse-Phase Protein Array (RPPA). In obese individuals, visceral adipose tissue (VAT), but not subcutaneous adipose tissue (SAT), shows activation of DNA damage response (DDR) markers including ATM, ATR, histone H2AX, KAP1, Chk1, and Chk2, alongside senescence markers p16 and p21. Additionally, stress-responsive metabolic markers, such as survivin, mTOR, and PFKFB3, are specifically elevated in VAT, suggesting both cellular stress and metabolic dysregulation. Conversely, peripheral blood mononuclear cells (PBMCs), while exhibiting elevated mTOR and JNK levels, did not present significant changes in DDR or senescence markers. Following BS, unexpected increases in phosphorylated ATM, ATR, and KAP1 levels, but not in Chk1 and Chk2 nor in senescence markers, were observed. This was accompanied by heightened levels of survivin and mTOR, along with improvement in markers of mitochondrial quality and health. This suggests that, following BS, pro-survival pathways involved in cellular adaptation to various stressors and metabolic alterations are activated in circulating PBMCs. Moreover, our findings demonstrate that the DDR has a dual nature. In the case of VAT from individuals with obesity, chronic DDR proves to be harmful, as it is associated with senescence and chronic inflammation. Conversely, after BS, the activation of DDR proteins in PBMCs is associated with a beneficial survival response. This response is characterized by metabolic redesign and improved mitochondrial biogenesis and functionality. This study reveals physiological changes associated with obesity and BS that may aid theragnostic approaches.
Heteromeric amyloid filaments of ANXA11 and TDP-43 in FTLD-TDP type C
Authors: Arseni Diana , Nonaka Takashi , Jacobsen Max H. , Murzin Alexey G. , Cracco Laura , Peak-Chew Sew Y. , Garringer Holly J. , Kawakami Ito , Suzuki Hisaomi , Onaya Misumoto , Saito Yuko , Murayama Shigeo , Geula Changiz , Vidal Ruben , Newell Kathy L. , Mesulam Marsel , Ghetti Bernardino , Hasegawa Masato , Ryskeldi-Falcon Benjamin 
Published: September 2024

AbstractNeurodegenerative diseases are characterized by the abnormal filamentous assembly of specific proteins in the central nervous system1. Human genetic studies have established a causal role for protein assembly in neurodegeneration2. However, the underlying molecular mechanisms remain largely unknown, which is limiting progress in developing clinical tools for these diseases. Recent advances in cryo-electron microscopy have enabled the structures of the protein filaments to be determined from the brains of patients1. All neurodegenerative diseases studied to date have been characterized by the self-assembly of proteins in homomeric amyloid filaments, including that of TAR DNA-binding protein 43 (TDP-43) in amyotrophic lateral sclerosis (ALS) and frontotemporal lobar degeneration with TDP-43 inclusions (FTLD-TDP) types A and B3,4. Here we used cryo-electron microscopy to determine filament structures from the brains of individuals with FTLD-TDP type C, one of the most common forms of sporadic FTLD-TDP. Unexpectedly, the structures revealed that a second protein, annexin A11 (ANXA11), co-assembles with TDP-43 in heteromeric amyloid filaments. The ordered filament fold is formed by TDP-43 residues G282/G284–N345 and ANXA11 residues L39–Y74 from their respective low-complexity domains. Regions of TDP-43 and ANXA11 that were previously implicated in protein–protein interactions form an extensive hydrophobic interface at the centre of the filament fold. Immunoblots of the filaments revealed that the majority of ANXA11 exists as an approximately 22 kDa N-terminal fragment lacking the annexin core domain. Immunohistochemistry of brain sections showed the colocalization of ANXA11 and TDP-43 in inclusions, redefining the histopathology of FTLD-TDP type C. This work establishes a central role for ANXA11 in FTLD-TDP type C. The unprecedented formation of heteromeric amyloid filaments in the human brain revises our understanding of amyloid assembly and may be of significance for the pathogenesis of neurodegenerative diseases.
Unveiling peripheral symmetric acceptors coupling with tetrathienylbenzene core to promote electron transfer dynamics in organic photovoltaics
Authors: Khalid Muhammad , Jabbar Aiman , Murtaza Shahzad , Arshad Muhammad , Braga Ataualpa A. C. , Ahamad Tansir 
Published: September 2024

AbstractNon-fullerene organic compounds are promising materials for advanced photovoltaic devices. The photovoltaic and electronic properties of the derivatives (TTBR and TTB1-TTB6) were determined by employing density functional theory (DFT) and time-dependent density functional theory (TD-DFT) analyses using the M06/6-311G(d,p) functional. To enhance the effectiveness of fullerene-free organic photovoltaic cells, modifications were applied to end-capped acceptors by using strong electron-withdrawing moieties. The structural tailoring showed a significant electronic impact for HOMO and LUMO for all chromophores, resulting in decreased band gaps (3.184–2.540 eV). Interestingly, all the designed derivatives exhibited broader absorption spectra in the range of 486.365–605.895 nm in dichloromethane solvent. Among all derivatives, TTB5 was observed to be the promising candidate because of its lowest energy gap (2.54 eV) and binding energy (0.494 eV) values, along with the bathochromic shift (605.895 nm). These chromophores having an A–π–A framework might be considered promising materials for efficient organic cells.
Efficient and fast arsenate removal from water by in-situ formed magnesium hydroxide
Authors: Zhou Juanjuan , Yang Ying , Li Zhanjun 
Published: September 2024

AbstractMgO nanoparticles have good As-adsorption capacity in treating As-contaminated wastewater but suffer from high production cost. In this study, instead of using pre-formed MgO nanoparticles, we found that in-situ formed Mg(OH)2 from MgCl2 and NaOH reaction exhibited super high arsenate (As(V)) removal efficiency. Only 1.5 mmol/L of in-situ formed Mg(OH)2 could remove more than 95% As(V) within 10 min to make the As contaminated water (10 mg-As(V)/L) meet the municipal wastewater treatment standard, whereas MgO nanoparticles failed. The Mg-As sludge has an amorphous crystal structure while no Mg(OH)2 phase could be observed. As(V) existed uniformly within the sludge which was confirmed by elemental mapping. A precipitation-adsorption-coagulation mechanism might exist, which could relieve the restriction of limited surface area of solid MgO adsorbents. This study not only reveals an applicable method for efficient removal of trace level As(V) from water but also implies the huge potential of in-situ formed adsorbents in water treatment.
Genetic analysis of tomato brown rugose fruit virus reveals evolutionary adaptation and codon usage bias patterns
Authors: Ghorbani Abozar 
Published: September 2024

AbstractTomato brown rugose fruit virus (ToBRFV) poses a significant threat to tomato production worldwide, prompting extensive research into its genetic diversity, evolutionary dynamics, and adaptive strategies. In this study, we conducted a comprehensive analysis of ToBRFV at the codon level, focusing on codon usage bias, selection pressures, and evolutionary patterns across multiple genes. Our analysis revealed distinct patterns of codon usage bias and selection pressures within the ToBRFV genome, with varying levels of genetic diversity and evolutionary constraints among different genes. We observed a transition/transversion bias of 2.07 across the entire ToBRFV genome, with the movement protein (MP) gene exhibiting the highest transition/transversion bias and SNP density, suggesting potential evolutionary pressures or a higher mutation rate in this gene. Furthermore, our study identified episodic positive selection primarily in the MP gene, highlighting specific codons subject to adaptive changes in response to host immune pressures or environmental factors. Comparative analysis of codon usage bias in the coat protein (CP) and RNA-dependent RNA polymerase (RdRp) genes revealed gene-specific patterns reflecting functional constraints and adaptation to the host's translational machinery. Our findings provide valuable insights into the molecular mechanisms driving ToBRFV evolution and adaptation, with implications for understanding viral pathogenesis, host-virus interactions, and the development of control strategies. Future research directions include further elucidating the functional significance of codon usage biases, exploring the role of episodic positive selection in viral adaptation, and leveraging these insights to inform the development of effective antiviral strategies and crop protection measures.
Evaluating the direct effect of vaccination and non-pharmaceutical interventions during the COVID-19 pandemic in Europe
Authors: Fajgenblat Maxime , Molenberghs Geert , Verbeeck Johan , Willem Lander , Crèvecoeur Jonas , Faes Christel , Hens Niel , Deboosere Patrick , Verbeke Geert , Neyens Thomas 
Published: September 2024

Abstract
Background
Across Europe, countries have responded to the COVID-19 pandemic with a combination of non-pharmaceutical interventions and vaccination. Evaluating the effectiveness of such interventions is of particular relevance to policy-makers.

Methods
We leverage almost three years of available data across 38 European countries to evaluate the effectiveness of governmental responses in controlling the pandemic. We developed a Bayesian hierarchical model that flexibly relates daily COVID-19 incidence to past levels of vaccination and non-pharmaceutical interventions as summarised in the Stringency Index. Specifically, we use a distributed lag approach to temporally weight past intervention values, a tensor-product smooth to capture non-linearities and interactions between both types of interventions, and a hierarchical approach to parsimoniously address heterogeneity across countries.

Results
We identify a pronounced negative association between daily incidence and the strength of non-pharmaceutical interventions, along with substantial heterogeneity in effectiveness among European countries. Similarly, we observe a strong but more consistent negative association with vaccination levels. Our results show that non-linear interactions shape the effectiveness of interventions, with non-pharmaceutical interventions becoming less effective under high vaccination levels. Finally, our results indicate that the effects of interventions on daily incidence are most pronounced at a lag of 14 days after being in place.

Conclusions
Our Bayesian hierarchical modelling approach reveals clear negative and lagged effects of non-pharmaceutical interventions and vaccination on confirmed COVID-19 cases across European countries.
Urban biodiversity is affected by human-designed features of public squares
Authors: Fairbairn Andrew J. , Meyer Sebastian T. , Mühlbauer Maximilian , Jung Kirsten , Apfelbeck Beate , Berthon Katherine , Frank Andrea , Guthmann Lea , Jokisch Jana , Kerler Kristel , Müller Nina , Obster Christina , Unterbichler Michaela , Webersberger Johanna , Matejka Juliane , Depner Paul , Weisser Wolfgang W. 
Published: September 2024

AbstractCities are designed primarily for the benefit of humans but also provide habitat for other species. However, understanding how different components of urban vegetation and other features of urban spaces enable different species or species groups to live in the city remains limited. Here we show that, for the City of Munich, designed features of public urban squares strongly determine the occurrence of different species groups. While taxon richness and abundance increased with increasing ‘greenness’ of the square, different taxa responded to different square features, such as the proportion of lawn, the volume of shrubs and the density of trees, as well as the number of people or pets on these squares. Our results highlight that urban design for human needs affects other species that may cohabit these spaces. Consequently, planning strategies for biodiverse cities that aim to enhance human–nature interactions need to be multifaceted, considering the needs of humans and other taxa to create diverse living cities.
CaMKII suppresses proteotoxicity by phosphorylating BAG3 in response to proteasomal dysfunction
Authors: Zhang Chenliang , Xu Huanji , Tang Qiulin , Duan Yichun , Xia Hongwei , Huang Huixi , Ye Di , Bi Feng 
Published: September 2024

AbstractProtein quality control serves as the primary defense mechanism for cells against proteotoxicity induced by proteasome dysfunction. While cells can limit the build-up of ubiquitinated misfolded proteins during proteasome inhibition, the precise mechanism is unclear. Here, we find that protein kinase Ca2+/Calmodulin (CaM)-dependent protein kinase II (CaMKII) maintains proteostasis during proteasome inhibition. We show that proteasome inhibition activates CaMKII, which phosphorylates B-cell lymphoma 2 (Bcl-2)-associated athanogene 3 (BAG3) at residues S173, S377, and S386. Phosphorylated BAG3 activates the heme-regulated inhibitor (HRI)- eukaryotic initiation factor-2α (eIF2α) signaling pathway, suppressing protein synthesis and the production of aggregated ubiquitinated misfolded proteins, ultimately mitigating the proteotoxic crisis. Inhibition of CaMKII exacerbates the accumulation of aggregated misfolded proteins and paraptosis induced by proteasome inhibitors. Based on these findings, we validate that combined targeting of proteasome and CaMKII accelerates tumor cell death and enhances the efficacy of proteasome inhibitors in tumor treatment. Our data unveil a new proteasomal inhibition-induced misfolded protein quality control mechanism and propose a novel therapeutic intervention for proteasome inhibitor-mediated tumor treatment.
Supramolecular tunnelling junctions with robust high rectification based on assembly effects
Authors: Roemer Max , Chen Xiaoping , Li Yuan , Wang Lejia , Yu Xiaojiang , Cazade Pierre-André , Nickle Cameron , Akter Romena , Del Barco Enrique , Thompson Damien , Nijhuis Christian A. 
Published: September 2024

The performance of molecular diodes can approach the performance of semiconductor devices but predictive structure–property design remains challenging. We show that the performance can be improved by optimizing several intertwined parameters.
Patient Motivation for Voice Therapy Increases After Stimulability Testing: Validation of a Voice Therapy Motivation and Voice Perception Inventory
Authors: Toles Laura E. , Turner Melanie , Harris Amy L. 
Published: September 2024

Objective:
Measuring patient motivation for voice therapy is an important component of determining prognosis and estimating compliance. Voice stimulability testing is assumed to influence the patient's motivation by improving their perception of the sound and/or feel of the voice. The purpose of this study was to validate a Voice Therapy Motivation and Voice Perception Inventory and to determine whether stimulability testing elicits improvements in motivation and patient-perceived voice status.

Method:
Seventy-five patients who underwent initial voice therapy evaluation completed a four-item inventory that queried their commitment to voice therapy, confidence that they could change their voice through voice therapy, perception of their voice severity, and ratings of their vocal effort. Inventories were completed shortly before and after stimulability testing. A psychometric analysis of the survey was conducted, including the internal consistency of each construct of the inventory along with content, predictive, and concurrent validity. Paired-samples statistical analyses were conducted to determine differences before and after stimulability testing, and Spearman correlations between voice and motivation ratings were conducted to determine relationships between the patient's perception of their voice and their motivation for voice therapy.

Results:
Internal consistency reliability was acceptable to good for each construct, particularly after stimulability testing. Motivation scales were predictive of returning for voice therapy sessions, subjective improvement of voice by the first therapy session, and likelihood of the patient practicing the home practice program. Patient ratings of voice severity and effort were positively correlated with clinician ratings of overall severity. Motivation and voice impairment perception improved following stimulability testing. Reduction in vocal effort was related to improved motivation, but change in voice severity was not.

Conclusions:
Voice stimulability testing can influence patient motivation for voice therapy and patient-perceived voice improvements. It should be considered a critical part of the voice evaluation.
The Use of Language Sample Analysis to Differentiate Developmental Language Disorder From Typical Language in Bilingual Children: A Systematic Review and Meta-Analysis
Authors: Ortiz José A. , Nolasco Jessica M. , Huang Yi Ting , Chow Jason C. 
Published: September 2024

Purpose:
Language sample analysis (LSA) is a commonly recommended method of assessment for bilingual children. This systematic review and meta-analysis provides a comprehensive overview of the literature on the use of LSA to differentiate between developmental language disorder (DLD) and typical language (TL) in bilingual children.

Method:
We conducted a search of several large electronic databases along with forward and backward searches and applied abstract and full-text screening procedures to identify all relevant studies. We then estimated standardized mean differences, representing the ability of LSA to differentiate between DLD and TL, using multilevel model and subgroup and moderator analyses to identify characteristics of LSA that may be associated with differences in effect size magnitude. We conducted assessments of publication bias and risk of bias by examining quality indicators for each study.

Results:

The search yielded 35 articles that met the inclusion criteria. Participants ranged in age from 2;0 (years;months) to 11;9, with over 40 languages represented. Across studies, the pooled standardized mean difference indicated that children with DLD performed 0.78
SD
lower on LSA measures than those with TL. Measures of morphosyntactic accuracy exhibited the largest pooled effect size. Elicitation method, language of task, and age were not associated with differences in effect size.

Discussion:
Results of this study provide evidence of the clinical utility of LSA in differentiating between DLD and TL in bilingual children. Further research is needed to examine classification accuracy as well as task characteristics that may improve its diagnostic utility.
A lightweight transformer with linear self‐attention for defect recognition
Authors: Zhai Yuwen , Li Xinyu , Gao Liang , Gao Yiping 
Published: September 2024

AbstractVisual defect recognition techniques based on deep learning models are crucial for modern industrial quality inspection. The backbone, serving as the primary feature extraction component of the defect recognition model, has not been thoroughly exploited. High‐performance vision transformer (ViT) is less adopted due to high computational complexity and limitations of computational resources and storage hardware in industrial scenarios. This paper presents LSA‐Former, a lightweight transformer architectural backbone that integrates the benefits of convolution and ViT. LSA‐Former proposes a novel self‐attention with linear computational complexity, enabling it to capture local and global semantic features with fewer parameters. LSA‐Former is pre‐trained on ImageNet‐1K and surpasses state‐of‐the‐art methods. LSA‐Former is employed as the backbone for various detectors, evaluated specifically on the PCB defect detection task. The proposed method reduces at least 18M parameters and exceeds the baseline by more than 2.2 mAP.
Efficient visual transformer transferring from neural ODE perspective
Authors: Niu Hao , Luo Fengming , Yuan Bo , Zhang Yi , Wang Jianyong 
Published: September 2024

AbstractRecently, the Visual Image Transformer (ViT) has revolutionized various domains in computer vision. The transfer of pre‐trained ViT models on large‐scale datasets has proven to be a promising method for downstream tasks. However, traditional transfer methods introduce numerous additional parameters in transformer blocks, posing new challenges in learning downstream tasks. This article proposes an efficient transfer method from the perspective of neural Ordinary Differential Equations (ODEs) to address this issue. On the one hand, the residual connections in the transformer layers can be interpreted as the numerical integration of differential equations. Therefore, the transformer block can be described as two explicit Euler method equations. By dynamically learning the step size in the explicit Euler equation, a highly lightweight method for transferring the transformer block is obtained. On the other hand, a new learnable neural memory ODE block is proposed by taking inspiration from the self‐inhibition mechanism in neural systems. It increases the diversity of dynamical behaviours of the neurons to transfer the head block efficiently and enhances non‐linearity simultaneously. Experimental results in image classification demonstrate that the proposed approach can effectively transfer ViT models and outperform state‐of‐the‐art methods.
Probabilistic co‐expansion planning for natural gas and electricity energy systems with wind curtailment mitigation considering uncertainties
Authors: Shabanian‐Poodeh Mostafa , Hooshmand Rahmat‐Allah , Kabiri‐Renani Yahya 
Published: September 2024

AbstractIn response to growing reliance on electricity and gas systems, this paper introduces a stochastic bi‐level model for the optimized integration of these systems. This integration is achieved through sizing and allocating of power‐to‐gas (P2G) and gas‐to‐power (G2P) units. The first level of the model focuses on decisions related to P2G and G2P unit installations, while the second level addresses optimal system operation considering decisions made from first level and stochastic scenarios. The primary aim is to enhance energy‐sharing capabilities through coupling devices and mitigate wind generation curtailment. An economic evaluation assesses the model's effectiveness in reducing costs. N − 1 contingency analysis gauges the integrated system's ability to supply load under emergency conditions. Two new indices, performance of the electricity system and performance of the natural gas system, are proposed for N − 1 contingency analysis. These indices quantify the proportion of the supplied load to the total load, thereby illustrating the system's capacity to meet demand. For numerical investigation, the proposed model is applied to a modified IEEE 14‐bus power system and a 10‐node natural gas system. Numerical results demonstrate a 9.426% reduction in investment costs and a significant 10.6% reduction in wind curtailment costs through proposed planning model.