bluuebunny/crossref_metadata_2025_split huggingface dataset:
Computational screen for sex-specific drug effects in a cardiac fibroblast signaling network model
Authors: Watts Kelsey M. , Nichols Wesley , Richardson William J. 
Published: October 2023

AbstractHeart disease is the leading cause of death in both men and women. Cardiac fibrosis is the uncontrolled accumulation of extracellular matrix proteins, which can exacerbate the progression of heart failure, and there are currently no drugs approved specifically to target matrix accumulation in the heart. Computational signaling network models (SNMs) can be used to facilitate discovery of novel drug targets. However, the vast majority of SNMs are not sex-specific and/or are developed and validated using data skewed towards male in vitro and in vivo samples. Biological sex is an important consideration in cardiovascular health and drug development. In this study, we integrate a cardiac fibroblast SNM with estrogen signaling pathways to create sex-specific SNMs. The sex-specific SNMs demonstrated high validation accuracy compared to in vitro experimental studies in the literature while also elucidating how estrogen signaling can modulate the effect of fibrotic cytokines via multi-pathway interactions. Further, perturbation analysis and drug screening uncovered several drug compounds predicted to generate divergent fibrotic responses in male vs. female conditions, which warrant further study in the pursuit of sex-specific treatment recommendations for cardiac fibrosis. Future model development and validation will require more generation of sex-specific data to further enhance modeling capabilities for clinically relevant sex-specific predictions of cardiac fibrosis and treatment.
Community structures of mangrove endophytic and rhizosphere bacteria in Zhangjiangkou National Mangrove Nature Reserve
Authors: Yuan Zongsheng , Zeng Zhihao , Liu Fang 
Published: October 2023

AbstractBacterial communities play an important role in mangrove ecosystems. In order to gain information on the bacterial communities in mangrove species and rhizospheres grown in Zhangjiangkou National Mangrove Nature Reserve, this study collected root, branch, and leaf samples from five mangrove species as well as rhizosphere and non-rhizosphere samples and analyzed the community structure of endophytic bacteria and bacteria in rhizosphere and non-rhizosphere using Illumina high-throughput sequencing technique. Bacteria in 52 phyla, 64 classes, 152 orders, 295 families, and 794 genera were identified, which mainly belonged to Proteobacteria, Cyanobacteria, Actinobacteria, Firmicutes, Bacteroidetes, Fusobacteria, and Nitrospirota. At each taxonomic level, the community structure of the rhizosphere bacteria varied slightly with mangrove species, but endophytic bacteria differed greatly with plant species. The diversity indices of endophytic bacteria in branch and leaf samples of Acanthus ilicifolius were significantly lower, and endophytic bacteria in the plant tissues had higher abundance in the replication/repair and translation Clusters of Orthologous Genes functional categories but lower abundance in the carbohydrate metabolism category. This study helps to understand the community structure and diversity characteristics of endophytic and rhizosphere bacteria in different mangrove plants. Provide a theoretical basis for in-depth research on the functions of mangrove ecosystems.
Identification of GUCA2A and COL3A1 as prognostic biomarkers in colorectal cancer by integrating analysis of RNA-Seq data and qRT-PCR validation
Authors: Hosseini Seyed Taleb , Nemati Farkhondeh 
Published: October 2023

AbstractBy 2030, it is anticipated that there will be 2.2 million new instances of colorectal cancer worldwide, along with 1.1 million yearly deaths. Therefore, it is critical to develop novel biomarkers that could help in CRC early detection. We performed an integrated analysis of four RNA-Seq data sets and TCGA datasets in this study to find novel biomarkers for diagnostic, prediction, and as potential therapeutic for this malignancy, as well as to determine the molecular mechanisms of CRC carcinogenesis. Four RNA-Seq datasets of colorectal cancer were downloaded from the Sequence Read Archive (SRA) database. The metaSeq package was used to integrate differentially expressed genes (DEGs). The protein–protein interaction (PPI) network of the DEGs was constructed using the string platform, and hub genes were identified using the cytoscape software. The gene ontology and KEGG pathway enrichment analysis were performed using enrichR package. Gene diagnostic sensitivity and its association to clinicopathological characteristics were demonstrated by statistical approaches. By using qRT-PCR, GUCA2A and COL3A1 were examined in colon cancer and rectal cancer. We identified 5037 differentially expressed genes, including (4752 upregulated, 285 downregulated) across the studies between CRC and normal tissues. Gene ontology and KEGG pathway analyses showed that the highest proportion of up-regulated DEGs was involved in RNA binding and RNA transport. Integral component of plasma membrane and mineral absorption pathways were identified as containing down-regulated DEGs. Similar expression patterns for GUCA2A and COL3A1 were seen in qRT-PCR and integrated RNA-Seq analysis. Additionally, this study demonstrated that GUCA2A and COL3A1 may play a significant role in the development of CRC.
Assessment of the available therapeutic approaches for severe COVID-19: a meta-analysis of randomized controlled trials
Authors: Marko Monika , Pawliczak Rafał 
Published: October 2023

AbstractThe study aimed to evaluate severe COVID-19 treatment approaches. We conducted a meta-analysis of randomized controlled trials (RTCs) with standard of care (SoC) as a control group and/or placebo. Database searching was performed separately for severe COVID-19 treatment such as anakinra, remdesivir, baricitinib, ivermectin, ritonavir, tocilizumab, sarilumab, sotrovimab, casirivimab/imdevimab. The results are presented as Risk Ratio (RR), 95% Confidence Interval (CI), and heterogeneity (I2). We obtained the most statistically significant outcomes favorable tocilizumab compared to SoC for death incidents RR 0.87 [95% CI 0.80, 0.95], overall effect p = 0.002, heterogeneity p = 0.85, I2 = 0%, need for mechanical ventilation RR 0.78 [95% CI 0.68, 0.89], overall effect p = 0.0004, heterogeneity p = 0.55, I2 = 0%, and number of patients discharged from hospital. RR 1.13 [95% CI 1.07, 1.20], overall effect p < 0.00001, heterogeneity p = 0.009, I2 = 85%. This meta-analysis has revealed that a considerable amount of research characterized by a very diverse methodology is available. Despite the limited data that met the criteria for inclusion in the meta-analysis, we showed that the available treatment options for severe COVID-19 are effective.
BRAFV600E genetic testing should be recommended for Bethesda III or V thyroid nodules based on fine-needle aspiration
Authors: Lu Yiran , Guo Xinghong , Yang Mengmeng , Wang Kewei , Cao Guanglei , Liu Yan , Hou Xinguo , Chen Li , Liang Kai 
Published: October 2023

AbstractThe preoperative diagnosis of thyroid nodules now routinely includes BRAFV600E genetic testing in most provincial and municipal hospitals in China. This study identified the most suitable patients of thyroid nodule for BRAFV600E genetic testing. We retrospectively collected data of patients from the Hospital Information System that had undergone fine needle aspiration biopsy (FNAB) from May 2019 to December 2021. Data of FNAB, BRAFV600E genetic testing, and post-surgical pathological diagnosis were collected. A total of 12,392 patients were included in this study. Among them, 7,010 patients underwent solely FNAB, while 5,382 patients had both FNAB and BRAFV600E genetic testing. In the FNAB group, 2,065 thyroid nodules were surgically removed, with a 93.12% malignancy rate. In the FNAB + BRAF group, 2,005 nodules were dissected, and the malignancy rate was 98.20%. However, it was evident that in the subgroups, the combination of FNAB and BRAFV600E genetic testing only benefited Bethesda III (p < 0.001) and V (p = 0.001) nodules. Overall, the combination of FNAB with BRAFV600E genetic testing significantly improved the malignancy rate of surgical thyroid nodes at our hospital when compared to FNAB alone. The subgroup analysis showed that BRAFV600E genetic testing only benefited Bethesda III and V nodules. These findings provide a clinical reference for rationally selecting the most suitable population for BRAFV600E genetic testing.
Adherence to pancreatic enzyme replacement therapy among patients with chronic pancreatitis in East China: a mixed methods study
Authors: Zhou You , Huang Ren-Qian , Wu Qi-Wei , Xu Jin-Jie , Yi Jin-Hui , Chen Cui , Lu Guo-Tao , Li Zhao-Shen , Wang Dan , Hu Liang-Hao 
Published: October 2023

AbstractPancreatic enzyme replacement therapy (PERT) has been recommended as the preferred method for pancreatic exocrine insufficiency caused by chronic pancreatitis (CP). However, at present, the patient-related factors for the poor PERT management are not clear, and there are no studies on the adherence to PERT in patients with CP in East China. This was a mixed-method study following the principle of sequential explanatory design and included two parts: a quantitative and qualitative study. A cross-sectional survey of medication adherence (MA) was first carried out, followed by a semi-structured interview to further explore and explain the influencing factors of adherence to PERT. Of the 148 patients included in this study, 48.0% had poor MA and only 12.8% had good MA. Multivariate logistic regression showed that lower levels of education and income were contributing factors for non-adherence to PERT. Semi-structured interviews with 24 patients revealed that the reasons for non-adherence also included lack of knowledge, self-adjustment of PERT, lifetime of medication, side effects of PERT, forgetfulness, financial burdens, and accessibility issues. The adherence to PERT was poor among patients with CP in East China. Healthcare providers should personalize medication strategies to improve patients’ MA.
Neanderthal introgression in SCN9A impacts mechanical pain sensitivity
Authors: Faux Pierre , Ding Li , Ramirez-Aristeguieta Luis Miguel , Chacón-Duque J. Camilo , Comini Maddalena , Mendoza-Revilla Javier , Fuentes-Guajardo Macarena , Jaramillo Claudia , Arias William , Hurtado Malena , Villegas Valeria , Granja Vanessa , Barquera Rodrigo , Everardo-Martínez Paola , Quinto-Sánchez Mirsha , Gómez-Valdés Jorge , Villamil-Ramírez Hugo , Silva de Cerqueira Caio C. , Hünemeier Tábita , Ramallo Virginia , Gonzalez-José Rolando , Schüler-Faccini Lavinia , Bortolini Maria-Cátira , Acuña-Alonzo Victor , Canizales-Quinteros Samuel , Poletti Giovanni , Gallo Carla , Rothhammer Francisco , Rojas Winston , Schmid Annina B. , Adhikari Kaustubh , Bennett David L. , Ruiz-Linares Andrés 
Published: October 2023

AbstractThe Nav1.7 voltage-gated sodium channel plays a key role in nociception. Three functional variants in theSCN9Agene (encoding M932L, V991L, and D1908G in Nav1.7), have recently been identified as stemming from Neanderthal introgression and to associate with pain symptomatology in UK BioBank data. In 1000 genomes data, these variants are absent in Europeans but common in Latin Americans. Analysing high-density genotype data from 7594 Latin Americans, we characterized Neanderthal introgression inSCN9A. We find that tracts of introgression occur on a Native American genomic background, have an average length of ~123 kb and overlap the M932L, V991L, and D1908G coding positions. Furthermore, we measured experimentally six pain thresholds in 1623 healthy Colombians. We found that Neanderthal ancestry inSCN9Ais significantly associated with a lower mechanical pain threshold after sensitization with mustard oil and evidence of additivity of effects across Nav1.7 variants. Our findings support the reported association of Neanderthal Nav1.7 variants with clinical pain, define a specific sensory modality affected by archaic introgression inSCN9Aand are consistent with independent effects of the Neanderthal variants on Nav1.7 function.
Dendritic deformation modes in additive manufacturing revealed by operando x-ray diffraction
Authors: Dass Adrita , Tian Chenxi , Pagan Darren C. , Moridi Atieh 
Published: October 2023

AbstractDynamic solidification behavior during metal additive manufacturing directly influences the as-built microstructure, defects, and mechanical properties of printed parts. How the formation of these features is driven by temperature variation (e.g., thermal gradient magnitude and solidification front velocity) has been studied extensively in metal additive manufacturing, with synchrotron x-ray imaging becoming a critical tool to monitor these processes. Here, we extend these efforts to monitoring full thermomechanical deformation during solidification through the use of operando x-ray diffraction during laser melting. With operando diffraction, we analyze thermomechanical deformation modes such as torsion, bending, fragmentation, assimilation, oscillation, and interdendritic growth. Understanding such phenomena can aid the optimization of printing strategies to obtain specific microstructural features, including localized misorientations, dislocation substructure, and grain boundary character. The interpretation of operando diffraction results is supported by post-mortem electron backscatter diffraction analyses.
Irreversible loss in marine ecosystem habitability after a temperature overshoot
Authors: Santana-Falcón Yeray , Yamamoto Akitomo , Lenton Andrew , Jones Chris D. , Burger Friedrich A. , John Jasmin G. , Tjiputra Jerry , Schwinger Jörg , Kawamiya Michio , Frölicher Thomas L. , Ziehn Tilo , Séférian Roland 
Published: October 2023

AbstractAnthropogenic warming of the oceans and associated deoxygenation are altering marine ecosystems. Current knowledge suggests these changes may be reversible on a centennial timescale at the ocean surface but irreversible at deeper depths even if global warming were to ameliorate. In contrast, the marine ecosystem’s response to these persistent changes remains poorly elucidated. Here we explore to what extent global warming may drive alterations in marine habitats by exploring the evolution of a metabolic index that captures marine organisms’ ecophysiological response to both temperature and oxygen changes, throughout an idealised ramp-up/ramp-down atmospheric carbon dioxide concentration and an overshoot scenarios. Using a multi-model approach; we find that changes in ocean temperature and oxygen drive a centuries-long irreversible loss in the habitable volume of the upper 1000 m of the world ocean. These results suggest that the combined effect of warming and deoxygenation will have profound and long-lasting impacts on the viability of marine ecosystems, well after global temperatures have peaked.
Assessing the dynamics and macromolecular interactions of the intrinsically disordered protein YY1
Authors: Donald Heather , Blane Ashleigh , Buthelezi Sindisiwe , Naicker Previn , Stoychev Stoyan , Majakwara Jacob , Fanucchi Sylvia 
Published: October 2023

Abstract
YY1 is a ubiquitously expressed, intrinsically disordered transcription factor involved in neural development. The oligomeric state of YY1 varies depending on the environment. These structural changes may alter its DNA binding ability and hence its transcriptional activity. Just as YY1’s oligomeric state can impact its role in transcription, so does its interaction with other proteins such as FOXP2. The aim of this work is to study the structure and dynamics of YY1 so as to determine the influence of oligomerisation and associations with FOXP2 on its DNA binding mechanism. The results confirm that YY1 is primarily a disordered protein, but it does consist of certain specific structured regions. We observed that YY1 quaternary structure is a heterogenous mixture of oligomers, the overall size of which is dependent on ionic strength. Both YY1 oligomerisation and its dynamic behaviour are further subject to changes upon DNA binding, whereby increases in DNA concentration result in a decrease in the size of YY1 oligomers. YY1 and the FOXP2 forkhead domain were found to interact with each other both in isolation and in the presence of YY1-specific DNA. The heterogeneous, dynamic multimerisation of YY1 identified in this work is, therefore likely to be important for its ability to make heterologous associations with other proteins such as FOXP2. The interactions that YY1 makes with itself, FOXP2 and DNA form part of an intricate mechanism of transcriptional regulation by YY1, which is vital for appropriate neural development.
A Preliminary Investigation of Stakeholders' Perspectives on Cognitive Fatigue After Childhood Brain Injury
Authors: Riccardi Jessica Salley 
Published: October 2023

Background:
Cognitive fatigue after childhood acquired brain injury (ABI) is known to negatively impact engagement in typical academic and social activities, yet limited evidence is available to inform speech-language pathologists' (SLPs') clinical practices. The purpose of this research study was to explore stakeholders' perspectives on cognitive fatigue for children with ABI to inform future directions for clinicians and researchers.

Method:
Twelve parents of children with traumatic brain injury and 35 SLPs participated in an online survey with 33 and 49 questions, respectively, including participant characteristics and perspectives on cognitive fatigue.

Results:
Parents reported being between “somewhat” and “highly aware” about cognitive fatigue, whereas SLPs reported being between “neither aware or not aware” and “somewhat aware.” Parents reported being between “somewhat comfortable” and “very comfortable,” whereas SLPs reported being between “neither comfortable or uncomfortable” and “somewhat comfortable” addressing cognitive fatigue in children with ABI. SLPs “somewhat” to “strongly” agreed that cognitive fatigue for children with ABI was within their scope of practice. Parents and SLPs reported accommodations and strategies useful to managing cognitive fatigue in children with brain injury, as well as factors that worsen and lessen cognitive fatigue.

Conclusions:
While additional foundational and translation research is needed, the perspectives of parents and SLPs begin to address a critical gap in SLPs' assessment and management of cognitive fatigue in children with ABI.

Supplemental Material:

https://doi.org/10.23641/asha.24216576
A polyphenol‐induced hydroxyapatite coating modulates corrosion resistance and biocompatibility of magnesium alloys
Authors: Chai Tao , Zhang Hao , Shen Xiaolong , Wang Haibo , Fan Xingping , Wang Binbin , He Dingying , Su Jia 
Published: October 2023

AbstractIn order to solve the problem of excessive degradation rate and insufficient biocompatibility of magnesium‐based bone implants, a polyphenol (EGCG) induced hydroxyapatite (HA) coating was prepared on the surface of AZ31 alloy. The physical and chemical properties and corrosion resistance of the coating were analysed in depth, and its biocompatibility was preliminarily explored in vitro. The results showed that the polyphenol (EGCG) conversion coating constructed on the AZ31 could successfully induce the formation of HA by complexing the phenolic hydroxyl group with calcium ions. The electrochemical and long‐term immersion experiments showed that the corrosion resistance of EGCG/HA composite coating was significantly improved. The self‐corrosion current density, hydrogen evolution and the increase of pH value of AZ31‐EGCG/HA were significantly lower than those of AZ31. On the basis of inhibiting the excessive corrosion of the substrate, the composite coating significantly improves the compatibility of pre‐osteoblasts, supports the adhesion and spreading and effectively reduces the haemolysis rate to less than 5%. The preparation method of the coating is simple, low cost and suitable for complex shape surfaces, which can significantly improve the corrosion resistance and biocompatibility of the AZ31 substrate. It is expected to provide a solution for the surface modification of magnesium‐based bone implants.
Distributed feedback optimisation based optimal power flow control in fully inverter based islanded AC microgrids
Authors: Cheng Y. , Liu Tao , Hill David John 
Published: October 2023

AbstractA novel distributed feedback optimisation (FO) based control method is proposed to control grid‐forming inverters (GFMIs) in fully inverter‐based islanded AC microgrids (MGs). The proposed controller has two control layers. The upper layer uses FO to calculate the frequency and voltage setpoints of GFMIs, whereas the lower layer makes GFMIs track these setpoints. The proposed control method takes advantage of the flexibility of voltage control to regulate the system frequency, maintain both active power and reactive power sharing accuracies, keep bus voltage within allowable range and meanwhile preserves the optimality of the closed‐loop system in term of optimal power flow. The gradient descent method is used to solve the proposed FO problem based on the real‐time measurements in the MGs, which is implemented in a distributed way, and thus eliminates the need for a central controller. Case studies show the effectiveness of the proposed method.The cover image is based on the Research Article Distributed feedback optimisation based optimal power flow control in fully inverter based islanded AC microgrids by Y. Cheng et al., https://doi.org/10.1049/stg2.12132.