bluuebunny/crossref_metadata_2025_split huggingface dataset:
Mode‐based morphometry: A multiscale approach to mapping human neuroanatomy
Authors: Cao Trang , Pang James C. , Segal Ashlea , Chen Yu‐Chi , Aquino Kevin M. , Breakspear Michael , Fornito Alex 
Published: March 2024

AbstractVoxel‐based morphometry (VBM) and surface‐based morphometry (SBM) are two widely used neuroimaging techniques for investigating brain anatomy. These techniques rely on statistical inferences at individual points (voxels or vertices), clusters of points, or a priori regions‐of‐interest. They are powerful tools for describing brain anatomy, but offer little insights into the generative processes that shape a particular set of findings. Moreover, they are restricted to a single spatial resolution scale, precluding the opportunity to distinguish anatomical variations that are expressed across multiple scales. Drawing on concepts from classical physics, here we develop an approach, called mode‐based morphometry (MBM), that can describe any empirical map of anatomical variations in terms of the fundamental, resonant modes—eigenmodes—of brain anatomy, each tied to a specific spatial scale. Hence, MBM naturally yields a multiscale characterization of the empirical map, affording new opportunities for investigating the spatial frequency content of neuroanatomical variability. Using simulated and empirical data, we show that the validity and reliability of MBM are either comparable or superior to classical vertex‐based SBM for capturing differences in cortical thickness maps between two experimental groups. Our approach thus offers a robust, accurate, and informative method for characterizing empirical maps of neuroanatomical variability that can be directly linked to a generative physical process.
External beam radiation therapy for recurrent or residual thyroid cancer: What is the best treatment time and the best candidate for long‐term local disease control?
Authors: Cavalcante Lara Bessa Campelo Pinheiro , Treistman Natalia , Gonzalez Fabiola Maria Teresa Torres , Fernandes Pollyanna Iemini Weyll , Alves Junior Paulo Alonso Garcia , Andrade Fernanda Accioly , Ferreira Elisa Napolitano , Brito Tarcisio Fontenele De , Pane Attilio , Corbo Rossana , Erlich Felipe , Bulzico Daniel Alves , Vaisman Fernanda 
Published: March 2024

AbstractIntroductionCervical disease control might be challenging in advanced thyroid cancer (DTC). Indications for cervical external beam radiation therapy (EBRT) are controversial.PurposeTo identify clinical and molecular factors associated with control of cervical disease with EBRT.MethodsRetrospective evaluation and molecular analysis of the primary tumor DTC patients who underwent cervical EBRT between 1995 and 2022 was performed.ResultsEighty adults, median age of 61 years, were included. T4 disease was present in 43.7%, lymph node involvement in 42.5%, and distant metastasis in 47.5%. Those with cervical progression were older (62.5 vs. 57.3, p = 0.04) with more nodes affected (12.1 vs. 2.8, p = 0.04) and had EBRT performed later following surgery (76.6 vs. 64 months, p = 0.05). EBRT associated with multikinase inhibitors showed longer overall survival than EBRT alone (64.3 vs. 37.9, p = 0.018) and better local disease control. Performing EBRT before radioiodine (RAI) was associated with longer cervical progression‐free survival (CPFS) than was RAI before (67.5 vs. 34.5, p < 0.01). EBRT ≥2 years after surgery was associated with worse CPFS (4.9 vs. 34, p = 0.04). The most common molecular alterations were ERBB2, BRAF, FAT1, RET and ROS1 and TERT mutation was predictive of worse disease control after EBRT (p = 0.04).ConclusionYounger patients, with fewer affected nodes and treated earlier after surgery had better cervical disease control. Combination of EBRT with MKI improved OS. TERT mutation might indicate worse responders to EBRT; however, further studies are necessary to clarify the role of molecular testing in selecting candidates for cervical EBRT.
A Fluorogenic Substrate for Quinoline Reduction: Pnictogen‐Bonding Catalysis in Aqueous Systems
Authors: Renno Giacomo , Zhang Qing‐Xia , Frontera Antonio , Sakai Naomi , Matile Stefan 
Published: March 2024

AbstractIt is often said that pnictogen‐bonding catalysis, and σ‐hole catalysis in general, would not work in aqueous systems because the solvent would interfere as an overcompetitive pnictogen‐bond acceptor. In this study, we show that the transfer of pnictogen‐bonding catalysis from hydrophobic solvents to aqueous systems is possible by replacing only hydrophobic with hydrophilic substrates, without changing catalyst or reaction. This differs from conventional covalent Lewis acid catalysts, which are instantaneously destroyed by ligand exchange. With their water‐proof substituents in place of exchangeable ligands, pnictogen‐bonding catalysts, the supramolecular counterpart of Lewis acid catalysts, are evinced to catalyze transfer hydrogenation of quinolines in neutral aqueous systems. To secure these results, we introduce a water‐soluble fluorogenic substrate that releases a coumarin upon the reduction of quinolines instead of activated quinolidiniums, and stiborane catalysts with deepened σ holes. They demonstrate that pnictogen‐bonding catalysts can operate in higher‐order architectures for supramolecular systems catalysis under biologically relevant conditions, and provide an operational assay for high‐throughput catalyst screening by fluorescence imaging, in situ under relevant aqueous conditions.
COMSOL Multiphysics simulation of hydromagnetic flow in horizontal channels with diverse media: Insights into momentum and heat diffusion limitations
Authors: Ahmed Sahin , Das Bikash 
Published: March 2024

AbstractThe Darcy–Forchheimer model for a two‐dimensional hydromagnetic flow in a horizontal channel, including the dynamic interaction of porous and nonporous media, is investigated in this study due to the importance of the consequences of heat exchange in porous materials. The novelty of the current investigation is to study the hydrodynamics of fluid flowing through a channel with free and non‐Darcy porous media linked next to one another influenced by the potent Lorentz force. The prime objective of this investigation is to analyze the influence of critical nondimensional parameters on the rate of heat transfer and shear forces exerted on the walls of the channel. Numerical simulations are carried out using the finite element method within the COMSOL Multiphysics program, which offers a versatile framework to explore the behavior of velocity and isothermal contours. The essential optimal stability of this adopted model is achieved for specific scenarios employing a finely meshed grid and grid‐independent analysis. It is noteworthy that larger Prandtl numbers enhance heat transmission rates from surfaces at high temperatures, whereas greater Eckert numbers are correlated with lower Nusselt numbers. On the lower surface, the Forchheimer and magnetic drag forces reduce skin friction, whereas the top surface displays a different pattern. The aforesaid findings have a variety of engineering applications by improving the flow dynamics in porous and nonporous materials. This study can be beneficial in designing heat exchanger devices.
Exploring landscape and geologic controls on spatial patterning of streambank groundwater discharge in a mixed land use watershed
Authors: Jackson Kevin E. , Moore Eric M. , Helton Ashley M. , Haynes Adam B. , Barclay Janet R. , Briggs Martin A. 
Published: March 2024

AbstractPreferential groundwater discharge features along stream corridors are ecologically important at local and stream network scales, yet we lack quantification of the multiscale controls on the spatial patterning of groundwater discharge. Here we identify physical attributes that best explain variation in the presence and lateral extent of preferential groundwater discharges along two 5th order streams, the Housatonic and Farmington Rivers, and 32 1st to 4th order reaches across the Farmington River network. We mapped locations of preferential groundwater discharge exposed along streambanks using handheld thermal infrared cameras paired with high‐resolution topographic and land use land cover datasets, surficial soil characteristic maps, and depth‐to‐bedrock geophysical measurements. The unconfined Housatonic River, MA, USA (12 km) had fewer discharge locations and less lateral extent (41 discharge locations with 38 m of active discharge/km of river) compared to the partially confined Farmington River, CT, USA (26 km; 169 discharge locations with 129 m of active discharge/km of river). Using a moving window analysis, we found along both rivers that discharge was more likely to occur where bank slopes were steeper, floodplain extent was narrower, and degree of confinement was higher. Along the Farmington River, groundwater discharge was more likely to occur where saturated hydraulic conductivity was higher and depth‐to‐bedrock was shallower. Among the 32 stream reaches surveyed (33.2 km of total stream length) within the Farmington River watershed, preferential discharge was observed in all but two stream reaches, varied from 0 to 25% of lateral extent along stream banks (mean = 6%), and was more likely to occur where stream reach slopes were steep, saturated hydraulic conductivity was high, and watershed urbanization was low. Our results show that, though both surface (e.g., topographic, land use land cover) and subsurface (e.g., soil characteristics, bedrock depth) factors control the prevalence of streambank preferential groundwater discharge, the dominant controls vary across valley settings and stream sizes.
The Transthyretin Protein and Amyloidosis – An Extraordinary Chemical Biology Platform
Authors: Hammarström Per 
Published: March 2024

AbstractThe amyloidoses are diseases caused by accumulation of amyloid fibrils from over 40 different human misfolded proteins in various organs of the body depending on precursor protein. Amyloidogenesis is a self‐perpetuating reaction with deleterious consequences causing degeneration in cells and organs where depositions occur. Transthyretin, TTR, is an amyloidogenic protein causing sporadic disease from the wild‐type protein during aging and from numerous different autosomal dominant familial mutations at earlier ages depending on the sequence of the hereditary variant. Until recently the disease process was poorly understood, and therapies were scarce. Over the past decades, spurred by clinical data, using chemical biology research, the mechanisms of TTR production and misfolding have been elucidated affording almost complete coverage of the TTR amyloidogenesis pathway to be targeted. This translational science success has provided a plethora of therapeutic options for the TTR amyloidoses providing an inspiring example for success in previously intractable diseases.
Using liquid chromatography and mass spectrometry to predict potential biomarkers for missed miscarriage and its metabolic pathways in a tertiary center: A cross‐sectional analytic study
Authors: Xia Lina , Zhao Huan , Shan Li , Ma Xiaohong , An Peixing , Duan Xiaoyan 
Published: March 2024

AbstractObjectiveTo determine and compare the serum metabolites in missed abortion versus normal early pregnancy using ultra‐high‐performance liquid chromatography and tandem time‐of‐flight mass spectrometry, and to determine how these metabolites can be used to predict the potential biomarkers and possible metabolic pathways of a missed abortion.MethodsThe serum of patients with a missed abortion was used as the experimental group and the serum of patients with an induced abortion during normal early pregnancy was used as the control group. Principal component analysis and orthogonal partial least square discriminant analysis were additionally used to observe the difference in metabolite distribution between the two groups. A variable weight value (variable importance in the projection; VIP) obtained from the orthogonal partial least squares discriminant analysis model more than 1 and P less than 0.05 were taken to indicate significant differences in metabolite screening. After this, enrichment analysis of the metabolic pathways of these metabolites was conducted using Fisher precise test in order to find the metabolic pathway with the highest correlation with the differential metabolites.ResultsIn total, 30 patients were included in the experimental group, with 30 patients in the control group. Fifty‐five metabolites (VIP > 1, P < 0.05) with significant differences related to missed abortion were selected, among which 35 metabolites increased and 20 decreased in patients with a missed abortion. KEGG pathway enrichment analysis showed that the four metabolic pathways with the highest correlation were cholesterol metabolism, arginine biosynthesis, cell apoptosis, and the FoxO signaling pathway.ConclusionThe missed abortion serum metabolites and changes in related metabolic pathways reported in this study provide a basis for the early prediction and diagnosis of a missed abortion.
Sexual quality of life and postoperative deep dyspareunia after vNOTES benign adnexal procedures
Authors: Berisha Laura , Hurni Yannick , Simonson Colin , Di Serio Marcello , Lachat Régine , Bodenmann Pauline , Seidler Stéphanie , Mathevet Patrice , Huber Daniela 
Published: March 2024

AbstractObjectiveThis study aimed to investigate the impact of vNOTES on postoperative sexual dysfunction in patients undergoing adnexal procedures.MethodsWe analyzed data from patients who underwent vNOTES adnexal surgeries for benign conditions between May 2020 and May 2023. The primary outcome was the presence of new postoperative deep dyspareunia (DD) or other sexual dysfunctions, which were assessed through a phone survey conducted 6 to 24 months after surgery. Secondary outcomes included surgical feasibility, operative times, complications rate, and postoperative pain evaluation.ResultsWe included 103 patients for primary and secondary outcomes and 111 patients for secondary outcomes analysis only. Newly postoperative DD was reported by three patients (2.9%), remained present at 12 postoperative months in one case (1.0%), and spontaneously disappeared in two cases (1.9%) after four and 10 postoperative months, respectively. In the remaining 100 patients (97.1%), no new DD or other sexual function disorders were reported after surgery. vNOTES procedures were successfully performed in all cases, with a mean operative time of 38.2 ± 19.6 min and a conversion rate to conventional laparoscopy of 0.9%. No significant complication was observed.ConclusionThis study suggests a very limited risk of developing postoperative sexual dysfunction after vNOTES benign adnexal procedures.
Lycopene prevents cell death in NRK‐52E cells by inhibition of high glucose‐activated DNA damage and apoptotic, autophagic, and necrotic pathways
Authors: Usta Ayşe , Yüksek Veysel , Çetin Sedat , Dede Semiha 
Published: March 2024

AbstractThis study aims to investigate the effects of lycopene on apoptotic, autophagic, and necrotic pathways, oxidative status, and DNA damage in diabetic nephropathy at the molecular level. The sample of the study includes seven groups: lycopene (L), high glucose (G), high glucose + lycopene (GL), and control (C) groups tested at 12 and 24 h. The expression levels of genes in oxidative, apoptotic, autophagic, and necrotic cell death pathways are determined by reverse transcription‐quantitative polymerase chain reaction analysis. The comet assay method is used for the analysis of DNA damage. It is observed that adding lycopene to high glucose for protective purposes reduces the expression of genes related to apoptosis, autophagy, and necrosis, as well as the DNA damage index, compared to cells given high glucose alone. Lycopene can be a safe and effective alternative agent.
Automatic classification of acute lymphoblastic leukemia cells and lymphocyte subtypes based on a novel convolutional neural network
Authors: MoradiAmin Morteza , Yousefpour Mitra , Samadzadehaghdam Nasser , Ghahari Laya , Ghorbani Mahdi , Mafi Majid 
Published: March 2024

AbstractAcute lymphoblastic leukemia (ALL) is a life‐threatening disease that commonly affects children and is classified into three subtypes: L1, L2, and L3. Traditionally, ALL is diagnosed through morphological analysis, involving the examination of blood and bone marrow smears by pathologists. However, this manual process is time‐consuming, laborious, and prone to errors. Moreover, the significant morphological similarity between ALL and various lymphocyte subtypes, such as normal, atypic, and reactive lymphocytes, further complicates the feature extraction and detection process. The aim of this study is to develop an accurate and efficient automatic system to distinguish ALL cells from these similar lymphocyte subtypes without the need for direct feature extraction. First, the contrast of microscopic images is enhanced using histogram equalization, which improves the visibility of important features. Next, a fuzzy C‐means clustering algorithm is employed to segment cell nuclei, as they play a crucial role in ALL diagnosis. Finally, a novel convolutional neural network (CNN) with three convolutional layers is utilized to classify the segmented nuclei into six distinct classes. The CNN is trained on a labeled dataset, allowing it to learn the distinguishing features of each class. To evaluate the performance of the proposed model, quantitative metrics are employed, and a comparison is made with three well‐known deep networks: VGG‐16, DenseNet, and Xception. The results demonstrate that the proposed model outperforms these networks, achieving an approximate accuracy of 97%. Moreover, the model's performance surpasses that of other studies focused on 6‐class classification in the context of ALL diagnosis.Research Highlights
Deep neural networks eliminate the requirement for feature extraction in ALL classification
The proposed convolutional neural network achieves an impressive accuracy of approximately 97% in classifying six ALL and lymphocyte subtypes.
Extracellular vesicles as a promising source of lipid biomarkers for breast cancer detection in blood plasma
Authors: Dorado Erika , Doria Maria Luisa , Nagelkerke Anika , McKenzie James S. , Maneta‐Stavrakaki Stefania , Whittaker Thomas E. , Nicholson Jeremy K. , Coombes Raoul Charles , Stevens Molly M. , Takats Zoltan 
Published: March 2024

AbstractExtracellular vesicles (EVs), including exosomes and microvesicles, mediate intercellular communication in cancer, from development to metastasis. EV‐based liquid biopsy is a promising strategy for cancer diagnosis as EVs can be found in cancer patients’ body fluids. In this study, the lipid composition of breast cancer‐derived EVs was studied as well as the potential of blood plasma EVs for the identification of lipid biomarkers for breast cancer detection. Initially, an untargeted lipidomic analysis was carried out for a panel of cancerous and non‐cancerous mammary epithelial cells and their secreted EVs. We found that breast cancer‐derived EVs are enriched in sphingolipids and glycerophospholipids compared to their parental cells. The initial in vitro study showed that EVs and their parental cells can be correctly classified (100% accuracy) between cancerous and non‐cancerous, as well as into their respective breast cancer subtypes, based on their lipid composition. Subsequently, an untargeted lipidomic analysis was carried out for blood plasma EVs from women diagnosed with breast cancer (primary or progressive metastatic breast cancer) as well as healthy women. Correspondingly, when blood plasma EVs were analysed, breast cancer patients and healthy women were correctly classified with an overall accuracy of 93.1%, based on the EVs’ lipid composition. Similarly, the analysis of patients with primary breast cancer and healthy women showed an overall accuracy of 95% for their correct classification. Furthermore, primary and metastatic breast cancers were correctly classified with an overall accuracy of 89.5%. This reveals that the blood plasma EVs’ lipids may be a promising source of biomarkers for detection of breast cancer. Additionally, this study demonstrates the usefulness of untargeted lipidomics in the study of EV lipid composition and EV‐associated biomarker discovery studies. This is a proof‐of‐concept study and a starting point for further analysis on the identification of EV‐based biomarkers for breast cancer.
SPINK5 inhibits esophageal squamous cell carcinoma metastasis via immune activity
Authors: Chen Jie , Lu Juncheng , Chen Zhiqiang , Liu Zihao , Sun Yuejun , He Shuyan , Mi Yedong , Gao Yi , Shen Dong , Lin Qingfeng 
Published: March 2024

AbstractBackgroundEsophageal squamous cell carcinoma (ESCC) is a predominant subtype of esophageal cancer with relatively high mortality worldwide. Serine peptidase inhibitor Kazal‐type 5 (SPINK5) is reported to be downregulated in ESCC. However, its explicit role in ESCC remains further investigation.MethodsThe tumor tissues and adjacent non‐cancerous tissues were obtained from 196 patients with ESCC for the determination of SPINK5 mRNA levels. Additionally, the relationship between SPINK5 mRNA levels and clinicopathological features of ESCC patients was explored. The effects of SPINK5 on the invasion and migration of ESCC cells were assessed using Transwell assays. Furthermore, SPINK5 mRNA and LEKTI protein were measured in ESCC cell lines after treatment with poly (I:C), lipopolysaccharide (LPS) or unmethylated CpG DNA. Moreover, the correlation between expression of SPINK5 and nuclear factor‐kappa B (NF‐κB) signaling pathway‐related genes was analyzed in the TCGA‐ESCC cohort, and the effects of SPINK5 on NF‐κB transcription was analyzed using a luciferase reporter gene assay. Finally, the correlations between SPINK5 and infiltration of immune cells, immune scores, stromal scores and ESTIMATE (i.e., Estimation of STromal and Immune cells in MAlignant Tumor tissues using Expression data) scores were explored.ResultsSPINK5 mRNA levels were downregulated in tumor tissues, which was significantly correlated with higher lymph node metastases. Overexpressed SPINK5 inhibited cell invasion and migration in ESCC cell lines. Mechanistically, LPS‐induced activation of Toll‐like receptor 4 (TLR4) decreased SPINK5 mRNA and LEKTI in KYSE150 and KYSE70 cells. Spearman correlation analysis revealed that SPINK5 mRNA was significantly negatively correlated with a total of seven NF‐κB signaling pathway‐related genes in TCGA‐ESCC patients. Moreover, downregulation of SPINK5 increased and upregulation of SPINK5 decreased the activity of the NF‐κB promoter in HEK293T cells. Finally, immune cells infiltration analysis revealed that SPINK5 was significantly correlated with the infiltration of various immune cells, stromal scores, immune scores and ESTIMATE scores.ConclusionsSPINK5 plays critical roles in the TLR4/NF‐κB pathway and immune cells infiltration, which might contribute to the ESCC metastasis. The findings of the present study may provide a promising biomarker for the diagnosis and treatment of esophageal squamous cell carcinoma.