bluuebunny/crossref_metadata_2025_split huggingface dataset:
Fast vibrational analysis of molecular systems
Authors: Petitjean Hugo , Giard Aude , Flament Jean‐Pierre , Berthomieu Catherine , Berthomieu Dorothée 
Published: June 2024

AbstractThe development of infrared difference spectroscopy provides unprecedented insights on structures of complex molecules like metalloproteins. However, the relevant information can be hard to find among the many bands of the vibrational spectra. The ab initio modeling is very helpful to assign the frequencies to vibrational modes but it is a challenge to process the huge quantity of data into descriptors useful for experimentalists. To this end, we developed a new tool called VIBMOL allowing to analyze vibrational modes of molecules from hessian matrices calculated with common quantum chemistry codes. VIBMOL program runs on Unix machines. Through a new graphical interface, the users can calculate the normal modes of molecules, visualize them, simulate infrared spectra, and explore the Potential Energy Distribution of normal modes among any set of vibration coordinates. It is combined with an interface program (gosdmu) formatting relevant data from the GAUSSIAN program. VIBMOL code is available upon request to the authors. A discussion is provided to help the readers to choose between a large choice of different software and it shows how VIBMOL can make the IR assignment easier in the context of collaborations with experimentalists.
Theoretical insights into solvent‐polarity‐associated excited state behaviors for a novel 2‐hydroxy‐1‐naphthaldehyde‐triphenylamine (TPHY) fluorophore: A TDDFT study
Authors: Hou Mengmeng , Zhang Meiyi , Zhao Jinfeng , Yang Liang , Tang Zhe 
Published: June 2024

AbstractInspired by the profound allure of the exquisitely regulated characteristics exhibited by 2‐hydroxy‐1‐naphthaldehyde‐triphenylamine (TPHY) and its derivatives in the realms of photochemistry and photophysics, our current endeavor primarily revolves around delving into the intricacies of photo‐induced excited state reactions for TPHY fluorophores within solvents boasting varying degrees of polarity. Our simulations, resulting from variations in geometry and vertical excitation charge reorganization, unveil solvent polarity‐dependent hydrogen bonding interactions and charge recombination induced by photoexcitation that can significantly enhance the excited state intramolecular proton transfer (ESIPT) reaction for TPHY chemosensor. By constructing potential energy surfaces (PESs), we reveal that the single ESIPT reaction of TPHY occurs concurrently with alternative dual intramolecular hydrogen bonds (O1‐H2···N3 and O4‐H5···N6). We sincerely hope that the regulation of solvent polarity on excited state behaviors may pave the way for the development of innovative luminescent materials.
Isolated liver gastrointestinal stromal tumor: A case report
Authors: Deng Yan , Zhang Min , Li Shi‐Yan 
Published: June 2024

ABSTACTGastrointestinal stromal tumors (GISTs) originate from the gastrointestinal tract. GISTs originate outside the gastrointestinal tract, referred to as extra GISTs, which is rare. Primary liver gastrointestinal stromal tumor (PLGIST) and liver metastasis of gastrointestinal stromal tumor (LMGIST) may present isolated liver lesion, making it difficult to determine their origin. A 38‐year‐old man who presented with isolated multiple giant cystic‐solid liver lesions, ultimately diagnosed as liver GIST through CT‐guided fine‐needle aspiration. However, distinguishing between PLGIST and LMGIST in this case is challenging due to the absence of detailed medical records of emergency small intestine resection 5 years ago. Over 2‐year follow‐up period, the maximum lesion size increased from 16 to 21 cm, still, no extra liver lesions were observed. This study aims to provide a review to enhance understanding of this rare liver entity, aiding in tumor diagnosis and staging.
Prenatal and postnatal cocaine exposure enhances the anxiety‐ and depressive‐like behaviors in rats: An ontogenetic study
Authors: Méndez Susana Barbosa , Salazar‐Juárez Alberto 
Published: June 2024

AbstractBackgroundPrenatal and postnatal exposure to drugs such as cocaine is a public health problem that causes deficits in brain development and function in humans and animals. One of the main effects of prenatal and postnatal cocaine exposure is increased vulnerability to developing the substance use disorder at an early age. Furthermore, the negative emotional states associated with cocaine withdrawal increase the fragility of patients to relapse into drug abuse. In this sense, prenatal and postnatal cocaine exposure enhanced the cocaine‐ and nicotine‐induced locomotor activity and locomotor sensitization, and rats exposed prenatally to cocaine displayed an increase in anxiety‐ and depressive‐like behaviors in adulthood (PND 60–70).ObjectiveTherefore, the objective of this study was to determine the effect of prenatal and postnatal cocaine exposure on anxiety‐ and depressive‐like behaviors at different ages (30, 60, 90, and 120 days of age) in rats.MethodsThe study was divided into two stages: prenatal and postnatal. In the prenatal stage, a group of pregnant female Wistar rats was administered daily from GD0 to GD21 cocaine (cocaine pre‐exposure group), and another group of pregnant female rats was administered daily saline (saline pre‐exposure group). In the postnatal stage, during lactation (PND0 to PND21), pregnant rats received administration of cocaine or saline, respectively. Of the litters resulting from the cocaine pre‐exposed and saline pre‐exposed pregnant female groups, only the male rats were used for the recording of the anxiety‐ and depressive‐like behaviors at different postnatal ages (30, 60, 90, and 120 days), representative of adolescence, adult, adulthood, and old age.ResultsThe study found that prenatal and postnatal cocaine exposure generated age‐dependent enhancement in anxiety‐ and depressive‐like behaviors, being greater in older adult (PND 120) rats than in adolescent (PND 30) or adults (PND 60–90) rats.ConclusionsThis suggests that prenatal and postnatal cocaine exposure increases anxiety‐ and depressive‐like behaviors, which may increase the vulnerability of subjects to different types of drugs in young and adult age.
Bone marrow‐fibroblast progenitor cell‐derived small extracellular vesicles promote cardiac fibrosis via miR‐21‐5p and integrin subunit αV signalling
Authors: Ranjan Prabhat , Dutta Roshan Kumar , Colin Karen , Li Jing , Zhang Qinkun , Lal Hind , Qin Gangjian , Verma Suresh Kumar 
Published: June 2024

AbstractCardiac fibrosis is the hallmark of cardiovascular disease (CVD), which is leading cause of death worldwide. Previously, we have shown that interleukin‐10 (IL10) reduces pressure overload (PO)‐induced cardiac fibrosis by inhibiting the recruitment of bone marrow fibroblast progenitor cells (FPCs) to the heart. However, the precise mechanism of FPC involvement in cardiac fibrosis remains unclear. Recently, exosomes and small extracellular vesicles (sEVs) have been linked to CVD progression. Thus, we hypothesized that pro‐fibrotic miRNAs enriched in sEV‐derived from IL10 KO FPCs promote cardiac fibrosis in pressure‐overloaded myocardium. Small EVs were isolated from FPCs cultured media and characterized as per MISEV‐2018 guidelines. Small EV's miRNA profiling was performed using Qiagen fibrosis‐associated miRNA profiler kit. For functional analysis, sEVs were injected in the heart following TAC surgery. Interestingly, TGFβ‐treated IL10‐KO‐FPCs sEV increased profibrotic genes expression in cardiac fibroblasts. The exosomal miRNA profiling identified miR‐21a‐5p as the key player, and its inhibition with antagomir prevented profibrotic signalling and fibrosis. At mechanistic level, miR‐21a‐5p binds and stabilizes ITGAV (integrin av) mRNA. Finally, miR‐21a‐5p‐silenced in sEV reduced PO‐induced cardiac fibrosis and improved cardiac function. Our study elucidates the mechanism by which inflammatory FPC‐derived sEV exacerbate cardiac fibrosis through the miR‐21a‐5p/ITGAV/Col1α signalling pathway, suggesting miR‐21a‐5p as a potential therapeutic target for treating hypertrophic cardiac remodelling and heart failure.
Amniotic fluid‐derived small extracellular vesicles for predicting postnatal severe outcome of congenital diaphragmatic hernia
Authors: Matsuo Seiko , Yokoi Akira , Yoshida Kosuke , Kitagawa Masami , Asano‐Inami Eri , Miura Mayo , Yasui Takao , Tano Sho , Ushida Takafumi , Imai Kenji , Kajiyama Hiroaki , Kotani Tomomi 
Published: June 2024

AbstractCongenital diaphragmatic hernia (CDH) is a life‐threatening condition with high morbidity and mortality rates. The survival rate of neonates with severe CDH is reportedly only 10%–15%. However, prenatal prediction of severe cases is difficult, and the discovery of new predictive markers is an urgent issue. In this study, we focused on microRNAs (miRNAs) in amniotic fluid‐derived small EVs (AF‐sEVs). We identified four miRNAs (hsa‐miR‐127‐3p, hsa‐miR‐363‐3p, hsa‐miR‐493‐5p, and hsa‐miR‐615‐3p) with AUC > 0.8 to classify good prognosis group and poor prognosis group in human study. The AUC for hsa‐miR‐127‐3p and hsa‐miR‐615‐3p, for predicting the poor prognosis, were 0.93 and 0.91, respectively. In addition, in the in vivo study, the miRNA profiles of the lung tissues of CDH rats were different from those of control rats. Additionally, two elevated miRNAs (rno‐miR‐215‐5p and rno‐miR‐148a‐3p) in the lung tissues of CDH rats were increased in the AF‐sEVs of CDH rats. Our results suggest that severe CDH neonates can be predicted prenatally with high accuracy using miRNAs contained in AF‐sEVs. Furthermore, miRNA profile changes in AF‐sEVs reflected the lung status in CDH. Our findings may contribute to the development of advanced perinatal care for patients with CDH.
A Nomogram Based on MRI Visual Decision Tree to Evaluate Vascular Endothelial Growth Factor in Hepatocellular Carcinoma
Authors: Dai Hanting , Yan Chuan , Huang Wanrong , Pan Yifan , Pan Feng , Liu Yamei , Wang Shunli , Wang Huifang , Ye Rongping , Li Yueming 
Published: June 2024

BackgroundsAnti‐vascular endothelial growth factor (VEGF) therapy has been developed and recognized as an effective treatment for hepatocellular carcinoma (HCC). However, there remains a lack of noninvasive methods in precisely evaluating VEGF expression in HCC.PurposeTo establish a visual noninvasive model based on clinical indicators and MRI features to evaluate VEGF expression in HCC.Study TypeRetrospective.PopulationOne hundred forty HCC patients were randomly divided into a training (N = 98) and a test cohort (N = 42).Field Strength/Sequence3.0 T, T2WI, T1WI including pre‐contrast, dynamic, and hepatobiliary phases.AssessmentThe fusion model constructed by history of smoking, albumin‐to‐globulin ratio (AGR) and the Radio‐Tree model was visualized by a nomogram.Statistical TestsPerformances of models were assessed by receiver operating characteristic (ROC) curves. Student's t‐test, Mann–Whitney U‐test, chi‐square test, Fisher's exact test, univariable and multivariable logistic regression analysis, DeLong's test, integrated discrimination improvement (IDI), Hosmer–Lemeshow test, and decision curve analysis were performed. P < 0.05 was considered statistically significant.ResultsHistory of smoking and AGR ≤1.5 were clinical independent risk factors of the VEGF expression. In training cohorts, values of area under the curve (AUCs) of Radio‐Tree model, Clinical‐Radiological (C‐R) model, fusion model which combined history of smoking and AGR with Radio‐Tree model were 0.821, 0.748, and 0.871. In test cohort, the fusion model showed highest AUC (0.844) than Radio‐Tree and C‐R models (0.819, 0.616, respectively). DeLong's test indicated that the fusion model significantly differed in performance from the C‐R model in training cohort (P = 0.015) and test cohort (P = 0.007).Data ConclusionThe fusion model combining history of smoking, AGR and Radio‐Tree model established with ML algorithm showed the highest AUC value than others.Evidence Level4Technical EfficacyStage 2
Explainable localization of premature ventricular contraction using deep learning‐based semantic segmentation of 12‐lead electrocardiogram
Authors: Kujime Kota , Seno Hiroshi , Nakajima Kenzaburo , Yamazaki Masatoshi , Sakuma Ichiro , Yamagata Kenichiro , Kusano Kengo , Tomii Naoki 
Published: June 2024

AbstractBackgroundPredicting the origin of premature ventricular contraction (PVC) from the preoperative electrocardiogram (ECG) is important for catheter ablation therapies. We propose an explainable method that localizes PVC origin based on the semantic segmentation result of a 12‐lead ECG using a deep neural network, considering suitable diagnosis support for clinical application.MethodsThe deep learning‐based semantic segmentation model was trained using 265 12‐lead ECG recordings from 84 patients with frequent PVCs. The model classified each ECG sampling time into four categories: background (BG), sinus rhythm (SR), PVC originating from the left ventricular outflow tract (PVC‐L), and PVC originating from the right ventricular outflow tract (PVC‐R). Based on the ECG segmentation results, a rule‐based algorithm classified ECG recordings into three categories: PVC‐L, PVC‐R, as well as Neutral, which is a group for the recordings requiring the physician's careful assessment before separating them into PVC‐L and PVC‐R. The proposed method was evaluated with a public dataset which was used in previous research.ResultsThe evaluation of the proposed method achieved neutral rate, accuracy, sensitivity, specificity, F1‐score, and area under the curve of 0.098, 0.932, 0.963, 0.882, 0.945, and 0.852 on a private dataset, and 0.284, 0.916, 0.912, 0.930, 0.943, and 0.848 on a public dataset, respectively. These quantitative results indicated that the proposed method outperformed almost all previous studies, although a significant number of recordings resulted in requiring the physician's assessment.ConclusionsThe feasibility of explainable localization of premature ventricular contraction was demonstrated using deep learning‐based semantic segmentation of 12‐lead ECG.Clinical trial registration: M26‐148‐8.
Applying Bradford Hill to assessing causality in systematic reviews: A transparent approach using process tracing
Authors: Shimonovich Michal , Thomson Hilary , Pearce Anna , Katikireddi Srinivasa Vittal 
Published: June 2024

AbstractBackgroundBradford Hill (BH) viewpoints are widely used to assess causality in systematic reviews, but their application has often lacked reproducibility. We describe an approach for assessing causality within systematic reviews (‘causal’ reviews), illustrating its application to the topic of income inequality and health. Our approach draws on principles of process tracing, a method used for case study research, to harness BH viewpoints to judge evidence for causal claims.MethodsIn process tracing, a hypothesis may be confirmed by observing highly unique evidence and disconfirmed by observing highly definitive evidence. We drew on these principles to consider the value of finding supportive or contradictory evidence for each BH viewpoint characterised by its uniqueness and definitiveness.ResultsIn our exemplar systematic review, we hypothesised that income inequality adversely affects self‐rated health and all‐cause mortality. BH viewpoints ‘analogy’ and ‘coherence’ were excluded from the causal assessment because of their low uniqueness and low definitiveness. The ‘experiment’ viewpoint was considered highly unique and highly definitive, and thus could be particularly valuable. We propose five steps for using BH viewpoints in a ‘causal’ review: (1) define the hypothesis; (2) characterise each viewpoint; (3) specify the evidence expected for each BH viewpoint for a true or untrue hypothesis; (4) gather evidence for each viewpoint (e.g., systematic review meta‐analyses, critical appraisal, background knowledge); (5) consider if each viewpoint was met (supportive evidence) or unmet (contradictory evidence).ConclusionsIncorporating process tracing has the potential to provide transparency and structure when using BH viewpoints in ‘causal’ reviews.
Dynamic changes in aromas and precursors of edible fungi juice: mixed lactic acid bacteria fermentation enhances flavor characteristics
Authors: Sun Hailan , Du Jiaxin , Yan Xingyue , Chen Xiao , Zhao Liyan 
Published: June 2024

AbstractBACKGROUNDLactic acid bacteria (LAB) fermentation technology has been increasingly used in the deep processing of edible fungi. However, the flavor profiles of edible fungi products after mixed LAB fermentation have received less attention and how aromas changes during the mixed LAB fermentation are still open questions. In the present study, fermented Hericium erinaceus and Tremella fuciformis compound juice (FHTJ) was prepared by mixed LAB strains. We aimed to systematically monitor the dynamic changes of aromas and precursors throughout the fermentation process and a data‐driven association network analysis was used to tentatively illustrate the mechanisms of formation between aromas and their precursors.RESULTSMixed LAB fermentation could enrich the aroma profile of FHTJ, reducing the unpleasant flavors such as nonanal and 1‐octen‐3‐ol, as well as increasing the floral flavors such as ethyl acetate and α‐pinene. Partial least squares‐discriminant analysis and relative odor activity values revealed that 11 volatile chemicals were recognized as aroma‐active markers. Volcano plot analysis showed that 3‐octen‐2‐one (green flavor) was the key aroma‐active marker in each stage, which was down‐regulated in fermentation stages I, II and IV, whereas it was up‐regulated in stage III. 3‐Octen‐2‐one was significantly negatively correlated with organic acids, particularly pyruvate (r2 = −0.89). Ethyl caprylate (floral flavor) was up‐regulated in the late fermentation stage, and showed a negative correlation with sugar alcohols and a positive correlation with organic acids, especially tartaric acid (r2 = 0.96).CONCLUSIONThe present study demonstrates the beneficial effect of mixed LAB fermentation on flavor characteristics, providing guidance for fermented edible fungi juice flavor quality monitoring and control. © 2024 Society of Chemical Industry.
Simultaneous determination of semi‐essential nutrients taurine, l‐carnitine and choline in infant formulas and adult/pediatric nutritional formulas by hydrophilic interaction liquid chromatography‐electrospray ionization‐tandem mass spectrometry
Authors: Bustamante‐Rangel Myriam , Rodríguez‐Gonzalo Encarnación , Pérez‐Pavón José Luis 
Published: June 2024

AbstractBACKGROUNDThe nutritional intake of formula‐fed newborns is often limited to a single source, so it must be supplemented with essential nutrients for the growth and proper development of infants. Taurine, l‐carnitine, and choline are considered conditionally essential nutrients especially in newborns and infants.RESULTSIn this work, a simple routine hydrophilic interaction liquid chromatography‐electrospray ionization‐tandem mass spectrometry (HILIC‐ESI‐MS/MS) method was developed and validated for the simultaneous determination of these semi‐essential nutrients in infant and adult/pediatric milk formulas. The extraction recoveries were between 90% and 114%. Precision of the method offered relative standard deviation below 5% and 7% for intra‐day and inter‐day precision, respectively. The proposed method was successfully applied to quantification of taurine, l‐carnitine, and choline in milk formula. The contents found were in good agreement with those provided on the product label for almost all samples.CONCLUSIONIn view of these results, it can be concluded that the developed method can be a useful approach for the simultaneous determination of taurine, l‐carnitine and choline in powdered milk samples, so it can be useful in the routine quality control of this kind of samples. © 2024 The Author(s). Journal of The Science of Food and Agriculture published by John Wiley & Sons Ltd on behalf of Society of Chemical Industry.
Moisture sorption isotherm and thermodynamic analysis of egg powders dried by foam‐mat‐assisted refractance window drying
Authors: Arslan‐Tontul Sultan , Gunisik Ayse , Tontul Ismail 
Published: June 2024

AbstractBACKGROUNDIn the designed study, the moisture sorption isotherm and thermodynamic properties of refractance‐window‐dried egg white powder (EWP), egg yolk powder (EYP) and whole egg powder (WEP) were determined.RESULTSThe adsorption isotherm of egg powders was classified as type II, giving a sigmoidal shape. Peleg showed the highest goodness of fitting for egg powder. The monolayer moisture content of egg powders varied between 0.02 and 0.09 g g−1. According to the thermodynamic analysis, an increase in moisture content led to a decrease in net isosteric heat of sorption (qst), and the highest decrease was observed in EWP. The qst of EWP was calculated as 18 637 kJ mol−1, while it decreased to 3104 kJ mol−1 at 0.2 g g−1 moisture content. Like qst, sorption entropy decreased from 52.07 to 7.14 J mol−1 K−1 with increasing water activity (aw) for EWP. Increasing temperature caused a decrease in spreading pressure and was higher in EWP samples. Increasing moisture content and temperature also decreased Gibbs free energy level.CONCLUSIONMoisture sorption isotherm (MSI) is used to predict the amount of bound water in a material at a specific relative humidity and temperature. To inhibit chemical and microbiological spoilage, the drying process must continue until the monolayer moisture content is reached. In this study, the monolayer moisture content of powdered eggs for safe storage was demonstrated by MSI. Additionally, by determining the thermodynamic functions of egg powder, valuable information was obtained related to predicting the energy requirement in drying processes. © 2024 Society of Chemical Industry.
Age Stratification and Prognostic Factor Analysis in Pediatric Differentiated Thyroid Cancer
Authors: Winder Ophir , Lazar Liora , Hod Roy , Shpitzer Thomas , Mizrachi Aviram , Bachar Gideon 
Published: June 2024

ObjectivesDifferentiated thyroid cancer (DTC) is rare in the pediatric population. It remains unclear whether younger children are at greater risk of more aggressive disease. We aimed to identify prognostic factors for aggressive pediatric DTC and to define an appropriate age stratification.MethodsThis retrospective cohort study included all patients aged 18 years or less who were treated for DTC between 1985 and 2021 in a tertiary medical center and were followed up for a minimum of 1.5 years after treatment.ResultsSeventy‐eight patients were included, all diagnosed with papillary thyroid carcinoma: 30 (38.5%) low‐risk, 21 (26.9%) intermediate‐risk, and 27 (34.6%) high‐risk according to the American Thyroid Association (ATA) risk stratification. The mean duration of follow‐up was 11.8 ± 7.8 years. No evidence of disease was documented in 52 patients (66.7%) at 1‐year post‐treatment and 64 patients (82.1%) at the end of follow‐up. On analysis by age, evidence of disease at 1‐year post‐treatment was found in 66.7% of children younger than 11 years, compared to 25.4% of older children (p = 0.002). There was no significant difference by age in evidence of disease at the last follow‐up (p = 0.453). Patients aged <11 years at diagnosis were associated with more aggressive disease features on histopathologic examination, metastatic disease, and high ATA risk level. Patients aged <8 years were associated with more frequent bilateral disease and extrathyroidal extension.ConclusionPediatric DTC patients who are younger than 11 years at diagnosis have more aggressive disease features and a lower early remission rate than older patients. Nevertheless, their long‐term outcome is satisfactory.Level of Evidence4‐retrospective cohort study Laryngoscope, 134:4818–4825, 2024