bluuebunny/crossref_metadata_2025_split huggingface dataset:
Tractography‐Based Automated Identification of Retinogeniculate Visual Pathway With Novel Microstructure‐Informed Supervised Contrastive Learning
Authors: Li Sipei , Zhang Wei , Yao Shun , He Jianzhong , Gao Jingjing , Xue Tengfei , Xie Guoqiang , Chen Yuqian , Torio Erickson F. , Feng Yuanjing , Bastos Dhiego C. A. , Rathi Yogesh , Makris Nikos , Kikinis Ron , Bi Wenya Linda , Golby Alexandra J. , O'Donnell Lauren J. , Zhang Fan 
Published: November 2024

ABSTRACTThe retinogeniculate visual pathway (RGVP) is responsible for carrying visual information from the retina to the lateral geniculate nucleus. Identification and visualization of the RGVP are important in studying the anatomy of the visual system and can inform the treatment of related brain diseases. Diffusion MRI (dMRI) tractography is an advanced imaging method that uniquely enables in vivo mapping of the 3D trajectory of the RGVP. Currently, identification of the RGVP from tractography data relies on expert (manual) selection of tractography streamlines, which is time‐consuming, has high clinical and expert labor costs, and is affected by inter‐observer variability. In this paper, we present a novel deep learning framework, DeepRGVP, to enable fast and accurate identification of the RGVP from dMRI tractography data. We design a novel microstructure‐informed supervised contrastive learning method that leverages both streamline label and tissue microstructure information to determine positive and negative pairs. We propose a new streamline‐level data augmentation method to address highly imbalanced training data, where the number of RGVP streamlines is much lower than that of non‐RGVP streamlines. In the experiments, we perform comparisons with several state‐of‐the‐art deep learning methods that were designed for tractography parcellation. Furthermore, to assess the generalizability of the proposed RGVP method, we apply our method to dMRI tractography data from neurosurgical patients with pituitary tumors. In comparison with the state‐of‐the‐art methods, we show superior RGVP identification results using DeepRGVP with significantly higher accuracy and F1 scores. In the patient data experiment, we show DeepRGVP can successfully identify RGVPs despite the effect of lesions affecting the RGVPs. Overall, our study shows the high potential of using deep learning to automatically identify the RGVP.
Brain morphometry in hepatic Wilson disease patients
Authors: Rahimi Parya , Mareček Stanislav , Brůha Radan , Dezortová Monika , Sojka Petr , Hájek Milan , Skowrońska Marta , Smoliński Łukasz , Urbánek Petr , Litwin Tomasz , Dušek Petr 
Published: November 2024

AbstractWilson disease (WD) primarily presents with hepatic and neurological symptoms. While hepatic symptoms typically precede the neurological manifestations, copper accumulates in the brain already in this patient group and leads to subclinical brain MRI abnormalities including T2 hyperintensities and atrophy. This study aimed to assess brain morphological changes in mild hepatic WD. WD patients without a history of neurologic symptoms and decompensated cirrhosis and control participants underwent brain MRI at 3T scanner including high‐resolution T1‐weighted images. A volumetric evaluation was conducted on the following brain regions: nucleus accumbens, caudate, pallidum, putamen, thalamus, amygdala, hippocampus, midbrain, pons, cerebellar gray matter, white matter (WM), and superior peduncle, using Freesurfer v7 software. Whole‐brain analyses using voxel‐ and surface‐based morphometry were performed using SPM12. Statistical comparisons utilized a general linear model adjusted for total intracranial volume, age, and sex. Twenty‐six WD patients with mild hepatic form (30 ± 9 years [mean age ± SD]); 11 women; mean treatment duration 13 ± 12 (range 0–42) years and 28 healthy controls (33 ± 9 years; 15 women) were evaluated. Volumetric analysis revealed a significantly smaller pons volume and a trend for smaller midbrain and cerebellar WM in WD patients compared to controls. Whole‐brain analysis revealed regions of reduced volume in the pons, cerebellar, and lobar WM in the WD group. No significant differences in gray matter density or cortical thickness were found. Myelin or WM in general seems vulnerable to low‐level copper toxicity, with WM volume loss showing promise as a marker for assessing brain involvement in early WD stages.
Dissociation Chemistry of Protonated α‐, β‐ and Other Amino Acids Using Multiple Stage Tandem Mass Spectrometry
Authors: Asakawa Daiki 
Published: November 2024

ABSTRACTTo discriminate amino acid isomers by multiple stage tandem mass spectrometry (MSn), the fragmentation of protonated amino acids were investigated by MSn with collision‐induced dissociation (CID) and density functional theory calculations. The CID of protonated α‐amino acids results in a loss of 46 Da, corresponding to H2O and CO, and iminium ions appear as resultant fragments. The CID of protonated β‐amino acids also produces iminium ions, but the corresponding loss is 60 Da instead of 46 Da. H2O loss initiates the fragmentation of protonated β‐amino acids, producing protonated β‐lactams as an intermediate. Subsequently, protonated β‐lactams are easily converted to iminium ions and CH2CO. By contrast, H2O loss from the protonated forms of γ‐ and ε‐amino acids provides protonated lactams with 5‐ and 7‐membered rings, respectively. Protonated lactams with more than 5‐membered rings provide stable fragments and do not undergo further degradation during CID. In addition, protonated forms of γ‐ and ε‐amino acids undergo NH3 loss as a competitive fragmentation pathway of H2O loss, producing protonated lactones. Because the fragmentation of protonated amino acid by CID depends on the position of amino and carboxyl groups, the tandem mass spectrometry with CID can discriminate α‐, β‐, and other amino acids.
Parental Severe Acute Respiratory Syndrome Coronavirus 2 (SARS‐CoV‐2) Predominates Over Coinfected SARS‐CoV‐2 Delta, Producing Less Lethal Variants in a Long‐Term Replication Mouse Model
Authors: Baek Kyeongbin , Kim Dongbum , Kang Bo Min , Kim Jinsoo , Demirev Atanas V. , Lee Sangyi , Kim Minyoung , Kim Suyeon , Park Sangkyu , Kim Jin Il , Park Man‐Seong , Lee Younghee , Kwon Hyung‐Joo 
Published: November 2024

ABSTRACTThe evolution of SARS‐CoV‐2, which limits public control and treatment, seems to have occurred through multiple mechanisms, including recombination of cocirculating strains in hosts. However, insufficient experimental data have been obtained after coinfection. Therefore, we investigated the emergence of variants after coinfection with parental SARS‐CoV‐2 and the SARS‐CoV‐2 Delta. We found that fewer (approximately 50%) mutations accumulated in Calu‐3 cells than in other cells after serial passaging. Previously, we established a long‐term replication mouse model by infecting Calu‐3 cell‐derived xenograft tumors with SARS‐CoV‐2. Here, we utilized our model to investigate the outcome after coinfection. More diverse viral mutations, along with multiple high‐frequency simultaneous mutations, were discovered in the tumors than during cell passaging. Viral isolates from the tumors showed no cytopathic effects and formed much smaller plaques. Phylogenetic analysis suggested that the genetic makeup of the variants remained largely the same as that of parental SARS‐CoV‐2 rather than the SARS‐CoV‐2 Delta. Viral challenge revealed that the isolates were less lethal than the parental SARS‐CoV‐2 and SARS‐CoV‐2 Delta strains. These findings suggest that parental SARS‐CoV‐2 predominates over the SARS‐CoV‐2 Delta when coinfected, but the SARS‐CoV‐2 Delta contributes to the evolution of parental SARS‐CoV‐2 variants toward better host adaptation without recombination.
Fibroblast Growth Factor Receptor (FGFR) Alterations in HPV Oropharyngeal Cancers
Authors: Bhateja Priyanka , Liu Xuefeng , Baliga Sujith , Gogineni Emile , Jhawar Sachin , Mitchell Darrion , Ma Sungjun , Zhu Simeng , Konieczkowski David , Blakaj Dukagjin , Old Matthew , Rocco James , Bonomi Marcelo 
Published: November 2024

ABSTRACTHPV viral E6 and E7 onco‐proteins play a well‐known role in carcinogenesis. Host genomic alterations also play a key role in the development of HPV‐related oropharyngeal cancer and have been under‐recognized. We describe a case series of 6 metastatic/locoregionally recurrent HPVOPSCC patients with FGFR alterations. HPVOPSCC presents with distinct pattern of spread both temporally and sites of recurrence compared to
non‐HPV‐related oropharyngeal cancer. Identification and reporting of genomic alterations in HPV are crucial to the understanding of disease biology and could aid in development of novel therapeutics for these patients. In addition, use of circulating tumor DNA may lead to early detection and supplement imaging in the follow up of these patients. Loco‐regional treatments may also play a key role in the management of metastatic HPV OPSCC depending on the pattern of presentation. Our case series highlights all these novelties that could lead to better treatment outcomes.
Discrepancy between Mexican paediatricians and ESPGHAN experts regarding cow's milk allergy
Authors: Hendricx Fabian , Robert Emma , Gestels Thomas , Delcourt Hanne , Negroe Benjamin Suarez , Vázquez‐Frias Rodrigo , Toro Monjaraz Erick Manuel , Monserrat Cazares Méndez Josefina , Ribes‐Koninckx Carmen , Huysentruyt K. , Vandenplas Yvan 
Published: November 2024

AbstractObjectivesCow's milk allergy (CMA) is a common food allergy in infants. Guidelines and recommendations for the diagnosis and management of CMA are based on scientific review of the available evidence. However, real‐world situations may oblige clinicians to adapt a different attitude.MethodsThis paper evaluated the opinion of 42 Mexican paediatricians on the 73 statements presented in the recent position paper of the European Society of Paediatric Gastroenterology, Hepatology and Nutrition (ESPGHAN). Voting on the statements and their interpretation were identical for both groups (online and anonymous). Both groups were unaware of the other's outcome at the moment of the voting.ResultsWhile the ESPGHAN group accepted all 73 statements, the Mexican group rejected 19 statements. Two rejections were due to the mean and median being below the predefined and agreed‐upon cut‐off, and 17 were due to over 75% of participants disagreeing with the statements. The greatest discrepancy was observed regarding the role of vitamin D in preventing CMA.ConclusionWhile opinions on the prevalence, diagnosis and management of CMA were comparable between European paediatric gastroenterologists and Mexican general paediatricians for the majority of statements, significant differences were observed. It is essential to gather information from various regions and healthcare levels to enhance the impact of recommendations.
Effects of microemulsions of Ocimum basilicum essential oil on the cooking quality of snakehead (Channa argus) under different impregnation methods
Authors: Shi Peng , Xie Yao , Mei Jun , Xie Jing 
Published: November 2024

AbstractBACKGROUNDThis study investigates the effect of microemulsions of 0.8% Ocimum basilicum essential oil (MOBO) on the cooking quality and shelf life of snakehead fillets using different impregnation methods (air environment treatment, vacuum impregnation, ultrasonic impregnation and vacuum impregnation with ultrasonic‐assisted). Basil essential oil, recognized for its antimicrobial and antioxidant properties, is utilized in a microemulsion form to enhance its efficacy and application in food preservation.RESULTSThe findings of the study demonstrated that MOBO markedly enhanced the cooking quality, flavor and overall acceptability of snakehead fillets. The incidence of microbial growth was markedly diminished in the MOBO‐treated fillets in comparison to the control group. On day 9, a reduction in the total viable count of a minimum of 1.7 lg CFU/g was observed in comparison to the control group. The treated group exhibited an extended shelf life, with an increase of 3–9 days in comparison to the control group. However, there was a higher cooking weight loss in the treated group compared to the control group. This is from the findings regarding moisture content. The digestibility of the MOBO‐treated fillets was enhanced by up to 4.13% in comparison to the control group, while the particle size was reduced by up to 40 nm. MOBO reduced the production of bitter amino acids and thiobarbituric acid.CONCLUSIONIncorporating MOBO in the marination process effectively enhances the cooking quality and extends the shelf life of snakehead fillets. These results indicate the potential of basil essential oil microemulsion as a natural and efficient food preservation method, offering significant benefits for the food industry in terms of product quality and safety improvement. © 2024 Society of Chemical Industry.
Rate coefficients for the gas‐phase reaction of OH radicals with the L4, L5, D5, and D6 permethylsiloxanes
Authors: Bernard François , Burkholder James B. 
Published: November 2024

AbstractRate coefficients, k(T), for the gas‐phase OH radical reaction with decamethyltetrasiloxane ((CH3)3SiO[Si(CH3)2O]2Si(CH3)3, L4, k1), dodecamethylpentasiloxane ((CH3)3SiO[Si(CH3)2O]3Si(CH3)3, L5, k2), and decamethylcyclopentasiloxane ([–Si(CH3)2O–]5, D5, k3), and dodecamethylcyclohexasiloxane ([–Si(CH3)2O–]6, D6, k4) were measured using a pulsed laser photolysis—laser induced fluorescence absolute method over the temperature range 270–370 K. The obtained room temperature rate coefficients, with quoted 2σ absolute uncertainties, and fitted temperature dependence are (cm−3 molecule−1 s−1):
The 2σ absolute rate coefficient uncertainty, for all compounds included in this study, is conservatively estimated to be ∼10% over the entire temperature range. The cyclic permethylsiloxanes were found to be less reactive than the analogous linear compound, while both linear and cyclic compounds show increasing reactivity with increasing number of CH3‐ groups. A structure activity relationship (SAR) parameterization for the permethylsiloxanes is presented. The estimated atmospheric lifetimes due to OH reaction for L4, L5, D5, and D6 are 5.2, 4.4, 6.8, and 5.2 days, respectively.
Leaf Accumulation Capacity of Herbaceous Plants Growing on Fields Contaminated With Anthropogenically Induced Potentially Toxic Elements Under Natural Soil Conditions
Authors: Asare Michael O. , Száková Jiřina , Najmanová Jana , Tlustoš Pavel 
Published: November 2024

ABSTRACTEstimation and knowledge of potentially toxic elements (PTEs) in soils and herbaceous plants are vital for ecotoxicological reasons. This study explored PTE accumulation in the aerial organ (leaf) of herbaceous plants in PTE‐contaminated soils in a linear transect of three localities close to the Litavka River in Pribram, Czech Republic. Leaf accumulation answers questions on PTE hyperaccumulation and removal during phytoremediation. The study adopted the pseudo‐total extraction (aqua regia soluble) of PTE contents (Cd, Cu, Zn, Pb, and Ni) of soil and leaf samples determined by inductively coupled plasma optical emission spectroscopy. Except for Ni, the contents of Cd, Cu, Pb, and Zn were above the permissible limits in soil following WHO with contamination factors ranging from moderate to serious contamination in the sites. Of the 118 herbaceous species in the sites, 43% (52 species) accumulated Cd above the WHO limit in leaves with
Geranium pusillum
Burm. f. having the highest content (0.84 mg kg−1) while only
Geum urbanum
L. (132 mg kg−1) and
G. pusillum
(166 mg kg−1) were above the limit that supports the principal option to clean the infested soils. There was a low bioaccumulation of all plants indicated by a bioaccumulation factor less < 1 (BAFleaf < 1) with PTE content lower than reported hyperaccumulator values. The hyperaccumulation status of PTE of plants stated by previous authors in leaves can be unreliable, under natural soil conditions, accumulations can even be lower than the permissible limits. Further studies requiring different soils and other plants are needed to make a reliable inference on which organs of plants support hyperaccumulation status.
Advancements in Understanding Beryllium Contamination: Novel Insights Into Environmental Risk Assessment
Authors: Kumar Amit , Kumar Vinod , Chawla Mrinalini , Thakur Monika , Bakshi Palak , Jasrotia Rakesh , Radziemska Maja , Kumar Rupesh 
Published: November 2024

ABSTRACTBeryllium (Be), a lightweight metal with significant industrial applications, poses notable environmental and health risks due to its toxicity and persistence, and widespread use, particularly in the mechanical, aerospace, and electronics sectors. It is commonly alloyed with other heavy metals to enhance material properties. The primary environmental pathways for Be release include emissions from coal and fossil fuels combustion, as well as the incineration of solid wastes. Once introduced into the natural environment, primarily Be associated with soil particles and sediments, particularly in terrestrial and aquatic ecosystems. This review examined the pathways through which Be enters the environment, including atmospheric deposition, industrial discharge, and leaching from natural geologic deposits. The paper highlights the bioavailability and mobility of Be in soil and water systems, emphasizing the geochemical and physical factors influencing its persistence and potential for bioaccumulation. Risk appraisal methodologies are evaluated, with a focus on human exposure routes, including inhalation of airborne particulates and ingestion of contaminated water and food. The toxicological impacts on human health are critically analyzed, detailing both acute and chronic effects, such as respiratory diseases and carcinogenicity. This review evaluates existing regulatory frameworks and remediation strategies, assessing their efficacy in mitigating environmental contamination and exposure to Be. By integrating interdisciplinary research, this paper provides an in‐depth understanding of the environmental behavior and toxicology of beryllium, offering insights that can inform robust policy frameworks and shape future research directions.
Evaluating the Therapeutic Potential of Microneedle Patch Laser With Multiple Wavelengths in Allergic Rhinitis: Insights From an Allergic Rhinitis Mouse Model
Authors: Ventura Reiza , Bae Jun‐Sang , Kim Eun Hee , Kim A. Young , Oh Min Hyuck , Kim Ji Hye , Yoo Shin Hyuk , Ryu Gwanghui , Mo Ji‐Hun 
Published: November 2024

ABSTRACTObjectiveThere is insufficient evidence to determine the effectiveness of treating allergic rhinitis with a patch laser affix to the skin as opposed to direct intranasal irradiation of the nasal mucosa. We aimed to evaluate the effect of the microneedle patch laser with multiple wavelengths in an allergic rhinitis (AR) mouse model and its underlying mechanism.MethodsThe microneedle patch laser was attached to the skin above the mouse's nasal cavity, transmitting light to the nasal mucosa. For 10 days, the microneedle patch laser administered simultaneous exposure to wavelengths of 670, 780, 850, and 910 nm at either 10 or 20 min each day. Multiple allergic parameters were evaluated following the microneedle patch laser treatment.ResultsMicroneedle patch laser treatment decreased allergic symptoms and inhibited OVA‐specific IgE levels. Additionally, it significantly reduced eosinophil infiltration, epithelial thickness of the nasal mucosa, and IL‐4 cytokine levels.ConclusionThe light emitted by the microneedle patch laser attached to the skin, penetrated effectively to the nasal mucosa within the nasal cavity, suggesting potential for treating allergic rhinitis in mice and could be extended in clinical applications.
Application of biomaterials in cardiac tissue engineering: Current status and prospects
Authors: Zhang Dongshan , He Rui , Qu Ying , He Chuan , Chu Bingyang 
Published: November 2024

AbstractCardiovascular diseases have become one of the leading causes of death and illness worldwide, posing significant challenges to global health. Due to the limited regenerative capacity of the heart, conventional approaches to treating heart diseases have demonstrated limited effectiveness. Therefore, leveraging biomaterials and biotechnologies in cardiac tissue engineering has emerged as a promising therapeutic strategy. This review aims to summarize the various characteristics of biomaterials in cardiac tissue engineering and their significance in addressing heart diseases. We categorize biomaterials into natural, synthetic, and conductive types based on their sources and unique properties, focusing on their applications in cardiac tissue engineering. We then present current applications of biomaterials in cardiac tissue engineering, followed by a discussion of existing challenges such as long‐term material stability, biocompatibility, adverse reactions, and precise application methodologies. Additionally, we provide insights into potential strategies for overcoming these challenges, aiming to enhance the effectiveness and safety of biomaterials in cardiac tissue engineering applications. Finally, this review highlights the potential of emerging biomaterials and technologies, underscoring the critical role of interdisciplinary collaboration in driving innovation and progress in cardiac tissue engineering.
Molecular Analysis of Genes CEBPA, NPM1, IDH1, and RUNX1 Polymorphisms as Biomarker Potential in Leukemia Patients
Authors: Bashir Kashif , Ghafar Sadia Abdul , Rehman Afifa Tur , Waris Tayyaba , Farooq Fatima , Alamin Amin A. 
Published: November 2024

ABSTRACTLeukemia is found in approximately 2.3 million people worldwide and causes many deaths all over the world. This research study was conducted to figure out the link of single nucleotide polymorphisms of genes CEBPA (rs34529039), NPM1 (rs753788683), IDH1 (of rs11554137) and RUNX1 (rs13051066) polymorphisms as biomarker potential in leukemia patients. A total of 600 subjects were included in the study which included 300 patients and 300 healthy controls with age and gender matched. After DNA extraction, PCR was carried out to analyze polymorphisms of selected genes. A significant association with increased risk of leukemia by almost twofolds is observed in homozygous mutant (AA) of rs34529039 SNP of gene CEBPA (odds ratio [OR] = 1.71; 95% confidence interval [CI] = 1.04–2.82; p = 0.03) while highly significant association but with decrease risk of leukemia is observed in heterozygote genotype (CA) of same SNP (OR = 0.36; 95% CI = 0.22–0.59; p = 0.0001). A highly significant association with increased risk of leukemia up to twofolds is observed in heterozygote genotype (AG) of rs753788683 of gene NPM1 (OR 2.10: 95% CI 1.32–3.36 p = 0.0017) while increasing risk by two‐fold and show significant association in homozygous mutant (AA) (OR = 1.75; 95% Cl = 1.09–2.79; p = 0.01). Leukemia risk increases by twofold and shows significant association in the homozygous mutant (AA) of rs11554137 (OR = 1.75; 95%Cl = 1.09–2.79; p = 0.01). Leukemia risk increases by twofold and shows significant association in the homozygous mutant (AA) of rs13051066 of gene RUNX1 (OR = 0.63; 95%Cl = 0.39–1.63; p = 0.06).