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17 pages, 824 KiB  
Article
A Machine Learning Approach to Understanding Sociodemographic Factors in Electric Vehicle Ownership in the U.S.
by Eazaz Sadeghvaziri, Ramina Javid, Hananeh Omidi and Mahmoud Arafat
Sustainability 2024, 16(23), 10202; https://doi.org/10.3390/su162310202 - 21 Nov 2024
Abstract
Electric vehicles (EVs) are rapidly gaining popularity due to their environmental benefits, such as reducing greenhouse gas emissions. Considering the sociodemographic factors that influence the adoption of EVs is essential when developing equitable and efficient transportation policies. This article leverages the National Household [...] Read more.
Electric vehicles (EVs) are rapidly gaining popularity due to their environmental benefits, such as reducing greenhouse gas emissions. Considering the sociodemographic factors that influence the adoption of EVs is essential when developing equitable and efficient transportation policies. This article leverages the National Household Travel Survey (NHTS) 2022 data to analyze the sociodemographic factors influencing the adoption of EVs in the U.S. A binary logistic regression model and three machine learning models were employed to predict EV ownership in the U.S. The results of the regression model suggested that the Pacific division leads in EV adoption, most likely due to legislation and improved infrastructure, while regions such as East South Central suffer from lower EV adoption. The findings indicate that higher household income and home ownership significantly correlate with increased EV adoption. In contrast, renters and rural households exhibit lower adoption rates suggesting an increase in charging facilities in these regions can promote EV adoption. The Random Forest model outperforms others with an accuracy of 82.72%, suggesting its robustness in handling complex relationships between variables. Policy implications include the need for financial incentives for low-income households and increased charging infrastructure in rural and underserved urban areas to promote equitable EV adoption. Full article
(This article belongs to the Section Sustainable Transportation)
22 pages, 1348 KiB  
Review
Galantamine-Memantine Combination in the Treatment of Parkinson’s Disease Dementia
by Emma D. Frost, Swanny X. Shi, Vishnu V. Byroju, Jamir Pitton Rissardo, Jack Donlon, Nicholas Vigilante, Briana P. Murray, Ian M. Walker, Andrew McGarry, Thomas N. Ferraro, Khalid A. Hanafy, Valentina Echeverria, Ludmil Mitrev, Mitchel A. Kling, Balaji Krishnaiah, David B. Lovejoy, Shafiqur Rahman, Trevor W. Stone and Maju Mathew Koola
Brain Sci. 2024, 14(12), 1163; https://doi.org/10.3390/brainsci14121163 (registering DOI) - 21 Nov 2024
Abstract
Parkinson’s disease (PD) is a progressive neurodegenerative disorder that affects over 1% of population over age 60. It is defined by motor and nonmotor symptoms including a spectrum of cognitive impairments known as Parkinson’s disease dementia (PDD). Currently, the only US Food and [...] Read more.
Parkinson’s disease (PD) is a progressive neurodegenerative disorder that affects over 1% of population over age 60. It is defined by motor and nonmotor symptoms including a spectrum of cognitive impairments known as Parkinson’s disease dementia (PDD). Currently, the only US Food and Drug Administration-approved treatment for PDD is rivastigmine, which inhibits acetylcholinesterase and butyrylcholinesterase increasing the level of acetylcholine in the brain. Due to its limited efficacy and side effect profile, rivastigmine is often not prescribed, leaving patients with no treatment options. PD has several derangements in neurotransmitter pathways (dopaminergic neurons in the nigrostriatal pathway, kynurenine pathway (KP), acetylcholine, α7 nicotinic receptor, and N-methyl-D-aspartate (NMDA) receptors) and rivastigmine is only partially effective as it only targets one pathway. Kynurenic acid (KYNA), a metabolite of tryptophan metabolism, affects the pathophysiology of PDD in multiple ways. Both galantamine (α7 nicotinic receptor) and memantine (antagonist of the NMDA subtype of the glutamate receptor) are KYNA modulators. When used in combination, they target multiple pathways. While randomized controlled trials (RCTs) with each drug alone for PD have failed, the combination of galantamine and memantine has demonstrated a synergistic effect on cognitive enhancement in animal models. It has therapeutic potential that has not been adequately assessed, warranting future randomized controlled trials. In this review, we summarize the KYNA-centric model for PD pathophysiology and discuss how this treatment combination is promising in improving cognitive function in patients with PDD through its action on KYNA. Full article
(This article belongs to the Section Neuropharmacology and Neuropathology)
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<p>Kynurenine pathway. An abbreviated depiction of the kynurenine pathway showing the major steps.</p>
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<p>Overview of the kynurenine pathway in the brain and its effects. Depiction of the differential expression of the KP in cells of the central nervous system. Astrocytes lack the full complement of KP enzymes, hence KP activation in astrocytes terminates in the production of neuroprotective KYNA. However, as microglia fully express KP enzymes, KP activation in microglia can result in the production of neurotoxic metabolites 3-HK and QUIN. KP = Kynurenine Pathway; TRP = Tryptophan; KYNA = Kynurenic Acid; IDO = Indoleamine 2,3-dioxygenase; TDO = Tryptophan-2,3-dioxygenase; QUIN = Quinolinic Acid; 3-HAA = 3 Hydroxyanthranilic Acid; 3-HK = 3-hydroxykynurenine; KMO = Kynurenin-3-monooxygenase; KYN = Kynurenine.</p>
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<p>Kynurenine pathway-centric pathophysiology model. Depiction of some of the receptors, pathways, and processes affected by increased levels of major kynurenine pathway metabolites KYN, KYNA, 3-HK, and QUIN after pathway activation. AhR = aryl hydrocarbon receptor; α7nAChR = Alpha7 nicotinic receptor; BCL-2 = B-cell Lymphoma 2; GABA = γ-aminobutyric acid; KYN = Kynurenine; KYNA = Kynurenic Acid; NMDA = N-methyl-D-aspartate; QUIN = Quinolinic Acid; 3-HK = 3-hydroxykynurenine. ↑, increased process; ↓, decreased process.</p>
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<p>Magic Bullet Versus Shotgun Approach. The magic bullet approach has long been thought to be the answer to treating complex medical conditions. Pharmaceutical companies hoped that they would be able to develop a single drug to treat many conditions. However, this has failed countless times. We argue that the shotgun approach is more effective. Using multiple drugs (shotgun approach) to target multiple pathways implicated in a disease is likely to a more effective treatment approach [<a href="#B225-brainsci-14-01163" class="html-bibr">225</a>].</p>
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14 pages, 1015 KiB  
Article
Evaluating Causal Reasoning Capabilities of Large Language Models: A Systematic Analysis Across Three Scenarios
by Lei Wang and Yiqing Shen
Electronics 2024, 13(23), 4584; https://doi.org/10.3390/electronics13234584 - 21 Nov 2024
Viewed by 26
Abstract
Large language models (LLMs) have shown their capabilities in numerical and logical reasoning, yet their capabilities in higher-order cognitive tasks, particularly causal reasoning, remain less explored. Current research on LLMs in causal reasoning has focused primarily on tasks such as identifying simple cause-effect [...] Read more.
Large language models (LLMs) have shown their capabilities in numerical and logical reasoning, yet their capabilities in higher-order cognitive tasks, particularly causal reasoning, remain less explored. Current research on LLMs in causal reasoning has focused primarily on tasks such as identifying simple cause-effect relationships, answering basic “what-if” questions, and generating plausible causal explanations. However, these models often struggle with complex causal structures, confounding variables, and distinguishing correlation from causation. This work addresses these limitations by systematically evaluating LLMs’ causal reasoning abilities across three representative scenarios, namely analyzing causation from effects, tracing effects back to causes, and assessing the impact of interventions on causal relationships. These scenarios are designed to challenge LLMs beyond simple associative reasoning and test their ability to handle more nuanced causal problems. For each scenario, we construct four paradigms and employ three types of prompt scheme, namely zero-shot prompting, few-shot prompting, and Chain-of-Thought (CoT) prompting in a set of 36 test cases. Our findings reveal that most LLMs encounter challenges in causal cognition across all prompt schemes, which underscore the need to enhance the cognitive reasoning capabilities of LLMs to better support complex causal reasoning tasks. By identifying these limitations, our study contributes to guiding future research and development efforts in improving LLMs’ higher-order reasoning abilities. Full article
(This article belongs to the Special Issue Feature Papers in Computer Science & Engineering, 2nd Edition)
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<p>Causal diagrams (i.e., directed acyclic graph) for the coin-flipping game case. (<b>a</b>) Original condition (i.e., without intervention): Shows the causal relationships between initial states <span class="html-italic">X</span>), individual actions (<span class="html-italic">A</span>, <span class="html-italic">B</span>, <span class="html-italic">C</span>, <span class="html-italic">D</span>), and final outcome (<span class="html-italic">Y</span>) for both coins. (<b>b</b>) With interventions: Illustrates how the causal structure changes when an intervention is introduced to set coin2’s state to heads up, regardless of previous actions.</p>
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<p>Causal diagrams for the File Downloading case. (<b>a</b>) Original condition (i.e., without intervention): Illustrates the causal relationships between initiating a file download (<span class="html-italic">X</span>), partial file download completion (<span class="html-italic">A</span>), installing an update (<span class="html-italic">B</span>), and the remaining download time (<span class="html-italic">Y</span>). (<b>b</b>) With interventions: Demonstrates how the causal structure changes when an intervention is introduced, setting the partial download completion (<span class="html-italic">A</span>) to zero (<math display="inline"><semantics> <mrow> <mi>a</mi> <mo>=</mo> <mn>0</mn> </mrow> </semantics></math>), effectively restarting the download process after the update installation.</p>
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<p>Causal diagrams illustrating Simpson’s Paradox in smallpox vaccination. (<b>a</b>) Original condition (i.e., without intervention): Shows the causal relationships between getting vaccinated (<span class="html-italic">X</span>), physical vulnerability (<span class="html-italic">A</span>), contracting smallpox (<span class="html-italic">B</span>), and fatality (<span class="html-italic">Y</span>). The numbers on the arrows represent probabilities of outcomes. (<b>b</b>) With interventions: Demonstrates how the causal structure changes when an intervention is introduced, altering the relationship between vaccination and physical vulnerability. We use * as a multiplication sign.</p>
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<p>Example responses from different LLMs to the zero-shot (vanilla) prompt for the cause-to-effect pattern in the Coin Flipping Game (Case 1). The figure illustrates the varying approaches and reasoning capabilities of Falcon-40B, LLaMA2, and GPT-4 when analyzing the causal relationships in the coin flipping scenario.</p>
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16 pages, 2647 KiB  
Article
Personalized Dose Selection for Treatment of Patients with Neuropsychiatric Disorders Using tDCS
by Sagarika Bhattacharjee, Rajan Kashyap, Vanteemar S. Sreeraj, Palanimuthu T. Sivakumar, Ganesan Venkatasubramanian, John E. Desmond, S. H. Annabel Chen, T. N. Sathyaprabha and Kaviraja Udupa
Brain Sci. 2024, 14(12), 1162; https://doi.org/10.3390/brainsci14121162 - 21 Nov 2024
Viewed by 130
Abstract
Background: Individualizing transcranial direct current stimulation (tDCS) parameters can improve precision in neuropsychiatric disorders. One important decision for the clinician is the selection of an appropriate montage—conventional or high-definition (HD)—to implement dose-controlled tDCS while maintaining the patient’s safety. Method: The present [...] Read more.
Background: Individualizing transcranial direct current stimulation (tDCS) parameters can improve precision in neuropsychiatric disorders. One important decision for the clinician is the selection of an appropriate montage—conventional or high-definition (HD)—to implement dose-controlled tDCS while maintaining the patient’s safety. Method: The present study simulated tDCS administration using T1-weighted brain images of 50 dementia, 25 depression patients, and 25 healthy individuals for two conventional and HD montages, targeting the regions of interest (ROIs) in the dorsal and ventral pathways that support language processing. For each tDCS configuration, the electric fields at the ROIs and the individualized dose required to achieve the desired current intensity at the target ROI across the subjects were estimated. Linear regression was performed on these parameters. Result: A significant relationship between atrophy and current dose that varies according to the disease was found. The dementia patients with significant brain atrophy required a higher personalized dosage for HD montage, as the current intensity at the target ROIs was lower and more variable than that of conventional montage. For dementia, tDCS individualization is pathway-dependent, wherein HD configuration of the dorsal route requires current dosages above the safety limit (>4 mA) for 46% of individuals. However, there was no significant difference in electrode configurations between the HD and traditional setups for depression and healthy volunteers without significant brain atrophy. Conclusions: HD-tDCS with fixed locations is limited, making conventional tDCS more effective for dose-controlled applications. In patients with atrophy, individualized adjustments based on simulations are needed due to the variable stimulation strength in the ROI. Full article
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<p>(<b>A</b>) Electric field simulation of tDCS dorsal and ventral pathway montages for both conventional and high-definition (HD) configurations demonstrating the (<b>i</b>) electrode positions, and (<b>ii</b>) electric field distributions across the brain regions. (<b>B</b>) Average current density (ACD) showing the electric field strength on the standard MNI brain (used as a reference for the calibration of doses) for conventional and HD configurations across (<b>i</b>) the dorsal pathway with two target ROIs: left inferior parietal lobule and left angular gyrus; and (<b>ii</b>) the ventral pathway with two target ROIs: left middle temporal gyrus and left inferior temporal gyrus. (<b>C</b>) Brain volumetric characteristics of the three groups (dementia, depression, and healthy) highlighting differences in the TBV [Total brain volume (GM + WM)] and TICV (Total intracranial volume (TBV + CSF)).</p>
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<p>The plot of mean ± standard deviations of ACD (<b>a</b>(<b>1</b>)–<b>a</b>(<b>4</b>)) highlighting their distribution across the subjects (<b>b</b>(<b>1</b>)–<b>b</b>(<b>4</b>)) for dorsal and ventral ROIs using conventional and high-definition montages for dementia, depression, and healthy volunteers. Level of significance denoted by * &lt;0.05. ** &lt;0.01, *** &lt;0.001.</p>
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<p>The plot of mean ± standard deviations of personalized dosages (<b>a</b>(<b>1</b>)–<b>a</b>(<b>4</b>)) highlighting their distribution across the subjects (<b>b</b>(<b>1</b>)–<b>b</b>(<b>4</b>)) for dorsal and ventral ROIs using conventional and high-definition montages for dementia, depression, and healthy volunteers. Level of significance denoted by ** &lt;0.01.</p>
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<p>Showing (<b>i</b>) The significant (<span class="html-italic">p</span> &lt; 0.001) relationship between the atrophy parameter and personalized doses at the target ROI at the left inferior parietal lobule, and (<b>ii</b>) its significant variation across the three groups: depression, dementia, and healthy volunteers. (*** denotes significance level &lt; 0.001).</p>
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15 pages, 6895 KiB  
Article
Curcumin Mitigates Gut Dysbiosis and Enhances Gut Barrier Function to Alleviate Metabolic Dysfunction in Obese, Aged Mice
by Gopal Lamichhane, Femi Olawale, Jing Liu, Da-Yeon Lee, Su-Jeong Lee, Nathan Chaffin, Sanmi Alake, Edralin A. Lucas, Guolong Zhang, Josephine M. Egan and Yoo Kim
Biology 2024, 13(12), 955; https://doi.org/10.3390/biology13120955 - 21 Nov 2024
Viewed by 188
Abstract
The gut microbiome plays a critical role in maintaining gut and metabolic health, and its composition is often altered by aging and obesity. This study aimed to investigate the protective effects of curcumin on gut dysbiosis, gut barrier integrity, and bile acid homeostasis [...] Read more.
The gut microbiome plays a critical role in maintaining gut and metabolic health, and its composition is often altered by aging and obesity. This study aimed to investigate the protective effects of curcumin on gut dysbiosis, gut barrier integrity, and bile acid homeostasis in aged mice fed a high-fat, high-sugar diet (HFHSD). Eighteen- to twenty-one-month-old male C57BL/6 mice were divided into groups fed a normal chow diet or HFHSD, with or without curcumin supplementation (0.4% w/w) for 8 and 15 weeks. We assessed body weight, food intake, insulin sensitivity, gut microbiota composition, and gene expression in the gut and liver and performed histological analysis of gut tissues. Curcumin supplementation prevented HFHSD-induced weight gain and metabolic disturbances. In the gut, curcumin-treated mice showed a higher abundance of beneficial bacterial genera, such as Lachnospiraceae, Akkermansia, Mucispirillum, and Verrucomicrobiota, alongside a lower abundance of harmful bacterial genera like Desulfobacteria, Alistipes, and Muribaculaceae compared to control. This shift in gut microbiota was associated with improved gut integrity, as demonstrated by increased expression of the tight junction protein occludin and reduced levels of the pro-inflammatory marker interleukin-1β in the ileum. Additionally, curcumin modulated hepatic gene expression involved in bile acid homeostasis, suggesting a positive effect on liver health. Curcumin supplementation can alleviate the negative effects of aging and an HFHSD on the gut microbiome, improve gut barrier integrity, and maintain bile acid homeostasis. These findings highlight curcumin’s potential as a dietary intervention for managing obesity- and age-associated gut health issues. Full article
(This article belongs to the Special Issue Gut Microbiome in Health and Disease (2nd Edition))
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<p>Curcumin supplementation mitigates body weight gain and improves insulin sensitivity in aged male mice. (<b>A</b>) Body weight gain (g), (<b>B</b>) accumulated food and food efficiency ratio, and (<b>C</b>) insulin tolerance test. (<span class="html-italic">n</span> = 9 for NCD and NCD+CUR; <span class="html-italic">n</span> = 6 for HFHSD; <span class="html-italic">n</span> = 9 for HFHSD+CUR). Results are expressed as mean ± SEM.</p>
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<p>Curcumin supplementation alters the beta diversity of the gut microbiome in the feces of aged male mice. (<b>A</b>) Observed ASVs, (<b>B</b>) Pielou’s evenness index, (<b>C</b>) Shannon index, (<b>D</b>) weighted UniFrac, and (<b>E</b>) unweighted UniFrac analysis of the feces from mice. (<span class="html-italic">n</span> = 6 per group). For (<b>A</b>–<b>C</b>): B, baseline and A, after the 15-week intervention. Dots above and below the bar graph in (<b>A</b>–<b>C</b>) represents outliers.</p>
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<p>Curcumin supplementation alters the relative abundance of the gut microbiome in the feces of aged male mice. The figure shows the relative abundance of the microbiome at (<b>A</b>,<b>B</b>) phylum level, (<b>C</b>) genus level, and (<b>D</b>) ASV level (<span class="html-italic">n</span> = 6 per group).</p>
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<p>LEfSe analysis of the abundance of the gut microbiome in the feces of aged male mice. The figure shows the relative abundance of the microbiome in (<b>A</b>) NCD vs. NCD+CUR and (<b>B</b>) HFHSD vs. HFHSD+CUR (<span class="html-italic">n</span> = 6 per group).</p>
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<p>Curcumin improves the integrity of the small intestine by decreasing inflammation and increasing the expression of tight junction proteins in aged mice. (<b>A</b>) Representative images from H&amp;E staining of jejunum tissues (scale bar = 200 µm), (<b>B</b>) expression of inflammatory markers in the ileum, and (<b>C</b>) expression of tight junction proteins in the ileum of mice. The results are presented as mean ± SEM, <span class="html-italic">n</span> = 6/group. Red arrow in the histological section highlights villous atrophy, which was not observed in HFHSD+CUR group.</p>
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<p>Curcumin has a modest effect on the colon of aged mice. (<b>A</b>) Representative images from H&amp;E staining of the colon (scale bar = 200 µm), (<b>B</b>) expression of inflammatory markers in the colon of aged mice. The results are presented as mean ± SEM, <span class="html-italic">n</span> = 6/group.</p>
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<p>Curcumin supplementation regulates biliary homeostasis-related genes in aged male mice. (<b>A</b>) Relative expression in NCD vs. NCD+CUR and (<b>B</b>) relative expression in HFHSD vs. HFHSD+CUR. Results are expressed as mean ± SEM, <span class="html-italic">n</span> = 6 per group.</p>
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19 pages, 367 KiB  
Article
The SEC Spanish Consortium: Foundations for Linguistic Gratuity and Language Documentation Among Latinx Populations in New Destination Communities of the U.S. South
by Stephen Fafulas, Chad Howe, Rafael Orozco, Alicia Cipria, Erin O’Rourke, Nina Moreno and Matthew J. Van Hoose
Languages 2024, 9(11), 354; https://doi.org/10.3390/languages9110354 - 20 Nov 2024
Viewed by 291
Abstract
Latinx populations in the USA have grown steadily in recent decades, with significant increases taking place in “new destination communities” of the U.S. South. The focus of our paper is to highlight opportunities for working with these populations, including traditional sociolinguistic ethnographies and [...] Read more.
Latinx populations in the USA have grown steadily in recent decades, with significant increases taking place in “new destination communities” of the U.S. South. The focus of our paper is to highlight opportunities for working with these populations, including traditional sociolinguistic ethnographies and community-engaged research. We highlight an initiative named “The SEC Spanish Consortium” which is an interinstitutional collaboration centered on scholarship and service involving Latinx populations in new destination communities of the U.S. South. We show that ongoing and future scholarly work in the U.S. South can act as a mechanism for documenting these emerging Latinx communities while simultaneously serving the underrepresented and minority speakers of these linguistic varieties. Full article
(This article belongs to the Special Issue Spanish in the US: A Sociolinguistic Approach)
22 pages, 334 KiB  
Review
Use of Epinephrine in Cardiac Arrest: Advances and Future Challenges
by Caitlin A. Williams, Hannah E. Fairley, Quincy K. Tran and Ali Pourmand
Medicina 2024, 60(11), 1904; https://doi.org/10.3390/medicina60111904 - 20 Nov 2024
Viewed by 242
Abstract
Epinephrine is the most common medication used in cardiac arrest. Although the medication has been a mainstay of treatment over the last century, the utility and efficacy of epinephrine has been re-evaluated in recent years. This study aims to evaluate the literature describing [...] Read more.
Epinephrine is the most common medication used in cardiac arrest. Although the medication has been a mainstay of treatment over the last century, the utility and efficacy of epinephrine has been re-evaluated in recent years. This study aims to evaluate the literature describing the efficacy, timing, and dosing of epinephrine use in cardiac arrest. We utilized an extensive PubMed and SCOPUS search that included randomized control trials, prospective observational studies, and secondary analysis of observational data. These articles evaluated the administration of epinephrine in cardiac arrest and reported patient outcomes, including survival rates, neurological function, and return of spontaneous circulation. Dosing of epinephrine has been standardized at 1 mg per administration in adults and studies show that higher doses may not have better outcomes and can potentially be harmful. Research on the optimal timing of epinephrine has shown that earlier administration of epinephrine in cardiac arrest is more likely to have improved outcomes compared to later administration and longer intervals, although there are still conflicting results on the improvement of neurological outcomes. Intravenous is the preferred route of administration for epinephrine, but new research suggests intramuscular administration may be beneficial. While epinephrine has been shown to improve the rates of return of spontaneous circulation and even survival to hospital discharge in several studies, epinephrine use may not provide patients who survive cardiac arrest with a meaningful neurological recovery. Full article
(This article belongs to the Special Issue Cardiopulmonary Resuscitation: Recent Advances and Future Challenges)
10 pages, 445 KiB  
Article
Beyond Borders and Genders: Unveiling Cultural Influences on Badminton Motivation Among Older Adult Players in Taiwan and the United States
by Wei-Chieh Liao, Yun-Dih Chia-Smith, David Cabello-Manrique, Chia-Min Wang and Li-An Liao
Sports 2024, 12(11), 313; https://doi.org/10.3390/sports12110313 - 20 Nov 2024
Viewed by 178
Abstract
This study explores and compares the motivations behind badminton participation among older adult players from Taiwan and the United States (U.S.), with a specific focus on cultural and gender differences. A total of 139 participants aged 60 and above took part in the [...] Read more.
This study explores and compares the motivations behind badminton participation among older adult players from Taiwan and the United States (U.S.), with a specific focus on cultural and gender differences. A total of 139 participants aged 60 and above took part in the study, with 55 from the United States (24 females, 31 males) and 84 from Taiwan (39 females, 45 males). Utilizing the Exercise Motivations Inventory-2 (EMI-2), this research examines differences in motivations across cultural and gender lines, identifying key factors such as health-related motivations, personal achievement, social interactions, and competition. The results reveal that Taiwanese players are more motivated by health benefits and stress reduction, while U.S. players emphasize personal achievement and recognition. Additionally, gender-specific motivations emerged, with female players from both countries placing greater importance on social interactions compared to their male counterparts. These findings underscore the need for culturally and gender-sensitive approaches to promote sports participation among older adults in diverse settings. Full article
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<p>Interaction between sex and region on motivation for social participation among badminton players.</p>
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14 pages, 3357 KiB  
Article
PRIMERS: Polydopamine Radioimmunotherapy with Image-Guided Monitoring and Enhanced Release System
by Shahinur Acter, Lindokuhle M. Ngema, Michele Moreau, Debarghya China, Akila Viswanathan, Kai Ding, Yahya E. Choonara, Sayeda Yasmin-Karim and Wilfred Ngwa
Pharmaceutics 2024, 16(11), 1481; https://doi.org/10.3390/pharmaceutics16111481 - 20 Nov 2024
Viewed by 195
Abstract
Background/Objectives: To overcome the side effects of conventional cancer treatment, multifunctional nanoparticles with image-guidance properties are increasingly desired to obtain enhanced therapeutic efficacy without any toxicity of the treatment. Herein, we introduce the potential of Polydopamine Radioimmunotherapy with Image-guided Monitoring and Enhanced (drug) [...] Read more.
Background/Objectives: To overcome the side effects of conventional cancer treatment, multifunctional nanoparticles with image-guidance properties are increasingly desired to obtain enhanced therapeutic efficacy without any toxicity of the treatment. Herein, we introduce the potential of Polydopamine Radioimmunotherapy with Image-guided Monitoring and Enhanced (drug) Release System (PRIMERS) to meet the challenges of currently used cancer therapy. Methods: The PDA nanobowls were synthesized using an emulsion-induced interfacial anisotropic assembly method followed by surface modification with high-Z material to obtained the final product PRIMERS. Results: The engineered multifunctional nanosystem “PRIMERS” could serve as fiducial markers with the potential for use in combination cancer therapy. By leveraging the advantages of the excellent surface functionalization capability of PDA, the anisotropic nanostructure (PDA nanobowls) has been successfully functionalized with gadolinium, which shows strong MRI contrast signal both in vitro in phantom and in vivo in animals. The results of anti-cancer drug loading and releasing efficiency of these functionalized nanobowls are presented. Moreover, the gadolinium-coated PDA nanobowls demonstrate the capacity for loading immunotherapy drugs (Anti-CD40) with activated release in acidic pH levels characteristic of the tumor microenvironment, with enhanced release following administration of radiation therapy in vitro. Conclusions: Overall, the results highlight the potential of this new technology for combining radiotherapy with activated image-guided drug delivery, which offers broad opportunities to overcome current challenges in cancer treatment. Full article
(This article belongs to the Section Nanomedicine and Nanotechnology)
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<p>Schematic diagram showing the functionalization of polydopamine bowl-shaped mesoporous nanoparticles (on <b>top</b> and on <b>bottom</b>) showing MRI contrast of the nanosystem in a mouse model.</p>
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<p>Transmission electron microscope (TEM) image of PDA nanobowls before functionalization (<b>a</b>,<b>b</b>), with (<b>b</b>) being a high-magnified view of the PDA nanobowl (<b>a</b>), and (<b>c</b>–<b>e</b>) showing PDA nanobowls coated with various concentrations of gadolinium (40, 100, and 150 µg/mL, respectively).</p>
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<p>Showing the MRI contrast of gadolinium-coated PDA mesoporous nanobowls in agar gel phantom. Image on the left: agar gel phantom only on the left, PDA nanoparticles in phantom on the bottom, and gadolinium-coated PDA nanobowls (gadolinium (III) chloride (100 µg/mL)) on the top right. MR image on the right: agar gel phantom only on the left, top right and bottom show gadolinium-coated PDA nanobowls with 100 µg/mL and 150 µg/mL of gadolinium (III) chloride, respectively. Herein, the letter A refers to the additive intensity value for an ellipse in a phantom image, L refers to Left and R refers to Right.</p>
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<p>(<b>A</b>) Showing the (3-[4,5-dimethylthiazol-2-yl]-2,5 diphenyl tetrazolium bromide) (MTT) assay of polydopamine (PDA) mesoporous nanobowls with and without gadolinium coating in TC-1 cells (concentration of gadolinium 100 µg/mL), <span class="html-italic">p</span> value (only cells vs. bowls_100 µg/mL—0.8380; only cells vs. bowls_500 µg/mL—0.4842; only cells vs. Gd_bowls_100 µg/mL—0.3737; Gd_bowls_500 µg/mL—0.4872), (<b>B</b>) MTT assay results showing biocompatibility of PDA mesoporous nanobowls on human umbilical vein endothelial cells (HUVEC). Herein, ns refer to non-significant value.</p>
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<p>(<b>A</b>) MRI images of the tumor showing PDA mesoporous nanobowls coated with 100 µg/mL of gadolinium (PRIMERS) and tumor visualization over time. Treatment means the PRIMERS is administered intratumorally, and control means no PRIMERS administration. (<b>B</b>) Showing the quantitative analysis of MRI images; on the left side, the two sets of images are treatment samples from day 1 and day 12. On the right side, the two sets of images are control samples from day 1 and day 12. Herein, treatment means the PRIMERS was intertumorally administered, and control means the PRIMERS was not administered. Herein, the pink box refers to the area of the tumour, where the MRI contrast is expected to observed.</p>
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<p>Transmission electron microscope (TEM) images of polydopamine mesoporous nanobowls coated with gadolinium (con. of gadolinium_100 µg/mL), before (<b>a</b>) and after (<b>b</b>) loading with doxorubicin, respectively, and (<b>c</b>) is the high-magnified view of image (<b>b</b>). Figure (<b>d</b>) shows the loading efficiency of DOX in gadolinium-coated PDA mesoporous nanobowls (con. of gadolinium_100 µg/mL) and figure (<b>e</b>) is the release of DOX from gadolinium-coated PDA mesoporous nanobowls (con. of gadolinium_100 µg/mL) in pH 5.6.</p>
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<p>Figure (<b>A</b>) confocal microscopy images, herein, (<b>a1</b>) is PDA nanobowls only, (<b>a2</b>) is fluorophore-tagged antiCD40 only, (<b>a3</b>,<b>a4</b>) are antiCD40 (fluorophore tagged) loaded PDA nanobowls, with and without coated with gadolinium respectively; herein, the white arrow pointing the TEM grid in the image (<b>a1</b>,<b>a2</b>), while the yellow arrow (<b>a1</b>–<b>a4</b>) pointing the sample. Figure (<b>B</b>) is the fluorescence intensity profile of antiCD40 (Alexa fluor 700) release from PDA mesoporous nanobowls in various pH environments; herein, for (<b>b1</b>,<b>b2</b>) the incubation time was 24 h only, and for (<b>b3</b>,<b>b4</b>) there are various incubation duration as it is time-point study (0, 4, and 24 h).</p>
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17 pages, 6822 KiB  
Article
LUCAT1-Mediated Competing Endogenous RNA (ceRNA) Network in Triple-Negative Breast Cancer
by Deepak Verma, Sumit Siddharth, Ashutosh S. Yende, Qitong Wu and Dipali Sharma
Cells 2024, 13(22), 1918; https://doi.org/10.3390/cells13221918 - 19 Nov 2024
Viewed by 347
Abstract
Breast cancer is a heterogeneous disease comprising multiple molecularly distinct subtypes with varied prevalence, prognostics, and treatment strategies. Among them, triple-negative breast cancer, though the least prevalent, is the most aggressive subtype, with limited therapeutic options. Recent emergence of competing endogenous RNA (ceRNA) [...] Read more.
Breast cancer is a heterogeneous disease comprising multiple molecularly distinct subtypes with varied prevalence, prognostics, and treatment strategies. Among them, triple-negative breast cancer, though the least prevalent, is the most aggressive subtype, with limited therapeutic options. Recent emergence of competing endogenous RNA (ceRNA) networks has highlighted how long noncoding RNAs (lncRNAs), microRNAs (miRs), and mRNA orchestrate a complex interplay meticulously modulating mRNA functionality. Focusing on TNBC, this study aimed to construct a ceRNA network using differentially expressed lncRNAs, miRs, and mRNAs. We queried the differentially expressed lncRNAs (DElncRNAs) between TNBC and luminal samples and found 389 upregulated and 386 downregulated lncRNAs, including novel transcripts in TNBC. DElncRNAs were further evaluated for their clinical, functional, and mechanistic relevance to TNBCs using the lnc2cancer 3.0 database, which presented LUCAT1 (lung cancer-associated transcript 1) as a putative node. Next, the ceRNA network (lncRNA–miRNA–mRNA) of LUCAT1 was established. Several miRNA–mRNA connections of LUCAT1 implicated in regulating stemness (LUCAT1-miR-375-Yap1, LUCAT1-miR181-5p-Wnt, LUCAT1-miR-199a-5p-ZEB1), apoptosis (LUCAT1-miR-181c-5p-Bcl2), drug efflux (LUCAT1-miR-200c-ABCB1, LRP1, MRP5, MDR1), and sheddase activities (LUCAT1-miR-493-5p-ADAM10) were identified, indicating an intricate regulatory mechanism of LUCAT1 in TNBC. Indeed, LUCAT1 silencing led to mitigated cell growth, migration, and stem-like features in TNBC. This work sheds light on the LUCAT1 ceRNA network in TNBC and implies its involvement in TNBC growth and progression. Full article
(This article belongs to the Special Issue Advances in the Biogenesis, Biology, and Functions of Noncoding RNAs)
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<p>Differentially expressed gene (DEG) profile of protein-coding and noncoding genes. DEG analysis of TNBC vs other subtypes with fold change filter of ≥1.5 and ≤ −1.5 FC was performed. Unsupervised clustering clearly showed two clusters. (<b>A</b>) Heat map shows all the variations including protein-coding and noncoding genes between TNBC and all other subtypes (Luminal A, Luminal B, Her2). (<b>B</b>) Heat map shows differential expression profile of lncRNA segregated through ENSEMBL-Biomart.</p>
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<p>Comprehensive analysis of LUCAT1 in TNBC. (<b>A</b>) The list of DElncRNA from GSE192341 was compared to the lnc2cancer3.0 database, which is a collection of experimentally validated mechanistic, functional, and clinically relevant lncRNAs. Venn diagram shows comparative result with GSE192341 and only LUCAT1 was common in all the 3 categories (mechanism, function, and clinical). (<b>B</b>) LUCAT1 expression in TNBC and non-TNBC samples. Outliers or extreme values are shown as * in the figure. (<b>C</b>) ceRNA network of LUCAT1 using lncACTdb database. (<b>D</b>) GSEA of hallmark in cancer (C1; MSigDb) and oncogene signature pathways (C6; MSigDb) with LUCAT1-correlated genes (r<sup>2</sup> ≥ 0.3) show a significant enrichment in hallmark apical junction pathway (NES:1.57), complement pathway (NES: 1.48), TNF signaling via NFKB (NES: 1.46), oncogene IL2 (NES:1.49), and MEK (1.44) upregulation signatures.</p>
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<p>LUCAT1 induces growth, proliferation and migration of TNBC cells. (<b>A</b>) Bar graph shows the expression profile of LUCAT1-associated miRNA (red bars) and mRNA (blue bars) in CCLE data of multiple breast cancer cell lines (TNBC vs. all other subtypes). (<b>B</b>) Bar graph shows the real-time mRNA expression profile of LUCAT1 in breast cancer subtype-specific cell lines. (<b>C</b>) TNBC cells were silenced for LUCAT1. RT-PCR results show mRNA expression level of LUCAT1 and GAPDH in TNBC cell lines. (<b>D</b>) MDA-MB-468 cells were silenced for LUCAT1 expression using siLUCAT1. The cell viability was evaluated using MTT assay and the data presented as % viability showing the mean viability ± SD of 6 independent replicates. (<b>E</b>) Trypan blue live–dead staining of MDA-MB-468 cells transfected with scramble-control and LUCAT1 siRNA was conducted. The bar graph shows the number of live cells only. *** <span class="html-italic">p</span> = 1.65046 × 10<sup>−6</sup>. (<b>F</b>) TNBC cells were silenced for LUCAT1 expression. Representative pictures of colony-formation assay in TNBC cells in the presence and absence of LUCAT1 are shown. (<b>G</b>) TNBC cells were silenced for LUCAT1 expression and subjected to transwell migration assay. Representative images show the cells migrated through the upper chamber in scramble-control and LUCAT1 siRNA group. Images captured at 10× magnification.</p>
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<p>LUCAT1 functions as an important axis regulating drug efflux, stemness, and programmed cell death in TNBC cells. (<b>A</b>) TNBC cells were silenced for LUCAT1. Identification of side population (SP) cells from multiple TNBC cells. SP = side population. SP cells of HCC1806, HCC1937 and Hs578t were analyzed by dual-wavelength flow cytometer after staining with Hoechst 33342. (<b>B</b>) Hs578t cells were silenced for LUCAT1, and mRNA-expression level of stemness markers (OCT-4, CMYC, and ZEB1) were examined. (<b>C</b>) HCC1806 cells were silenced for LUCAT1, and CD49F level was examined using FACS analysis. (<b>D</b>) HCC1937 cells were silenced for LUCAT1 and ALDH activity assay was performed. (<b>E</b>) Total protein lysates from HCC1806 cells transfected with scramble-control and LUCAT1-siRNA were immunoblotted for the expression of BAX, Bcl2-xL, and T-PARP. (<b>F</b>) Flow cytometry analysis of cell distribution in respective phases of cell cycle of HCC1806 cells transfected with scramble-control and LUCAT1 siRNA. Sub-G1 cells correspond to apoptotic cells. (<b>G</b>) mRNA expression level of WNT1, WNT2, LUCAT1 and GAPDH in HCC1806 cells transfected with scramble-control and LUCAT1 siRNA. (<b>H</b>) TOPflash/FOPflash reporter assay in HCC1937 cells transfected with scramble-control and LUCAT1 siRNA (** <span class="html-italic">p</span> = 0.00252).</p>
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<p>Association between LUCAT1 and miRNA, and LUCAT1 and mRNAs in TNBC. (<b>A</b>) Kaplan–Meier plots of triple-negative breast cancer survival in relation to high LUCAT1 + low miRs (miR-375 + miR-642a + miR-200c + miR-181-5p + miR-199a-5p + miR-493-5p + miR-181c-5p). (<b>B</b>) Kaplan–Meier plots of triple-negative breast cancer survival in relation to high LUCAT1 + high target genes (WNT + YAP + DNMT + ABACb + Zeb + LRP + ROCK + ADAM + ABCC).</p>
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13 pages, 337 KiB  
Article
A Spatial–Temporal Bayesian Model for a Case-Crossover Design with Application to Extreme Heat and Claims Data
by Menglu Liang, Zheng Li, Lijun Zhang and Ming Wang
Stats 2024, 7(4), 1379-1391; https://doi.org/10.3390/stats7040080 - 19 Nov 2024
Viewed by 210
Abstract
Epidemiological approaches for examining human health responses to environmental exposures in observational studies frequently address confounding by employing advanced matching techniques and statistical methods grounded in conditional likelihood. This study incorporates a recently developed Bayesian hierarchical spatiotemporal model within a conditional logistic regression [...] Read more.
Epidemiological approaches for examining human health responses to environmental exposures in observational studies frequently address confounding by employing advanced matching techniques and statistical methods grounded in conditional likelihood. This study incorporates a recently developed Bayesian hierarchical spatiotemporal model within a conditional logistic regression framework to capture the heterogeneous effects of environmental exposures in a case-crossover (CCO) design. Spatial and temporal dependencies are modeled through random effects incorporating multivariate conditional autoregressive priors. Flexible frailty structures are introduced to explore strategies for managing temporal variables. Parameter estimation and inference are conducted using a Monte Carlo Markov chain method within a Bayesian framework. Model fit and optimal model selection are evaluated using the deviance information criterion. Simulations assess and compare model performance across various scenarios. Finally, the approach is illustrated with workers’ compensation claims data from New York and Florida to examine spatiotemporal heterogeneity in hospitalization rates related to heat prostration. Full article
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<p>Case-crossover (CCO) design in our study.</p>
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26 pages, 1685 KiB  
Review
Myeloproliferative Neoplasms: Challenging Dogma
by Jerry L. Spivak
J. Clin. Med. 2024, 13(22), 6957; https://doi.org/10.3390/jcm13226957 - 19 Nov 2024
Viewed by 423
Abstract
Myeloproliferative neoplasms, polycythemia vera, essential thrombocytosis, and primary myelofibrosis are a unique group of clonal hematopoietic stem cell neoplasms that share somatic, gain-in-function driver mutations in JAK2, CALR, and MPL. As a consequence, these disorders exhibit similar phenotypic features, the [...] Read more.
Myeloproliferative neoplasms, polycythemia vera, essential thrombocytosis, and primary myelofibrosis are a unique group of clonal hematopoietic stem cell neoplasms that share somatic, gain-in-function driver mutations in JAK2, CALR, and MPL. As a consequence, these disorders exhibit similar phenotypic features, the most common of which are the ceaseless production of normal erythrocytes, myeloid cells, platelets alone or in combination, extramedullary hematopoiesis, myelofibrosis, and a potential for leukemic transformation. In the case of polycythemia vera and essential thrombocytosis, however, prolonged survival is possible. With an incidence value in the range of 0.5–2.0/100,000, myeloproliferative neoplasms are rare disorders, but they are not new disorders, and after a century of scrutiny, their clinical features and natural histories are well-defined, though their individual management continues to be controversial. With respect to polycythemia vera, there has been a long-standing dispute between those who believe that the suppression of red blood cell production by chemotherapy is superior to phlebotomy to prevent thrombosis, and those who do not. With respect to essential thrombocytosis, there is a similar dispute about the role of platelets in veinous thrombosis, and the role of chemotherapy in preventing thrombosis by suppressing platelet production. Linked to these disputes is another: whether therapy with hydroxyurea promotes acute leukemia in disorders with a substantial possibility of longevity. The 21st century revealed new insights into myeloproliferative neoplasms with the discovery of their three somatic, gain-of-function driver mutations. Almost immediately, this triggered changes in the diagnostic criteria for myeloproliferative neoplasms and their therapy. Most of these changes, however, conflicted with prior well-validated, phenotypically driven diagnostic criteria and the management of these disorders. The aim of this review is to examine these conflicts and demonstrate how genomic discoveries in myeloproliferative neoplasms can be used to effectively complement the known phenotypic features of these disorders for their diagnosis and management. Full article
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<p>The hematopoietic stem cell (HSC) hierarchy (modified from Yamamoto et al. [<a href="#B14-jcm-13-06957" class="html-bibr">14</a>]). HSCs are organized in a hierarchy in which the most primitive HSC, the long-term HSC (CD34+CD38-LT-HSC), is mainly dormant in endosteal bone marrow niches, tethered to osteoblasts through adhesive proteins and thrombopoietin. These LT-HSCs also require the presence of closely opposed megakaryocytes, which maintain HSC quiescence though the secretion of thrombopoietin and CXCL4 [<a href="#B15-jcm-13-06957" class="html-bibr">15</a>]. The daily requirement of committed hematopoietic progenitor cells is provided by short-term HSCs (ST-HSCs), which have a limited self-renewal capacity, but a large proliferative capacity. Importantly, the only hematopoietic growth factor receptor expressed by LT-HSCs is the thrombopoietin receptor, MPL. The default commitment pathway for LT-HSCs is to give rise to myeloid repopulating HSCs (MyRPs) with restricted lineage specificity, including megakaryocyte HSCs (MkRPs); megakaryocyte–erythroid HSCs (MERPs), and a common myeloid HSCs (CMRPs), which gives rise to myeloid, erythroid, and megakaryocytic cells. This arrangement reflects the need of LT-HSCs for megakaryocytes as well as thrombopoietin to remain quiescent. It also explains why thrombocytosis is a common presenting manifestation of all three MPNs, and also the pleiomorphic presenting manifestations of MPNs and MPN clonal succession. MPC, multipotent myeloid progenitor cell; LPC, multipotent lymphoid progenitor cell; n/m, neutrophil/monocyte progenitor cell; ery, erythroid progenitor cell; mk, megakaryocytic progenitor cell; B, B-cell progenitor cell; T, T-cell progenitor cell; G-CSFR, granulocyte colony stimulating factor receptor; EPOR, erythropoietin receptor; MPL, thrombopoietin receptor. * Represents the presence of an MPN driver mutation.</p>
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<p>The correlation between the total body red cell mass measured directly and the peripheral blood hematocrit level in PV patients. The data from reference [<a href="#B24-jcm-13-06957" class="html-bibr">24</a>] have been replotted to illustrate the important fact that the peripheral blood hematocrit in untreated PV patients fails to correlate with the actual total body hematocrit, even at values falling within the normal hematocrit ranges for normal men and women. As a corollary, even for hematocrits greater than normal, until the hematocrit is greater than 59%, the possibility of a reduced plasma volume still exists (pseudopolycythemia). The red arrows represent the recommended phlebotomy target hematocrits for men and women PV patients, as well as for PV patients with splanchnic vein thrombosis or who are pregnant, respectively.</p>
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<p>An algorithm for the evaluation of isolated erythrocytosis. In this situation, the frequency of benign causes for an elevated hematocrit or red cell count far outnumbers PV as a cause of isolated erythrocytosis, and an assay for the <span class="html-italic">JAK</span>2 or <span class="html-italic">LNK</span> mutation is rarely necessary. * this MAB distinguishes PV from CHIP.</p>
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28 pages, 5179 KiB  
Article
Sugar Composition of Thai Desserts and Their Impact on the Gut Microbiome in Healthy Volunteers: A Randomized Controlled Trial
by Sayamon Senaprom, Nuttaphat Namjud, Thunnicha Ondee, Akkarach Bumrungpert and Krit Pongpirul
Nutrients 2024, 16(22), 3933; https://doi.org/10.3390/nu16223933 - 18 Nov 2024
Viewed by 373
Abstract
Background: The relationship between consuming Thai desserts—predominantly composed of carbohydrates—and gut microbiome profiles remains unclear. This study aimed to evaluate the effects of consuming various Thai desserts with different GI values on the gut microbiomes of healthy volunteers. Methods: This open-label, parallel randomized [...] Read more.
Background: The relationship between consuming Thai desserts—predominantly composed of carbohydrates—and gut microbiome profiles remains unclear. This study aimed to evaluate the effects of consuming various Thai desserts with different GI values on the gut microbiomes of healthy volunteers. Methods: This open-label, parallel randomized clinical trial involved 30 healthy individuals aged 18 to 45 years. Participants were randomly assigned to one of three groups: Phetchaburi’s Custard Cake (192 g, low-GI group, n = 10), Saraburi’s Curry Puff (98 g, medium-GI group, n = 10), and Lampang’s Crispy Rice Cracker (68 g, high-GI group, n = 10), each consumed alongside their standard breakfast. Fecal samples were collected at baseline and 24 h post-intervention for metagenomic analysis of gut microbiome profiles using 16S rRNA gene sequencing. Results: After 24 h, distinct trends in the relative abundance of various gut microbiota were observed among the dessert groups. In the high-GI dessert group, the abundance of Collinsella and Bifidobacterium decreased compared to the low- and medium-GI groups, while Roseburia and Ruminococcus showed slight increases. Correlation analysis revealed a significant negative relationship between sugar intake and Lactobacillus abundance in the medium- and high-GI groups, but not in the low-GI group. Additionally, a moderately negative association was observed between Akkermansia abundance and sugar intake in the high-GI group. These bacteria are implicated in energy metabolism and insulin regulation. LEfSe analysis identified Porphyromonadaceae and Porphyromonas as core microbiota in the low-GI group, whereas Klebsiella was enriched in the high-GI group, with no predominant bacteria identified in the medium-GI group. Conclusions: The findings suggest that Thai desserts with varying GI levels can influence specific gut bacteria, though these effects may be temporary. Full article
(This article belongs to the Special Issue Nutrition–Microbiome Interaction in Healthy Metabolism)
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<p>Nutritional value per 50 g of available carbohydrates (one serving size) of Thai desserts for testing. Note: Nutritional value data were retrieved from Namjud et al. [<a href="#B21-nutrients-16-03933" class="html-bibr">21</a>], except for total sugar content, which was assessed in this study. The serving size was 50 g of available carbohydrates [<a href="#B26-nutrients-16-03933" class="html-bibr">26</a>]. ND = not detected; GI = glycemic index; low GI ≤ 55, medium GI = 56–69, and high GI ≥ 70 [<a href="#B27-nutrients-16-03933" class="html-bibr">27</a>].</p>
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<p>CONSORT flow chart of the experimental design in this study.</p>
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<p>The relative abundance of the identified phyla, classes, orders, families, and genera of only the top 100 taxa. The relative abundance data of all identified taxa are presented in <a href="#app1-nutrients-16-03933" class="html-app">Supplementary Tables S1–S5</a>.</p>
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<p>Boxplots showing the comparison of changes in relative abundance of the gut microbiota after the 24 h consumption of testing Thai desserts. The gut microbiome profiles were compared at the level of phylum (<b>A</b>), class (<b>B</b>), order (<b>C</b>), family (<b>D</b>), and genus (<b>E</b>). Data were analyzed using the Kruskal–Wallis test and Dunn’s post hoc test. Asterisks (*) indicate significant differences at <span class="html-italic">p</span> &lt; 0.05. More detailed data on changes in relative abundance are presented in <a href="#app1-nutrients-16-03933" class="html-app">Supplementary Table S6</a>.</p>
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<p>The gut microbial taxa determined as dominant biomarkers for association with the consumption of Thai desserts. After the 24 h intervention in the low-GI and high-GI dessert groups, the three taxa, the family Porphyromonadaceae, and the genera <span class="html-italic">Porphyromonas</span> and <span class="html-italic">Klebsiella</span> were determined as dominant biomarkers as analyzed by LEfSe with an LDA score ≥ 1.0 (<b>A</b>). Cladogram exhibiting the phylogenetic distributions of gut microbiota (<b>B</b>).</p>
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<p>The alpha diversity indices of the dessert groups are shown by boxplots. The indices consist of observed ASVs, Chao1, Shannon, and PD whole tree. Black dots represent 20 samples obtained from combining the index values of both baseline and after the 24 h intervention for each dessert group. Alpha diversity values of each sample and quartiles of the distribution (minimum, first quartile, median, third quartile, and maximum of boxes) are demonstrated. No significant differences between dessert groups were observed by One-Way ANOVA or the Kruskal–Wallis test on any indices.</p>
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<p>The beta diversity indices between dessert groups as shown by 2-dimentional plots. The indices consist of PCoA on weighted (<b>A</b>) and unweighted (<b>B</b>) UniFrac distances, or GUniFrac distances (<b>C</b>), and NMDS based on Bray–Curtis dissimilarity (<b>D</b>). Colored dots represent samples at baseline or after the 24 h intervention for each dessert group. No significant difference between dessert groups was observed by the PERMANOVA test in any indices.</p>
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<p>Correlation between dietary nutrient intake and the relative abundance of gut microbiota at the genus level. The correlation data were analyzed by Spearman’s rank correlation coefficient. Asterisks (*) indicate statistically significant Spearman’s rho (<span class="html-italic">ρ</span>) values at <span class="html-italic">p</span> &lt; 0.05, while daggers (†) indicate the tendency of correlation at 0.05 ≤ <span class="html-italic">p</span> &lt; 0.10.</p>
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25 pages, 1576 KiB  
Review
Parkinson’s Disease: Biomarkers for Diagnosis and Disease Progression
by Rakesh Arya, A. K. M. Ariful Haque, Hemlata Shakya, Md. Masum Billah, Anzana Parvin, Md-Mafizur Rahman, Khan Mohammad Sakib, Hossain Md. Faruquee, Vijay Kumar and Jong-Joo Kim
Int. J. Mol. Sci. 2024, 25(22), 12379; https://doi.org/10.3390/ijms252212379 - 18 Nov 2024
Viewed by 381
Abstract
Parkinson’s disease (PD) is a progressive neurological disease that causes both motor and nonmotor symptoms. While our understanding of putative mechanisms has advanced significantly, it remains challenging to verify biomarkers with sufficient evidence for regular clinical use. Clinical symptoms are the primary basis [...] Read more.
Parkinson’s disease (PD) is a progressive neurological disease that causes both motor and nonmotor symptoms. While our understanding of putative mechanisms has advanced significantly, it remains challenging to verify biomarkers with sufficient evidence for regular clinical use. Clinical symptoms are the primary basis for diagnosing the disease, which can be mild in the early stages and overlap with other neurological disorders. As a result, clinical testing and medical records are mostly relied upon for diagnosis, posing substantial challenges during both the initial diagnosis and the continuous disease monitoring. Recent biochemical, neuroimaging, and genetic biomarkers have helped us understand the pathophysiology of Parkinson’s disease. This comprehensive study focuses on these biomarkers, which were chosen based on their relevance, methodological excellence, and contribution to the field. Biochemical biomarkers, including α-synuclein and glial fibrillary acidic protein (GFAP), can predict disease severity and progression. The dopaminergic system is widely used as a neuroimaging biomarker to diagnose PD. Numerous genes and genome wide association study (GWAS) sites have been related to the development of PD. Recent research on the SNCA gene and leucine-rich repeat protein kinase 2 (LRRK2) has shown promising results. By evaluating current studies, this review intends to uncover gaps in biomarker validation and use, while also highlighting promising improvements. It emphasizes the need for dependable and reproducible indicators in improving PD diagnosis and prognosis. These biomarkers may open up new avenues for early diagnosis, disease progression tracking, and the development of personalized treatment programs. Full article
(This article belongs to the Special Issue New Challenges of Parkinson’s Disease)
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<p>Schematic representation of PD biomarkers. The three primary categories of PD biomarkers are genetic, biochemical, and neuroimaging biomarkers, each leading to insights into disease mechanisms and progression. Created with <a href="http://www.BioRender.com" target="_blank">www.BioRender.com</a>.</p>
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<p>Possible blood-based biomarker of Parkinson’s disease. This figure provides evidence supporting the potential of the blood-based biomarker for Parkinson’s disease, shows significant differences in levels between PD patients and controls, good diagnostic accuracy, correlation with disease severity, dynamic changes over time, and reproducibility in an independent cohort. Total α-synuclein levels show inconsistent results, with some studies reported increase (↑), others decrease (↓), and some no significant difference (↔) between PD patients and HC. This variability may stem from differences in sample sources or detection methods. Phosphorylated α-synuclein is consistently elevated (↑) in PD patients as compared to HC. Levels of oligomeric forms of α-synuclein are increased (↑) in PD patients' plasma, serum, and red blood cells, which is more closely associated with neurotoxicity and PD pathology. Exosomal α-synuclein is also elevated (↑) in PD patients compared to HC, supporting its role as a biomarker for PD. Blood NfL levels are significantly higher (↑) in advanced stages of PD, reflecting neurodegeneration and disease progression. Tau protein levels, both in plasma and serum, are generally increased (↑) in PD, but other studies report no significant change (↔). Aβ42 levels in PD are unchanged (↔) or reduced (↓) compared to HC, reflecting study variability and potential differences in disease mechanisms. Levels of phosphorylated tau (p-tau) and Aβ42 are increased (↑) in FTD patients compared to PD or APS. CRP protein levels, both in whole blood and serum, are generally elevated (↑) in PD patients as compared to HC. PD; Parkinson’s disease, HC; Healthy control, FTD; Frontotemporal dementia, APS; Atypical parkinsonian syndromes, CRP; C-Reactive protein, Aβ42; amyloid-beta 42, NfL; Neurofilament light chain, ↑; upregulated, ↓; downregulated, ↔; unchanged.</p>
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<p>Cerebrospinal fluid (CSF) biomarkers of PD. This figure illustrates the complex pathways involved in PD pathology and highlights key cerebrospinal fluid (CSF) biomarkers associated with the disease. The molecular mechanisms underlying PD facilitate early diagnosis and the development of targeted therapies.</p>
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14 pages, 2094 KiB  
Review
65 Years on—Aflatoxin Biomarkers Blossoming: Whither Next?
by Thomas W. Kensler and David L. Eaton
Toxins 2024, 16(11), 496; https://doi.org/10.3390/toxins16110496 - 18 Nov 2024
Viewed by 345
Abstract
Aflatoxins are mycotoxins produced by Aspergillus flavus and several other related organisms and are common contaminants of numerous grains and nuts, especially maize (corn) and peanuts. Although, undoubtedly, aflatoxins have been present in the food of humans for millennia, their toxic effects were [...] Read more.
Aflatoxins are mycotoxins produced by Aspergillus flavus and several other related organisms and are common contaminants of numerous grains and nuts, especially maize (corn) and peanuts. Although, undoubtedly, aflatoxins have been present in the food of humans for millennia, their toxic effects were not discovered until 1960, first becoming evident as a non-infectious outbreak of poisoning of turkeys (Turkey X disease) arising from contaminated groundnut meal. The elucidation of specific chemical structures in 1963 led to the rapid characterization of aflatoxins as among the most potent chemical carcinogens of natural origin ever discovered. As a frontispiece to the Special Issue “65 Years on from Aflatoxin Discovery—A Themed Issue in Honor of Professor John D. Groopman”, we highlight many of Professor Groopman’s important contributions utilizing urinary (aflatoxin–N7–guanine) and, especially, serum (aflatoxin–albumin adducts) biomarkers; this work focused on over 40+ years of the development of analytical methods to measure biomarkers of aflatoxin exposure and their application in experimental and clinical studies. Collectively, this work serves as a template for using chemical-specific biomarkers as key tools to probe ‘exposure–disease relationships’—in this instance, dietary aflatoxins and liver cancer. New approaches to measuring carcinogen biomarkers will build upon this ‘aflatoxin paradigm’ to inform the public health implications of diverse exposures around the world. Full article
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<p>Dose–response relationship between AFB<sub>1</sub> dose and malignant liver tumors in male rats. The numbers of animals with tumors out of the total number of animals is shown for each dose point. Also shown are the first ‘time to tumor’ data for each dose point. See Wogan et al., 1974 for details [<a href="#B17-toxins-16-00496" class="html-bibr">17</a>].</p>
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<p>AFB<sub>1</sub> metabolites used as biomarkers from biofluids. Various cytochromes, P450, form oxidative metabolites, of varying toxicity. AFB-8,9-oxide is highly toxic and responsible for most, if not all, of the toxic and carcinogenic effects of AFB<sub>1</sub>. However, it can be detoxified by conjugation with glutathione, via specific glutathione <span class="html-italic">S</span>-transferases. Formation of DNA and protein adducts provide stable urinary and serum biomarkers of exposure with biological half-lives of ~8 h and ~30 days, respectively. Yellow: urine; red: serum or plasma.</p>
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<p>Pioneers of AFB<sub>1</sub> discovery and biomarker development. (<b>A</b>) Proposed structures of AFB<sub>1</sub> and AFG<sub>1</sub> by George Büchi on 22 March 1963 and reported later that year by Büchi, Wogan and colleagues [<a href="#B6-toxins-16-00496" class="html-bibr">6</a>]. Professor Gerald Wogan was the doctoral mentor for Prof. Groopman. Courtesy of Prof John Essigmann, MIT. (<b>B</b>) Initial chromatography of aflatoxin–N<sup>7</sup>–guanine by HPLC and photodiode array detection in human urine in 1987 by Groopman. (<b>C</b>) Dr Groopman with his first HPLC (1981). Courtesy of Prof. John Groopman. (<b>D</b>) Mass spectrometry of aflatoxin–lysine adduct standard and in rat serum. * Indicates position of stable isotope labels for internal standard. (<b>E</b>) John Groopman with his first mass spectrometer for biomarker quantification, a Thermo LCQ (2000). Photo courtesy of Thomas Kensler. (<b>F</b>) John Groopman measuring volumes of urine in samples collected during molecular epidemiology studies and chemoprevention clinical trials in Qidong, China, an endemic area for aflatoxin exposure, with a high incidence of liver cancer (2016). Photo courtesy of Thomas Kensler.</p>
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<p>Timeline for key events in the discovery, biomarker development and molecular epidemiology, and regulation of aflatoxins. FDA, Food and Drug Administration; IARC, International Agency for Research on Cancer; IAC, immunoaffinity chromatography; CHL, chlorophyllin. Red boxes highlight seminal contributions of Professor John Groopman over the last 4 decades. Photo credits: original “Rosetta” groundnut meal used in initial characterization of aflatoxin toxicities, courtesy of John Groopman; and broccoli sprouts grown in the Qidong Liver Cancer Institute, China for the first clinical trials, courtesy of Thomas Kensler.</p>
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