bluuebunny/crossref_metadata_2025_split huggingface dataset:
Causal relationship between gut microbiota and thyroid nodules: a bidirectional two-sample Mendelian randomization study
Authors: Yan Shaoshuai , He Jiawei , Yu Xudong , Shang Jianwei , Zhang Yaosheng , Bai Han , Zhu Xingyu , Xie Xiaoming , Lee Leanne 
Published: August 2024

ObjectiveEmerging evidence suggests alterations in gut microbiota (GM) composition following thyroid nodules (TNs) development, yet the causal relationship remains unclear. Utilizing Mendelian Randomization (MR), this study aims to elucidate the causal dynamics between GM and TNs.MethodsEmploying summary statistics from the MiBioGen consortium (n=18,340) and FinnGen consortium (1,634 TNs cases, 263,704 controls), we conducted univariable and multivariable MR analyses to explore the GM-TNs association. Techniques including inverse variance weighted, MR-Egger regression, weighted median, and MR-PRESSO were utilized for causal inference. Instrumental variable heterogeneity was assessed through Cochran’s Q statistic and leave-one-out analysis. Reverse MR was applied for taxa showing significant forward MR associations, with multivariate adjustments for confounders.ResultsOur findings suggest that certain microbiota, identified as Ruminococcaceae_NK4A214_group (OR, 1.89; 95%CI, 0.47-7.64; p = 0.040), Senegalimassilia (OR, 1.72; 95%CI, 1.03-2.87; p =0.037), Lachnospiraceae (OR,0.64; 95%CI,0.41-0.99; p =0.045), exhibit a protective influence against TNs’ development, indicated by negative causal associations. In contrast, microbiota categorized as Desulfovibrionales (OR, 0.63; 95%CI, 0.41-0.95; p =0.028), Prevotella_7 (OR, 0.79; 95%CI, 0.63-1.00; p =0.049), Faecalibacterium (OR, 0.66; 95%CI, 0.44-1.00; p =0.050), Desulfovibrionaceae (OR, 0.55; 95%CI, 0.35-0.86; p =0.008), Deltaproteobacteria (OR, 0.65; 95%CI, 0.43-0.97; p =0.036) are have a positive correlation with with TNs, suggesting they may serve as risk factors. Reverse MR analyses did not establish significant causal links. After comprehensive adjustment for confounders, taxa Desulfovibrionales (Order), Desulfovibrionaceae (Family), Deltaproteobacteria (Class) remain implicated as potential contributors to TNs’ risk.DiscussionThis study substantiates a significant causal link between GM composition and TNs development, underscoring the thyroid-gut axis’s relevance. The findings advocate for the integration of GM profiles in TNs’ prevention and management, offering a foundation for future research in this domain.
Developing an SSA-optimized attention-ConvGRU model for predicting and assessing soil contaminant distribution
Authors: Liang Yajie , Zhao Jieyu , Zhang Yiting , Li Jisheng , Ding Jieran , Jing Changyong , Ji Jiukun , Wu Dongtan 
Published: August 2024

Introduction: Soil pollution, which includes a variety of contaminants such as heavy metals and organic compounds, poses significant environmental and health risks, making effective prediction and assessment techniques essential. Current predictive models often struggle with the complexity and diversity of soil contaminant behaviors, leading to limitations in their accuracy and applicability.Methods: Recognizing the importance of capturing the temporal dynamics influenced by seasonal variations and agricultural practices, our study introduces an SSA-optimized Attention-ConvGRU model. This model integrates convolutional neural networks, gated recurrent units, and attention mechanisms, enhanced through optimization with the Sparrow Search Algorithm to improve predictive performance.Results: Experimental results confirm that our model significantly outperforms traditional methods, demonstrating over 30% improvement in prediction accuracy across multiple datasets.Discussion: This research underscores the potential of advanced machine learning techniques to revolutionize the assessment of soil pollution, providing substantial benefits for environmental management and public health protection.
In pancreatic cancer patients, chemotherapy reshapes the gene expression profile and antigen receptor repertoire of T lymphocytes and enhances their effector response to tumor-associated antigens
Authors: Brugiapaglia Silvia , Bulfamante Sara , Curcio Claudia , Arigoni Maddalena , Calogero Raffaele , Bonello Lisa , Genuardi Elisa , Spadi Rosella , Satolli Maria Antonietta , Campra Donata , Giordano Daniele , Cappello Paola , Cordero Francesca , Novelli Francesco 
Published: August 2024

IntroductionPancreatic Ductal Adenocarcinoma (PDA) is one of the most aggressive malignancies with a 5-year survival rate of 13%. Less than 20% of patients have a resectable tumor at diagnosis due to the lack of distinctive symptoms and reliable biomarkers. PDA is resistant to chemotherapy (CT) and understanding how to gain an anti-tumor effector response following stimulation is, therefore, critical for setting up an effective immunotherapy.MethodsProliferation, and cytokine release and TCRB repertoire of from PDA patient peripheral T lymphocytes, before and after CT, were analyzed in vitro in response to four tumor-associated antigens (TAA), namely ENO1, FUBP1, GAPDH and K2C8. Transcriptional state of PDA patient PBMC was investigated using RNA-Seq before and after CT.ResultsCT increased the number of TAA recognized by T lymphocytes, which positively correlated with patient survival, and high IFN-γ production TAA-induced responses were significantly increased after CT. We found that some ENO1-stimulated T cell clonotypes from CT-treated patients were expanded or de-novo induced, and that some clonotypes were reduced or even disappeared after CT. Patients that showed a higher number of effector responses to TAA (high IFN-γ/IL-10 ratio) after CT expressed increased fatty acid-related transcriptional signature. Conversely, patients that showed a higher number of regulatory responses to TAA (low IFN-γ/IL-10 ratio) after CT significantly expressed an increased IRAK1/IL1R axis-related transcriptional signature.ConclusionThese data suggest that the expression of fatty acid or IRAK1/IL1Rrelated genes predicts T lymphocyte effector or regulatory responses to TAA in patients that undergo CT. These findings are a springboard to set up precision immunotherapies in PDA based on the TAA vaccination in combination with CT.
Multi-omics pan-cancer analysis reveals the prognostic values and immunological functions of PPA2, with a spotlight on breast cancer
Authors: Zhang Jia-Ning , Yang Bei-Bei , Li Lin-Wei , Xu Hao , Wang Bin , Yi Zi-Lu , Zhou Xi-Rui , Liu Hong 
Published: August 2024

BackgroundRecently, the role of inorganic pyrophosphatase 2 (PPA2) has been remaining merely superficial in many tumors. Hence, the aim was to analyze the potential functions of PPA2 in pan-cancer, focusing on its role in breast cancer.MethodsA systematic pan-cancer analysis conducted primarily utilizing various open databases such as TCGA and GTEx. We explored the clinical value of PPA2 as well as various biological functions, including expression levels and subcellular localization, multi-dimensional immune-correlation analysis, co-expression networks, and gene heterogeneity. In addition, we not only verified the function of PPA2 through cell experiments but also analyzed PPA2 at the single-cell level and its drug sensitivity.ResultsPPA2 is abnormally expressed in various tumors, and it is mainly distributed in mitochondria. Furthermore, the indicators (OS, DSS, DFI, and PFI) of analysis hint that PPA2 exhibits significant prognostic value. At the same time, the genomic heterogeneity (including TMB, MSI, MATH, and NEO) of PPA2 in pan-cancer was analyzed. Across multiple tumors, the results showed a close correlation between PPA2 expression levels and different immune signatures (such as immune cell infiltration). All of these indicate that PPA2 could potentially be applied in the guidance of immunotherapy. We also have demonstrated that PPA2 promoted the process of breast cancer. Finally, some potential therapeutic agents (such as Fulvestrant) targeting the abnormal expression of PPA2 are revealed.ConclusionIn conclusion, the results demonstrated the great value of PPA2 in pan-cancer research, as well as its potential as a therapeutic target for breast tumors.
Finite element analysis and automation of a medium scale grinder applied to the manufacture of cassava starch
Authors: Oroun’Gobi Idayatou , Guo Chen Guang 
Published: August 2024

This research is based on the modeling, internal structure analysis, and automation of a cassava grinding machine. For the design, the single-cylinder grinder was chosen due to its advantages, notably simplicity and versatility. The grinding method used in this type of grinder is compression. The mechanical design and simulation software first allowed for the design of the grinder and then for performing static analyses under three loads (P1 = 10000N, P2 = 15000N, and P3 = 20000N). The results of these tests led to the selection of P3 = 20000N as the straightening load, with a maximum stress value in the static analysis of 88,18 MPa and a maximum deformation of 0,000358 under the force of load P3. Additionally, the frequency analysis distinguished five resonance modes. The results for each mode concluded that no resonance would affect the machine, thus ensuring stable operation. Furthermore, fatigue, frequency, and safety factor studies showed that the machine could withstand a load of m3 = 2000 kg without damage, with a service life of 1e+09 cycles. Considering the total number of life cycles, which is 1e+09 cycles, this means that the machine will have a service life of 347000 years, with a total grinding output of 2e+12 kg of cassava and 5840000 kg per year. The factor of safety is FoS = 1,78, indicating a sufficient margin for safe operating conditions. The automation of the grinder was carried out using a GRAFCET model and a sophisticated human-machine interface (HMI), providing an additional safety point for the machine and allowing the operator to monitor the operation via a simple graphical interface. This automation enables continuous operation with minimal human intervention, thereby improving the efficiency and safety of the cassava grinding process.
The memory binding test can anticipate Alzheimer’s disease diagnosis at an early preclinical stage: a longitudinal study in the INSIGHTpreAD cohort
Authors: Raposo Pereira Filipa , George Nathalie , Dalla Barba Gianfranco , Dubois Bruno , La Corte Valentina 
Published: August 2024

IntroductionAnticipating the diagnosis of Alzheimer’s disease (AD) at an early asymptomatic at-risk stage, where therapeutics can more effectively delay conscious cognitive decline, is currently among the biggest challenges in the field. Herein, we aimed to compare the capacity of the Memory Binding Test (MBT) with the official diagnostic tool, the Free and Cued Selective Reminding Test (FCSRT), to anticipate AD diagnosis at an early preclinical stage based on the associative memory component of MBT (binding), suggested as more sensitive to the emergence of subtle episodic memory (EM) deficits (AD hallmark).MethodsWe assessed the tests performance longitudinally (over 5 years) in 263 cognitively-normal elderly individuals at risk of AD (&gt;6 months of subjective memory complaints) using linear mixed-effect models controlled for age, sex, and education. We stratified participants in 2 models: amyloid-β (Aβ)/neurodegeneration (N) model, assessing Aβ burden and neurodegeneration effect [3 groups: controls (Aβ-/N-); stable/N- (Aβ+); stable/N+ (Aβ+)]; and the stable/progressors model, assessing progression to prodromal-AD effect [2 groups: stable (Aβ+); progressors (Aβ+)], based on 15 subjects who progressed to AD during follow-up (excluded once diagnosed).ResultsAβ burden was associated with significantly less MBT-intrusions, while Aβ burden and neurodegeneration together, with the most. Progression status had a strong negative effect on both tests performance. When compared with the FCSRT, the MBT seems to anticipate diagnosis based on a worst performance in a higher number of scores (including binding) in at least a year.DiscussionAnticipation of diagnosis to an asymptomatic at-risk stage, while participants remain cognitively-normal according to FCSRT cut-offs and unaware of objective EM deficits, has the potential to delay the onset of AD-linked cognitive decline by applying promising therapeutics before decline becomes too advanced.
Risk factors of in-stent restenosis after carotid angioplasty and stenting: long-term follow-up study
Authors: Park Sangil , Kim Bum Joon , Choi Hye-Yeon , Chang Dae-Il , Woo Ho Geol , Heo Sung Hyuk 
Published: August 2024

BackgroundAfter carotid artery angioplasty with stenting (CAS), it is unclear which risk factors are related to long-term outcomes, including in-stent restenosis (ISR). This study aimed to assess the factors associated with restenosis after CAS with a median follow-up of 35.7 months.Materials and methodsPatients who underwent CAS from January 2013 to December 2018 were included if they had symptomatic or asymptomatic carotid artery stenosis. The carotid Doppler ultrasonography (CDU) was followed up after the procedure. We defined at least 50% restenosis using the criteria that the internal carotid artery (ICA) peak systolic velocity (PSV) was greater than 224 cm/s or the ICA to common carotid artery PSV ratio was higher than 3.4. The risk factors for ISR were also assessed.ResultsOf the 189 patients, 122 had symptomatic carotid artery stenosis, and 67 had asymptomatic carotid artery stenosis. Patients were evaluated by CDU for a median of 35.7 months (interquartile range 19.5 to 70.0). Kaplan–Meier analysis showed that the longest time to ISR was 39 months, and ISR-free was better in the asymptomatic CAS group. In all groups, ISR was independently associated with current smoker [adjusted odds ratio (aOR), 3.425; 95% confidence interval (CI), 1.086 to 10.801] and elevated ICA PSV at baseline (aOR, 1.004; 95% CI, 1.001 to 1.007).ConclusionIndependent risk factors for ISR in the CAS group included current smoking and elevated ICA PSV at baseline. In the symptomatic CAS group, alcohol was independently associated with the ISR. ISR did not occur after 39 months from the CAS procedure in our study patients. Future studies with extended follow-up are necessary to fully understand the long-term outcomes of CAS.
Leveraging design of experiments to build chemometric models for the quantification of uranium (VI) and HNO3 by Raman spectroscopy
Authors: Sadergaski Luke R. , Einkauf Jeffrey D. , Delmau Laetitia H. , Burns Jonathan D. 
Published: August 2024

Partial least squares regression (PLSR) and support vector regression (SVR) models were optimized for the quantification of U(VI) (10–320 g L−1) and HNO3 (0.6–6 M) by Raman spectroscopy with optimized calibration sets chosen by optimal design of experiments. The designed approach effectively minimized the number of samples in the calibration set for PLSR and SVR by selecting sample concentrations with a quadratic process model, despite complex confounding and covarying spectral features in the spectra. The top PLS2 model resulted in percent root mean square errors of prediction for U(VI), HNO3, and NO3− of 3.7%, 3.6%, and 2.9%, respectively. PLS1 models performed similarly despite modeling an analyte with a majority linear response (i.e., uranyl symmetric stretch) and another with more covarying vibrational modes (i.e., HNO3). Partial least squares (PLS) model loadings and regression coefficients were evaluated to better understand the relationship between weaker Raman bands and covarying spectral features. Support vector machine models outperformed PLS1 models, resulting in percent root mean square error of prediction values for U(VI) and HNO3 of 1.5% and 3.1%, respectively. The optimal nonlinear SVR model was trained using a similar number of samples (11) compared with the PLSR model, even though PLS is a linear modeling approach. The generic D-optimal design presented in this work provides a robust statistical framework for selecting training set samples in disparate two-factor systems. This approach reinforces Raman spectroscopy for the quantification of species relevant to the nuclear fuel cycle and provides a robust chemometric modeling approach to bolster online monitoring in challenging process environments.
Precision nutrition for type 2 diabetes in Benin: leveraging linear goal programming to optimize diets with emphasis on adequacy, affordability, accessibility, and culture
Authors: Alaofè Halimatou , Mahdavimanshadi Mahdi , Mizéhoun-Adissoda Carmelle , Okechukwu Abidemi , Hounkpatin Waliou Amoussa , Bedrick Edward John , Gninkoun Jules , Fan Neng , Ehiri John 
Published: August 2024

BackgroundNutrition and diet are critical to managing Type 2 diabetes (T2D). Low-income households often face challenges maintaining a healthy and balanced diet due to food insecurity, availability, and cost. To address this issue, we used a linear goal programming (LGP) model to develop nutritionally adequate, affordable, accessible, and culturally acceptable diets for persons with T2D in Benin, a French-speaking sub-Saharan country. The goal was to help persons with T2D manage their condition more effectively.MethodsWe compiled a robust list of local commonly consumed foods in Benin, and calculated their nutritional value using West African food composition tables and food costs per serving from a market survey. Using mathematical optimization techniques, we designed dietary plans that meet the daily nutrient intake recommended by the World Health Organization (WHO) to prevent chronic diseases in normal adults. While adhering to dietary constraints of T2D, we developed optimized diet plans with varying energy levels that meet all nutrient requirements while considering availability, acceptability, and budgetary constraints.ResultsFifty-two food items and recipes were evaluated to create six low-cost daily menus. Menu 1 was the most affordable at CFA 1,127 (USD 1.88), providing 1890 kcal of energy, while Menu 6 was the most expensive at CFA 1,227 (USD 2.05), providing 1749 kcal. All the menus met the daily WHO minimum requirements for carbohydrates, fat, cholesterol, and fiber content, while other nutrients such as protein, vitamin C, and iron reached the upper limits of the acceptable value range.ConclusionLinear goal programming can be an effective tool in helping to obtain optimized adequate, accessible, and culturally acceptable diets at minimal cost by interpreting and translating dietary recommendations into a nutritional model, based on local market prices.
Dietary advanced glycation end-products and their associations with body weight on a Mediterranean diet and low-fat vegan diet: a randomized, cross-over trial
Authors: Kahleova Hana , Znayenko-Miller Tatiana , Motoa Giulianna , Eng Emma , Prevost Alex , Uribarri Jaime , Holubkov Richard , Barnard Neal D. 
Published: August 2024

ObjectiveEvidence suggests that changes in dietary advanced glycation end-products (AGEs) may influence body weight, but the effects of different dietary patterns remain to be explored.The aim of this study was to compare the effects of a Mediterranean and a low-fat vegan diet on dietary AGEs and test their association with body weight.Materials and methodsIn this randomized cross-over trial, 62 overweight adults were assigned to a Mediterranean or a low-fat vegan diet for 16-week periods in random order, separated by a 4-week washout. Body weight was the primary outcome. Three-day diet records were analyzed using the Nutrition Data System for Research software and dietary AGEs were estimated, using an established database. Statistical approaches appropriate for crossover trials were implemented.ResultsDietary AGEs decreased by 73%, that is, by 9,413 kilounits AGE/day (95% −10,869 to −7,957); p &lt; 0.001, compared with no change on the Mediterranean diet (treatment effect −10,303 kilounits AGE/day [95% CI −13,090 to −7,516]; p &lt; 0.001). The participants lost 6.0 kg on average on the vegan diet, compared with no change on the Mediterranean diet (treatment effect −6.0 kg [95% CI −7.5 to −4.5]; p &lt; 0.001). Changes in dietary AGEs correlated with changes in body weight (r = +0.47; p &lt; 0.001) and remained significant after adjustment for total energy intake (r = +0.39; p = 0.003).ConclusionDietary AGEs did not change on the Mediterranean diet but decreased on a low-fat vegan diet, and this decrease was associated with changes in body weight, independent of energy intake.Clinical trial registrationhttps://clinicaltrials.gov/, identifier NCT03698955
Efficacy and safety evaluation of mixed nutrition for postoperative esophageal cancer patients in China: a meta-analysis
Authors: Liu Shui , Qiao Lin , Liu Yang , Liu Hangmei , Li Yiwen , Sun Jingbo , Chen Wei , Shang Rongguo , Zhang Lili , Liu Xiaochuan 
Published: August 2024

ObjectiveThe purpose of this study was to evaluate the clinical effect of mixed nutrition and parenteral nutrition support on postoperative patients with esophageal cancer.MethodBy searching PubMed, Web of Science, Cochrane, CNKI, Wanfang and other databases, all the literatures until March 2024 about the comparison of randomized controlled Trial (RCT) of mixed nutrition and parenteral nutrition support in postoperative patients with esophageal cancer were screened. The inclusion criteria were that the patients were from randomized controlled trials or clinical trials in China, and the patients were all diagnosed with esophageal cancer by pathological biopsy. The exclusion criteria were the literature other than the above, including repeated published literature, non-Chinese and English literature, incomplete or missing analysis data, etc. After two researchers independently screened the literature, extracted the data and evaluated the risk of bias according to the criteria, Meta-analysis was carried out with RevMan 5.4 software.ResultsA total of 11 studies were included, including 1216 patients. Meta-analysis showed that, compared with parenteral nutrition, mixed nutrition can improve the levels of transferrin, serum albumin, prealbumin and lymphocyte counts in patients with esophageal cancer after surgery, shorten the time of anal recovery of exhaust, defecation and hospital stay after surgery, and reduce the incidence of pulmonary infection, abdominal distension, incision infection and anastomotic fistula, with statistical significance between the two groups (P &lt; 0.05). The heterogeneity of individual results in this study is relatively high, the analysis comes from clinical heterogeneity, and the publication bias is analyzed through Funnel plot. Taking the incidence of lung infection as an example, the results are evenly distributed on both sides of the Funnel plot, and the publication bias has little impact on the results of the study.ConclusionCompared with parenteral nutrition, mixed nutrition can improve the prognosis of postoperative patients with esophageal cancer and reduce the incidence of related adverse events.