bluuebunny/crossref_metadata_2025_split huggingface dataset:
IL‐27 produced during acute malaria infection regulates Plasmodium‐specific memory CD4+ T cells
Authors: Macalinao Maria Lourdes , Inoue Shin‐Ichi , Tsogtsaikhan Sanjaadorj , Matsumoto Hirotaka , Bayarsaikhan Ganchimeg , Jian Jiun‐Yu , Kimura Kazumi , Yasumizu Yoshiaki , Inoue Tsuyoshi , Yoshida Hiroki , Hafalla Julius , Kimura Daisuke , Yui Katsuyuki 
Published: October 2023

AbstractMalaria infection elicits both protective and pathogenic immune responses, and IL‐27 is a critical cytokine that regulate effector responses during infection. Here, we identified a critical window of CD4+ T cell responses that is targeted by IL‐27. Neutralization of IL‐27 during acute infection with Plasmodium chabaudi expanded specific CD4+ T cells, which were maintained at high levels thereafter. In the chronic phase, Plasmodium‐specific CD4+ T cells in IL‐27‐neutralized mice consisted mainly of CD127+KLRG1− and CD127−KLRG1+ subpopulations that displayed distinct cytokine production, proliferative capacity, and are maintained in a manner independent of active infection. Single‐cell RNA‐seq analysis revealed that these CD4+ T cell subsets formed independent clusters that express unique Th1‐type genes. These IL‐27‐neutralized mice exhibited enhanced cellular and humoral immune responses and protection. These findings demonstrate that IL‐27, which is produced during the acute phase of malaria infection, inhibits the development of unique Th1 memory precursor CD4+ T cells, suggesting potential implications for the development of vaccines and other strategic interventions.
Evaluation of the antimicrobial potential of digested and undigested carob phenolic extracts: Impact on selected gut microbiota
Authors: Chaalal M. , Ydjedd S. , Chemache L. , López-Nicolás R. , Sánchez-Moya T. , Frontela-Saseta C. , Ros-Berruezo G. , Kati D.E. 
Published: October 2023

AbstractCarob pulp is a natural source of polyphenols, which have been shown to possess health benefits. These compounds play a crucial role in initiating, shaping, and modulating the gut microbiota. The objective of this study was to evaluate the impact of carob pulp phenolic extracts on nine specific groups of human gut microbiota before and after in vitro gastrointestinal digestion. The effects of pure gallic and coumaric acids were also tested. The results showed that the treated phenolic compounds exhibited inhibitory effects on the growth of most pathogenic bacteria. Gallic acid, in particular, demonstrated the most potent antimicrobial effect on Listeria monocytogenes, reducing its growth to below 5%. Staphylococcus aureus and Escherichia coli showed a growth reduction of up to 10%. Furthermore, both phenolic acids, before and after digestion, led to a slight reduction in E. coli O157:H7 numbers. Probiotic bacteria experienced minimal decrease following exposure to phenolic extracts. However, the growth of Lactobacillus casei ssp. rhamnosus was significantly inhibited by almost 50%. Interestingly, the in vitro digestion process exhibited a stronger antibacterial effect against pathogenic bacteria compared to probiotic bacteria. These results highlight the potential of carob phenolic extracts in modulating the intestinal microbiota, thereby offering interesting prospects for the development of diet-based health strategies.
Standardisation of low clinker cements containing calcined clay and limestone: a review by RILEM TC-282 CCL
Authors: Kanavaris Fragkoulis , Vieira Manuel , Bishnoi Shashank , Zhao Zengfeng , Wilson William , Tagnit Hamou Arezki , Avet Francois , Castel Arnaud , Zunino Franco , Visalakshi Talakokula , Martirena Fernando , Bernal Susan A. , Juenger Maria C. G. , Riding Kyle 
Published: October 2023

AbstractMaterials used in concrete construction are highly regulated through national standards that set minimum material reactivity, composition, and performance. Advances have shown that the combination of calcined clay and limestone fines in cementitious systems can have a synergistic reaction that allows for high levels of clinker replacement while maintaining adequate mechanical properties and durability. Recent modifications to national standards and codes have been made to allow for the use of calcined clay and limestone fines in concrete, albeit with some restrictions on use. Building codes also impose limits such as maximum water-to-cement/binder)-ratio, minimum strength, and minimum cement content as means to meet design service life requirements in lieu of measuring durability properties. This paper reviews the major standards and codes related to calcined clay materials and their use in concrete and suggests changes that could increase adoption and clinker replacement. It is hoped that this review will provide insights that can help facilitate the wider adoption of these materials in the construction industry as well as to identify potential changes in standards or creation of new ones which might be needed to enable the rapid widespread uptake of this promising technology.
Filtering eye-tracking data from an EyeLink 1000: Comparing heuristic, savitzky-golay, IIR and FIR digital filters
Authors: Raju Mehedi Hasan , Friedman Lee , Bouman Troy , Komogortsev Oleg 
Published: October 2023

In a prior report (Raju et al., 2023) we concluded that, if the goal was to preserve events such as saccades, microsaccades, and smooth pursuit in eye-tracking recordings, data with sine wave frequencies less than 75 Hz were the signal and data above 75 Hz were noise. Here, we compare five filters in their ability to preserve signal and remove noise. We compared the proprietary STD and EXTRA heuristic filters provided by our EyeLink 1000 (SR-Research, Ottawa, Canada), a Savitzky-Golay (SG) filter, an infinite impulse response (IIR) filter (low-pass Butterworth), and a finite impulse filter (FIR). For each of the non-heuristic filters, we systematically searched for optimal parameters. Both the IIR and the FIR filters were zero-phase filters. All filters were evaluated on 216 fixation segments (256 samples), from nine subjects. Mean frequency response profiles and amplitude spectra for all five filters are provided. Also, we examined the effect of our filters on a noisy recording. Our FIR filter had the sharpest roll-off of any filter. Therefore, it maintained the signal and removed noise more effectively than any other filter. On this basis, we recommend the use of our FIR filter. We also report on the effect of these filters on temporal autocorrelation.
Correlações entre perfil socioacadêmico, habilidades sociais e uso de substâncias psicoativas por estagiários da saúde
Authors: SILVA Meire Luci da , Dias Marcela Doescher , Correa Kelly Cristina , Rondina Regina Cassia , Silva Nilson Rogério 
Published: October 2023

Introdução: O estágio supervisionado na área da saúde é período de relacionar teoria e prática, podendo ser permeado de desafios e instabilidades. Objetivo: Investigar correlações entre variáveis socioacadêmicas, habilidades sociais e uso de substâncias psicoativas em estagiários da área da saúde. Metodologia: Pesquisa quantitativa e transversal. Amostra composta por estagiários da área da saúde de uma universidade pública paulista. Foram utilizados três instrumentos: Questionário socioacadêmico, Alcohol, Smoking and Substance Involvement Screening Test e Inventário de Habilidades Sociais. Para análise foram utilizados cálculos de estatística descritiva, protocolos dos instrumentos e Teste de Correlação de Pearson. Resultados: Participaram 113 estagiários, com média de idade de 22 anos, maioria do gênero feminino e solteira e, que já fizeram uso de substâncias. As substâncias mais utilizadas foram álcool, tabaco e maconha. Parte expressiva apresentou repertório de habilidades sociais deficitário, destacando-se os fatores: Enfrentamento e autoafirmação com risco e Conversação e Desenvoltura Social. Observaram-se correlações positivas: maconha e tabaco; maconha e autocontrole da agressividade; curso e conversação e desenvoltura social; correlações negativas: maconha e religião; lazer e conversação e desenvoltura social. Conclusão: Necessidade de programas de atenção à saúde do estagiário voltado a prevenção do uso de substâncias e treino de habilidades sociais.
Evolutionary dynamics of chromatin structure and duplicate gene expression in diploid and allopolyploid cotton
Authors: Hu Guanjing , Grover Corrinne , Vera Daniel , Lung Pei-Yau , Girimurugan Senthil , Miller Emma , Conover Justin , Ou Shujun , Xiong Xianpeng , Zhu De , Li Dongming , Gallagher Joseph , Udall Joshua , Sui Xin , Zhang Jinfeng , Bass Hank , Wendel Jonathan 
Published: October 2023

Abstract

Polyploidy is a prominent mechanism of plant speciation and adaptation, yet the mechanistic understandings of duplicated gene regulation remain elusive. Chromatin structure dynamics are suggested to govern gene regulatory control. Here we characterized genome-wide nucleosome organization and chromatin accessibility in allotetraploid cotton, Gossypium hirsutum (AADD, 2n=4X=52), relative to its two diploid parents (AA or DD genome) and their synthetic diploid hybrid (AD), using DNS-seq. The larger A-genome exhibited wider average nucleosome spacing in diploids, and this inter-genomic difference diminished in the allopolyploid but not hybrid. Allopolyploidization also exhibited increased accessibility at promoters genome-wide and synchronized cis-regulatory motifs between subgenomes. A prominent cis-acting control was inferred for chromatin dynamics and demonstrated by transposable element removal from promoters. Linking accessibility to gene expression patterns, we found distinct regulatory effects for hybridization and later allopolyploid stages, including nuanced establishment of homoeolog expression bias and expression level dominance. Histone gene expression and nucleosome organization are coordinated through chromatin accessibility. Our study demonstrates the capability to track high resolution chromatin structure dynamics and reveals their role in the evolution of cis-regulatory landscapes and duplicate gene expression in polyploids, illuminating regulatory ties to subgenomic asymmetry and dominance.
Distinct Molecular Profiles and Drug Vulnerabilities in
Pancreatic Metastases of Renal Cell Carcinoma
Authors: Juusola Matilda , Kallio Pauliina , Luck Tamara , Polso Minttu , Kumari Romika , Mikkonen Piia , Välimäki Katja , Malmstedt Minna , Ellonen Pekka , Pellinen Teijo , Heckman Caroline , Mustonen Harri , Puolakkainen Pauli , Alitalo Kari , Kallioniemi Olli , Mirtti Tuomas , Rannikko Antti , Pietiäinen Vilja , Seppänen Hanna 
Published: October 2023

Abstract

Pancreatic metastases (PM) of clear cell renal cell carcinoma (ccRCC) are rare, and little is known about them at patient level. The aim of this study was to define the patient-specific characteristics of PM-ccRCC and matching patient-derived cell (PDC) cultures.
We describe the genomic and single-cell transcriptomic profiles of five patients with PM-ccRCC as well as the functional drug sensitivities of their PDCs­­. First, the patients’ tumors depicted both common and novel somatic mutations and copy number alterations, which were maintained in their PDCs. Second, we show that PM-ccRCC transcriptomes differ from previously reported signatures for bone metastasis and primary ccRCC. Finally, we find both shared (e.g., PIK3, mTOR inhibitors) and patient-specific (e.g., EGFR, MEK1/2 inhibitors) drug sensitivities. We use integrated multi-omics to illuminate pathway-level deregulations explaining drug sensitivities, and to propose patient-specific druggable pathways. Altogether, our findings suggest enriched molecular profiles in PM-ccRCC and target pathways for PM-ccRCC treatment.
Research on User Review Analysis Based on Text Mining and ISM
Authors: Li Na , Liu Yutao , Chen Zhan 
Published: October 2023

Abstract
Effective keywords are extracted from the massive milk product user review data to construct thematic terms and explore the elemental influence relationships to assist manufacturers, and E-Commerce platforms in understanding user behaviour and preferences and further optimise product design and marketing strategies. By fusing two different text mining methods, TF-IDF and Word2vec, we explore the semantic relationships, then visualise the relevance of user reviews by drawing knowledge graphs with Neo4j, and finally, be able to explore the relationship between the themes of the mined reviews, ISM was used for a comprehensive evaluation, and the effectiveness of the method was verified on the Suning.com website dataset. The fusion of text mining and systematic analysis helps users to locate products quickly and precisely from the huge review information. The six elements of user reviews were categorized as Freshness of taste, Discounted prices, Logistics, Customer Repurchase, Product Packaging, Nutritional composition, and their element levels were divided into three layers. the first layer was Discounted prices, Customer Repurchase, and Logistics; the second layer was Product Packaging and Nutritional composition; and the third layer was Taste freshness.
Response mechanism of overexpress LBA0625 in Lactococcus lactis NZ9000 at freeze-drying process revealed by transcriptomic analysis
Authors: Sun Xiaoqian , Zeng Xiaoqun , Sun Jie , Wu Zhen , Du Qiwei , Guo Yuxing , Tu Maolin , Pan Daodong 
Published: October 2023

Abstract

Background:
Uridine diphosphate glucose pyrophosphorylase (UGPase) is an important cytosolic enzyme in polysaccharide synthesis, which plays an important role in the growth and development of bacteria. However, the regulatory mechanisms of UGPase in freeze-drying resistance are still unclear.
Results:
In this work, the LBA0625 gene of Lactobacillus acidophilus ATCC4356 which is able to induct of the production of UGPase-0625 were overexpressed in Lactococcus lactis NZ9000. And the physiological changes and transcriptomics of the strains were analyzed to determine possible survival mechanisms. The results showed that LBA0625 overexpression significantly enhanced survival rate from 57.14 % to 79.29% and increased UGPase activity by 48.35%, which indicating that there has a positive relationship between stress tolerance and LBA0625 overexpression. Transcriptome analysis showed that there were total 441 differentially expressed genes (DEGs) after LBA0625 overexpression, including 433 upregulated DEGs and 8 downregulated DEGs. Many of the upregulated DEGs are related to oxidative phosphorylation and exopolysaccharide to facilitate L. lactis NZ9000 biochemical reactions, eventually enhanced freeze-drying resistance.
Conclusions:
The results of this study suggested the mechanisms involved in overexpression of LBA0625 in L. lactis NZ9000 and would construct in the field of stress-resistant to lactic acid bacteria.
Dynamic Multi-Layered Image Encryption scheme using User Driven Chaotic Sequences
Authors: Mathivanan P. , Ashwini K , Aljaedi Amer , Bouye Mohamed , Bassfar Zaid 
Published: October 2023

Abstract

With technological advances, sharing sensitive information, such as multimedia data, especially images, is common. To protect the integrity of such data, advanced encryption algorithms are utmost necessary. The proposed encryption scheme introduces a novel approach that capitalizes on the distinct characteristics of users' authenticated usernames to dictate the sequence in which image blocks are encrypted. The methodology encompasses two key strategies. Initially, a set of four individual chaotic maps - Sin, Chebyshev, Logistic, and Gaussian - are employed for encryption. Also, the image blocks are encrypted with a novel 4D chaotic map. The process begins with segmenting an N×N×3 color image into its red, blue, and green constituents, each of size N×N. These constituents are further subdivided into four arrays, each sized (4×4) × (N/4) × (N/4). The encryption process for various image bands is based on the use of chaotic sequences generated by schemes 1 and 2. These resulting sequences serve as the fundamental encryption keys, guiding a variety of processes including both confusion and diffusion. The proposed encryption schemes, Scheme 1 and Scheme 2 were rigorously evaluated through extensive simulations, comparing their performance with a traditional algorithm. Both procedures demonstrated robustness against statistical analysis differential attacks and showcased NPCR and UACI values closely approximating ideal standards of 99.6 and 33.4, respectively. Notably, Scheme 2, employing the proposed 4D map, outperformed Scheme 1, which used four different chaotic maps, particularly in terms of NPCR and UACI. The schemes exhibited a significant key space of 2540, rendering decryption infeasible within an astronomical time frame of 9.449 × 10130 years. Further, entropy and correlation analysis validation revealed values close to 7.99 and 0, aligning with traditional algorithms' values. Additionally, pixel distribution analyses indicated uniformity along horizontal, vertical, and diagonal directions. The paper introduces an innovative encryption approach that capitalizes on user-specific characteristics and demonstrates superior security and performance compared to conventional methods.
Thermodynamic properties of propanol using DFT in the gas phase
Authors: Lopes Franklin dos Santos , Arouche TIAGO da Silva , Reis Arthur Felipe Vasconcelos Ferreira , Neto Abel Ferreira Gomes , Pereira Tais , de Almeida Ossalin , Junior Raul Nunes Carvalho , Costa Fabio Lopes Paranhos , Lima Romulo Costa , Costa Manuel , Costa José Franscisco Silva , Neto Antonio Maia de Jesus Chaves 
Published: October 2023

Abstract

This study aims to assess the impact of thermodynamic properties of propanols (propan-1-ol, propan-2-ol) and their isomers (2-methylpropan-1-ol and 2-methylpropan-2-ol) on fuel mixtures with gasoline, diesel, and kerosene. The evaluation is conducted using the Functional Density Theory, which determines various thermodynamic properties like specific molar heat at constant pressure, entropy, Gibbs free energy, and variation of formation enthalpy for calculating the heat of combustion. The simulation is performed using the functional hybrid B3LYP structures with bases 6–311 + + g (d, p) and 6-31g (d) through the software Gaussian 09W and the semi-empirical method PM3. Notably, 2-methylpropan-1-ol and 2-methylpropan-2-ol show higher energy gains, generating 13.38 KJ/g and 13.88 KJ/g more energy per unit mass compared to ethanol (22.73 KJ/g) and methanol (12.70 KJ/g), respectively. As the fraction of propanols increases by 10%, propan-1-ol with 33.49 KJ/g and propan-2-ol with 33.53 KJ/g exhibit the highest energy losses when compared to gasoline, which recorded 13.81 KJ/g and 13.77 KJ/g, respectively, under similar pressure and temperature conditions. The combustion of propan-1-ol shows the lowest values in all scenarios, particularly with diesel fuel at 11.31 KJ/g and kerosene at 12.71 KJ/g. Additionally, the study highlights the potential of these propanol-based mixtures as viable alternatives in the combustion phase, offering potential benefits in terms of energy efficiency and reduced emissions.
Pathomics models based on H&amp;E slides to predict the survival prognosis of patients with head and neck squamous cell carcinoma
Authors: Wang xinbin , Wang Fang , Liu Zhonglong , Li Hui , ONG Huishan , Guo Bing , Zhang Wenhao , Meng Zexiang , Qu Xingzhou , Xu Guangzhou , Chen Minjie , Yang X 
Published: October 2023

Abstract
Head and neck squamous cell carcinoma is the most common tumor of the head and neck region and has a low survival rate. This study innovatively proposes the use of pathomics to determine the correlation between clinicopathological and genomic data and patient prognosis, while exploring the underlying molecular mechanisms behind histology subtypes. In this study, hematoxylin and eosin slides were subjected to image segmentation and feature extraction, followed by unsupervised clustering analysis, to establish a predictive model for survival. Differential gene expression and pathways were explored based on the pathological subtypes, and transcriptome data from our hospital were used for validation. A total of 485 samples with complete pathological images and clinical information were included in this study, with 271 from the TCGA dataset and 214 from patients from our hospital with a 5-year follow-up. Thirteen pathomechanical features were selected based on different survival rates. In the training and validation set, there were significant differences in the pathological grade among the different pathological histology subtypes. In addition, different pathological classification also differed in early-stage tumor (Histologic grade G1/G2). A total of 76 differentially expressed genes were identified among the different pathological subtypes that were enriched in energy metabolism-related pathways. Visualization of mutation profiles for different pathomic subtypes revealed high mutation rates in PI3K-AKT, MAPK, and apoptosis pathways. Finally, using TCGA and our hospital's transcriptome data, we identified the differential expression of MTOR, COL9A1, and CD44 among pathological subtypes. The pathological histological subtype model had excellent predictive performance for survival. MTOR, COL9A1, and CD44 may regulate tumor differentiation and the immune microenvironment to ultimately drive pathological changes.
Computer-aided rational design strategy based on protein surface charge to improve the thermal stability of a novel esterase from Geobacillus jurassicus
Authors: Song Runfei , Zhang Jin , Zhu Mengyu , Lin Lin , Wei Wei , Wei Dongzhi 
Published: October 2023

Abstract
Objectives
Although Geobacillus are significant thermophilic bacteria source, there are no reports of thermostable esterase gene in G. jurassicus or rational design strategies to increase the thermal stability of esterases.
Results
Gene gju768 showed a highest similarity of 15.20% to esterases from Geobacillus sp. with detail enzymatic properties. Using a combination of Gibbs Unfolding Free Energy (∆∆G) calculator and the distance from the mutation site to the catalytic site (DsCα−Cα) to screen suitable mutation sites with elimination of negative surface charge, the mutants (D24N, E221Q, and E253Q) displayed stable mutants with higher thermal stability than the wild-type (WT). Mutant E253Q exhibited the best thermal stability, with a half-life (T1/2) at 65°C of 32.4 min, which was 1.8-fold of the WT (17.9 min).
Conclusion
Cloning of gene gju768 and rational design based on surface charge engineering contributed to the identification of thermostable esterase from Geobacillus sp. and the exploration of evolutionary strategies for thermal stability.