bluuebunny/crossref_metadata_2025_split huggingface dataset:
Effect of intercropping of paulownia and buckwheat on soil microbial biodiversity and enzymatic activity
Authors: Woźniak Małgorzata , Jama-Rodzeńska Anna , Gębarowska Elżbieta , Liszewski Marek , Siebielec Sylwia , Kaczmarek-Pienczewska Agata , Kucińska Jolanta , Gałka Bernard , Zalewski Dariusz , Bąbelewski Przemysław 
Published: July 2024

Abstract

The aim of this study was to capture microbiological changes in the soil environment during intercropping of paulownia with buckwheat using randomized block method experiment conducted at Wroclaw University of Environmental and Life Sciences in 2019–2022. The soil samples were characterized by measuring abundance of microorganisms determining the microbial and fungal community structure using Illumina MiSeq sequencing, the activity of dehydrogenase (DHA) and total glomalin-related soil proteins (T-GRSP). In addition, we assessed the buckwheat roots' colonisation by fungi, as well as yield and biometric traits of the plant. The calculated alpha indicators of the bacterial microbiome diversity and abundance show higher bacterial diversity in the intercropping samples, when compared to the control site. NGS (Next-Generation Sequencing) analysis showed that Actionobacteria, Proteobacteria and Acidobacteria were dominant in the microbiome in every variant of the experiment, regardless of the crop. By contrast, the mycobiome was dominated by fungi classified as the Ascomycota and Mortierellomycota. At the first sampling date (T1), intercropping sample analysis showed significant increase in DHA activity, but not in glomalin concentration. As a rule, the biometric traits’ values were higher when buckwheat was intercropped with paulownia compared to the control culture, both in terms of buckwheat yield and the total kernels of weight per plant.
Experimental study on Down-hole Dynamic Compaction to reinforce the deep slag miscellaneous fill foundation of highways
Authors: Chen Tao , Wang Weizhong , Guo Yancheng 
Published: July 2024

Abstract

Down-hole dynamic compaction is one of the important engineering technology to solve the problems of insufficient bearing capacity and uneven settlement after construction for deep slag miscellaneous fill foundation. Based on the deep slag miscellaneous fill foundation treatment project of an expressway, several groups of field tests were carried out, such as different pile forming processes and different pile spacing. Through the super heavy dynamic penetration test and foundation bearing capacity test, the reinforcement effect of down-hole dynamic compaction on the soil between piles of miscellaneous fill foundation is studied. The results show that the down-hole dynamic compaction has a significant reinforcement effect on the deep slag miscellaneous fill. After treatment, the compactness of the undisturbed slag miscellaneous fill changes from loose to medium dense or dense, and the soil compression modulus increases significantly. In addition, according to the compaction effect of soil between piles, the improvement effect of punching pile with small pile diameter on the bearing and deformation capacity of foundation is better than that of rotary digging pile with large diameter. Finally, deep dynamic compaction in the hole will have a certain disturbance on the shallow soil. In engineering applications, after the completion of the pile, the surface soil should be tamped to ensure the overall treatment effect of the foundation.
Nasal microbiota homeostasis regulates host anti-influenza immunity via the IFN and autophagy pathways in beagles
Authors: Geng Jinzhu , Dong Yuhao , Huang Hao , Wen Xia , Xu Ting , Zhao Yanbing , Liu Yongjie 
Published: July 2024

Abstract

Background
The respiratory tract houses a specialized microbial ecosystem, and despite the close anatomical and physiological ties between the oral, upper respiratory, and lower respiratory tracts, there is a substantial discrepancy in microbial quantity, spanning multiple orders of magnitude. The potential for commensal bacteria to prevent infection lies in their ability to regulate innate and adaptive host immune responses. Influenza virus predominantly targets and replicates within the epithelial cells of both upper and lower respiratory tracts. Given this, we hypothesize that the nasal-lung-microbe cross-talk plays a crucial role in influencing influenza susceptibility. In this study, we investigated viral presence, gene expression profiles of host, and the nasal and lung microbiota in a beagle dog model with antibiotic-induced nasal dysbiosis during influenza virus infection.
Results
In this study, using 16S rRNA sequencing, combined with comparative anatomy, transcriptomics and histological examination, we investigated viral presence, gene expression profiles of host, and the nasal and lung microbiota in influenza-infected beagles with antibiotic-induced nasal dysbiosis. Our data showed that dysbiosis of the nasal microbiome exacerbates influenza-induced respiratory disease and the epithelial barrier disruption, and impairs host antiviral responses in the nasal cavity and lung. Moreover, dysregulation of nasal microbiota worsens the influenza-induced disturbance in lung microbiota. Further, we identified one strain of Lactobacillus plantarum with a significant antiviral effect, which is exerted by activating the IFN pathway and modulating the impaired autophagy flux induced by influenza virus. Our data collectively indicate a close connection between the microbiomes of different ecological niches in the nasal and lung regions. This connection significantly influences subsequent host-microbe cross-talk, which was associated with an increased susceptibility to influenza.
Conclusions
Our investigation reveals that nasal microbiota dysbiosis not only increases host susceptibility to influenza virus infection but also contributes to the exacerbation of influenza-induced lung microbiota dysregulation. This intricate relationship extends to the microbiome composition, demonstrating correlations with critical factors such as host antiviral responses, inflammation thresholds, and mucosal barrier integrity. Together, these findings underscore the substantial impact of nasal microbiota dysbiosis on the overall outcome during influenza infections.
The symmetric 2-adic complexity of Tang-Gong interleaved sequences from Legendre sequence pair
Authors: Yan Feifei , Ke Pinhui , Chang Zuling 
Published: July 2024

Abstract

The symmetric 2-adic complexity of a class of Tang-Gong interleaved binary sequences with period 4N (where N ≡ 3 (mod 4)) constructed from the Legendre sequence pair is open (Yang et al., Designs, Codes and Cryptography, 2024, online first). By analysing the algebraic structure of the sequences and calculating the autocorrelation and crosscorrelation distributions of the column sequences in the interleaved structure, we completely determine the symmetric 2-adic complexity of the sequences. Our result shows that the symmetric 2-adic complexity of these sequences is equal to their 2-adic complexity.
An Adaptive Matrix-Based Evolutionary Computation Framework for EEG Feature Selection
Authors: Duan Dan-Ting , Sun Bing , Yang Qiang , Ye Long , Zhang Qin , Zhang Jun 
Published: July 2024

Abstract

Electroencephalogram (EEG) plays a significant role in emotion recognition because it contains abundant information. However, due to the highly correlated EEG channels, a lot of redundant EEG features exist, which not only potentially degrade the emotion recognition accuracy, but also bring high computational cost. To address this challenge, this paper proposes an adaptive matrix-based evolutionary computation (MEC) framework to select as a small number of informative EEG features as possible for effective emotion recognition. Unlike most existing EC algorithms that utilize vector-based operations, this framework leverages matrix-based operations to reduce feature redundancy and improve classification accuracy by dynamically adjusting the feature subset size according to the characteristics of the dataset. In such a way, the selection efficiency is largely improved. To verify the effectiveness and efficiency of this framework, the classical Genetic Algorithm (GA), the typical Particle Swarm Optimization (PSO) algorithm, and the classical Differential Evolution (DE) algorithm, are respectively embedded into this framework for EEG feature selection, and then evaluated on three widely used public EEG datasets for emotion recognition. Compared with several state-of-the-art EEG feature selection algorithms, the devised framework is much more effective in terms of the classification accuracy, the feature subset optimization, and the computational efficiency. In addition, the experimental results further reveal that the selected feature subsets are very different for different genders. This indicates the demand of gender-sensitive EEG feature selection for emotion recognition.
Tumor-specific CXCR6 positive precursor CD8 + T cells mediate tumor control in metastatic melanoma
Authors: Song Yang , Chen Ji , Zhang Yaqin , Wu Ning , Zhu Yongjun , Chen Gang , Miao Feng , Chen Zhiming , Wang Yiqing 
Published: July 2024

Abstract

Background
Adoptive cell therapy (ACT) mediates durable and complete regression of various cancers. However, its efficacy is limited by the long-term persistence of cytotoxic T lymphocytes, given their irreversible dysfunction within the tumor microenvironment. Herein, we aimed to establish an artificial lung metastasis model to examine T-lymphocyte subsets, in order to identify potential effective cell subsets for ACT.
Methods
A metastatic lung melanoma mouse model was established using OVA-expressing melanoma B16 cells. Flow cytometry analysis was conducted to examine the surface markers, transcription factors, and secreted cytokines of tumor-specific CD8+ T cells within metastatic tissues. The infiltrated cells were sorted by flow cytometry for in vitro tumor cell killing assays or in vivo cell infusion therapy combined with chemotherapeutic drugs and immune checkpoint blockade antibodies.
Results
Exhausted CD8+ T cells (Tex) exhibited high heterogeneity in metastatic tissues. Among Tex cells, the CXCR6− precursor cell showed certain memory characteristics, including phenotype, transcription factors, and maintenance, whereas the CXCR6+ subpopulation partially lost these traits. Moreover, CXCR6+ precursor cells effectively replenished effector-like Tex cells in metastatic tissues and exerted direct cytotoxicity against tumor cells. Notably, transferring these tumor-specific CXCR6+ precursor-exhausted T (Texp) cells into recipients induced a substantial regression of metastasis. In addition, these cells could respond to immune checkpoint blockade, which could better control tumor metastasis.
Conclusions
In our study, a subset of antigen-specific CXCR6-expressing Texp cells was observed within the metastatic tissue. The cells served as a crucial source of effector-like Tex cells and exerted direct cytotoxic effects on tumor cells. Adoptive transfer of CXCR6+ Texp cells effectively mitigated lung metastasis in mice. This study helps elucidate the role of Texp cells in metastasis, thereby offering novel insights into enhancing the efficacy and durability of immunotherapy.
ChromoGen: Diffusion model predicts single-cell chromatin conformations
Authors: Zhang Bin , Schuette Greg , Lao Zhuohan 
Published: July 2024

Abstract

Breakthroughs in high-throughput sequencing and microscopic imaging technologies have revealed that chromatin structures vary considerably between cells of the same type. However, a thorough characterization of this heterogeneity remains elusive due to the labor-intensive and time-consuming nature of these experiments. To address these challenges, we introduce ChromoGen, a generative model based on state-of-the-art artificial intelligence techniques that efficiently predicts three-dimensional, single-cell chromatin conformations \emph{de novo} with both region- and cell type-specificity. These generated conformations accurately reproduce experimental results at both the single-cell and population level. Moreover, ChromoGen successfully transfers to cell types excluded from the training data using just DNA sequence and widely available DNase-seq data, thus providing access to chromatin structures in myriad cell types. These achievements come at a remarkably low computational cost. Therefore, ChromoGen enables the systematic investigation of single-cell chromatin organization, its heterogeneity, and its relationship to sequencing data, all while remaining economical.
Microheater hotspot engineering for repeatable multi-level switching in foundry-processed phase change silicon photonics
Authors: Ocampo Carlos A. Rios , Sun Hongyi , Lian Chuanyu , Vásquez-Aza Francis , Kari Sadra Rahimi , Huang Yi-Siou , Restelli Alessandro , Vitale Steven A. , Takeuchi Ichiro , Hu Juejun , Youngblood Nathan , Pavlidis Georges 
Published: July 2024

Abstract

Nonvolatile photonic integrated circuits employing phase change materials have relied either on optical switching mechanisms with precise multi-level control but poor scalability or electrical switching with seamless integration and scalability but mostly limited to a binary response. Recent works have demonstrated electrical multi-level switching; however, they relied on the stochastic nucleation process to achieve partial crystallization with low demonstrated repeatability and cyclability. Here, we re-engineer waveguide-integrated microheaters to achieve precise spatial control of the temperature profile (i.e., hotspot) and, thus, switch deterministic areas of an embedded phase change material cell. We experimentally demonstrate this concept using a variety of foundry-processed doped-silicon microheaters on a silicon-on-insulator platform to trigger multi-step amorphization and reversible switching of Sb2Se3 and Ge2Sb2Se4Te alloys. We further characterize the response of our microheaters using Transient Thermoreflectance Imaging. Our approach combines the deterministic control resulting from a spatially resolved glassy-crystalline distribution with the scalability of electro-thermal switching devices, thus paving the way to reliable multi-level switching towards robust reprogrammable phase-change photonic devices for analog processing and computing.
Structure-Guided Design of Partial Agonists at an Opioid Receptor
Authors: Che Tao , Varga Balazs , Bernhard Sarah M , Daibani Amal El , Zaidi Saheem , Lam Jordy , Aguilar Jhoan , Appourchaux Kevin , Nazarova Antonina , Kouvelis Alexa , Eans Shainnel , Margolis Elyssa , Fay Jonathan , Pradhan Amynah , Katritch Vsevolod , McLaughlin Jay , Majumdar Susruta 
Published: July 2024

Abstract

The persistence of chronic pain and continuing overdose deaths from pain-relieving opioids targeting µ opioid receptor (µOR) have fueled the need for reliable long-term analgesics which use different targets and mechanisms. The δ opioid receptor (δOR) is a potential alternative target for non-addictive analgesics to alleviate chronic pain, made more attractive by its lack of respiratory depression associated with µOR agonists. However, early δOR full agonists were found to induce seizures, precluding clinical use. Partial δOR agonists may offer more controlled activation of the receptor compared to full agonists, but the development of such ligands has been hindered by uncertainty over the molecular mechanism mediating partial agonism. Using a structure-based approach, we explored the engagement of the sodium binding pocket in δOR and developed a bitopic ligand, C6-Quino, predicted to be a selective δOR partial agonist. Functional studies of C6-Quino revealed that it displayed δOR partial agonist activity at both G-protein and arrestin pathways. Its interaction with the sodium pocket was confirmed and analyzed using a single particle cryo-EM. Additionally, C6-Quino demonstrated favorable chemical and physiological properties like oral activity, and analgesic activity in multiple chronic pain models. Notably, µOR-related hyperlocomotion and respiratory depression, and δOR-related convulsions, were not observed at analgesic doses of C6-Quino. This fundamentally new approach to designing δOR ligands provides a blueprint for the development of partial agonists as safe analgesics and acts as a generic method to optimize signaling profiles of other Class A GPCRs.
Effect and clinical evaluation of postoperative intraperitoneal hyperthermic perfusion therapy on disease control and survival in patients with locally advanced colorectal cancer
Authors: wang Xue , Hu Xiang , Sun Yichiao , Star Sparkle 
Published: July 2024

Abstract

Objective
To investigate the effect of postoperative intraperitoneal hyperthermic perfusion (IPHP) combined with nutritional support on disease control and survival in patients with locally advanced colorectal cancer (CRC).
Methods
From August 2019 to August 2020, we arbitrarily divided 80 patients with locally advanced CRC into two groups. Each group contained 40 cases. In the control group, the patients were given simple nutritional support after operation, and in the observation group, the patients were cured with intraperitoneal thermal perfusion combined with nutritional support based on the control group. The clinical efficacy was observed. And the recurrence rate, metastasis rate, survival rate, serum thymidine kinase 1 (TK1), cyclooxygenase-2 (COX-2), soluble intercellular adhesion molecule-1 (ICAM-1) levels and life quality scores were compared before and after treatment.
Results
In the observation group, the objective remission rate (ORR) was 80.00%, and the disease control rate (DCR) was 97.50%. In the control group, the ORR was 57.50% and the DCR was 77.50%. There was a remarkable increase in ORR and DCR in the observation group (P < 0.05). Comparatively to the control group (35.00% and 40.00%), the observation group had the lower recurrence and metastasis rates (12.50% and 17.50%, respectively). As compared to the control group (55.00%), the observation group's survival rate was remarkably higher (77.50%) and its survival time was remarkably longer (77.50%). The serum levels of TKI, COX-2 and soluble ICAM-1 were remarkably lessened, and the serum levels in the observation group were lower (P < 0.05). After treatment, the scores of social, physical, role and cognitive functions of patients were remarkably elevated. In the control and observation groups, the incidence of adverse reactions was 27.50% and 5.00% respectively.
Conclusion
IPHP plus with nutritional support is effective in postoperative patients with locally advanced CRC, which can successfully enhance the life quality, reduce the rate of recurrence, prolong the survival time. The treatment approach has been highly safe, which may be relevant to the remarkable reduction of serum TK1, COX-2 and solution ICAM-1 levels.
Formability Assessment of 3D-Printed ABS Sheets Using Nakajima Test
Authors: Kami Abdolvahed , Fakhri Hamed , Hosseini Mehdi , Mirtorabi Hamid 
Published: July 2024

Abstract

This study explores the formability of acrylonitrile butadiene styrene (ABS) sheets produced by the fused filament fabrication 3D-printing process. The ABS sheets, fabricated with a diameter of 80 mm, were subjected to the Nakajima test. The investigation focused on assessing the impact of printing pattern (rectilinear, concentric, concentric/rectilinear), sheet thickness (0.8 mm, 1.4 mm, and 2 mm), and forming temperature (35°C, 70°C, and 90°C) on forming depth, utilizing a full factorial design of experiments comprising 27 conditions. Through the application of analysis of variance (ANOVA), a linear model for forming depth was derived, demonstrating high precision and reliability. Results indicate that as temperature increases, formability improves, reaching a maximum at 90°C with a rectilinear print pattern (15.95 mm depth). Conversely, the lowest forming depth (1.45 mm) occurred at 35°C with a concentric printing pattern. Sheet thickness showed minimal impact on forming depth, but forming force increased with thickness.
Rapid worldwide spread of 17MPLF spike insertion mutants (JN.1-JN.1.25, KP.1, KP.2, KQ.1, KR.1, XDD, XDP, XDK, XDQ subvariants) of omicron coronaviruses and spike gene 5’-end sequencing problem
Authors: Chakraborty Asit Kumar 
Published: July 2024

Abstract

We postulated a higher omicron JN.1/BA.2.86.1.1 coronavirus transmission due to unique 17MPLF spike insertion compensating 24LPP, 69HV, 145Y, 211N and 483V deletions [Journal of Future Medicine and Healthcare Innovation, 2(3):1–20, 2024]. After six months of our publication in Research Square preprint, I am updating our analysis of omicron spike insertion mutants. Database analysis suggested that JN.1-JN.1.25 subvariants had such insertion and such mutants were predominantly spreading worldwide. But we found some new coronavirus variants spread in the database like KP.1, KP.2, KP.1.1, KQ.1, XDD, XDK, XDP, XDQ, XDQ.1 and more which was contradictory to our hypothesis. Similarly, previously compared HV.1, EG.5.1.1, XBB.1.1-XBB.1.103, FL.1.5.1 like variants with no 17MPLF insertion but with termination codon mutation in the ORF8 gene, was diminishing comparatively in 2024. Surprisingly, the newly spreading subvariants also contained 17MPLF insertion in the spike. Originally, KP.1 was BA.2.86.1.1.11.1 while XDQ variant was a composite of BA.2.86.1 and FL1.5.1.1 suggesting JN.1, KP.1, XDK and XDQ subvariants were very similar. As the other genetic variations were found minimal, our hypothesis was fundamentally proved. On the other hand, critical search indicated omission of ORF8 protein in some 17MPLF insertion mutants likely diminishing viral load and disease severity but frequently found ORF7a deletions were not found. We also detected unique 32S deletion in the spike of few 17MPLF insertion mutants increasing to nine AAs spike deletion in JN.1 lineages. BLASTP search using oligopeptides at the new mutations (F59L, H146Q, R346T) and deletion (32S) boundaries demonstrated the penetration of insertion mutants in the USA, UK, Russia and Japan. Contrary to our hypothesis, Opentrons P (AN: PP889628, PP916105, PP938531, PP938533, PQ009953), Sadri N (AN: PP887470, PP88747474, PP887480, PP887481), Dragon J et al. (PP938086, PP938087), and Reev V et al (AN: PP871683, PP934270, PQ012208) reported JN.1 lineages without 17MPLF spike insertion.
Mortalidad materno-infantil entre las localidades de Bogotá D.C. según terciles de pobreza, 2011-2021
Authors: Montenegro Martínez Gino , Acosta Romo María Fernanda 
Published: July 2024

Objetivo: analizar la mortalidad materno-infantil entre las localidades de Bogotá D.C. según terciles de pobreza para el periodo 2011-2021. Metodología: diseño ecológico longitudinal con información retrospectiva. Los indicadores de salud se tomaron del Observatorio de Salud de Bogotá; los datos de pobreza monetaria corresponden a las mediciones de la Encuesta Multipropósito de Bogotá D.C. Se realizó un análisis del comportamiento de las tendencias mediante la regresión de Jointpoint. Para la medición de la desigualdad de los resultados en salud entre las localidades según terciles de pobreza, se utilizó el Índice Relativo de Desigualdad (IRD). Resultados: los indicadores de salud se comportan de manera distinta entre las agrupaciones de localidades por terciles de pobreza. Se identificaron desigualdades en el comportamiento de la mortalidad en menores de 5 años por terciles de pobreza en Bogotá D.C, los cuales se mantuvieron a lo largo del periodo de observación. Para el caso de la mortalidad perinatal, mortalidad infantil y mortalidad materna, se presentaron desigualdades para algunos años del periodo 2011-2021. Conclusiones: los resultados de este estudio permiten entender las dinámicas de las desigualdades en salud materno-infantil, a partir de lo cual, los profesionales de salud pueden desempeñar un rol activo en la formulación de políticas de salud y en la promoción de un enfoque integral, integrado y equitativo en salud.