bluuebunny/crossref_metadata_2025_split huggingface dataset:
Dynamics-Based Control and Path Planning Method for Long-Reach Coupled Tendon-Driven Manipulator
Authors: Takata Atsushi ,   Editorial Office, Endo Gen 
Published: February 2024

The Fukushima power station in Japan was affected by a major earthquake and tsunami in March 2011, inspecting the primary containment vessel remains difficult due to high radioactivity.	Long-reach robot arms are useful in inspecting such hazardous environments,	and a coupled tendon-driven mechanism enables realizing a long, light-weight, and thin manipulator.	However, high elastic elongation of tendons due to gravity may lead to unstable joint control.	In this paper, we introduce dynamics-based control as a feasible strategy for a long-reach tendon-driven robotic arm.	Additionally, a planning method to identify the joint angle path ensuring stability is proposed.	Considering stability analysis, the potential due to the tendon elasticity and gravity is evaluated and used as an index of joint stability.	The rapidly exploring random tree is used as the planning algorithm.	The effectiveness of the proposed method was demonstrated through the successful manipulation of a 5-kg payload by a 10-m long robotic arm.
Determination of the Thickness and Fracture Toughness of Shale Interfacial Transition Zone Near Various Micromineral Aggregates Using Nano-Scratch Tests
Authors: Nie Yuanxun , Wu Bisheng , Zhang Guangqing , Zhang Li , Li Shiyuan , Yang Liu , Liu Zhaoyang 
Published: February 2024

Summary
Heterogeneously distributed micromineral aggregates (MMAs) are common in shale reservoirs. The interfaces between these MMAs and the surrounding minerals significantly affect fracture propagation behaviors during shale oil exploitation. In this paper, the concept of interfacial transition zone (ITZ) between the MMAs (e.g., striped barite, pyrite, calcite, apatite blocks, and bedding plane) and the surrounding mineral in shale is introduced. Due to the small thickness of the ITZ, its thickness and mechanical properties are very difficult to determine by traditional standard methods. To address this issue, this paper proposes a method combining nano-scratch tests, scanning electron microscopy (SEM), and quantitative evaluation of minerals by SEM (QEMSCAN) techniques to investigate the thickness and fracture toughness of the ITZ near typical MMAs. The results show that the thickness of the ITZ determined by the transverse force FT and scratch depth (-d2) varies from 3.2 μm to 17.3 μm. In addition, the fracture toughness of both MMAs and ITZs is characterized by high heterogeneity ranging from 0.1 MPa·m0.5 to 2.1 MPa·m0.5. Moreover, a formula evaluating the fracture toughness of the ITZ is proposed taking into account the type and content of minerals in the ITZ. A strong linear relationship is observed between the thickness of the ITZ and the average fracture toughness ratio. In addition, a relationship is established between the fracture toughness of the ITZ and MMAs, and an evaluation equation is derived. This study is helpful for understanding the characteristics (i.e., mainly thickness and fracture toughness) of the ITZ within shales.
PPI-hotspotID: A Method for Detecting Protein-Protein Interaction Hot Spots from the Free Protein Structure
Authors: Chen Yao Chi , Sargsyan Karen , Wright Jon D , Chen Yu-Hsien , Huang Yi-Shuian , Lim Carmay 
Published: February 2024

Abstract

Experimental detection of residues critical for protein-protein interactions (PPI) is a time-consuming, costly, and labor-intensive process. Hence, high-throughput PPI-hot spot prediction methods have been developed, but they have been validated using relatively small datasets, which may compromise their predictive reliability. Here, we introduce PPI-hotspotID, a novel method for identifying PPI-hot spots using the free protein structure, and validated it on the largest collection of experimentally confirmed PPI-hot spots to date. We show that PPI-hotspotID outperformed FTMap and SPOTONE, the only available webservers for predicting PPI hotspots given free protein structures and sequences, respectively. When combined with the AlphaFold-Multimer-predicted interface residues, PPI-HotspotID, yielded better performance than either method alone. Furthermore, we experimentally verified the PPI-hot spots of eukaryotic elongation factor 2 predicted by PPI-hotspotID. Notably, PPI-hotspotID unveils PPI-hot spots that are not obvious from complex structures, which only reveal interface residues, thus overlooking PPI-hot spots in indirect contact with binding partners. Thus, PPI-hotspotID serves as a valuable tool for understanding the mechanisms of PPIs and facilitating the design of novel drugs targeting these interactions. A freely accessible web server is available at https://ppihotspotid.limlab.dnsalias.org/ and the source code for PPI-hotspotID at https://github.com/wrigjz/ppihotspotid/.
Stingless bee, Tetragonula iridipennis as a pollinator in Bell pepper, Capsicum annum under protected cultivation
Authors: N Rakshitha T 
Published: February 2024

Abstract
Stingless bees are common visitor to flowering plants in the tropics, and play a vital role as a pollinator both in open and closed environment. The present study was carried out to know the efficiency of stingless bee, Tetragonula iridipennis Smith on bell pepper, Capsicum annum cultivated under greenhouses during two seasons, summer (2021) and winter (2021-2022). At the time of flower initiation three stingless bee colonies were introduced inside the greenhouse. The peak activity of outgoing foragers recorded at 11.00 h to 12.00 h (12.90 bees/m2/10 min) during summer. In winter, activity of bees was maximum at 11:00 h to 12:00 h (11.35 bees/m2/10 min). The floral handling time of bees on flower in both the seasons, irrespective of the hours in a day, the maximum flower handling time was observed in the afternoon hours (44.60 s/flower) compared to forenoon hours (20.57 s/flower). Even in often cross pollinated bell pepper significant increase in number of fruits/plant (10.40 and 8.98), percentage of fruit set (90.04 % and 81.86 %), yield/plant (0.71 g and 0.46 g), fruit length (7.38 mm and 6.50 mm), fruit girth (22.86 mm and 19.43 mm), fruit weight (98.38 g and 83.08 g), TSS (5.20 % and 4.52 %), ascorbic content (93.64 mg/100 g and 89.15 mg/100 g) and moisture content (95.37 % and 40.93 %) was recorded between bee pollinated and control plots, respectively.
Kinetics of Organic Matter Removal in Olive Mill Wastewater and Cheese Whey Effluent using Microfiltration Membrane
Authors: Akdemir Ezgi Oktav 
Published: February 2024

Abstract

In this study, a laboratory-scale microfiltration membrane system was operated with olive oil industry wastewater (OMW) and cheese whey effluent (CWE) with chemical oxygen demand (COD) concentrations of 54 and 65.6 g/L at flow rates (Q) of 100, 150, and 200 L/h, pressures of 1 and 2 bar, filtration times considered as four different hydraulic retention time (q) of 30, 60, 90, and 120 min, respectively. COD removal efficiencies decreased with decreasing q from 120 min to 30 min and increasing pressure. In this study, mathematical models such as first-order kinetics, Grau second-order, and Modified Stover-Kincannon models were applied to determine the organic matter removal kinetics of the microfiltration membrane system. The model’s kinetic parameters were determined by linear regression using the experimental data. The predicted effluent COD concentrations were calculated using the kinetic constants. Grau second-order and Modified Stover-Kincannon models were found to be more consistent with the observed data. Moreover, the correlation coefficient (R2) obtained for the experimental and predicted effluent COD concentration also confirmed the suitability of the kinetic models and showed that the models can be used in the kinetics of organic matter removal in microfiltration membrane system design, thus predicting the behavior of the membrane for treating olive oil industry wastewater and cheese whey effluent. The experimental results obtained in this study are expected to be used as a reference for the determination of organic matter removal kinetics in membrane systems.
Stability analysis of spherical pendulum with rotational spatial vibrating suspension point
Authors: Luo Yan , Sheng Kaicheng 
Published: February 2024

Abstract
We consider a spherical pendulum whose suspension point performs high-frequency spatial vibrations. Dynamics of this pendulum can be described by averaging of its Hamiltonian over phases of vibrations. We impose conditions on vibrations such that that the averaged Hamiltonian has a rotational symmetry. Under these conditions we present a bifurcation diagram for the phase portraits of the averaged system. We show numerical simulations of different examples of vibrations. Bifurcation of phase portraits of spherical physical pendulum with vibrating suspension point are considered as well.
Causal associations between human gut microbiota and Multiple Myeloma: a mendelian randomization study
Authors: Zhang Jingtao , Hu Minhua , Liu Shitao , Zeng Wenxing , Zhou Qishi 
Published: February 2024

Abstract

Background: Numerous clinical studies have indicated a close connection between the human gut microbiome and multiple myeloma, yet the presence of a causal genetic link between them remains unclear. This study employs a two-sample Mendelian Randomization (MR) approach to assess the potential causal relationship between these two factors.
Methods:We used genome-wide association study (GWAS) statistics for the human gut microbiome obtained from the MiBioGen database, and multiple myeloma data from the UK Biobank (UKB). The primary analysis was conducted using the inverse variance weighted (IVW) method for two-sample MR to assess the causal relationship between the gut microbiome and multiple myeloma. Sensitivity analyses were performed to ensure the robustness of the results.
Results:Our findings, predominantly based on the IVW method, support a causal relationship between six gut microbial taxa and multiple myeloma. We observed positive associations with increased risk of multiple myeloma for Anaerotruncus from the human colon (p=0.033) and the Bilophila genus (p=0.033), suggesting these microbiota may elevate the risk of the disease.
Conversely, negative correlations potentially related to reduced risk were found for the Slackia genus (p=0.022), Victivallis genus (p=0.046), Butyrivibrio genus (p=0.044), and Ruminiclostridium5 genus (p=0.032). No reverse causality was detected between multiple myeloma and the six specific gut microbial taxa.
Conclusion:Our team pioneered a Mendelian Randomization study on the causal relationship between specific gut microbiota and multiple myeloma, providing meaningful insights into the potential mechanisms from a genetic perspective. This research offers valuable references for the early prevention of multiple myeloma and the improvement of disease progression.
An Experimental Study on Oxygen Assisted Plasma Air Cutting of Low Carbon Steel
Authors: Petare Anand C. , Khan Anas Ullah , Madhukar Yuvraj K 
Published: February 2024

Abstract

Air plasma cutting technology is widely used for cutting complex profiles, geometrics, shapes, and sections in electrically conducting materials at high speed. In this experimental research, oxygen was introduced along with compressed air during plasma air cutting of 10 mm thick C-20 carbon steel plates and their effect on cut surface quality was studied. A total of twenty experiments with compressed air were performed using a full-factorial design of experiments to identify the optimum ranges of process parameters. Further, based on the obtained results from preliminary experiments, twenty experiments were designed using a central composite design (CCD) approach of response surface method (RSM) using compressed air and a mixture of compressed air and oxygen. The cut surface quality was analysed for both conditions in terms of kerf width, dross height, bevel angle, surface roughness, maximum cutting temperature and heat-affected zone (HAZ). A comparative study between compressed air plasma cutting and oxygen assisted compressed air plasma cutting reveals that the addition of oxygen with compressed air improves the arc quality of plasma, which consequently reduced cutting time, kerf width, dross height, and surface roughness of the work materials. The microstructure study of both the cut surfaces reveals that the addition of oxygen with compressed air reduced the length of HAZ significantly compared to compressed air plasma cutting. The outcome of this study would be beneficial for the researcher and engineers working in the area of plasma-assisted cutting of metals.
New Glycosyltransferase RpUGT2 from Rheum palmatum involved in the flavonoid glycoside Biosynthesis
Authors: Zou Jianzhen , Zou Jing , Zhang Shiwen , Zhang Gang , Liu Mengmeng 
Published: February 2024

Abstract
Uridine diphosphate-dependent glycosyltransferases (UGTs) serve as key mediators in the glycosylation of plant metabolites, thereby inducing alterations in their physicochemical properties and bioactivities. Particularly, flavonoid glycosides are synthesized from aglycones through reactions catalyzed by typical UGTs. In our present investigation, we successfully cloned a novel UGT, RpUGT2, originating from Rheum palmatum, a highly regarded traditional Chinese herb known for its abundant genetic diversity. Sequence alignment and phylogenetic analysis indicated the close phylogenetic proximity of RpUGT2 to Vitis vinifera. The recombinant RpUGT2 protein, produced heterologously in Escherichia coli, displayed robust catalytic activity towards a spectrum of flavonoids. Mutational analyses revealed that specific amino acid sequence modifications could result in the loss of enzymatic activity in RpUGT2. This study has thus provided potential candidate genes, RpUGT2, for prospective applications in the metabolic engineering of flavonoid compounds in plants.
Intraovarian Injection of 3D-MSC-EVs-ECM Gel Significantly Improved Rat Ovarian Function After Chemotherapy
Authors: Zhang Yaping , Li Dong , Han Yi , Wu Min , Zhang Shule , Dong Na , Ma Huixian , Liu Linghong , Ju Xiuli 
Published: February 2024

Abstract

Background
Restoring the function of the ovary is important for chemotherapy-induced ovarian failure (COF) patients. Stem cell and extracellular vesicles (EVs) therapy show promise but need further improvement.
Methods
Human umbilical cord mesenchymal stem cells (hUC-MSCs) were primarily cultured and further three-dimensional (3D) cultured using an ultra-low attachment surface method. The expression levels of nutritional cytokines and immunomodulatory and stemness-related genes of 3D-cultured hUC-MSCs were analyzed. EVs were isolated by ultracentrifugation and characterized. Ovaries were decellularized with sodium dodecyl sulfate to obtain extracellular matrix (ECM). Lyophilized EVs from three-dimensional (2D) or 3D hUC-MSCs were mixed with ECM to prepare the 2D/3D-MSC-EVs-ECM gels. The therapeutic effect of the MSC-EVs-ECM gel on cyclophosphamide (CTX) -treated rats was analyzed through various tests. RNA sequencing was used to analyze the expression changes of genes before and after treatment.
Results
After culturing in ultra-low attachment dishes, hUC-MSCs aggregated into spheroids and significantly upregulated the expression levels of immunomodulatory and stemness-related genes. The total EVs yield was also upregulated (5.6-fold) after 3D culture. The cell viability of CTX-treated ovarian granulosa cells (OGCs) was significantly rescued by coculture with the 3D-MSC-EVs-ECM gel. Hormones indicative of ovarian function, AMH, E2, and FSH, were recovered in both the CTX + 2D-MSC-EVs-ECM gel group and the CTX + 3D-MSC-EVs-ECM gel group, while the apoptosis-related protein Bax was significantly downregulated. The 3D-MSC-EVs-ECM gel was more effective than the 2D-MSC-EVs-ECM gel. Significantly differentially expressed genes, such as Hbb-b1, Gpd1, and Sirpa, were detected by RNA sequencing. Hbb-b1 was increased in the ovaries of CTX-treated rats, and this increase was attenuated by injecting the 2D/3D-MSC-EVs-ECM gel. Gpd1 was increased after CTX treatment, and this increase was reversed by the 3D-MSC-EVs-ECM gel. Sirpa was decreased in the ovaries of CTX-treated rats, and this decrease was attenuated by injecting the 3D-MSC-EVs-ECM gel.
Conclusions
Our study demonstrated that the 3D-MSC-EVs-ECM gel is an efficient strategy for the recovery of ovarian function in CTX-induced ovarian failure.
Leveraging the Histidine Kinase-Phosphatase Duality to Sculpt Two-Component Signaling
Authors: Möglich Andreas , Meier Stefanie , Multamäki Elina , Ranzani Américo , Takala Heikki 
Published: February 2024

Abstract

Bacteria need to constantly read out their environment for the rapid adaptation to variable conditions. This crucial need is most frequently served by two-component systems (TCS) which decode environmental stimuli into intracellular responses. As one component, sensor histidine kinases (SHK) control the phosphorylation status of the second component, i.e., the response regulator (RR), which in turn determines the downstream responses. These responses can be highly stringent, acute, and sensitive as SHKs commonly exert both kinase and phosphatase activity towards their RRs. With a bacteriophytochrome TCS as a paradigm, we here interrogate how this catalytic duality underlies the signal responses and their reprogramming. Derivative systems exhibit tenfold enhanced sensitivity to red light, owing to an altered balance between the elementary kinase and phosphatase activities. Modifications of the linker intervening the SHK sensor and catalytic entities likewise tilt this balance and provide novel TCSs with hitherto unavailable, inverted output that increases under red light. Not only do the derivative TCSs support novel applications in synthetic biology and optogenetics, but also, they showcase how deliberate perturbations of the kinase-phosphatase duality underpin the rapid exploration of novel signal-response regimes. Arguably, these aspects equally pertain to the engineering and the natural evolution of TCSs.
Identification of apoptosis-related biomarkers of apoptosis in pulpitis based on biological informatics
Authors: Huang Xiaoshan , 李 霞 
Published: February 2024

Abstract

Background Pulpitis (PPS) is a dental disease caused by the destruction of dental hard tissue around the dental pulp. Studies have confirmed that apoptosis has a role in the production of PPS. Hence, it was vital to screen apoptosis related biomarkers for PPS. Methods To identify differentially expressed genes (DEGs) in GSE77459, we conducted a differential expression analysis (normalversusPPS). Then, apoptosisrelated differential expression genes (AR-DEGs) were got via overlapping DEGs and apoptosis related genes (ARGs). The five algorithms of cytoHubba in protein-protein interaction (PPI) network and receiver operating characteristic (ROC) were applied to screen apoptosis related biomarkers. Subsequently, we further conducted gene functional enrichment and immune microenvironment analyses for these biomarkers. We finally verified the expression in clinical tissue samples by RT-qPCR. Results A sum of 4,089 DEGs were obtained between PPS and normal groups. Soon afterwards, 19AR-DEGs were screened by the intersection of DEGs and ARGs. Moreover, we got 5 apoptosis related biomarkers via five machine learning algorithms, includingTNFSF10,BIRC3,IL1A,NFKBIAandCASP10.We found that these three biomarkers participated immune-related processes ‘immunoglobulin complex’. In additional, we discovered thatTNFSF10was correlated with Neutrophil and MAIT in immune microenvironment of PPS. In agreement with the results of the public database data analysis, the expression ofTNFSF10,BIRC3,IL1A,NFKBIAandCASP10was markedly over-expressed in clinical PPS samples versus normal samples. Conclusion Overall, we obtained five apoptosis related biomarkers (TNFSF10,BIRC3,IL1A,NFKBIAandCASP10) associated with PPS, which laid a theoretical foundation for the treatment of PPS.
Extraction and Analysis of Surface Quality Characteristics of Turning Workpieces Based on Finite Element Methods
Authors: Chen Taoming , Li Chun , Zou Zhexiang , Han Qi , Gu Fengshou , Ball Andrew D 
Published: February 2024

Abstract
Selecting appropriate cutting parameters can enhance surface quality and extend component lifespan. In addressing challenges such as prolonged duration and low efficiency in multi-parameter turning experiments, constructing precise finite element models is the primary task. Subsequently, to obtain comprehensive distributions of the cutting force and temperature under various cutting parameters, an orthogonal turning experiment was designed, and numerical simulations were conducted. To acquire the surface roughness information of the machined surface, image processing techniques were introduced, encompassing surface mesh calibration, workpiece edge extraction, and edge fitting, with the aim of calculating surface roughness values based on the results of finite element simulation. An in-depth exploration of the interrelationships between the cutting parameters and cutting force, turning temperature, and surface roughness was conducted through range analysis and multiple-factor linear regression analysis. Consequently, a multivariate regression model was developed to address this relationship. Finally, the practical feasibility of the proposed method was verified through turning experiments. This study establishes a foundation for constructing linear regression models between workpiece surface quality and cutting parameters, and demonstrates the innovative application of image processing techniques to overcome the difficulties in obtaining and measuring workpiece surface quality.