bluuebunny/crossref_metadata_2025_split huggingface dataset:
In-depth analysis of erythrose reductase homologs in Yarrowia lipolytica
Authors: Szczepańczyk Mateusz , Rzechonek Dorota A. , Neuvéglise Cécile , Mirończuk Aleksandra M. 
Published: March 2023

Abstract
The unconventional yeast Yarrowia lipolytica produces erythritol as a response to osmotic stress. In this study, the array of putative erythrose reductases, responsible for the conversion of d-erythrose to erythritol, was analyzed. Single knockout and multiple knockout strains were tested for their ability to produce polyols in osmotic stress conditions. Lack of six of the reductase genes does not affect erythritol significantly, as the production of this polyol is comparable to the control strain. Deletion of eight of the homologous erythrose reductase genes resulted in a 91% decrease in erythritol synthesis, a 53% increase in mannitol synthesis, and an almost 8-fold increase in arabitol synthesis as compared to the control strain. Additionally, the utilization of glycerol was impaired in the media with induced higher osmotic pressure. The results of this research may shed new light on the production of arabitol and mannitol from glycerol by Y. lipolytica and help to develop strategies for further modification in polyol pathways in these microorganisms.
Frequency, Characteristics, and Preventability of Adverse Drug Reactions in Perioperative Neurosurgery: Analysis Over 11 Years
Authors: Kashiwazaki Daina , Tomita Takahiro , Hori Emiko , Akioka Naoki , Akai Takuya , Kuroda Satoshi 
Published: March 2023

Abstract

Introduction: Despite the importance of adverse drug reactions (ADRs), little is known about their role in perioperative neurosurgery. This study aimed to determine the prevalence of ADRs in perioperative neurosurgery in the past 11 years and clarify the characteristics, severity, preventability, and risk factors of ADRs.
Methods: Data for all patients who underwent neurosurgical procedures over an 11-year period were analyzed. During the study period, 3648 surgical procedures were performed for 2695 patients, including 1440 males and 1255 females. The average age was 57.3 ± 22.7 years(range, 0-100). Demographic and clinical information documented included sex, age, body mass index, medical history, allergic history, diagnosis, surgical method, suspected drugs, concomitant medications, and drug details. Multivariate logistic regression analyses were performed to identify independent parameters that were correlated with ADRs.
Results: In total, 467 ADRs (18.3% ADRs/all neurosurgical procedures) were experienced by 401 patients. Anticonvulsants were associated with the highest number of ADRs (16.0%), followed by antibiotics (14.7%). Patients with ADRs were older than patients without ADRs (P < 0.01). The total number of drugs in patients with ADRs was 8.8 ± 3.6, compared to 5.2 ± 2.4 for patients without ADRs (P < 0.01). There were no significant differences in sex, allergic history, severe renal dysfunction (eGFR < 30 ml/min/1.73 m2), hypertension, diabetes, urgency of surgery, and type of surgery. Multivariate analysis showed that a high total number of drugs (odds = 3.2; 95%CI 1.9–5.1) and older age (odds = 2.1; 95%CI 1.3–3.8) were independent risk factors for ADRs in perioperative neurosurgery.
Conclusion: The frequency of suspected and severe ADRs was higher than expected. Polypharmacy and older age were independent risk factors for ADRs in perioperative neurosurgery. To decrease ADRs during perioperative neurosurgery, polypharmacy must be discouraged, especially among older adult patients.
Transcription-replication interactions reveal principles of bacterial genome regulation
Authors: Yanai Itai , Pountain Andrew , Jiang Peien , Yao Tianyou , Homaee Ehsan , Guan Yichao , Podkowik Magdalena , Shopsin Bo , Torres Victor , Golding Ido 
Published: March 2023

Abstract
Organisms determine the transcription rates of thousands of genes through a few modes of regulation that recur across the genome1. These modes interact with a changing cellular environment to yield highly dynamic expression patterns2. In bacteria, the relationship between a gene’s regulatory architecture and its expression is well understood for individual model gene circuits3,4. However, a broader perspective of these dynamics at the genome-scale is lacking, in part because bacterial transcriptomics have hitherto captured only a static snapshot of expression averaged across millions of cells5. As a result, the full diversity of gene expression dynamics and their relation to regulatory architecture remains unknown. Here we present a novel genome-wide classification of regulatory modes based on each gene’s transcriptional response to its own replication, which we term the Transcription-Replication Interaction Profile (TRIP). We found that the response to the universal perturbation of chromosomal replication integrates biological regulatory factors with biophysical molecular events on the chromosome to reveal a gene’s local regulatory context. While the TRIPs of many genes conform to a gene dosage-dependent pattern, others diverge in distinct ways, including altered timing or amplitude of expression, and this is shaped by factors such as intra-operon position, repression state, or presence on mobile genetic elements. Our transcriptome analysis also simultaneously captures global properties, such as the rates of replication and transcription, as well as the nestedness of replication patterns. This work challenges previous notions of the drivers of expression heterogeneity within a population of cells, and unearths a previously unseen world of gene transcription dynamics.
Application of Micro-textured Surface Prepared by an Integrated Molding Process in Sustainable Turning of Titanium Alloy
Authors: Li Jinhua , Zhang Gaofeng , Wu Gaocan , Chen Bingxing 
Published: March 2023

Abstract

Titanium alloys have been widely used as an aerospace material owing to their excellent mechanical properties. However, ordinary tools can suffer from severe chip adhesion and surface abrasion when turning titanium alloys. To address these problems, micro-textured cutting tools have become a topic of significant research. Here, to improve the preparation process of textured tools, a novel tool prepared by an integrated molding process was proposed. The performance of this novel textured tool in terms of turning Ti-6Al-4V was investigated under dry conditions and minimal quantities of lubricant (MQL). Textured surfaces with four types of patterns and dimensions were used in the turning experiment to draw a comparison with traditional cutting tools. The results showed that the textured surface exhibited a uniform and smooth appearance with no obvious defects, indicating that the integrity of the textured surface was maintained. The combination of a micro-textured surface and the MQL method decreased the process temperature and cutting force. The narrower parallel type of textured tool exhibited the best performance. The process temperature reduced to 124 ℃ for the narrower parallel textured tool under MQL, decreasing by ~ 14.5% compared with the traditional tool; the lowest main cutting force and feed force were obtained for the narrower parallel textured tool, approximately 212 N and 171 N, respectively. Significant improvements in chip adhesion and tool wear were observed for the textured tool. Application of textured surface and MQL method are both decreased the adhesive scale layer area on the rake face of tools compared with ordinary tools.
Application of big data search based on collaborative filtering algorithm in cross-border e-commerce product recommendation
Authors: Wu Xiaoli , Wu Zhihao 
Published: March 2023

Abstract
With the deepening of cross-border e-commerce, the trend of buying and selling goods through the Internet is rising. It is necessary to establish a cross-border e-commerce platform that meets the above functions, and improve the ability to process big data in search. For example, the emergence of large amounts of data can not only help users make choices, but also increase the difficulty of users in choosing. At present, there are many problems in the big data search system in the market, such as inaccurate user personality analysis and low importance of product recommendation. E-commerce is developing rapidly in the new era, and new users are increasing every day. Many researchers invest in finding excellent cross-border e-commerce recommendation system as a business platform. The number of information in cross-border e-commerce shows a rapid growth pattern, and the rapid growth of data and information has seriously affected people's judgment. The big data search system based on collaborative filtering algorithm can meet the product recommendation system of cross-border e-commerce. The user matrix label is an attribute of construction. For the label quantification, the new user preference is the model of building the label, and the concept of weight is added to the label. The collaborative filtering algorithm works based on the created weight label.
Experimental and Theoretical investigations of the Inhibition of the Corrosion of Mild Steel in HCl by Synthesized Piperazin Derivatives
Authors: Singaravelu Ponnusamy. , Anand Balu , Loganathan S. , Eddy Nnabuk 
Published: March 2023

Abstract

In this study, two organic molecues namely, [4-(4-aminobenzoyl)-piperazin-1-yl)] furan − 2-yl) methanone (4-4-ABPFM) and 4-(4-aminophenylpiperazin-1-yl) furan-2-yl) methanone (4-4-APPFM) were synthesized and characterized using FTIR, UV-visible, thin layer chromatography, C-13 and proton NMR. The corrosion inhibition efficiencies of these molecules were tested using weight loss, polarization and AC impedance methods. Quantum chemical calculations (which included local selectivity, global reactivity and Monte Carlo simulation) were also implemented to complement the experimental data. The results obtained provided information confirmed that the synthesized compound has some inherent corrosion inhibition potentials due to the presence of aromatic rings, pi-electron systems, heteroatoms and corrosion structure parameters. The maximum inhibition efficiencies were 95 and 91% for 4,4-ABPFM and 4,4-APPFM respectively. The ideal fitness of the Langmuir isotherm with slope and R2 values approximating unity was also upheld. Theoretical calculation results showed strong accord to experimental values and supported higher efficiency for 4,4-ABPFM than 4,4-APPFM. Monte Carlo simulation showed that the adsorption energy is negative and also supported evidence drawn from the experiment, which is the spontaneous adsorption of the inhibitors on the metal surface.
Insights from a 3-Year Genomic Evolution of SARS-CoV-2 Shows a Predominance of Variants from Developing Countries
Authors: Abdelmounim ESSABBAR , Safae EL MAZOURI , Azeddine IBRAHIMI 
Published: March 2023

Abstract
Since the emergence of SARS-CoV-2, the virus has rapidly disseminated globally, with consequential genetic changes that have profoundly affected its pathogenicity, transmissibility, and immune evasion. Therefore, the pressing need to gain a comprehensive understanding of the genetic evolution and dissemination of this virus across diverse regions is paramount. In light of this, the present study aimed to investigate the spatial and temporal distribution of SARS-CoV-2 variants by leveraging genomic sequencing data.
We analyzed a representative dataset of 14,759 genomic sequences of SARS-CoV-2 obtained from 142 countries, spanning the period from January 2020 to January 2023. The findings showed that the early spread of certain SARS-CoV-2 lineages was geographically limited. However, the subsequent lifting of quarantine and travel restrictions facilitated the homogenization of the virus' genetic diversity across diverse regions. Moreover, our temporal analysis demonstrated that the lifespan of SARS-CoV-2 variants has been significantly truncated over time, with dominant strains frequently being outcompeted by more adaptive variants. We further observed that a significant proportion of newly emerged SARS-CoV-2 variants were identified in developing countries, particularly in sub-Saharan Africa, South America, and South Asia. Lastly, our results underscore the impact of weakened health systems, a high prevalence of immunocompromised individuals, and delayed reporting of these variants on the spread and severity of the virus in these regions.
Vegetable lignocellulosic residues and chitosan as valuable resources in the superabsorbent bio-aerogels development for food conservation
Authors: Sanchez Laura Mabel , Rincón Esther , Niza Jorge de Haro , Martín Ramón Morcillo , Espinosa Eduardo , Rodríguez Alejandro 
Published: March 2023

Abstract
Superabsorbent bio-aerogels were developed from TEMPO-oxidized cellulose nanofibers (isolated from vegetables lignocellulosic residues) and two different commercial chitosan reactants (low and high molecular weight) by polyelectrolyte complex formation at room temperature. Three different thickness values were considered, and two different aging times were employed, thus leading to twelve different bio-aerogels samples. Remarkably, no crosslink agents nor organic solvents were used. All the developed materials were characterized and deeply studied. The bio-aerogels components were strongly interacting through hydrogen bonding, leading to highly porous and stable materials able to absorb high amounts of water and soybean oil. Then, the specific tests to visualize the material’s potential use as food absorbent pads showed: i) they were able to absorb simulated food exudates under a specific pressure in higher quantities (≈ 4000%) than some commercial pads (≈ 1600%); ii) the materials have low to moderate antibacterial activities exposing better reduction effectiveness for Listeria monocytogenes than for Salmonella typhimurium; and iii) the antioxidant properties were in general low. In the light of all the results achieved, the bio-aerogels prepared from H-CH with an aging time of 24 h and whose thickness was around 2.1 mm (H-10g-24) were selected as the most appropriate for the desired application.
Insight into the effect of physicochemical properties on CO2 absorption behavior of imidazole anion-functionalized ionic liquids
Authors: Wang JIanni , He Yuxin , Chen Tingting , Xu Yingjie , Chen Bin 
Published: March 2023

Abstract
Three imidazole anion-functionalized ionic liquids (IFILs) with tributylethylphosphonium ([P4442]+) cation and imidazolate ([Im]−), 4-methylimidazolate ([4-MeIm]−), or 4-bromimidazolate ([4-BrIm]−) anions were prepared to study the effect of physicochemical properties on CO2 absorption behavior. Density (ρ), viscosity (η), speed of sound (u) of the studied IFILs were measured, and molecular volume (Vm), standard entropy (S0), lattice energy (UPOT), and isentropic compressibility coefficient (κs) were calculated accordingly. CO2 absorption behavior of [P4442][Im] at T = 313.15-333.15 K and p = 0.2 and 1 bar were investigated as an example. The results show that with the increase of temperature, ρ, η, u, and UPOT decrease, while Vm, S0, and κs increase, due to a decrease in electrostatic interaction correspondingly. The orders of ρ, u, η, Vm, and S0 values are as follows: [P4442][Im] < [P4442][4-MeIm] < [P4442][4-BrIm], while UPOT and κs are in reverse order. Interestingly, CO2 capture capacity of IFILs is approximately linear with η or κs. Due to low η and high κs, CO2 absorption capacity of [P4442][Im] is almost independent of temperature and partial pressure, as high as 0.90 mol CO2/mol IL at 333.15 K and 0.2 bar, indicating that [P4442][Im] has potential applications for CO2 absorption at high temperature and low pressure.
Phylogenetic diversity, distribution, and gene structure of the pyruvic oxime dioxygenase involved in heterotrophic nitrification
Authors: Tsujino Shuhei , Masuda Ryota , Shimizu Yoshiyuki , Azuma Yuichi , Kanada Yutaro , Fujiwara Taketomo 
Published: March 2023

Abstract
Pyruvic oxime dioxygenase (POD) is the enzyme that is involved in the heterotrophic nitrification process in Alcaligenes faecalis. Genes encoding POD were found in bacteria of the phyla Proteobacteria and Actinobacteria, and in fungi of the phylum Ascomycota, and their gene products were found to be active in recombinant experiments. No pod genes were found in the well-known heterotrophic nitrifying species such as Paracoccus and Bacillus, suggesting that heterotrophic nitrification in these bacteria proceeds without the involvement of POD. Phylogenetic analysis of amino acid sequences classified POD into three groups. Group 1 POD is mainly found in heterotrophic nitrifying Betaproteobacteria and fungi, and is assumed to be involved in heterotrophic nitrification. It is not clear whether group 2 POD, found mainly in species of the Gammaproteobacteria and Actinobacteria, and group 3 POD, found simultaneously with group 1 POD, are involved in heterotrophic nitrification. The genes of bacterial group 1 POD comprised a single transcription unit with the genes related to the metabolism of aromatic compound, and many of the genes group 2 POD consisted of a single transcription unit with the gene encoding the protein homologous to 4-hydroxy-tetrahydrodipicolinate synthase (DapA). POD may be involved not only in nitrification, but also in certain metabolic processes whose functions are currently unknown, in coordination with members of gene clusters.
Identification of cholesterol metabolism-related subtypes in Nonfunctioning Pituitary neuroendocrine tumors and analysis of immune infiltration
Authors: feng tians , Hou Pengwei , Fang Yi , Li Xinxiong , Li Ziqi , Wang Di , Chen Li , Lu Lingling , Lin Kunzhe , Mu Shuwen , Wang Shousen 
Published: March 2023

Abstract

Objective: This study aimed to investigate the role of cholesterol metabolism-related genes in nonfunctioning pituitary neuroendocrine tumor (NF-PitNETs) invading the cavernous sinus and analyze the differences in immune cell infiltration between invasive and noninvasive NF-PitNETs.
Methods: First, a retrospective analysis of single-center clinical data was performed. Second, the immune infiltration between invasive and noninvasive NF-PitNETs in the GSE169498 dataset was further analyzed, and statistically different cholesterol metabolism-related gene expression matrices were obtained from the dataset. The hub cholesterol metabolism genes in NF-PitNETs were screened by constructing machine learning models. In accordance with the hub gene, 73 cases of NF-PitNETs were clustered into two subtypes, and the functional differences and immune cell infiltration between the two subtypes were further analyzed.
Results: The clinical data of 146 NF-PitNETs were evaluated, and the results showed that the cholesterol(P=0.034) between invasive and noninvasive NF-PitNETs significantly differed. After binary logistic analysis, Cholesterol was found to be an independent risk factor for cavernous sinus invasion (CSI) in NF-PitNETs. Bioinformatics analysis found 3 immune cells between invasive and non-invasive NF-PitNETs were statistically significant in the GSE169498 dataset, and 34 cholesterol metabolism-related genes with differences between the two groups were obtained 12 hub genes were selected by crossing the two machine learning algorithm results. Subsequently, cholesterol metabolism-related subgroups, A and B, were obtained by unsupervised hierarchical clustering analysis. The results showed that 12 immune cells infiltrated differentially between the two subgroups. Chi-square test revealed that the two subgroups had statistically significance in the invasive and non-invasive samples (P=0.001). KEGG enrichment analysis showed that the differentially expressed genes were mainly enriched in the neural ligand–receptor pathway. GSVA analysis showed that the mTORC signaling pathway was upregulated and played an important role in the two-cluster comparison.
CONCLUSION: By clinical data and bioinformatics analysis, Cholesterol metabolism-related genes may promote the infiltration abundance of immune cells in NF-PitNETs and the invasion of cavernous sinuses by NF-PitNETs through the mTOR signaling pathway. This study provides a new perspective to explore the pathogenesis of cavernous sinus invasion by NF-PitNETs and determine potential therapeutic targets for this disease.
Rationally designed PMAP-23 derivatives with enhanced bactericidal and anticancer activity based on the molecular mechanism of peptide-membrane interactions
Authors: Lee Hyunhee , Shin Sung-Heui , Yang Sungtae 
Published: March 2023

Abstract
Antimicrobial peptides (AMPs) are a crucial component of the natural defense system that the host employs to protect itself against invading pathogens. PMAP-23, a cathelicidin-derived AMP, has potent and broad spectrum antimicrobial activity. Our earlier studies led us to hypothesize that PMAP-23 adopts a dynamic helix-hinge-helix structure, initially attaching to membrane surfaces through the N-helix and subsequently inserting the C-helix into the lipid bilayer. Here, we rationally designed PMAP-NC with increased amphipathicity and hydrophobicity in the N- and C-helix, respectively, based on the hypothesis of the interaction of PMAP-23 with membranes. Compared to the parental PMAP-23, PMAP-NC showed 2–8 fold improved bactericidal activity against both gram-positive and gram-negative strains with fast killing kinetics. Fluorescence studies demonstrated that PMAP-NC largely disrupted membrane integrity, indicating that efficiency and kinetics of bacterial killing are associated with the membrane permeabilization. Interestingly, PMAP-NC exhibited much better anticancer activity against tumor cells than PMAP-23 but displayed low hemolytic activity against human erythrocytes. Collectively, our findings suggest that PMAP-NC, with the structural arrangement of an amphipathic helix–hinge–hydrophobic helix that plays a critical role in rapid and efficient membrane permeabilization, can be an attractive candidate for novel antimicrobial and/or anticancer drugs.
Green Alternatives in Pharmaceutical and Bioanalytical Analysis of TDM Required Drugs: Procainamide
Authors: Ülgen Murat , Can Eylem Cemil , Dogan Aysegul , Akduman Nursabah Elif Basci 
Published: March 2023

Introduction:In drug analysis, using non-hazardous solvents instead of the ones harmful to humans and the environment is a green strategy to protect analysts and environmental health.Objective:Procainamide (PCA) is an antiarrhythmic drug requiring therapeutic drug monitoring (TDM) because of its narrow therapeutic window and serious side effects.Aim:The aim of this study is to develop validated green HPLC methods to be used in drug quality control and TDM analysis for PCA, thus indicating the further applicability in the analysis of TDM-required drugs, such as immunosuppressants, anti-cancer drugs, and psychiatric drugs.Methods:Human-friendly ethanol was selected as an organic solvent in the mobile phase. PCA was eluted from NUCLEODUR 100-5 C8 ec (5 μm, 150 x 4.6 mm) column by a mobile phase containing ethanol and 50 mM NaH2PO4 buffer (5:95, v/v). The mobile phase flow rate was 1.0 ml min-1, the column temperature was 35 °C, and the wavelength at the PDA detector was 278 nm.Results:Retention time for PCA was 5.0 min and 7.7 min for paracetamol as an internal standard (IS). In the green HPLC method for pharmaceutical analysis, the highest relative standard deviation (RSD) and mean recovery values were 1.32% and 98.89%, respectively. In the analysis of plasma, the sample preparation step was only smooth protein precipitation by ethanol. Thus, the bioanalytical method was fully green having a limit of detection (LOD) of 0.3 μg ml-1 and a limit of quantification (LOQ) of 0.8 μg ml-1. The therapeutic plasma concentration for PCA was reported in the range of 4–12 μg ml−1.Conclusion:As a result, the green HPLC methods developed and validated in this study were selective, accurate, precise, reproducible, and trustable and have the quality for the application in pharmaceutical and TDM analysis of PCA, thus encouraging green HPLC analysis of other TDM required drugs.