bluuebunny/crossref_metadata_2025_split huggingface dataset:
Diffusion-based Generative AI for Exploring Transition States from 2D Molecular Graphs
Authors: Kim Seonghwan , Woo Jeheon , Kim Woo Youn 
Published: May 2023

Abstract
The exploration of transition state (TS) geometries is crucial for elucidating chemical reaction mechanisms and modeling their kinetics. Recently, machine learning (ML) models have shown remarkable performance for prediction of TS geometries. However, they require 3D conformations of reactants and products often with their appropriate orientations as input, which demands substantial efforts and computational cost. Here, we propose a generative approach based on the stochastic diffusion method, namely TSDiff, for prediction of TS geometries just from 2D molecular graphs. TSDiff outperformed the existing ML models with 3D geometries in terms of both accuracy and efficiency. Moreover, it enables to sample various TS conformations, because it learned the distribution of TS geometries for diverse reactions in training. Thus, TSDiff was able to find more favorable reaction pathways with lower barrier heights than those in the reference database. These results demonstrate that TSDiff shows promising potential for an efficient and reliable TS exploration.
Factors affecting the penetration in microneedles and PLGA nanoparticle-assisted drug delivery: Importance of preparation and formulation
Authors: Lu Geng , Li Baohua , Deng Qiyi , Lin Luping , Liao Liqi , Li Xiaofang , Lu Zhufen , BAN JUNFENG 
Published: May 2023

Abstract
Purpose
Oral administration of the first-line antidepressant paroxetine (PAX) has certain limitations, including difficulty in reaching the brain due to oral absorption. Although there are many invasive and non-invasive strategies available to cross the blood–brain barrier (BBB), they run counter to long-term administration and convenience for patients.
Methods
We herein designed a simple PAX-loaded nanoparticle-integrated dissolving microneedles system (PAX-NP-DMNs), aiming to improve the bioavailability of PAX through the synergistic permeation-enhancing effect of microneedles (MNs) and nanoparticles (NPs).
Results
We assessed the NPs characteristics before and after MNs preparation and confirmed the successful construction of PAX-NP-DMNs based on differential scanning calorimetry, X-ray diffraction, and Fourier transform infrared spectroscopy. In the mechanical strength test, the addition of NPs increased the mechanical strength of dissolving MNs by 0.43 times and prolonged the release of PAX from 1 h to 48 h; PAX-NP-DMNs has over 40 times than PAX solution in the isolated skin penetration in permeability experiments. Moreover, PAX-NP-DMNs has good biocompatibility and does not cause adverse reactions.
Conclusion
Loading PAX into polylactic glycolic copolymer NPs and adding them into MNs can effectively improve the bioavailability of PAX and the mechanical strength problem of dissolving MNs. PAX-NP-DMNs can easily penetrate the skin to provide rapid and painless delivery without causing adverse effects, thus offering a more convenient and effective method for the treatment of central nervous diseases.
Molecular Detection of Leishmania spp.and blood source of female sandflies in theParque Estadual do Rio Doce, the municipality of Timóteo, Minas Gerais, Brazil
Authors: Souza Cristian Ferreira , Santos Carlos Alberto , Bevilacqua Paula Dias , Filho José Dilermando Andrade , Brazil Reginaldo Peçanha 
Published: May 2023

Abstract
Background Leishmaniasis is a group of diseases caused by protozoa of the Leishmania genus (Kinetoplastida: Trypanosomatidae) and transmitted by the bite of female sand fly insects (Diptera: Psychodidae: Phlebotominae). The present work was characterized as a descriptive study comparing two areas: a wild area where the Parque Estadual do Rio Doce (PERD) is located and another urban area, located in the municipality of Timóteo-MG (AUT) with a propose to identify the presence of Leishmania spp. and the blood source of collected female sand flies.Methods Sand flies were collected with CDC light trap, between September 2012 and February 2014.We used 19 traps in the Urban Area of ​​Timóteo and 12 in the Parque Estadual do Rio Doce. For molecular studies of Leishmania spp. DNA we used ITS1 gene and in the search of blood source, the CytB gene was used and positive samples were sequenced.Results In the municipality of Timóteo there are at least three species of Leishmania: Leishmania (Viannia) braziliensis, Leishmania (Leishmania) amazonensis and Leishmania (V.) guyanensis. Nyssomyia whitmani and Pressatia choti predominated in urban area and PERD, respectivelly, both species were positive for the presence of Leishmania braziliensis DNA. We found also the presence of blood of Gallus gallus (chicken) and Sus scrofa (pig) in sand flies, which helps to maintain the flies in the urban area of ​​the municipality.Conclusion The present study demonstrates that Leishmania braziliensis is the main agent of cutaneous leishmaniasis in the study area, with effective participation of Nyssomyia whitmani as a vector and boths Gallus gallus (chicken) and Sus scrofa (pig) are fundamental in maintaining the cycle in urban areas.
Growth patterns of Pseudomonas aeruginosa in milk fortified with chitosan and selenium nanoparticles during refrigerated storage
Authors: Atia Rehab M. , Mohamed Hamdi A. , ELRoos Nahla A. Abo , Awad Dina A.B. 
Published: May 2023

Abstract
Pseudomonas spp are considered the most common milk-associated psychotropic bacteria, leading to milk deterioration during storage so, our study aimed to study the growth behavior of Pseudomonas aeruginosa in milk after employing chitosan nanoparticles (CsNP 50, 25 and15 mg/100ml) and selenium nanoparticles (SeNP 0.5, 0.3 and 0.1mg/100ml) as a trial to control the bacterial growth in milk during five days of cooling storage. Our study relies on using ion gelation method and green synthesis for conversion chitosan and selenium to nanosized particles, respectively, we subsequently confirmed their size and shape using SEM and TEM. Depending on using Pseudomonas selective agar medium supplemented by glycerol for monitoring the bacterial growth along the cooling storage. Our findings reported that, both synthesized nanoparticles exhibit antibacterial activity in a dose dependent manner. Moreover, the uniform aggregated with average size 60 ± 5 nm CsNP50 could inhibit the P. aeruginosa survival growth to mean average 2.62 ± 1.18 log10cfu/ml in the fifth day of milk cooling storage, also it was noted that the hexagonal particles with average size 20 ± 5nm SeNP0.5 could inhibit 2.49 ± 11 log10cfu/ml in comparison to, the control P. aeruginosa milk group exhibited growth survival 7.24 ± 2.57 log10cfu/ml under the same conditions. As conclusion, in order to improve milk safety, we suggest employing chitosan and selenium nanoparticles.
Sub-classifying Neuroblastoma: A Comparative Study of Clinical Characteristics and Survival Outcomes in Neuroblastoma and Ganglioneuroblastoma
Authors: Wu Xiongwei , Wang Jianyong , Liu Yao , Dong Qian 
Published: May 2023

AbstractObjective:Neuroblastoma (NB) and Ganglioneuroblastoma (GNB) are the most common extracranial solid tumors in children, with different clinicopathological features and survival outcomes. The aim of this study is to compare the demographic, clinical features, and survival outcomes of patients with NB and GNB.Method:We retrospectively extracted data from patients with NB and GNB from the Surveillance, Epidemiology, and End Results (SEER) database between 2004 and 2019. We analyzed the demographic and clinical characteristics using Pearson’s chi-squared test or Fisher’s exact test. Kaplan-Meier curves were utilized to compare cancer-specific survival (CSS) and overall survival (OS) among different subgroups. Multivariable Cox proportional hazards regression analysis was used to estimate the independent prognostic factors for CSS and OS.Results:A total of 1,968 patients under 14 years of age were included in this study, of whom 1,609 (81.7%) were diagnosed with NB and 359 (19.3%) with GNB. The majority of GNB patients were over 2 years old (83.57%), while most NB patients were under 2 years old (58.42%). Survival analysis revealed that the OS of GNB patients was superior to that of NB patients. In addition, multivariate Cox regression analysis identified chemotherapy and tumor site as independent prognostic factors for GNB patients, while age, surgery, chemotherapy, tumor size, and tumor site were independent prognostic factors for NB patients.Conclusions:This study provides insights into the significant differences between NB and GNB in terms of demographic, clinical features, and survival outcomes. Our findings have important implications for informing clinical decision-making and providing more targeted therapeutic options for patients with these tumors. Further studies are necessary to validate our findings and explore the underlying biological mechanisms.
On the dynamic of discrete-time Rayleigh-Duffing oscillators
Authors: Khajoei Najmeh , Nia Mehdi Fatehi , Nurkanović Zehra 
Published: May 2023

Abstract
This paper investigates the dynamics of discrete-time Rayleigh-Duffing oscillator by applying the forward Euler's scheme. It is shown that the system undergoes Hopf bifurcation and flip bifurcation by using the center manifold theorem and bifurcation theory. Also, it is proven the system possesses chaotic behavior in the sense of Marotto's definition. We compute the Lyapunov exponents numerically to show sensitive dependence to initial conditions and chaotic behavior.
MSC Classification: 39A10 , 39A20 , 39A23 , 39A30 , 65L20
Effects of Clostridium autoethanogenum protein on growth performance, intestine and liver health of turbot Scophthalmus maximus during grow-out phase
Authors: Bai Nan , Li Qing , Pan Shihui , Qi Zezheng , Deng Wanzhen , Gu Min 
Published: May 2023

Abstract
Clostridium autoethanogenum protein (CAP) is an emerging protein source with several key advantages and it has investigated on juvenile turbot (9.13 g). However, it was indicated that fish growth stage is a decisive factor for CAP performance and the influence of CAP on turbot intestine health has not been reported. Thus, it is worth investigating the effects of CAP on turbot extensively. In the present study, a 67-day feeding experiment was conducted to evaluate the effects of CAP on turbot in the grow-out phase from growth performance, intestine and liver health. Six hundred and thirty turbot with an initial body weight of about 150 g were randomly divided into 6 groups, which were fed with fishmeal-based control diet or diet with CAP to replace 15%, 30%, 45%, 60% and 75% of fishmeal protein in control diet, respectively. From growth and feed utilization, the substitution level of CAP should no more than 30%, which was less than previous reported on juvenile turbot. The palatability of the feed was linearly reduced. Although CAP did not induce enteritis, it decreased the intestine villi height in middle and intestine villi density in distal intestine. Except for decreasing the size of hepatocytes by CAP at 45% or higher substitution levels, no other abnormality observed in liver histology. However, dietary CAP reduced the triglyceride and cholesterol levels in the plasma at 30% or higher levels and linearly down-regulated genes related to lipogenesis in liver. The genes related lipid transportation and oxidation were up-regulated by CAP at the substitution levels of 15–60%. The present work confirmed the safety of CAP in fish feed and suggested more work should be conducted before it widely used in aquafeed.
Enhanced electric field and charge polarity modulate the microencapsulation and stability of electrosprayed probiotic cells (Streptococcus thermophilus, ST44)
Authors: Dima Panagiota , Stubbe Peter Reimer , Mendes Ana C. , Chronakis Ioannis S. 
Published: May 2023

Abstract
The “organization” of Streptococcus thermophilus (ST44) probiotic cells within maltodextrin microcapsules was investigated, using electrospray processing. The generated electrostatic forces between the negatively surface-charged probiotic cells and the applied negative polarity on the electrospray nozzle, allowed to control the location of the cells towards the core of the electrosprayed microcapsules. The “organization” of the cells affected the evaporation of the solvent (water) and subsequently the glass transition temperature (Tg) of the electrosprayed microcapsules. Moreover, the utilization of auxiliary ring-shaped electrodes, between the nozzle and the collector, enhanced the electric field strength and contributed further to the increase of the Tg. Numerical simulation, through Finite Element Method (FEM), shed light to the effects of the additional ring-electrode on the electric field strength, potential distribution, and controlled deposition of the capsules. Moreover, the viability of the encapsulated cells was significantly improved for up to 2 weeks of storage at 25°C and 35% RH, when the cells were located at the core of the microcapsules, compared to the probiotics distributed towards the surface. Overall, this study presents a novel method to manipulate the encapsulation of the surface charged probiotic cells within electrosprayed microcapsules, utilizing the polarity of the electric field and additional ring-electrodes.
Colonic Microbiota Improves Fiber Digestion Ability and Enhances Absorption of SCFAs in Hainan Local Pigs
Authors: Xue Pengxiang , Luo Yabiao , Song Yanxia , Tang Qiguo , Wang Feng , Sun Ruiping , Chao Zhe , Fang Meiying 
Published: May 2023

Abstract
Background
Compared to commercial breeds, Chinese local pig breeds have a greater ability to digest dietary fiber, which may be due to differences in intestinal microbiota. Previous studies on the adaptation of dietary fiber either considered only feed factors or breed factors. Therefore, this study took both of these factors into consideration for the experimental design in order to explore the potential causes of high dietary fiber adaptation of Ding’an pigs.
Results
Compared with commercial pigs, Ding’an pigs have a stronger ability to digest dietary fiber. Prevotella was more prevalent in Ding’an pigs than in DLY pigs, which may be an important reason for the stronger ability of fiber degradation in Ding’an pigs. When the effects of feed and breed factors are considered, differences in abundance of 31 species and 14 species, respectively, may result in a greater ability of fiber degradation in Ding’an pigs. Among them, Prevotella. sp. CAG:520 may be a newly discovered bacterium related to fiber degradation, which positively correlated with many fiber-degrading bacteria. We also found that the concentration of plant metabolites with anti-inflammatory and antioxidant effects was higher in the colonic chyme of Ding’an pigs after increasing the fiber content, which resulted in down-regulated expression of inflammatory factors in colonic mucosa. Spearman’s correlation coefficient revealed a strong correlation between microbiota and apparent digestibility of dietary fiber. The mRNA expressions of SLC16A1, PYY and GCG were significantly increased in the colonic mucosa of Ding’an pigs fed on high-fiber diets, which indicates that Ding’an pigs have an enhanced absorption of SCFAs.
Conclusions
Our results suggested that an appropriate increase in dietary fiber content can reduce the inflammatory response and improve feed efficiency in Ding'an pigs, and differences in the intestinal microbial composition may be an important reason for the difference in the fiber degradation capacity between the two breeds of pigs.
Identification of immune subtypes and response prediction to immune-checkpoint inhibitors for MDM4 gain/amplification luminal A type breast cancer
Authors: Zhao Fei , Wang Na-Na 
Published: May 2023

Abstract

Objective:The aim of this work was to identify the consensus immune subtypes and predict the response to immune checkpoint inhibitor (ICIs) therapy for MDM4 gain/amplification luminal A type breast cancer (BC).Materials and Methods:Luminal A type BC expression data, copy number and corresponding clinical information were downloaded and pre-processed for subsequently analysis from The Cancer Genome Atlas (TCGA) and Molecular Taxonomy of Breast Cancer International Consortium (METABRIC). Furthermore, gene set enrichment analysis (GSEA) was performed to identify transcripts functions between MDM4 gain/amplification and control samples. Subsequently, weighted gene co-expression network analysis (WGCNA) was applied to screen out gene modules related biomarkers for ICIs therapy response in luminal A type BC. We perform an unsupervised consensus clustering in MDM4 gain/amplification luminal A type BC from TCGA BC dataset based immune-related gene signatures (IRGs) and then used luminal A type BC from METABRIC BC as validation datasets. We performed the Tumor Immune Dysfunction and Exclusion (TIDE) analysis to predict ICIs response and explore significant relationship with immune subtype.Results:The results from GSEA indicated that luminal A type BC with MDM4 gain/amplification were significantly enriched in immunological signature gene sets. Significantly, we also identified three gene modules significantly association with immune checkpoint, DNA damage, and immune cell infiltering in luminal A type BC. Luminal A type BC could be categorized into two distinct immune subtypes based on the expression of IRGs. Luminal A type BC in one subtype showed high response to ICIs therapy, characterized by higher immune checkpoint genes score and CD8+T-cell score compared to tumors in a second subtype.Conclusion:Our findings demonstrated that immune subtype for MDM4 gain/amplification luminal A type BC was beyond the current luminal A/B classification and a subset of luminal A type BC patients may benefit from ICIs therapy.
The Effect of Distribution of the Perforation Density on the Production Through Perforated Horizontal Wellbore
Authors: Kareem¹ Hasanain J. , Hasini Hasril , Abdulwahid Mohammed A. 
Published: May 2023

Abstract
With depletion of oil reserve around the world, focus has been shifted towards deeper exploration in the field that is difficult to reach. Oil production rate is influenced by perforation density distribution's along horizontal wells, specifically in reservoirs with high permeability and low-pressure drawdown. This study investigated the behaviours of the total pressure drop, mixture’s superficial velocity, void fraction and liquid film thickness that occurs with various flow patterns (i.e., bubble, slug, stratified and stratified wave flows). Two perforation density conditions are studied, namely perforation density increase at outlet and perforation density increase at inlet. The friction factor was fulfilled through the perforated and unperforated horizontal wellbore. Production is greater with a perforated horizontal wellbore than with a smooth (unperforated) horizontal wellbore. The total pressure drop, mixture superficial velocity and void fraction increases with the air superficial velocity when the water superficial was constant. The liquid film thickness decreases when the air superficial velocity increased, while the pressure drops increase with increases of mixture Reynolds number. The liquid and air products increase when the perforation density increases at the inlet section (and decreased at the outlet section) of the perforated horizontal wellbore. It was noted that the air product increased with the air flow rate. Liquid product increases with the bubble flow as the transition point of the bubble/stratified flow decreased. Validation with experimental data, as well as data from other researchers show good agreement, conforming the reliability of the numerical code used in this study. The convergence between the results is good through the patterns (bubble flow, dispersed bubble flow, slug flow, transition bubble/stratified flow, and transition stratified/stratified wave flow).
Transcriptomic and lipidomic analysis reveals the salt-adapted in Salicornia europaea
Authors: Yang Lei , Bai Yang , Yang Jiahui , Gao Yunyan , Shi Panpan , Hou Chenxue , Wang Yanzhi , Gu Xinlu , Liu Weizhong 
Published: May 2023

Abstract
Halophytes have evolved unique strategies to cope with salinity. Salicornia europaea, a succulent euhalophyte plant, show optimal reproduction under 200 mM NaCl. However, the role of lipid metabolism caused by salinity in S. europaea is not fully understood. To gain insight into this, we conducted a combined lipidomic and transcriptomic analysis to investigate the molecular basis of lipid metabolism in response to 0 and 200 mM NaCl. GO and KEGG analysis revealed that salt treatment mainly affected glycosylphosphatidylinositol (GPI) anchored biosynthesis, secondary metabolite synthesis, plant hormone signal transduction, peroxisome, and glycosphingoipid biosynthesis. We identifited 485 lipid compounds, 27 of which showed altered abundances under salt treatment. Notably, lysophosphatidylcholine (LPC) and phytosphingosine-1-phosphate (S1P) significantly increased, while polyunsaturated monogalactosyldiacylglycerols (PA), lysophosphatidylinositol (LPI), phytoceramides with hydroxylated fatty acyl (PhytoCer-OHFA), phyto-glucosylceramide (Phyto-GluCer), sphingosine (Sph), and phytosphingosine (PhytoSph) markedly decreased. Additionally, the increase in DBI index was mostly phospholipids and sphingolipids, indicating that the lipid saturation was reduced, and the fluidity was higher, which may be related to the strong salt resistance of S. europaea. By comparing the average carbon chain length (ACL), it can be seen that the ACL coefficient of S1P is significantly reduced with 200 mM NaCl concentration, so we speculate that S1P may be related to the salt resistance.
[(EtO) 3 Si(CH 2 ) 3 N + H 3 ][CH 3 COO - ] as basic ionic liquid catalyst promoted green synthesis of benzo[a]pyrano[2,3-c]phenazine derivatives
Authors: Shirzaei Farhad , Shaterian Hamid Reza 
Published: May 2023

Abstract
An efficient, one-pot quantitative procedure for the preparation of benzo[a]pyrano[2,3-c]phenazine derivatives from four-component condensation reaction of 2-hydroxynaphthalene-1,4-dione, benzene-1,2-diamine, aromatic aldehydes, and malononitrile in the presence of [(EtO)3Si(CH2)3N+H3][CH3COO−] as basic ionic liquid as catalyst under solvent-free conditions is described. Simple procedure, high yields, short reaction times, and an environmentally benign method are advantages of this protocol. The [(EtO)3Si(CH2)3N+H3][CH3COO−] can be recovered and reused several times without loss of its activity.