bluuebunny/crossref_metadata_2025_split huggingface dataset:
Genetic algorithm for obtaining potential energy curve of diatomic molecules based on dispersed fluorescence spectra
Authors: Urbańczyk Tomasz , Koperski Jarosław , Kaszewski Gabriel , Synak Mikołaj , Swenda Jakub , Krośnicki Marek 
Published: October 2023

AbstractThe method for reconstruction of an adiabatic potential energy curve from experimental dispersed fluorescence spectra has been developed. The novelty of the method relies on a unique approach of simultaneous use of $$bound \rightarrow bound$$

b
o
u
n
d
→
b
o
u
n
d

and $$bound \rightarrow free$$

b
o
u
n
d
→
f
r
e
e

parts of the spectrum. The method is based on the Genetic Algorithm (GA) procedure and determines potential energy curve integrally, below and above the dissociation energy limit. The method was tested on the artificially generated reference spectrum as well as experimental spectrum of $$G0_u^+(\upsilon ^{\prime }=39) \rightarrow X0_g^+$$

G

0
u
+

(

υ
′

=
39
)

→
X

0
g
+

transition in Hg$$_2$$

2

. The tests show very good accuracy of simulation based on GA results with artificially generated reference spectrum as well as with the experimental one.
Characterization and structural analysis of the endo-1,4-β-xylanase GH11 from the hemicellulose-degrading Thermoanaerobacterium saccharolyticum useful for lignocellulose saccharification
Authors: Kim In Jung , Kim Soo Rin , Kim Kyoung Heon , Bornscheuer Uwe T. , Nam Ki Hyun 
Published: October 2023

AbstractXylanases are important for the enzymatic breakdown of lignocellulose-based biomass to produce biofuels and other value-added products. We report functional and structural analyses of TsaGH11, an endo-1,4-β-xylanase from the hemicellulose-degrading bacterium, Thermoanaerobacterium saccharolyticum. TsaGH11 was shown to be a thermophilic enzyme that favors acidic conditions with maximum activity at pH 5.0 and 70 °C. It decomposes xylans from beechwood and oat spelts to xylose-containing oligosaccharides with specific activities of 5622.0 and 3959.3 U mg−1, respectively. The kinetic parameters, Km and kcat towards beechwood xylan, are 12.9 mg mL−1 and 34,015.3 s−1, respectively, resulting in kcat/Km value of 2658.7 mL mg−1 s−1, higher by 102–103 orders of magnitude compared to other reported GH11s investigated with the same substrate, demonstrating its superior catalytic performance. Crystal structures of TsaGH11 revealed a β-jelly roll fold, exhibiting open and close conformations of the substrate-binding site by distinct conformational flexibility to the thumb region of TsaGH11. In the room-temperature structure of TsaGH11 determined by serial synchrotron crystallography, the electron density map of the thumb domain of the TsaGH11 molecule, which does not affect crystal packing, is disordered, indicating that the thumb domain of TsaGH11 has high structural flexibility at room temperature, with the water molecules in the substrate-binding cleft being more disordered than those in the cryogenic structure. These results expand our knowledge of GH11 structural flexibility at room temperature and pave the way for its application in industrial biomass degradation.
Exploring the performance of implicit neural representations for brain image registration
Authors: Byra Michal , Poon Charissa , Rachmadi Muhammad Febrian , Schlachter Matthias , Skibbe Henrik 
Published: October 2023

AbstractPairwise image registration is a necessary prerequisite for brain image comparison and data integration in neuroscience and radiology. In this work, we explore the efficacy of implicit neural representations (INRs) in improving the performance of brain image registration in magnetic resonance imaging. In this setting, INRs serve as a continuous and coordinate based approximation of the deformation field obtained through a multi-layer perceptron. Previous research has demonstrated that sinusoidal representation networks (SIRENs) surpass ReLU models in performance. In this study, we first broaden the range of activation functions to further investigate the registration performance of implicit networks equipped with activation functions that exhibit diverse oscillatory properties. Specifically, in addition to the SIRENs and ReLU, we evaluate activation functions based on snake, sine+, chirp and Morlet wavelet functions. Second, we conduct experiments to relate the hyper-parameters of the models to registration performance. Third, we propose and assess various techniques, including cycle consistency loss, ensembles and cascades of implicit networks, as well as a combined image fusion and registration objective, to enhance the performance of implicit registration networks beyond the standard approach. The investigated implicit methods are compared to the VoxelMorph convolutional neural network and to the symmetric image normalization (SyN) registration algorithm from the Advanced Normalization Tools (ANTs). Our findings not only highlight the remarkable capabilities of implicit networks in addressing pairwise image registration challenges, but also showcase their potential as a powerful and versatile off-the-shelf tool in the fields of neuroscience and radiology.
Unravelling the skills and motivations of Magdalenian artists in the depths of Atxurra Cave (Northern Spain)
Authors: Garate Diego , Rivero Olivia , Rios-Garaizar Joseba , Medina-Alcaide Mª Ángeles , Arriolabengoa Martin , Intxaurbe Iñaki , Ruiz-López Juan F. , Marín-Arroyo Ana Belén , Rofes Juan , García Bustos Paula , Torres Antonio , Salazar Sergio 
Published: October 2023

AbstractAtxurra cave has a decorated assemblage composed of more than a hundred engraved animal depictions. All of them are located in deep parts of the cave and most of them are hidden in raised areas, away from the main path. The main sector is the “Ledge of the Horses”, located at 330 m from the entrance of the cave. It is a space of 12 m long and 1.5 m wide, elevated 4 m above the cave floor. This area includes almost fifty engraved and painted animals accompanied by a dozen flint tools, three fireplaces, and around one hundred charcoal fragments from torches. This extraordinary archaeological record allows us to value the complexity of the artistic production inside the caves during the Upper Palaeolithic. Our study has confirmed that there is planning prior to artistic production, both in terms of the iconographic aspects (themes, techniques, formats), its location (visibility, capacity), and the lighting systems. Furthermore, the data indicates the panel was decorated to be seen by third parties from different positions and was expressly illuminated for this purpose. This evidence supports the role of rock art as a visual communication system in Upper Palaeolithic societies.
Trace impurities in sodium phosphate influences the physiological activity of Escherichia coli in M9 minimal medium
Authors: Soma Yuki , Tominaga Saki , Tokito Kanako , Imado Yuri , Naka Kosuke , Hanai Taizo , Takahashi Masatomo , Izumi Yoshihiro , Bamba Takeshi 
Published: October 2023

AbstractIn the field of applied microbiology, reproducibility and experimental variability are important factors that influence both basic research as well as process development for industrial applications. Experimental reproducibility and accuracy depend not only on culture conditions such as temperature and aeration but also on raw materials and procedures used for media preparation. The M9 minimal medium is one of the most common synthetic media for culturing Escherichia coli and other bacteria. This synthetic medium can be used to observe and evaluate the physiological activity of microbes under minimal nutritional requirements and determine the limiting factor for the desired phenotype. Although one of the advantages using the M9 medium is that its composition can be modulated, it is difficult to control presence of trace components and impurities from the reagents for preparing this medium. Herein, we showed that trace ingredients present in the reagents used for M9 media preparation affect the bacterial physiological activities (e.g., cell growth, substrate consumption, and byproduct formation). Additionally, we systematically identified the trace ingredient that influenced phenotypic differences. Our results showed that the selection of reagents and accuracy during reagent preparation is important for experimental reproducibility in the field of bio-engineering and systems biology focused on the systematic and continuous development of biomolecular systems (e.g., biorefinery, metabolic engineering, and synthetic biology).
Memory-induced alignment of colloidal dumbbells
Authors: Krishna Kumar Karthika , Caspers Juliana , Ginot Félix , Krüger Matthias , Bechinger Clemens 
Published: October 2023

AbstractWhen a colloidal probe is forced through a viscoelastic fluid which is characterized by a long stress-relaxation time, the fluid is excited out of equilibrium. This is leading to a number of interesting effects including a non-trivial recoil of the probe when the driving force is removed. Here, we experimentally and theoretically investigate the transient recoil dynamics of non-spherical particles, i.e., colloidal dumbbells. In addition to a translational recoil of the dumbbells, we also find a pronounced angular reorientation which results from the relaxation of the surrounding fluid. Our findings are in good agreement with a Langevin description based on the symmetries of a director (dumbbell) as well as a microscopic bath-rod model. Remarkably, we find an instability with amplified fluctuations when the dumbbell is oriented perpendicular to the direction of driving. Our results demonstrate the complex behavior of non-spherical objects within a relaxing environment which are of immediate interest for the motion of externally but also self-driven asymmetric objects in viscoelastic fluids.
Spin independence of the strongly enhanced effective mass in ultra-clean SiGe/Si/SiGe two-dimensional electron system
Authors: Melnikov M. Yu. , Shakirov A. A. , Shashkin A. A. , Huang S. H. , Liu C. W. , Kravchenko S. V. 
Published: October 2023

AbstractThe effective mass at the Fermi level is measured in the strongly interacting two-dimensional (2D) electron system in ultra-clean SiGe/Si/SiGe quantum wells in the low-temperature limit in tilted magnetic fields. At low electron densities, the effective mass is found to be strongly enhanced and independent of the degree of spin polarization, which indicates that the mass enhancement is not related to the electrons’ spins. The observed effect turns out to be universal for silicon-based 2D electron systems, regardless of random potential, and cannot be explained by existing theories.
Transcriptomic analysis of the antimicrobial activity of prodigiosin against Cutibacterium acnes
Authors: Kim Hyun Ju , Lee Moo-Seung , Jeong Se Kyoo , Lee Sang Jun 
Published: October 2023

AbstractProdigiosin, a red pigment produced by Hahella chejuensis, a marine-derived microorganism, has several biological functions, including antimicrobial activity and inflammatory relief. In this study, the antibacterial activity of prodigiosin against skin microorganisms was explored. Paper disc assay on skin bacterial cells revealed that Cutibacterium acnes related to acne vulgaris highly susceptible to prodigiosin. MIC (Minimal Inhibitory Concentration) and MBC (Minimal Bactericidal Concentration) were determined on Cutibacterium species. The RNA-seq analysis of prodigiosin-treated C. acnes cells was performed to understand the antibacterial mechanism of prodigiosin. Among changes in the expression of hundreds of genes, the expression of a stress-responsive sigma factor encoded by sigB increased. Conversely, the gene expression of cell wall biosynthesis and energy metabolism was inhibited by prodigiosin. Specifically, the expression of genes related to the metabolism of porphyrin, a pro-inflammatory metabolite, was significantly reduced. Therefore, prodigiosin could be used to control C. acnes. Our study provided new insights into the antimicrobial mechanism of prodigiosin against C. acnes strains.
Seroprevalence of hepatitis A virus antibodies among children and adolescents living in Northern Thailand: an implication for hepatitis A immunization
Authors: Kunanitthaworn Natchaya , Mueangmo Oramai , Saheng Jutamad , Wongjak Worawan , Lertsiriladakul Tanin , Chaito Tanachot , Nantarat Pasawat , Sudjaritruk Tavitiya 
Published: October 2023

AbstractThis cross-sectional study aimed to assess seroprevalence of hepatitis A virus (HAV) antibodies and identify factors associated with HAV seropositivity among children and adolescents aged 1–18 years who resided in Chiang Mai, Thailand. Sociodemographic characteristics, sanitation/hygiene, and history of HAV vaccination were collected. Anti-HAV IgG antibody was determined, and a level ≥ 1.0 S/CO defined HAV seropositivity. We enrolled 300 participants; median age 8.7 years, 54% male, and 13% overweight (BMI z-score: + 1 to + 2 standard deviation [SD]). Sixty-five participants (22%) were vaccinated against HAV. Overall, 84/300 participants (28%) demonstrated HAV seropositivity, of whom 55/65 (85%) and 29/235 (12%) were among vaccinated and unvaccinated participants (P < 0.001), respectively. Previous HAV vaccination (adjusted odds ratio [aOR] 47.2; 95% CI 20.0–111.8) and overweight (aOR 4.4; 95% CI 1.7–11.3, compared with normal weight [BMI z-score: − 2 to + 1 SD]) were significantly associated with seropositivity of HAV. In the stratified analyses, crowded bedroom (aOR 3.2; 95% CI 1.3–7.8, per one person increase) and overweight (aOR 5.0; 95% CI 1.8–13.7) were factors associated with HAV seropositivity among vaccinated and unvaccinated participants, respectively. Seroprevalence of HAV antibodies in healthy Thai children and adolescents was relatively low. Recommendation of HAV vaccination for these populations, particularly those with high-risk conditions, should be considered.
Development of nomograms for predicting the survival of intestinal-type gastric adenocarcinoma patients after surgery
Authors: Liu Chu-Yun , Yang Yu-Shen , Ye Kai , He He-fan 
Published: October 2023

AbstractIntestinal-type gastric adenocarcinoma (IGA) is a common phenotype of gastric cancer. Currently, few studies have constructed nomograms that may predict overall (OS) and cancer-specific survival (CSS) probability after surgery. This study is to establish novel nomograms for predicting the survival of IGA patients who received surgery. A total of 1814 IGA patients who received surgery between 2000 and 2018 were selected from Surveillance, Epidemiology, and End Results database and randomly assigned to the training and validating sets at a ratio of 7:3. Then univariate and multivariate cox regression analyses were performed to screen significant indictors for the construction of nomograms. The calibration curve, the area under the receiver operating characteristic (receiver operating characteristic, ROC) curve (the area under curve, AUC), C-index, net reclassification index (NRI), integrated discrimination improvement (IDI) and decision curve analysis (DCA) curves were applied to assess the performance of the model. The significant outcomes of multivariate analysis revealed that ten variables (age, sex, race, surgery type, summary stage, grade, AJCC TNM stage, radiotherapy, number of regional nodes examined, number of regional nodes positive) were demonstrated to construct the nomogram for OS and ten variables (age, sex, race, surgery type, summary stage, grade, AJCC TNM stage, chemotherapy, number of regional nodes examined, number of regional nodes positive) for CSS. The calibration and AUC uncovered their favorable predictive performance. Subsequently, C-index, NRI, IDI and DCA curves further validated the predicative superiority of nomograms over 7th AJCC Stage System. The validated nomogram provides more reliable OS and CSS predictions for postoperative IGA patients with good accuracy, which can help surgeons in treatment decision-making and prognosis evaluation.
Network pharmacology and experimental verification of the potential mechanism of Er-Xian decoction in aplastic anemia
Authors: Ye Mei , Liu Guangxian , Yang Yujun , Yang Hongyu , Ren Juan , Chen Wenfei , Gao Zeli 
Published: October 2023

AbstractTo investigate the potential mechanism of Er-Xian decoction (EXD) in treating aplastic anemia (AA), the active components of EXD were screened by the Traditional Chinese Medicine Systems Pharmacology Database and Analysis Platform (TCMSP), and the targets of the components were predicted by the Swiss Target Prediction database. AA targets were collected from the GeneCards, OMIM, DisGeNET, PharmGKB, DrugBank, and TTD databases, the intersection of AA targets and EXD targets was calculated, and an herb-component-target network was constructed by Cytoscape 3.7.2 software. The STRING database was used for protein‒protein interaction (PPI) analysis, and Cytoscape 3.7.2 software was used to construct a PPI network and perform topology analysis. The core targets were imported into the DAVID database for gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses. The molecular docking software AutoDock was used to measure the affinity between active components and key targets. Finally, we established a mouse model of AA and verified the key targets and signaling pathways of EXD by RT‒PCR, ELISA and Western blot analysis. A total of 53 active components were screened from EXD, 2516 AA-related targets were collected, and 195 common targets were obtained. An herb-component-target network and a PPI network were successfully constructed, and 36 core targets were selected from the PPI network. The main active components of EXD include luteolin, kaempferol, berberine, etc., and key targets include PIK3CA, AKT1, STAT3, etc. GO functional enrichment analysis showed that cell components, molecular functions and biological processes with significant correlations were macromolecular complexes, protein serine/threonine/tyrosine kinase activity and protein phosphorylation, respectively. KEGG pathway analysis showed that the pathways with significant correlations included the PI3K-Akt signaling pathway and JAK-STAT signaling pathway. Molecular docking results showed that the tested key targets had good affinity for the corresponding active components. In AA mice, we found that EXD significantly increased white blood cell count, red blood cell count, platelet count and hemoglobin levels, increased mRNA levels of PIK3CA, PIK3CD, AKT1, JAK2, STAT3 and MAPK1, and promoted phosphorylation of PI3K, AKT, ERK1/2 and STAT3. In summary, EXD acts on PI3K, AKT, STAT3 and other targets through berberine, luteolin, quercetin and other components to regulate the PI3K-Akt pathway, JAK-STAT pathway and other pathways, thus exerting its therapeutic effect on AA. This study explained the Chinese medicine theory of treating AA with EXD by tonifying kidney-yang and provides a scientific basis for the use of EXD in treating AA.
LncRNA RARA-AS1 could serve as a novel prognostic biomarker in pan-cancer and promote proliferation and migration in glioblastoma
Authors: Huang Yue , Deng Song , Jiang Qiaoji , Shi Jinlong 
Published: October 2023

AbstractLong non-coding RNAs (lncRNAs) have emerged as crucial regulators of cancer progression and are potential biomarkers for diagnosis and treatment. This study investigates the role of RARA Antisense RNA 1 (RARA-AS1) in cancer and its implications for diagnosis and treatment. Various bioinformatics tools were conducted to analyze the expression patterns, immune-related functions, methylation, and gene expression correlations of RARA-AS1, mainly including the comparisons of different subgroups and correlation analyses between RARA-AS1 expression and other factors. Furthermore, we used short hairpin RNA to perform knockdown experiments, investigating the effects of RARA-AS1 on cell proliferation, invasion, and migration in glioblastoma. Our results revealed that RARA-AS1 has distinct expression patterns in different cancers and exhibits notable correlation with prognosis. Additionally, RARA-AS1 is highly correlated with certain immune checkpoints and mismatch repair genes, indicating its potential role in immune infiltration and related immunotherapy. Further analysis identified potential effective drugs for RARA-AS1 and demonstrated its potential RNA binding protein (RBP) mechanism in glioblastoma. Besides, a series of functional experiments indicated inhibiting RARA-AS1 could decrease cell proliferation, invasion, and migration of glioblastoma cell lines. Finally, RARA-AS1 could act as an independent prognostic factor for glioblastoma patients and may serve as a promising therapeutic target. All in all, Our study provides a comprehensive understanding of the functions and implications of RARA-AS1 in pan-cancer, highlighting it as a promising biomarker for survival. It is also an independent risk factor affecting prognosis in glioblastoma and an important factor affecting proliferation and migration in glioblastoma, setting the stage for further mechanistic investigations.
Towards eliminating friction and wear in plain bearings operating without lubrication
Authors: Kharanzhevskiy Evgeny V. , Ipatov Aleksey G. , Makarov Aleksey V. , Gil’mutdinov Faat Z. 
Published: October 2023

AbstractPlain bearings, renowned for their versatility and simplicity, are extensively utilized in engineering design across various industries involving moving parts. Lubrication is vital to the functioning of these bearings, yet their usage is inhibited under dynamic load conditions, or at elevated or reduced temperatures due to this dependency on lubrication. This study introduces an innovative method to significantly mitigate friction and wear in plain bearings operating without lubrication. The plain bearings were constructed from steel–bronze pairs, where the steel shafts were alloyed with bismuth oxide via short-pulse laser treatment. MnO2 was utilized as a carrier to incorporate the bismuth oxide into the surface layers of the steel. Insights from transmission electron microscopy and X-ray photoelectron spectroscopy revealed a highly non-equilibrium state of matter, unattainable through conventional engineering methods. The tribological performance of the modified steel disks was assessed via a block-on-ring sliding test, demonstrating superior wear and friction performance without lubrication, as well as an ultra-low coefficient of friction. Remarkably, the modified friction pairs remained functional after 200 km of linear sliding at a load of 250 N (12.5 MPa) and a sliding speed of 9 m/s. To substantiate the technique’s viability, we tested the performance of an internal combustion engine turbocharger fitted with a modified steel shaft. The turbocharger’s performance validated the long-term effectiveness of the steel–bronze coupling operating without lubrication at 75,000 rpm. The simplicity and resilience of this technique for modifying steel–bronze pairs offer a ground-breaking and promising approach for a wide range of applications.