bluuebunny/crossref_metadata_2025 huggingface dataset:
Identification and Characterization of ten Escherichia coli Strains Encoding Novel Shiga Toxin 2 Subtypes, Stx2n as Well as Stx2j, Stx2m, and Stx2o, in the United States
Authors: Lindsey Rebecca L. , Prasad Arjun , Feldgarden Michael , Gonzalez-Escalona Narjol , Kapsak Curtis , Klimke William , Melton-Celsa Angela , Smith Peyton , Souvorov Alexandre , Truong Jenny , Scheutz Flemming
Published: October 2023

The sharing of genome sequences in online data repositories allows for large scale analyses of specific genes or gene families. This can result in the detection of novel gene subtypes as well as the development of improved detection methods. Here, we used publicly available WGS data to detect a novel Stx subtype, Stx2n in two clinical E. coli strains isolated in the USA. During this process, additional Stx2 subtypes were detected; six Stx2j, one Stx2m strain, and one Stx2o, were all analyzed for variability from the originally described subtypes. Complete genome sequences were assembled from short- or long-read sequencing and analyzed for serotype, and ST types. The WGS data from Stx2n- and Stx2o-producing STEC strains were further analyzed for virulence genes pro-phage analysis and phage insertion sites. Nucleotide and amino acid maximum parsimony trees showed expected clustering of the previously described subtypes and a clear separation of the novel Stx2n subtype. WGS data were used to design OMNI PCR primers for the detection of all known stx1 (283 bp amplicon), stx2 (400 bp amplicon), intimin encoded by eae (221 bp amplicon), and stx2f (438 bp amplicon) subtypes. These primers were tested in three different laboratories, using standard reference strains. An analysis of the complete genome sequence showed variability in serogroup, virulence genes, and ST type, and Stx2 pro-phages showed variability in size, gene composition, and phage insertion sites. The strains with Stx2j, Stx2m, Stx2n, and Stx2o showed toxicity to Vero cells. Stx2j carrying strain, 2012C-4221, was induced when grown with sub-inhibitory concentrations of ciprofloxacin, and toxicity was detected. Taken together, these data highlight the need to reinforce genomic surveillance to identify the emergence of potential new Stx2 or Stx1 variants. The importance of this surveillance has a paramount impact on public health. Per our description in this study, we suggest that 2017C-4317 be designated as the Stx2n type-strain.
Genesis of the Graphite from the Tugeman Graphite Deposit, Xinjiang, China: Evidence for Carbon Isotope Refining by Fluids Associated with the Ductile Shear Zone
Authors: Li Hang , Hong Tao , Liu Shanke , Ke Qiang , Yang Zhiquan , Ma Yince , Wang Xuehai , Niu Lei , Kang Kai , Xu Xingwang
Published: October 2023

The Altun orogenic belt is situated along the northern boundary of the Tibetan Plateau. In this study, we present an analysis of the ore deposit, mineral composition, and carbon isotope signatures of the Tugeman graphite deposit within the Altun orogenic belt. The graphite in the Tugeman graphite deposit occurs within graphite-bearing schists and marble. Graphite enrichment is observed in the ductile shear zone. The carbon isotope values of graphite range between −18.90‰ and −10.03‰ (with an average value of −12.70‰). These values differ significantly from those observed in organic matter and marine carbonates, suggesting the occurrence of a mixing process involving reduced carbon fluid derived from biological organic material during regional metamorphism as well as a potential influx of oxidized carbon fluid from external sources. In addition, the metamorphic temperature of Tugeman graphite calculated from Raman spectroscopy is between 494 °C and 570 °C, which indicates that the disordered material is transformed from greenschist-amphibolite facies metamorphism to moderate-crystalline graphite. Combining the geological and carbon isotope characteristics of the Tugeman graphite deposit, we argue that the Tugeman graphite deposit is a regional metamorphic graphite deposit of biogenic origin, and during the late stage of metamorphism, it underwent interaction with fluids.
New Approach for Direct Determination of Manganese Valence State in Ferromanganese Nodules by X-ray Fluorescence Spectrometry
Authors: Chubarov Victor M.
Published: October 2023

A new X-ray fluorescence technique is proposed as an alternative to the labor-consuming volumetric method for the estimation of manganese valence state in ferromanganese nodules. The approach is based on the measurement of the relative intensities of some X-ray fluorescence spectrum characteristic spectral lines and satellites (MnKβ5 and MnKβ′) preconditioned by electron transfer from the valence shell. Calibration curves were created using manganese oxide samples (MnO, Mn2O3, MnO2) and 12 certified reference materials of ferromanganese nodules, cobalt-bearing ferromanganese crusts, and manganese ores with certified (or determined by approved methods) total and tetravalent manganese content. The presence of high iron content was taken into account. A set of oceanic ferromanganese nodules samples collected in the Magellan Seamounts (Pacific Ocean) were analyzed. Differences between the results of the X-ray fluorescence method and volumetric techniques for tetravalent manganese content were 4.9 rel.%, which is comparable with the accuracy of the volumetric technique (3.6 rel.%).
Characterization of the Sedimentary Environment of the Shanxi Formation in the Southeastern Ordos Basin Revealed by Detrital Zircon and Geochemical Analyses
Authors: Li Jiandong , Li Xianqing , Tian Wen , Xiao Chunhui , Zhao Yingfan , Xiang Jie , Sun Deyao
Published: October 2023

The interpretation of the sedimentary paleogeographic environment of the Lower Permian Shanxi Formation (P1s) coal strata in the southeastern Ordos Basin remains a subject of significant debate. In this paper, based on detrital zircon U–Pb source analysis, paleosalinity assessment, the sandstone modal composition, and other methods, we analyzed the P1s source system and constructed a model of the sedimentary evolution. The findings reveal that the primary source of the clastic materials in the study area stems from a mixed-source within the recycling orogenic belt. During the deposition period, the Shanxi Formation developed two predominant material source systems: one in the north, primarily linked to the Paleo-Yinshan Fold Orogenic Belt (YFOB), and the other in the south, originating from the North Qinling Orogenic Belt (NQinOB). These two major source systems converged in the Yichuan–Fuxian area. From the early stages of the Shanxi Formation period (Shan1), there was a regional retreat of the sea in the area. The seawater receded in a southeastward direction, leading to a gradual reduction in the paleosalinity and Sr/Ba-ratio variability during the Shan1 period. The influence of the seawater diminished, transitioning into a deltaic depositional system. This shift towards a terrestrial lakeshore basin reached its full development during the Lower Xiashihezi period. This study concludes that the Shanxi Formation in this area represents the evolution of a deltaic depositional system originating from a shallow sea shelf. This evolution can be divided into three major stages: remnants of the shallow sea shelf, barrier island–lagoon–littoral, and deltaic deposition. Within this framework, the shoreline underwent frequent lateral migration, influencing a broad range of characteristics. In the vertical direction, numerous alternating sets of sandstone bodies and mudstone, shale, and coal beds formed, creating a significant relationship between coal hydrocarbon sources and reservoirs. This study also establishes the stratigraphic-sequence framework of the basin for this period. These results hold great importance for the expansion of natural gas exploration and development efforts.
Recent Computational Advances Regarding Amyloid-β and Tau Membrane Interactions in Alzheimer’s Disease
Authors: Nguyen Phuong H. , Derreumaux Philippe
Published: October 2023

The interactions of amyloid proteins with membranes have been subject to many experimental and computational studies, as these interactions contribute in part to neurodegenerative diseases. In this review, we report on recent simulations that have focused on the adsorption and insertion modes of amyloid-β and tau proteins in membranes. The atomistic-resolution characterization of the conformational changes of these amyloid proteins upon lipid cell membrane and free lipid interactions is of interest to rationally design drugs targeting transient oligomers in Alzheimer’s disease.
Costa Rican Propolis Chemical Compositions: Nemorosone Found to Be Present in an Exclusive Geographical Zone
Authors: Umaña Eduardo , Solano Godofredo , Zamora Gabriel , Tamayo-Castillo Giselle
Published: October 2023

Background: The chemistry of Costa Rican propolis from Apis mellifera remains underexplored despite its potential applications. This study identified its chemical composition, linking chemotypes to antioxidant potential. Methods: Proton nuclear magnetic resonance (1H NMR) spectra were obtained for 119 propolis extracts and analyzed using multivariate analyses. In parallel, 2,2-diphenyl-1-picrylhydrazyl (DPPH) radical scavenging assay was used to assess antioxidant activity. A generalized linear regression model (GLM) correlated this with its chemical profiles and geographical origin. Chromatographic methods were used to isolate active and inactive compounds, which were identified using nuclear magnetic resonance (NMR) and high-resolution mass spectrometry (HRMS). Results: Principal component analysis (PCA) revealed three chemical profile groups for the 119 propolis extracts, explaining 73% of the total variance with two components. Radical scavenging activity was found to correlate with chemical composition. Isolation yielded n-coniferyl benzoate in type I (EC50 = 190 µg/mL, ORAC = 0.60 µmol TE/µmol) and nemorosone in type II (EC50 = 300 µg/mL, ORAC = 0.7 µmol TE/µmol). Type III was represented in terpene-like components, which exhibited lower antioxidant activity. Conclusions: This study categorizes Costa Rican propolis into three chemical types and identifies two key components linked to antioxidant activity. Notably, nemorosone, a valuable natural product, was found to be highly concentrated in a particular region of Costa Rica.
Strategy of Coniferous Needle Biorefinery into Value-Added Products to Implement Circular Bioeconomy Concepts in Forestry Side Stream Utilization
Authors: Klavins Linards , Almonaitytė Karolina , Šalaševičienė Alvija , Zommere Alise , Spalvis Kaspars , Vincevica-Gaile Zane , Korpinen Risto , Klavins Maris
Published: October 2023

Sustainable development goals require a reduction in the existing heavy reliance on fossil resources. Forestry can be considered a key resource for the bioeconomy, providing timber, energy, chemicals (including fine chemicals), and various other products. Besides the main product, timber, forestry generates significant amounts of different biomass side streams. Considering the unique and highly complex chemical composition of coniferous needle/greenery biomass, biorefinery strategies can be considered as prospective possibilities to address top segments of the bio-based value pyramid, addressing coniferous biomass side streams as a source of diverse chemical substances with applications as the replacement of fossil material-based chemicals, building blocks, food, and feed and applications as fine chemicals. This study reviews biorefinery methods for coniferous tree forestry biomass side streams, exploring the production of value-added products. Additionally, it discusses the potential for developing further biorefinery strategies to obtain products with enhanced value.
The Tetrel Bonds of Hypervalent Halogen Compounds
Authors: Niu Zhihao , McDowell Sean A. C. , Li Qingzhong
Published: October 2023

The tetrel bond between PhXF2Y(TF3) (T = C and Si; X = Cl, Br, and I; Y = F and Cl) and the electron donor MCN (M = Li and Na) was investigated at the M06-2X/aug-cc-pVDZ level of theory. As the electronegativity of the halogen atom X increases, the strength of the tetrel bond also increases, but as the electronegativity of the halogen atom Y increases, the strength of the tetrel bond decreases. The magnitude of the interaction energy in most –CF3 complexes was found to be less than 10 kcal/mol, but to exceed 11 kcal/mol for PhClF2Cl(CF3)⋯NCNa. The tetrel bond is greatly enhanced when the –SiF3 group interacts with LiCN or NaCN, with the largest interaction energy approaching 100 kcal/mol and displaying a covalent Si⋯N interaction. Along with this enhancement, the Si⋯N distance was found to be less than the X–Si bond length, the –SiF3 group to be closer to the N atom, and in most –SiF3 systems, the X–Si–F angle to be less than 90°; the –SiF3 group therefore undergoes inversion and complete transfer in some systems.
A Study of the Mechanical Behaviour of Boron Nitride Nanosheets Using Numerical Simulation
Authors: Sakharova Nataliya A. , Pereira André F. G. , Antunes Jorge M.
Published: October 2023

Hexagonal boron nitride (h-BN) nanosheets are attractive materials for various applications that require efficient heat transfer, surface adsorption capability, biocompatibility, and flexibility, such as optoelectronics and power electronics devices, nanoelectromechanical systems, and aerospace industry. Knowledge of the mechanical behavior of boron nitride nanosheets is necessary to achieve accurate design and optimal performance of h-BN-based nanodevices and nanosystems. In this context, the Young’s and shear moduli and Poisson’s ratio of square and rectangular boron nitride nanosheets were evaluated using the nanoscale continuum modeling approach, also known as molecular structural mechanics. The latter allows robust and rapid assessment of the elastic constants of nanostructures with graphene-like lattices. To date, there is a lack of systematic research regarding the influence of input parameters for numerical simulation, loading conditions, size, and aspect ratio on the elastic properties of the h-BN nanosheets. The current study contributes to filling this gap. The results allow, on the one hand, to point out the input parameters that lead to better agreement with those available in the literature. On the other hand, the Young’s and shear moduli, and Poisson’s ratio calculated in the present work contribute to a benchmark for the evaluation of elastic constants of h-BN nanosheets using theoretical methods.
Burgeoning Single-Atom Nanozymes for Efficient Bacterial Elimination
Authors: Shi Tongyu , Cui Yuanyuan , Yuan Huanxiang , Qi Ruilian , Yu Yu
Published: October 2023

To fight against antibacterial-resistant bacteria-induced infections, the development of highly efficient antibacterial agents with a low risk of inducing resistance is exceedingly urgent. Nanozymes can rapidly kill bacteria with high efficiency by generating reactive oxygen species via enzyme-mimetic catalytic reactions, making them promising alternatives to antibiotics for antibacterial applications. However, insufficient catalytic activity greatly limits the development of nanozymes to eliminate bacterial infection. By increasing atom utilization to the maximum, single-atom nanozymes (SAzymes) with an atomical dispersion of active metal sites manifest superior enzyme-like activities and have achieved great results in antibacterial applications in recent years. In this review, the latest advances in antibacterial SAzymes are summarized, with specific attention to the action mechanism involved in antibacterial applications covering wound disinfection, osteomyelitis treatment, and marine antibiofouling. The remaining challenges and further perspectives of SAzymes for practical antibacterial applications are also discussed.
Gastrointestinal Fermentable Polysaccharide Is Beneficial in Alleviating Loperamide-Induced Constipation in Mice
Authors: Liu Buyu , Zhang Zhiguo , Liu Xingquan , Hu Weiwei , Wu Weicheng
Published: October 2023

To investigate the role of gastrointestinal (GI) polysaccharide fermentation in alleviating constipation, two polysaccharide fractions were isolated from a soluble fiber extract with determined anti-constipation activity: a 2.04 kDa neutral fraction (SSP-1) contained 99.29% glucose, and a 41.66 kDa acidic fraction (SSP-2) contained 63.85% uronic acid. After mice were given loperamide for 14 d to induce constipation, the GI transit rate increased significantly in the SSP-1 group (p < 0.05) but not in the SSP-2 group. The stool weight in the SSP-2 group was significantly higher than that in SSP-1 (383.60 mg vs. 226.23 mg) (p < 0.05). Both SSP-1 and SSP-2 groups had significantly increased serum gastrin and motilin levels (p < 0.05) and changes in their fecal short-chain fatty acid (SCFA) profiles, while SSP-1 showed better fermentation properties than SSP-2 in terms of statistically higher fecal contents of acetic acid and total SCFAs (p < 0.05). Bioinformatic analysis indicated that SSP-1 upregulated bacteria such as Oscillibacter to improve SCFA metabolism and stimulate GI hormone secretion, while SSP-2 had less influence on the gut microbiota. These results suggest that the neutral polysaccharide with superior GI fermentation properties exerted beneficial effects on constipation, while the less fermentable pectic fraction might act as a stool-bulking agent.
Enhancing Chronic-Disease Education through Integrated Medical and Social Care: Exploring the Beneficial Role of a Community Teaching Kitchen in Oregon
Authors: Tanumihardjo Jacob P. , Davis Heidi , Zhu Mengqi , On Helen , Guillory Kayla K. , Christensen Jill
Published: October 2023

Teaching kitchens (TKs) are rapidly being utilized as models to integrate culinary education and chronic-disease education into healthcare settings. Our observational study details the structure and organizational processes (e.g., referral, services, medical and social care integration) of the Community TK at Providence Milwaukie Hospital in Portland, OR. We utilize electronic medical-record data from engaged TK participants (n = 3077) to evaluate between the association of engagement and clinical outcomes (e.g., HbA1c, blood pressure, weight and cholesterol). Mean baseline HbA1c of Highly Engaged TK patients with diabetes (n = 88) reduced from 9.8% to 8.6% at 6 months (p < 0.0001) and sustained significant reductions at 12, 18, 24, 30, and 36 months (p < 0.05). Highly Engaged patients with hypertension (n = 152) had significant, sustained reductions in blood pressure (p < 0.0001). Engaged patients in the same high-risk groups also had significant improvements in HbA1c and blood pressure. Both engagement subgroups had moderate improvements in weight change and cholesterol. This study shows promising associations of TK services that promote chronic-disease self-management with improved clinical outcomes among higher risk patients (e.g., high blood pressure, high HbA1c, high low-density lipoprotein) with different medical issues (e.g., diabetes, obesity) and social barriers (e.g., food insecurity).
Nasal CPAP in the Pediatric Ward to Reduce PICU Admissions for Severe Bronchiolitis?
Authors: Aricò Melodie O. , Wrona Diana , Lavezzo Giovanni , Valletta Enrico
Published: October 2023

In treating acute bronchiolitis in infants, the decision to use continuous positive airway pressure (CPAP) often involves infant referral from the pediatric ward to the pediatric intensive care unit (PICU). We present our experience of CPAP use in a general pediatric ward, aiming to reduce the pressure on the PICU in recent outbreaks of bronchiolitis. Clinical data of patients less than 12 months of age and admitted for bronchiolitis from 1 October 2021 to 31 March 2023 were retrospectively collected. Of 82 infants admitted for bronchiolitis, 16 (19%) were treated with nasal CPAP (nCPAP group); of the remaining 66, 21 (26%) were treated with a low-flow nasal cannula (LFNC) only, 1 (1%) was also treated a with high-flow nasal cannula (HFNC), 12 (15%) were treated with an HFNC only, and 41 (50%) were treated without oxygen support (no-nCPAP group). Overall, coinfection with RSV and SARS-CoV-2 was observed in three patients and SARS-CoV-2 infection was observed in two patients. None of them required any type of oxygen support. Only 3/16 (19%) infants in the nCPAP group were referred to the PICU due to worsening clinical conditions despite nCPAP support. In our experience of treating epidemic bronchiolitis, nCPAP can be safely managed in a general pediatric ward, thus reducing the burden of admissions to the PICU. Training and regular updating of the pediatric staff, careful monitoring of the patient, and close cooperation with the PICU were instrumental for our team.
A New Cathepsin D Targeting Drug Delivery System Based on Immunoliposomes Functionalized with Lipidated Pepstatin A
Authors: Kozak Andreja , Mikhaylov Georgy , Khodakivskyi Pavlo , Goun Elena , Turk Boris , Vasiljeva Olga
Published: October 2023

Cathepsin D is an aspartic protease and one of the most abundant proteases. It is overexpressed in many cancers and plays an important role in tumor development, progression, and metastasis. While it is a physiologically intracellular protein, cathepsin D is secreted into the extracellular matrix under pathological conditions, making it an appealing target for drug delivery systems. Here, we present the development and evaluation of a new delivery system for tumor targeting based on immunoliposomes functionalized with pepstatin A—a natural peptide inhibitor of cathepsin D. A lipid tail was added to pepstatin A, enabling its incorporation into the liposomal lipid bilayer. The successful targeting of cathepsin D was confirmed using recombinant cathepsin D and in tumor cell lines, showing the feasibility of this targeting approach and its potential for in vivo use in theragnostic applications.
Predicting Maternal and Infant Tetrahydrocannabinol Exposure in Lactating Cannabis Users: A Physiologically Based Pharmacokinetic Modeling Approach
Authors: Shenkoya Babajide , Yellepeddi Venkata , Mark Katrina , Gopalakrishnan Mathangi
Published: October 2023

A knowledge gap exists in infant tetrahydrocannabinol (THC) data to guide breastfeeding recommendations for mothers who use cannabis. In the present study, a paired lactation and infant physiologically based pharmacokinetic (PBPK) model was developed and verified. The verified model was used to simulate one hundred virtual lactating mothers (mean age: 28 years, body weight: 78 kg) who smoked 0.32 g of cannabis containing 14.14% THC, either once or multiple times. The simulated breastfeeding conditions included one-hour post smoking and subsequently every three hours. The mean peak concentration (Cmax) and area under the concentration–time curve (AUC(0–24 h)) for breastmilk were higher than in plasma (Cmax: 155 vs. 69.9 ng/mL; AUC(0–24 h): 924.9 vs. 273.4 ng·hr/mL) with a milk-to-plasma AUC ratio of 3.3. The predicted relative infant dose ranged from 0.34% to 0.88% for infants consuming THC-containing breastmilk between birth and 12 months. However, the mother-to-infant plasma AUC(0–24 h) ratio increased up to three-fold (3.4–3.6) with increased maternal cannabis smoking up to six times. Our study demonstrated the successful development and application of a lactation and infant PBPK model for exploring THC exposure in infants, and the results can potentially inform breastfeeding recommendations.
Research on Adaptive Transmit Diversity Strategy for Reducing Interference in Underwater Optical Multi-Beam Non-Orthogonal Multiple Access Systems
Authors: Li Yanlong , Jiang Yutong , Chen Xiao , Jiang Pengcheng , Li Shuaixing , Hu Yu
Published: October 2023

With the rapid development of the underwater Internet of Things (IoT), the number of underwater communication nodes is rapidly increasing. The access capacity of a traditional multi-antenna communication system is limited by the number of transmitting antennas, and multi-beam communication systems using non-orthogonal multiple access (NOMA) technology can enhance the access capacity of the system. However, this can lead to serious inter-beam and intra-beam interference. To address the severe issues of inter-beam and intra-beam interference in underwater multi-beam NOMA systems, we propose an adaptive transmit diversity strategy. We design an algorithm for adaptive selection and merging beams based on the degree of interference between beams in space, which merges LED beams with high interference. Diversity technology is used to reduce interference between beams, and spatial multiplexing is still performed between LED groups with low interference. Within the same beam, we use an OFDM-NOMA scheme to match and group the users. Signals from different user groups are sent through different subcarriers to improve resource utilization. This enhances access capacity while reducing NOMA inter-user interference. Simulation results show that the bit error rate (BER) of users with the adaptive transmit diversity strategy satisfies the forward error correction (FEC) limits in the presence of high inter-beam interference and has a better reachable rate and BER performance compared to the multi-beam access system without interference management. We also analyze the system BER performance of the proposed strategy in the multi-user case, and the BER of all 32 access nodes are lower than the FEC threshold at a communication distance of 5 m. This demonstrates that the strategy can effectively reduce the interference of the multi-beam NOMA system.
Precision Spectroscopy of Radiation Transitions between Singlet Rydberg States of the Group IIb and Yb Atoms
Authors: Glukhov Igor L. , Kamenski Aleksandr A. , Ovsiannikov Vitaly D. , Palchikov Vitaly G.
Published: October 2023

The measurements of microwave (μw) and radio-frequency (RF) radiation quantitative parameters may be based on the quantum–optical approach to determine the spectral characteristics of radiation transitions between the Rydberg states of atoms. Frequencies and matrix elements are calculated for dipole transitions between opposite-parity Rydberg states nL 1L and n′L±1 1L±1 (where n′= n,n±1,n±2) of the singlet series in the alkaline–earth–metal-like atoms of group IIb (Zn, Cd, Hg) and Yb. The matrix elements determine the shifts of Rydberg-state energy levels in the field of resonance μw or RF radiation, splitting the resonance of electromagnetically induced transparency (EIT) for intensely absorbed probe radiation. Numerical computations based on the single-electron quantum defect method (QDM) and the Fues’ model potential (FMP) approach with the use of the most reliable data from the current literature on quantum defect values are performed for frequencies and matrix elements of transitions between singlet Rydberg states of 1S0-, 1P1-, 1D2-, and 1F3-series in Zn, Cd, Hg, and Yb atoms. The calculated data are approximated by polynomials in the powers of the principal quantum numbers. The polynomial coefficients are determined with the use of a standard curve-fitting interpolation polynomial procedure for numerically calculated functions. These approximation expressions provide new possibilities for accurately evaluating the frequencies and matrix elements of dipole transitions between Rydberg states over a wide range of quantum numbers n >> 1, accompanied by the emission and absorption of μw and RF photons.
Capture Dynamics of Dielectric Microparticles in Hollow-Core-Fiber-Based Optical Traps
Authors: Li Kun , Wang Rui , Shao Shuangyun , Xie Fang , Jiang Yi , Xie Shangran
Published: October 2023

Optical traps formed in hollow-core fibers (HCFs) can overcome several limitations of conventional free-space optical tweezers. One of the key issues is to load particles from free space into the hollow core with high efficiency, in which process the capture dynamics of the particles in front of the HCF endface plays an important role. In this work, a comprehensive model of the trapping and capture process of the dielectric particles in front of HCF is established by taking into account the features of the fiber modes and the motional parameters of the particles. Stable capture positions are predicted based on analytical calculations of optical forces, and the dependencies of the equilibrium axial trapping position on the beam numerical aperture, the fiber core and particle diameters are provided. In addition, the trajectories and the capture dynamics of the particles are studied by solving the equation of motion for the particles under the impact of optical forces, predicting feasible parameter ranges of the initial amplitude and direction of particle launch velocity for achieving successful particle capture in front of HCF. The results can provide guidance for further improving the particle-loading efficiencies of the HCF-based optical traps, which may find applications of flying particle sensors and long-range particle binding in HCFs.
Dendrological Secrets of the Pazaislis Monastery in Central Lithuania: DNA Markers and Morphology Reveal Tilia × europaea L. Hybrids of an Impressive Age
Authors: Jurkšienė Girmantė , Danusevičius Darius , Kembrytė-Ilčiukienė Rūta , Baliuckas Virgilijus
Published: October 2023

We benefited from the availability of a species-specific DNA marker to describe the morphometry of T. cordata × platyphyllos hybrids of an impressive age (ca. 150 years) grown in the Pazaislis baroque monastery yard in Central Lithuania. In an earlier study on a country-wide set of 543 T. cordata individuals from natural forest populations in Lithuania, we detected a nuclear microsatellite locus Tc8 well-differentiating between T. cordata and T. platyphyllos. The Tc8 locus contained a 140 bp allele in T. cordata (541 sampled individuals) and alleles above 160 bp in the two trees with a T. platyphyllos-like morphology (sampled in a national park). To verify the Tc8 locus as species specific, we sampled a further four T. platyphyllos-like individuals, which all contained the Tc8 locus alleles above 160 bp. We subsequently genotyped the six old-growth individuals from the Pazaislis monastery with mixed T. cordata × platyphyllos morphology. Results revealed that all six old-growth Tilia individuals from the Pazaislis monastery were heterozygous for the Tc8 locus with alleles of 140 bp (indicative of T. cordata) and 162 bp (indicative of T. platyphyllos). This finding confirms the morphological observations that these individuals are hybrids between T. cordata and T. platyphyllos. Additionally, the genotyping of a set of 14 nuclear microsatellite loci revealed that all six trees from the Pazaislis monastery are clones, possessing identical microsatellite genotypes. After the molecular identification, we morphotyped leaves, bracts, twigs, and nuts of the 6 old-growth T. cordata × platyphyllos hybrids from the Pazaislis monastery, 16 T. cordata old-growth trees, 4 T. × europaea var. europaea ‘Pallida’ trees growing near the Pazaislis monastery, and 4 mature T. platyphyllos trees from a nearby Girionys park. The morphotyping showed that T. cordata × platyphyllos hybrids may be the easiest to distinguish from T. cordata by raised and horizontally tertiary veins of leaves.
Road Impact on Plant Colonization in the Arid Timanfaya National Park
Authors: Bernardos María , Cornejo Natalia Sierra , Torres Hassan Antonio Daniel , Cabrera Raimundo , Arévalo José Ramón
Published: October 2023

Roads have the potential to alter local environmental conditions, such as the availability of water and nutrients, and rapidly create suitable habitats for the establishment of both native and non-native plant species, transforming the ecosystems. This is a challenge in Timanfaya National Park and Los Volcanes Natural Park on Lanzarote Island, protected areas that have experienced primary succession after recent volcanic eruptions. In arid ecosystems, changes in abiotic conditions along roadsides might facilitate colonization and plant growth. We analyzed the effect of roads and road type on plant species composition and richness at a spatiotemporal scale. Vascular plant species were systematically recorded at three distances from the road edge on both sides, across fourteen zones in the wet and dry seasons, for three years. Results showed that there were slight differences on species composition depending on the distance to the road edge, as well as on the zones. Species richness was also determined by the interaction of the position, zones, and season, being higher at the road edge. Furthermore, zones with higher traffic intensity showed a higher presence of both native and non-native species. This study highlights the importance of the awareness about the road impacts on species composition by enhancing the colonization capacity of species while facilitating the entry of invasive ones. Good management practices regarding infrastructures in natural protected areas are crucial for the conservation of their unique flora, landscapes, and natural succession processes.
Comparison of Phenolic Compounds and Evaluation of Antioxidant Properties of Porophyllum ruderale (Jacq.) Cass (Asteraceae) from Different Geographical Areas of Queretaro (Mexico)
Authors: Vargas-Madriz Ángel Félix , Luzardo-Ocampo Ivan , Chávez-Servín Jorge Luis , Moreno-Celis Ulisses , Roldán-Padrón Octavio , Vargas-Madriz Haidel , Vergara-Castañeda Haydé Azeneth , Kuri-García Aarón
Published: October 2023

Porophyllum ruderale (P. ruderale) is a well-known Mexican plant from the group of “Quelites”, widely consumed plant species used for several food and medicinal purposes. As the production is very heterogeneous and the diverse agroclimatic conditions significantly impact the plant’s phytochemical composition, this research aimed to compare the phenolic compound composition and the antioxidant capacity of the P. ruderale plant from three different collection sites (Queretaro, Landa de Matamoros, and Arroyo Seco) in the State of Queretaro (Mexico). Plants collected from Queretaro displayed the lowest total phenolic compounds, flavonoids, and condensed tannins, reflected in a lower antioxidant capacity (DPPH, FRAP, ABTS), compared to the other collection places. Flavones (epicatechin and epigallocatechin gallate) were the most abundant (36.1–195.2 μg equivalents/g) phenolics quantified by HPLC-DAD, while 31 compounds were identified by UHPLC-DAD-QToF/MS-ESI. Most compounds were linked to biological mechanisms related to the antioxidant properties of the leaves. A PCA analysis clustered Landa de Matamoros and Arroyo Seco into two groups based on flavones, hydroxybenzoic acids, the antioxidant capacity (ABTS and DPPH), and total phenolic compounds, the main contributors to its variation. The results indicated contrasting differences in the polyphenolic composition of collected P. ruderale in Queretaro, suggesting the need to standardize and select plants with favorable agroclimatic conditions to obtain desirable polyphenolic compositions while displaying potential health benefits.
Water Stress Alters Physiological, Spectral, and Agronomic Indexes of Wheat Genotypes
Authors: Tavares Cássio Jardim , Ribeiro Junior Walter Quadros , Ramos Maria Lucrécia Gerosa , Pereira Lucas Felisberto , Muller Onno , Casari Raphael Augusto das Chagas Noqueli , de Sousa Carlos Antonio Ferreira , da Silva Anderson Rodrigo
Published: October 2023

Selecting drought-tolerant and more water-efficient wheat genotypes is a research priority, specifically in regions with irregular rainfall or areas where climate change is expected to result in reduced water availability. The objective of this work was to use high-throughput measurements with morphophysiological traits to characterize wheat genotypes in relation to water stress. Field experiments were conducted from May to September 2018 and 2019, using a sprinkler bar irrigation system to control water availability to eighteen wheat genotypes: BRS 254; BRS 264; CPAC 01019; CPAC 01047; CPAC 07258; CPAC 08318; CPAC 9110; BRS 394 (irrigated biotypes), and Aliança; BR 18_Terena; BRS 404; MGS Brilhante; PF 020037; PF 020062; PF 120337; PF 100368; PF 080492; and TBIO Sintonia (rainfed biotypes). The water regimes varied from 22 to 100% of the crop evapotranspiration replacement. Water stress negatively affected gas exchange, vegetation indices, and grain yield. High throughput variables TCARI, NDVI, OSAVI, SAVI, PRI, NDRE, and GNDVI had higher yield and morphophysiological measurement correlations. The drought resistance index indicated that genotypes Aliança, BRS 254, BRS 404, CPAC 01019, PF 020062, and PF 080492 were more drought tolerant.
Chiranthodendron pentadactylon Larreat (Sterculiaceae), a Potential Nephroprotector against Oxidative Damage Provoked by STZ-Induced Hyperglycemia in Rats
Authors: Santiago-Balmaseda Eira , Segura-Cobos David , Garín-Aguilar María Eugenia , San Miguel-Chávez Rubén , Cristóbal-Luna José Melesio , Madrigal-Santillán Eduardo , Gutierrez-Rebolledo Gabriel Alfonso , Chamorro-Cevallos Germán Alberto , Pérez-Pastén-Borja Ricardo
Published: October 2023

Background: Chiranthodendron pentadactylon, known in Mexico as the “tree of the little hands”, flower’s infusion is used to treat kidney failure associated with diseases such as diabetes. The aim of this work is to evaluate the antioxidant effect of the methanolic extract of its flowers on oxidative damage in kidneys caused by streptozotocin in rats. Methods: The extract phytochemical profile was performed with HPLC. Antioxidant potential in vitro was determined with DPPH and total phenolic tests; antioxidant evaluation in vivo was performed in diabetic rats administered daily via the intragastric route (100 and 200 mg/kg) for 6 weeks; serum glucose/creatinine, food/water consumption, and urinary volume were measured. Relative weight, protein/DNA ratios and oxidative stress were measured in renal tissue. Results: The extract showed 20.53% of total phenolic content and IC50 of 18.05 µg/mL in DPPH, and this was associated with ferulic acid, phloretin and α-amyrin. Both doses showed a moderate decrease in the protein/DNA ratio in renal tissue, and the same behavior was observed for total urinary protein loss and serum creatinine, while the best antioxidant effect was exerted by a lower dose, which increased catalase activity and decreased lipid peroxidation in the kidneys. Conclusions: Results demonstrated that C. pentadactylon methanolic flower’s extract improves renal function through antioxidant mechanisms during experimental diabetes.
In Silico Verification of Predicted Potential Promoter Sequences in the Rice (Oryza sativa) Genome
Authors: Bubnova Anastasiya N. , Yakovleva Irina V. , Korotkov Eugene V. , Kamionskaya Anastasiya M.
Published: October 2023

The exact identification of promoter sequences remains a serious problem in computational biology, as the promoter prediction algorithms under development continue to produce false-positive results. Therefore, to fully assess the validity of predicted sequences, it is necessary to perform a comprehensive test of their properties, such as the presence of downstream transcribed DNA regions behind them, or chromatin accessibility for transcription factor binding. In this paper, we examined the promoter sequences of chromosome 1 of the rice Oryza sativa genome from the Database of Potential Promoter Sequences predicted using a mathematical algorithm based on the derivation and calculation of statistically significant promoter classes. In this paper TATA motifs and cis-regulatory elements were identified in the predicted promoter sequences. We also verified the presence of potential transcription start sites near the predicted promoters by analyzing CAGE-seq data. We searched for unannotated transcripts behind the predicted sequences by de novo assembling transcripts from RNA-seq data. We also examined chromatin accessibility in the region of the predicted promoters by analyzing ATAC-seq data. As a result of this work, we identified the predicted sequences that are most likely to be promoters for further experimental validation in an in vivo or in vitro system.
Antioxidant Properties and Prediction of Bioactive Peptides Produced from Flixweed (sophia, Descurainis sophia L.) and Camelina (Camelina sativa (L.) Crantz) Seed Meal: Integrated In Vitro and In Silico Studies
Authors: Ngo Na Thi Ty , Senadheera Tharindu R. L. , Shahidi Fereidoon
Published: October 2023

Flixweed (sophia) seed meal and camelina, both by-products of oil processing, were employed to generate protein hydrolysates by applying Flavourzyme and Alcalase. This study aimed to integrate in vitro and in silico methods to analyze sophia and camelina protein hydrolysates for releasing potent antioxidative, dipeptidyl peptidase IV (DPP IV) inhibitors and angiotensin-converting enzyme (ACE) inhibitory peptides. In vitro methods were used to investigate the antioxidant potential of sophia/camelina protein hydrolysates. Bioinformatics techniques, including Peptideranker, BIOPEP, Toxinpred, AlgPred, and SwissADME, were employed to obtain the identification of bioactive peptides produced during the hydrolysis process. Protein hydrolysates produced from sophia and camelina seed meal exhibited higher ABTS and DPPH radical scavenging activities Ithan their protein isolates. Among the produced protein hydrolysates, Alcalase-treated samples showed the highest oxygen radical absorbance capacity and hydroxyl radical scavenging activity. In addition, sophia/camelina hydrolysates prevented hydroxyl and peroxyl radical-induced DNA scission and LDL cholesterol oxidation. In silico proteolysis was conducted on Alcalase-treated samples, and resultant peptides showed potential DPP IV and ACE-inhibitory activities. Identified peptides were further assessed for their toxicity and medicinal properties. Results indicate that all digestive-resistant peptides were non-toxic and had desirable drug-like properties. The findings of this study suggest that sophia/camelina protein hydrolysates are promising candidates for functional foods, nutraceuticals, and natural therapeutics.
Effects of Nd2O3 Nanoparticles on the Structural Characteristics and Dielectric Properties of PVA Polymeric Films
Authors: Alshammari Khulaif , Alashgai Thamer , Alshammari Alhulw H. , Abdelhamied Mostufa M. , Alotibi Satam , Atta Ali
Published: October 2023

Polyvinyl alcohol (PVA) and Neodymium (III) oxide (Nd2O3) were combined to synthesized flexible innovative PVA/Nd2O3 polymer composite samples utilizing a solution casting approach for use in dielectric devices. The XRD, FTIR, and SEM methods are all investigated to characterize the composite films. In a frequency of 50 Hz to 5 MHz, the effects of additive Nd2O3 on the dielectric behavior of PVA were recorded. The PVA/Nd2O3 composite films were successfully fabricated, as shown by XRD and infrared spectroscopy. The scanning microscopy pictures showed that the Nd2O3 was loaded and distributed uniformly throughout the PVA. After the incorporation of Nd2O3, the composite PVA/Nd2O3 has a conductivity of 6.82 × 10−9 S·cm−1, while the PVA has a conductivity of 0.82 × 10−9 S·cm−1. Another improvement is the decrease in the relaxation time from 14.2 × 10−5 s for PVA to 6.35 × 10−5 s for PVA/Nd2O3, and an increase in the dielectric constant of 0.237 for PVA to 0.484 at a frequency of 100 Hz. The results showed that the composite samples have considerable changes as flexible films in different applications, including batteries and electronic circuits.
Spray Drying Enzyme-Treated Cellulose Nanofibrils
Authors: Hwang Sungjun , Walker Colleen C. , Johnson Donna , Han Yousoo , Gardner Douglas J.
Published: October 2023

Enzyme-treated cellulose nanofibrils (CNFs) were produced via a lab-scale mass colloider using bleached kraft pulp (BKP) to evaluate their processability and power requirements during refining and spray-drying operations. To evaluate the energy efficiency in the CNF refining process, the net energy consumption, degree of polymerization (DP), and viscosity were determined. Less energy was consumed to attain a given fines level by using the endoglucanase enzymes. The DP and viscosity were also decreased using the enzymes. The morphological properties of the enzyme-pretreated spray-dried CNF powders (SDCNFs) were measured. Subsequently, the enzyme-pretreated SDCNFs were added to a PP matrix with MAPP as a coupling agent. The mixture was then compounded through a co-rotating twin-screw extruder to determine whether the enzyme treatment of the CNFs affects the mechanical properties of the composites. Compared to earlier studies on enhancing PMCs with SDCNF powders, this research investigates the use of enzyme-pretreated SDCNF powders. It was confirmed that the strength properties of PP increased by adding SDCNFs, and the strength properties were maintained after adding enzyme-pretreated SDCNFs.
UV-Cured Bio-Based Acrylated Soybean Oil Scaffold Reinforced with Bioactive Glasses
Authors: Bergoglio Matteo , Najmi Ziba , Cochis Andrea , Miola Marta , Vernè Enrica , Sangermano Marco
Published: October 2023

In this study, a bio-based acrylate resin derived from soybean oil was used in combination with a reactive diluent, isobornyl acrylate, to synthetize a composite scaffold reinforced with bioactive glass particles. The formulation contained acrylated epoxidized soybean oil (AESO), isobornyl acrylate (IBOA), a photo-initiator (Irgacure 819) and a bioactive glass particle. The resin showed high reactivity towards radical photopolymerisation, and the presence of the bioactive glass did not significantly affect the photocuring process. The 3D-printed samples showed different properties from the mould-polymerised samples. The glass transition temperature Tg showed an increase of 3D samples with increasing bioactive glass content, attributed to the layer-by-layer curing process that resulted in improved interaction between the bioactive glass and the polymer matrix. Scanning electron microscope analysis revealed an optimal distribution on bioactive glass within the samples. Compression tests indicated that the 3D-printed sample exhibited higher modulus compared to mould-synthetized samples, proving the enhanced mechanical behaviour of 3D-printed scaffolds. The cytocompatibility and biocompatibility of the samples were evaluated using human bone marrow mesenchymal stem cells (bMSCs). The metabolic activity and attachment of cells on the samples’ surfaces were analysed, and the results demonstrated higher metabolic activity and increased cell attachment on the surfaces containing higher bioactive glass content. The viability of the cells was further confirmed through live/dead staining and reseeding experiments. Overall, this study presents a novel approach for fabricating bioactive glass reinforced scaffolds using 3D printing technology, offering potential applications in tissue engineering.
On the Analogy of Processes in Thermodynamic and Microeconomic Systems
Authors: Tsirlin Anatoly M. , Balunov Alexander I.
Published: October 2023

This work states the typical problems in thermodynamic optimization. The authors present an overview of the results of studies focused on the ultimate capabilities of macrosystems in thermodynamics and microeconomics, taking into account the irreversibility of the processes occurring in them. The research methodology is based on adding an entropy balance to energy and matter balances. This allows for the refining of reversible indicators, such as the reversible efficiency coefficient, by accounting for kinetic factors, such as transfer coefficients, which indirectly reflect the size of devices, kinetic equation forms, and others. For processes that use heat energy, the set of feasible solutions within the ‘target flow intensity–energy expenses’ plane is convex upwards and limited. This paper also provides conditions for the minimum dissipation of processes at a given intensity. These conditions define the boundary of the feasibility set. Finally, this paper compares and lists the similarities between thermodynamic and microeconomic systems and demonstrates the ultimate capabilities of an intermediary in microeconomic systems and the optimal parameters of a working medium in thermodynamic systems. These are divided into active and passive subsystems. The latter, in turn, can have finite and infinite capacity (reservoirs).