bluuebunny/crossref_metadata_2025 huggingface dataset:
High-angle deflection of metagrating-integrated laser emission for high-contrast microscopy
Authors: Juodėnas Mindaugas , Strandberg Erik , Grabowski Alexander , Gustavsson Johan , Šípová-Jungová Hana , Larsson Anders , Käll Mikael
Published: October 2023

Flat metaoptics components are looking to replace classical optics elements and could lead to extremely compact biophotonics devices if integrated with on-chip light sources and detectors. However, using metasurfaces to shape light into wide angular range wavefronts with high efficiency, as is typically required in high-contrast microscopy applications, remains a challenge. Here we demonstrate curved GaAs metagratings integrated on vertical-cavity surface-emitting lasers (VCSELs) that enable on-chip illumination in total internal reflection and dark field microscopy. Based on an unconventional design that circumvents the aspect ratio dependent etching problems in monolithic integration, we demonstrate off-axis emission centred at 60° in air and 63° in glass with > 90% and > 70% relative deflection efficiency, respectively. The resulting laser beam is collimated out-of-plane but maintains Gaussian divergence in-plane, resulting in a long and narrow illumination area. We show that metagrating-integrated VCSELs of different kinds can be combined to enable rapid switching between dark-field and total internal reflection illumination. Our approach provides a versatile illumination solution for high-contrast imaging that is compatible with conventional microscopy setups and can be integrated with biophotonics devices, such as portable microscopy, NIR-II range bioimaging, and lab-on-a-chip devices.
Chemogenetic activation of CRF neurons as a model of chronic stress produces sex-specific physiological and behavioral effects
Authors: Montgomery Kristen R. , Bridi Morgan S. , Folts Lillian M. , Marx-Rattner Ruth , Zierden Hannah C. , Wulff Andreas B. , Kodjo Emmanuela A. , Thompson Scott M. , Bale Tracy L.
Published: October 2023

Trauma and chronic stress exposure are the strongest predictors of lifetime neuropsychiatric disease presentation. These disorders often have significant sex biases, with females having higher incidences of affective disorders such as major depression, anxiety, and PTSD. Understanding the mechanisms by which stress exposure heightens disease vulnerability is essential for developing novel interventions. Current rodent stress models consist of a battery of sensory, homeostatic, and psychological stressors that are ultimately integrated by corticotropin-releasing factor (CRF) neurons to trigger corticosteroid release. These stress paradigms, however, often differ between research groups in the type, timing, and duration of stressors utilized. These inconsistencies, along with the variability of individual animals’ perception and response to each stressor, present challenges for reproducibility and translational relevance. Here, we hypothesized that a more direct approach using chemogenetic activation of CRF neurons would recapitulate the effects of traditional stress paradigms and provide a high-throughput method for examining stress-relevant phenotypes. Using a transgenic approach to express the Gq-coupled Designer Receptor Exclusively Activated by Designer Drugs (DREADD) receptor hM3Dq in CRF-neurons, we found that the DREADD ligand clozapine-N-oxide (CNO) produced an acute and robust activation of the hypothalamic-pituitary-adrenal (HPA) axis, as predicted. Interestingly, chronic treatment with this method of direct CRF activation uncovered a novel sex-specific dissociation of glucocorticoid levels with stress-related outcomes. Despite hM3Dq-expressing females producing greater corticosterone levels in response to CNO than males, hM3Dq-expressing males showed significant typical physiological stress sensitivity with reductions in body and thymus weights. hM3Dq-expressing females while resistant to the physiological effects of chronic CRF activation, showed significant increases in baseline and fear-conditioned freezing behaviors. These data establish a novel mouse model for interrogating stress-relevant phenotypes and highlight sex-specific stress circuitry distinct for physiological and limbic control that may underlie disease risk.
Prognostic indices in diffuse large B-cell lymphoma: a population-based comparison and validation study of multiple models
Authors: Jelicic Jelena , Juul-Jensen Karen , Bukumiric Zoran , Roost Clausen Michael , Ludvigsen Al-Mashhadi Ahmed , Pedersen Robert Schou , Poulsen Christian Bjørn , Brown Peter , El-Galaly Tarec Christoffer , Stauffer Larsen Thomas
Published: October 2023

Currently, the International Prognostic Index (IPI) is the most used and reported model for prognostication in patients with newly diagnosed diffuse large B-cell lymphoma (DLBCL). IPI-like variations have been proposed, but only a few have been validated in different populations (e.g., revised IPI (R-IPI), National Comprehensive Cancer Network IPI (NCCN-IPI)). We aimed to validate and compare different IPI-like variations to identify the model with the highest predictive accuracy for survival in newly diagnosed DLBCL patients. We included 5126 DLBCL patients treated with immunochemotherapy with available data required by 13 different prognostic models. All models could predict survival, but NCCN-IPI consistently provided high levels of accuracy. Moreover, we found similar 5-year overall survivals in the high-risk group (33.4%) compared to the original validation study of NCCN-IPI. Additionally, only one model incorporating albumin performed similarly well but did not outperform NCCN-IPI regarding discrimination (c-index 0.693). Poor fit, discrimination, and calibration were observed in models with only three risk groups and without age as a risk factor. In this extensive retrospective registry-based study comparing 13 prognostic models, we suggest that NCCN-IPI should be reported as the reference model along with IPI in newly diagnosed DLBCL patients until more accurate validated prognostic models for DLBCL become available.
Interfacial co-assembly strategy towards gradient mesoporous hollow sheet for molecule filtration
Authors: Dong Yangbo , Feng Danyang , Li Wei , Zhang Rui , Dou Shuzhen , Wang Luoqi , Yang Yan , Wang Li , Yang Yang , Wei Feng , Qiao Zhen-An
Published: October 2023

Gradient porous structures enable the fast capillary-directed mass transport and enhance the chemical reaction rate with optimal efficiency and minimal energy consumption. Rational design and facile synthesis of functional mesoporous materials with sheet structure and gradient mesopores still face challenges of stacked structures and unadjustable pore sizes. Herein, an interfacial co-assembly strategy for gradient mesoporous hollow silica sheets is reported. The modulated oil-water interface allows the assembly of gradient mesoporous silica layers on the water-removable ammonium sulfate crystals. The obtained mesoporous silica layers possess narrow pore size distributions (~2.2 nm and ~6.6 nm). Owing to the good mono-dispersity, sheet structure and proper pore size, the designed gradient mesoporous hollow silica sheets can serve as flexible building blocks for fabricating nanoscale molecule filtration device. Experiments reveal that the obtained nanofiltration device shows remarkable gradient rejection rates (range from 23.5 to 99.9%) for molecules with different sizes (range from 1.2 to 4.4 nm).
Tunable encapsulation of sessile droplets with solid and liquid shells
Authors: Lathia Rutvik , Nagpal Satchit , Modak Chandantaru Dey , Mishra Satyarthi , Sharma Deepak , Reddy Bheema Sankar , Nukala Pavan , Bhat Ramray , Sen Prosenjit
Published: October 2023

Droplet encapsulations using liquid or solid shells are of significant interest in microreactors, drug delivery, crystallization, and cell growth applications. Despite progress in droplet-related technologies, tuning micron-scale shell thickness over a large range of droplet sizes is still a major challenge. In this work, we report capillary force assisted cloaking using hydrophobic colloidal particles and liquid-infused surfaces. The technique produces uniform solid and liquid shell encapsulations over a broad range (5–200 μm shell thickness for droplet volume spanning over four orders of magnitude). Tunable liquid encapsulation is shown to reduce the evaporation rate of droplets by up to 200 times with a wide tunability in lifetime (1.5 h to 12 days). Further, we propose using the technique for single crystals and cell/spheroid culture platforms. Stimuli-responsive solid shells show hermetic encapsulation with tunable strength and dissolution time. Moreover, scalability, and versatility of the technique is demonstrated for on-chip applications.
Self-protection soft fluidic robots with rapid large-area self-healing capabilities
Authors: Tang Wei , Zhong Yiding , Xu Huxiu , Qin Kecheng , Guo Xinyu , Hu Yu , Zhu Pingan , Qu Yang , Yan Dong , Li Zhaoyang , Jiao Zhongdong , Fan Xujun , Yang Huayong , Zou Jun
Published: October 2023

Soft fluidic robots have attracted a lot of attention and have broad application prospects. However, poor fluidic power source and easy to damage have been hindering their development, while the lack of intelligent self-protection also brings inconvenience to their applications. Here, we design diversified self-protection soft fluidic robots that integrate soft electrohydrodynamic pumps, actuators, healing electrofluids, and E-skins. We develop high-performance soft electrohydrodynamic pumps, enabling high-speed actuation and large deformation of untethered soft fluidic robots. A healing electrofluid that can form a self-healed film with excellent stretchability and strong adhesion is synthesized, which can achieve rapid and large-areas-damage self-healing of soft materials. We propose multi-functional E-skins to endow robots intelligence, making robots realize a series of self-protection behaviors. Moreover, our robots allow their functionality to be enhanced by the combination of electrodes or actuators. This design strategy enables soft fluidic robots to achieve their high-speed actuation and intelligent self-protection, opening a door for soft robots with physical intelligence.
Digital data storage on DNA tape using CRISPR base editors
Authors: Sadremomtaz Afsaneh , Glass Robert F. , Guerrero Jorge Eduardo , LaJeunesse Dennis R. , Josephs Eric A. , Zadegan Reza
Published: October 2023

While the archival digital memory industry approaches its physical limits, the demand is significantly increasing, therefore alternatives emerge. Recent efforts have demonstrated DNA’s enormous potential as a digital storage medium with superior information durability, capacity, and energy consumption. However, the majority of the proposed systems require on-demand de-novo DNA synthesis techniques that produce a large amount of toxic waste and therefore are not industrially scalable and environmentally friendly. Inspired by the architecture of semiconductor memory devices and recent developments in gene editing, we created a molecular digital data storage system called “DNA Mutational Overwriting Storage” (DMOS) that stores information by leveraging combinatorial, addressable, orthogonal, and independent in vitro CRISPR base-editing reactions to write data on a blank pool of greenly synthesized DNA tapes. As a proof of concept, this work illustrates writing and accurately reading of both a bitmap representation of our school’s logo and the title of this study on the DNA tapes.
A lightweight cow mounting behavior recognition system based on improved YOLOv5s
Authors: Wang Rong , Gao Ronghua , Li Qifeng , Zhao Chunjiang , Ma Weihong , Yu Ligen , Ding Luyu
Published: October 2023

To improve the detection speed of cow mounting behavior and the lightness of the model in dense scenes, this study proposes a lightweight rapid detection system for cow mounting behavior. Using the concept of EfficientNetV2, a lightweight backbone network is designed using an attention mechanism, inverted residual structure, and depth-wise separable convolution. Next, a feature enhancement module is designed using residual structure, efficient attention mechanism, and Ghost convolution. Finally, YOLOv5s, the lightweight backbone network, and the feature enhancement module are combined to construct a lightweight rapid recognition model for cow mounting behavior. Multiple cameras were installed in a barn with 200 cows to obtain 3343 images that formed the cow mounting behavior dataset. Based on the experimental results, the inference speed of the model put forward in this study is as high as 333.3 fps, the inference time per image is 4.1 ms, and the model mAP value is 87.7%. The mAP value of the proposed model is shown to be 2.1% higher than that of YOLOv5s, the inference speed is 0.47 times greater than that of YOLOv5s, and the model weight is 2.34 times less than that of YOLOv5s. According to the obtained results, the model proposed in the current work shows high accuracy and inference speed and acquires the automatic detection of cow mounting behavior in dense scenes, which would be beneficial for the all-weather real-time monitoring of multi-channel cameras in large cattle farms.
Pressure driven polymorphic transitions in nanocrystalline Lu2O3, Tm2O3 and Eu2O3
Authors: Bura Neha , Bhoriya Ankit , Yadav Deepa , Velaga Srihari , Govind Bal , Singh Jasveer , Poswal Himanshu Kumar , Sharma Nita Dilawar
Published: October 2023

The crystallite size of the materials considerably influences the material properties, including their compressibility and resistance to external forces and the stability of the crystalline structure; a corresponding study for which, so far, has been limited for the important class of nanocrystalline Rare Earth Sesquioxides (REOs). In the present study, we report the crystallographic structural transitions in nanocrystalline Rare Earth Oxides (REOs) under the influence of pressure, investigated via high-energy X-Ray Diffraction (XRD) measurements. The study has been carried out on three of the REOs, namely Lutetium oxide (Lu2O3), Thulium oxide (Tm2O3) and Europium oxide (Eu2O3) up to the pressures of 33, 22 and 11 GPa, respectively. The diffraction data of Lu2O3 and Tm2O3 suggests the occurrence of irreversible structural transitions from cubic to monoclinic phase, while Eu2O3 showed a transition from the cubic to hexagonal phase. The transitions were found to be accompanied by a collapse in the volume and the resulting Pressure–Volume (P–V) graphs are fitted with the 3rd order Birch-Murnaghan (BM) equation of state (EOS) to estimate the bulk moduli and their pressure derivatives. Our study establishes a qualitative relationship between the crystallite size and various material properties such as the lattice parameters, transition pressure, bulk modulus etc., and strengthens the knowledge regarding the behaviour of this technologically important class of materials.
Transcervical artificial insemination in the brown brocket deer (Subulo gouazoubira): a promising method for assisted reproduction in deer
Authors: Duarte Gabriella Saloni , Galindo David Javier , Baldini Maria Helena Mazzoni , da Fonseca Jeferson Ferreira , Duarte José Mauricio Barbanti , Oliveira Maria Emilia Franco
Published: October 2023

The present study aimed to test the efficiency of transcervical artificial insemination techniques with cervical immobilization (TCAI-CI) or cervical traction (TCAI-CT), associated or not with the use of oxytocin (OT) as a protocol for cervical dilation, in the brown brocket deer (Subulo gouazoubira). The study was carried out in a crossover design using four adult females in two replicates with an interval of 60 days. Estrus was synchronized with oral melengestrol acetate (MGA) associated with estradiol benzoate and sodium cloprostenol. TCAI techniques were performed from 18 to 24 h after estrus onset. All females received either an i.v. application of 50 IU of OT (G-OT, n = 4) or 1 mL of saline solution (G-Control, n = 4) 20 min before the TCAI procedure. The TCAIs were performed using frozen-thawed semen motility 40%, vigor 3, acrosome integrity 87%, membrane integrity of 95% and 13% of total post-thaw defects from the same batch. Behavioral estrus was observed in 100% of the females, in both replicates. It was achieved a 50% (4/8) success of cervical transposition with semen deposition in the uterine. Regarding inseminations, most of them (87.5%) were performed using the TCAI-CT technique, and the overall conception rate was 50%. Cervical transposition times (< 1 min) and TCAI procedures (~ 17 min) were considered satisfactory. Thus, the performance of the TCAI-CI and TCAI-CT techniques was successful, regardless of using OT as a cervical dilation protocol. This procedure is proposed as a method of choice for artificial insemination with greater applicability in different conservation centers, compared to more advanced reproductive biotechniques, and with a favorable impact on the conservation of deer species.
Retest variability and patient reliability indices of quantitative fundus autofluorescence in age-related macular degeneration: a MACUSTAR study report
Authors: von der Emde Leon , Mallwitz Merten , Vaisband Marc , Hasenauer Jan , Saßmannshausen Marlene , Terheyden Jan Henrik ,   MACUSTAR Consortium, Agostini H. , Altay L. , Atia R. , Bandello F. , Basile P. G. , Batuca J. , Behning C. , Belmouhand M. , Berger M. , Binns A. , Boon C. J. F. , Böttger M. , Bouchet C. , Brazier J. E. , Butt T. , Carapezzi C. , Carlton J. , Carneiro A. , Charil A. , Coimbra R. , Cozzi M. , Crabb D. P. , Cunha-Vaz J. , Dahlke C. , de Sisternes L. , Dunbar H. , Finger R. P. , Fletcher E. , Floyd H. , Francisco C. , Gutfleisch M. , Hinz S. , Hogg R. , Holz F. G. , Hoyng C. B. , Kilani A. , Krätzschmar J. , Kühlewein L. , Larsen M. , Leal S. , Lechanteur Y. T. E. , Luhmann U. F. O. , Lüning A. , Marques I. , Martinho C. , Montesano G. , Mulyukov Z. , Paques M. , Parodi B. , Parravano M. , Penas S. , Peters T. , Peto T. , Pfau M. , Poor S. , Priglinger S. , Rowen D. , Rubin G. S. , Sahel J. , Sánchez C. , Sander O. , Saßmannshausen M. , Schmid M. , Schmitz-Valckenberg S. , Siedlecki J. , Silva R. , Skelly A. , Souied E. , Staurenghi G. , Stöhr L. , Taylor D. J. , Terheyden J. H. , Thiele S. , Tufail A. , Varano M. , Vieweg L. , Wintergerst L. , Wolf A. , Zakaria N. , Sloan Kenneth R. , Schmitz-Valckenberg Steffen , Finger Robert P. , Holz Frank G. , Ach Thomas
Published: October 2023

This study aimed to determine the retest variability of quantitative fundus autofluorescence (QAF) in patients with and without age-related macular degeneration (AMD) and evaluate the predictive value of patient reliability indices on retest reliability. A total of 132 eyes from 68 patients were examined, including healthy individuals and those with various stages of AMD. Duplicate QAF imaging was conducted at baseline and 2 weeks later across six study sites. Intraclass correlation (ICC) analysis was used to evaluate the consistency of imaging, and mean opinion scores (MOS) of image quality were generated by two researchers. The contribution of MOS and other factors to retest variation was assessed using mixed-effect linear models. Additionally, a Random Forest Regressor was trained to evaluate the extent to which manual image grading of image quality could be replaced by automated assessment (inferred MOS). The results showed that ICC values were high for all QAF images, with slightly lower values in AMD-affected eyes. The average inter-day ICC was found to be 0.77 for QAF segments within the QAF8 ring and 0.74 for peripheral segments. Image quality was predicted with a mean absolute error of 0.27 on a 5-point scale, and of all evaluated reliability indices, MOS/inferred MOS proved most important. The findings suggest that QAF allows for reliable testing of autofluorescence levels at the posterior pole in patients with AMD in a multicenter, multioperator setting. Patient reliability indices could serve as eligibility criteria for clinical trials, helping identify patients with adequate retest reliability.
The importance of planning CT-based imaging features for machine learning-based prediction of pain response
Authors: Llorián-Salvador Óscar , Akhgar Joachim , Pigorsch Steffi , Borm Kai , Münch Stefan , Bernhardt Denise , Rost Burkhard , Andrade-Navarro Miguel A. , Combs Stephanie E. , Peeken Jan C.
Published: October 2023

Patients suffering from painful spinal bone metastases (PSBMs) often undergo palliative radiation therapy (RT), with an efficacy of approximately two thirds of patients. In this exploratory investigation, we assessed the effectiveness of machine learning (ML) models trained on radiomics, semantic and clinical features to estimate complete pain response. Gross tumour volumes (GTV) and clinical target volumes (CTV) of 261 PSBMs were segmented on planning computed tomography (CT) scans. Radiomics, semantic and clinical features were collected for all patients. Random forest (RFC) and support vector machine (SVM) classifiers were compared using repeated nested cross-validation. The best radiomics classifier was trained on CTV with an area under the receiver-operator curve (AUROC) of 0.62 ± 0.01 (RFC; 95% confidence interval). The semantic model achieved a comparable AUROC of 0.63 ± 0.01 (RFC), significantly below the clinical model (SVM, AUROC: 0.80 ± 0.01); and slightly lower than the spinal instability neoplastic score (SINS; LR, AUROC: 0.65 ± 0.01). A combined model did not improve performance (AUROC: 0,74 ± 0,01). We could demonstrate that radiomics and semantic analyses of planning CTs allowed for limited prediction of therapy response to palliative RT. ML predictions based on established clinical parameters achieved the best results.
Ramadan intermittent fasting is associated with ameliorated inflammatory markers and improved plasma sphingolipids/ceramides in subjects with obesity: lipidomics analysis
Authors: Madkour Mohamed Ibrahim , Islam Md Torikul , Tippetts Trevor S. , Chowdhury Kamrul H. , Lesniewski Lisa A. , Summers Scott A. , Zeb Falak , Abdelrahim Dana N. , AlKurd Refat , Khraiwesh Husam M. , AbuShihab Katia H. , AlBakri Asma , Obaideen Khaled , Faris MoezAlIslam E.
Published: October 2023

Intermittent fasting (IF) is associated with enormous metabolic alterations that underpin its diverse health effects. Changes in lipid metabolism, particularly ceramides, and other sphingolipids, are among the most notable of these alterations. This study investigated the lipidomic alterations associated with 29–30 days of Ramadan diurnal intermittent fasting (RIF) in metabolically healthy overweight and obese subjects. A prospective cohort of 57 overweight and obese adults (70% males, 38.4 ± 11.2 years), with an age range of 18–58 years was observed prior to and at the conclusion of Ramadan. At both time points, anthropometric, biochemical (lipid profile, glycemic, and inflammatory markers), and dietary intake measurements were taken. Using liquid chromatography-mass spectrometry, a lipidomic analysis of ceramides and other sphingolipids was conducted. Using paired sample t-tests, pre- and post-Ramadan anthropometric, biochemical, and dietary values were compared. RIF was associated with improved levels of lipid profile compartments and inflammatory markers. In addition, RIF was associated with a decrease in plasma sphingosine and sphinganine, which was accompanied by a decrease in sphingosine 1-phosphate and sphinganine 1-phosphate. In addition, RIF was associated with decreased C17, C22, and C24 sphingomyelin, but not C14, C16, C18, C20, and C24:1 sphingomyelin, as well as C20, C22, C24, and C24:1 dihydrosphingomyelin, but not C16 and C18 dihydrosphingomyelin. This study demonstrates that RIF is associated with improvements in plasma sphingosine, sphinganine sphingomyelin, and dihydrosphingomyelin lipid species, as well as improved lipid profile and inflammatory markers, which may confer short-term protection against cardiometabolic problems in patients with overweight/obesity.
Research on panic spread and decision behaviour in a delayed SEIR evolutionary game model under an emergency
Authors: Lv Rongjian , Li Hua , Sun Qiubai , Li Bowen
Published: October 2023

Taking major emergencies as the research background, the transmission mechanism for panic spread and the decision behaviour of the opinion field are explored in this paper. By using evolutionary game theory to explore the game relationship between the official opinion field and the public opinion field and by considering the existence of strategy dependency in the same game group, the dependence coefficient is introduced to improve replicator dynamics. The dynamic delayed SEIR evolutionary game model is built by combining the epidemic model with the delay effect within the group, and the stability of the proposed model is analysed. The research results show that the strategy dependency among the same game group has positive and negative effects on the evolution process. The evolution of the dynamic delayed panic SEIR evolutionary game spread model under the effect of a positive effect is simulated. The results suggest that the official opinion field and the public opinion field should actively deal with emergencies, formulate effective control strategies to make the panic within the group disappear, and provide theoretical guidance for the relevant government to formulate plans.
Dormancy-break and germination requirements for seeds of the threatened Austral papaya (Carica chilensis)
Authors: Loayza Andrea P. , García-Guzmán Patricio , Carozzi-Figueroa Giovanni , Carvajal Danny E.
Published: October 2023

Seed dormancy is one of the most important adaptive mechanisms in plants, optimizing germination, seedling emergence, and establishment to ensure these processes occur when environmental conditions are favorable for plant survival and growth. Endemic to rocky environments of the southern Atacama Desert, the Austral papaya (Carica chilensis) is the papaya species with the southernmost distribution within the Caricaceae, thriving in the most extreme environmental conditions. This threatened plant exhibits low natural regeneration, primarily attributed to low germination, yet no information regarding seed dormancy release is available. In this study, we investigated the dormancy-break and germination requirements ofC. chilensis. We hypothesized that ifC. chilensisseeds exhibit physiological dormancy, then seeds with reduced moisture content and those treated with chemicals or growth hormones would exhibit higher germination percentages and faster germination than control seeds akin to other members of Caricacea. Our results confirmed this prediction and revealed that ultra-drying (< 3% moisture content) and treating seeds with sulfuric acid, gibberellic acid, or potassium nitrate are the most effective methods for germinatingC. chilensis. Consequently, we suggest using these treatments to propagate this threatened papaya species.
Characterization of three-nucleate Rhizoctonia AG-E based on their morphology and phylogeny
Authors: Moliszewska Ewa , Maculewicz Dagna , Stępniewska Hanna
Published: October 2023

The genus Rhizoctonia has been classified into two main groups according to the number of nuclei. Binucleate Rhizoctonia strains have two nuclei in each cell, whereas multinucleate Rhizoctonia fungi were observed to have a variable number of nuclei ranging from 4 to 16 in each cell. In the study, twelve Polish isolates were tested. According to ITS1-5,8S-ITS2 rDNA sequences, the isolates were classified in the AG-E. Their affiliation to AG was confirmed by anastomosis reactions with tester isolates. The number of nuclei was counted with DAPI staining under a fluorescent microscope, and the diameter of the hyphae was also measured. Not all AG-E isolates had the same number of nuclei in their cells: one group among these fungi produced cells with a diverse number of nuclei, usually 3; however, this number ranged from 2 to 4, making the average number of nuclei close to 3. It can be assumed that all isolates with three nuclei belong to this group, which may greatly facilitate the preliminary identification of trinucleate isolates of Rhizoctonia spp. belonging to AG-E. Based on these characters, we call these isolates AG-E-3n isolates. The thiamine requirement is not helpful in classifying and describing the AG-E strains.
The novel sterilization device: the prototype testing
Authors: Nowak Robert , Wityk Paweł , Wierzbicka-Woś Anna , Gos Waldemar , Kostrzewa-Nowak Dorota
Published: October 2023

Currently, there are numerous methods that can be used to neutralize pathogens (i.e., devices, tools, or protective clothing), but the sterilizing agent must be selected so that it does not damage or change the properties of the material to which it is applied. Dry sterilization with hydrogen peroxide gas (VHP) in combination with UV-C radiation is well described and effective method of sterilization. This paper presents the design, construction, and analysis of a novel model of sterilization device. Verification of the sterilization process was performed, using classical microbiological methods and flow cytometry, on samples containing Geobacillus stearothermophilus spores, Bacillus subtilis spores, Escherichia coli, and Candida albicans. Flow cytometry results were in line with the standardized microbiological tests and confirmed the effectiveness of the sterilization process. It was also determined that mobile sterilization stations represent a valuable solution when dedicated to public institutions and businesses in the tourism sector, sports & fitness industry, or other types of services, e.g., cosmetic services. A key feature of this solution is the ability to adapt the device within specific constraints to the user’s needs.
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

The 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 $$bound \rightarrow bound$$

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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 $$G0_u^+(\upsilon ^{\prime }=39) \rightarrow X0_g^+$$

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. 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

Xylanases 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

Pairwise 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

Atxurra 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

In 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

When 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

The 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

Prodigiosin, 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

This 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

Intestinal-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.