bluuebunny/crossref_metadata_2025_split huggingface dataset:
Streamlined instrument-free lysis for the detection of Candida auris
Authors: Jin Mei , Trick Alexander Y. , Totten Marissa , Lee Pei-wei , Zhang Sean X. , Wang Tza-Huei 
Published: December 2023

AbstractThe continued spread of Candida auris in healthcare facilities has increased the demand for widely available screening to aid in containment and inform treatment options. Current methods of detection can be unreliable and require bulky and expensive instruments to lyse and identify fungal pathogens. Here, we present a quick, low-cost, instrument-free method for lysis of C. auris suitable for streamlined sample processing with polymerase chain reaction (PCR) detection. Chemical, thermal, and bead beating lysis techniques were evaluated for lysis performance and compatibility with nucleic acid extraction and downstream PCR reactions. Using only 10 s of manual shaking with glass beads, this method demonstrated a limit of detection (LOD) of C. auris at 500 colony forming units per mL, a 20-fold improvement compared to the LOD without manual shaking, and a 60-fold reduction in time compared to common fungal lysis kits, all while maintaining repeatability and reproducibility across multiple users. This work highlights a simple method for increasing sensitivity and reducing turnaround time of PCR-based C. auris detection and exhibits promise for integration into point-of-care platforms towards real-time triage of colonized patients.
Foam formation during drainage of a surfactant solution in a microfluidic porous medium model
Authors: Lima Nicolle , Parsa Shima , Paciornik Sidnei , Carvalho Marcio S. 
Published: December 2023

AbstractFoam has been shown to have great potential to significantly improve sweep efficiency during gas injection in oil recovery, remediation of contaminated sites, gas storage, and acidification processes. The gas mobility reduction largely depends on the generation and stability of lamellae in the pore space that traps the gas phase. Most available analyses focus on foam formation during the co-injection of gas and liquid phases at different fractional flow (foam quality) or flow of foam formed before being injected in the porous media. During surfactant-alternating-gas (SAG) injection, foam is formed as the aqueous phase is displaced by the gas slug that follows. The dynamics of lamellae formation and their stability are different from that of a co-injection process, since the amount of surfactant available to stabilize the gas-liquid interfaces is fixed as fresh surfactant solution is not injected together with the gas phase. This work studies foam formation during the drainage of a surfactant solution by gas injection at a fixed flow rate. A transparent microfluidic model of a porous medium is used in order to enable the correlation of pore-scale phenomena and macroscopic flow behavior. The results show that the maximum number of lamellae increases with surfactant concentration, even much above the critical micelle concentration (CMC). The availability of surfactant molecules needed to stabilize newly formed gas-liquid interfaces rises with concentration. The higher number of lamellae formed at higher surfactant concentration leads to stronger mobility reduction of the gas phase and longer time needed for the gas to percolate through the porous medium.
The effects of challenge or social buffering on cortisol, testosterone, and antler growth in captive red deer (Cervus elaphus) males
Authors: Bartoš Luděk , Esattore Bruno , Kotrba Radim , Pluháček Jan , Ceacero Francisco , Komárková Martina , Dušek Adam , Bartošová Jitka 
Published: December 2023

AbstractWe equipped 17 captive red deer males (Cervus elaphus) with GPS collars to measure inter-individual distances throughout the 5-months of the antler growth period. We expected some individuals to associate regularly with others while others would not. We predicted that males aggregating with others within a socially stable environment (Associates) would benefit from a form of “social buffering” and would likely have lowered cortisol (C) and testosterone (T) concentrations. Males only irregularly joining social groupings would experience elevated levels of aggression; according to the “Challenge hypothesis”, their T and C concentrations should increase. Interacting with a higher proportion of Associates did indeed reduce C concentrations. Conversely, avoiding Associates and challenging other males stimulated the T secretion. Admittedly, males avoiding regular proximity to others tended to develop the largest antlers. They probably benefited from frequent successful agonistic threats to conspecifics, resulting in elevated T concentrations. Regular association with tolerant, conspecifics and “social buffering” did not seem sufficient for producing larger antlers despite reducing C concentrations. Alternative social strategies were adopted within the same group of individuals and showed how the trade-off between these strategies could have an essential impact on C and T concentrations.
Oxidation-treated carbon nanotube yarns accelerate neurite outgrowth and induce axonal regeneration in peripheral nerve defect
Authors: Kunisaki Atsushi , Kodama Akira , Ishikawa Masakazu , Ueda Takahiro , Lima Marcio D. , Kondo Takeshi , Adachi Nobuo 
Published: December 2023

AbstractCarbon nanotubes (CNTs) have the potential to promote peripheral nerve regeneration, although with limited capacity and foreign body reaction. This study investigated whether CNTs hydrophilized by oxidation can improve peripheral nerve regeneration and reduce foreign body reactions and inflammation. Three different artificial nerve conduit models were created using CNTs treated with ozone (O group), strong acid (SA group), and untreated (P group). They were implanted into a rat sciatic nerve defect model and evaluated after 8 and 16 weeks. At 16 weeks, the SA group showed significant recovery in functional and electrophysiological evaluations compared with the others. At 8 weeks, histological examination revealed a significant increase in the density of regenerated neurofilament and decreased foreign body giant cells in the SA group compared with the others. Oxidation-treated CNTs improved biocompatibility, induced nerve regeneration, and inhibited foreign-body reactions.
A multi-modal attention neural network for traffic flow prediction by capturing long-short term sequence correlation
Authors: Huang Xiaohui , Jiang Yuan , Wang Junyang , Lan Yuanchun , Chen Huapeng 
Published: December 2023

AbstractAccurate traffic flow prediction information can help traffic managers and drivers make more rational decisions and choices. To make an effective and accurate traffic flow prediction, we need to consider not only the spatio-temporal dependencies between data, but also the temporal correlation between data. However, most existing methods only consider temporal continuity and ignore temporal correlation. In this paper, we propose a multi-modal attention neural network for traffic flow prediction by capturing long-short term sequence correlation (LSTSC). In the model, we employed attention mechanisms to capture the spatio-temporal correlations of the sequences, and the model based on multiple decision forms demonstrated higher accuracy and reliability. The superiority of the model is demonstrated on two datasets, PeMS08 and PeMSD7(M), particularly for long-term predictions.
A bead-based multiplex assay covering all coronaviruses pathogenic for humans for sensitive and specific surveillance of SARS-CoV-2 humoral immunity
Authors: Stern Daniel , Meyer Tanja C. , Treindl Fridolin , Mages Hans Werner , Krüger Maren , Skiba Martin , Krüger Jan Philipp , Zobel Christian M. , Schreiner Maximilian , Grossegesse Marica , Rinner Thomas , Peine Caroline , Stoliaroff-Pépin Anna , Harder Thomas , Hofmann Natalie , Michel Janine , Nitsche Andreas , Stahlberg Silke , Kneuer Antje , Sandoni Anna , Kubisch Ulrike , Schlaud Martin , Mankertz Annette , Schwarz Tatjana , Corman Victor M. , Müller Marcel A. , Drosten Christian , de la Rosa Kathrin , Schaade Lars , Dorner Martin B. , Dorner Brigitte G. 
Published: December 2023

AbstractSerological assays measuring antibodies against SARS-CoV-2 are key to describe the epidemiology, pathobiology or induction of immunity after infection or vaccination. Of those, multiplex assays targeting multiple antigens are especially helpful as closely related coronaviruses or other antigens can be analysed simultaneously from small sample volumes, hereby shedding light on patterns in the immune response that would otherwise remain undetected. We established a bead-based 17-plex assay detecting antibodies targeting antigens from all coronaviruses pathogenic for humans: SARS-CoV-2, SARS-CoV, MERS-CoV, HCoV strains 229E, OC43, HKU1, and NL63. The assay was validated against five commercial serological immunoassays, a commercial surrogate virus neutralisation test, and a virus neutralisation assay, all targeting SARS-CoV-2. It was found to be highly versatile as shown by antibody detection from both serum and dried blot spots and as shown in three case studies. First, we followed seroconversion for all four endemic HCoV strains and SARS-CoV-2 in an outbreak study in day-care centres for children. Second, we were able to link a more severe clinical course to a stronger IgG response with this 17-plex-assay, which was IgG1 and IgG3 dominated. Finally, our assay was able to discriminate recent from previous SARS-CoV-2 infections by calculating the IgG/IgM ratio on the N antigen targeting antibodies. In conclusion, due to the comprehensive method comparison, thorough validation, and the proven versatility, our multiplex assay is a valuable tool for studies on coronavirus serology.
SOCS2 inhibits hepatoblastoma metastasis via downregulation of the JAK2/STAT5 signal pathway
Authors: Lv Yong , Xie Xiaolong , Zou Guoyou , Kong Meng , Yang Jiayin , Chen Jing , Xiang Bo 
Published: December 2023

AbstractMetastasis of hepatoblastoma (HB) is a key factor that impairs the prognosis and treatment of children. The suppressor of cytokine signaling 2 (SOCS2) is a classical negative feedback protein that regulates cytokine signal transduction and has been known to be downregulated in several tumor, but the molecular mechanisms of its involvement in HB metastasis are unknown. We found that SOCS2 was a gene down-regulated in hepatoblastoma and associated with HB metastasis through bioinformatics. The qRT-PCR, Western blot and IHC showed that SOCS2 was significantly lower in HB tissues. Clinicopathological correlation analysis revealed that low expression of SOCS2 was significantly correlated with tumor metastasis (P = 0.046) and vascular invasion (P = 0.028), associated with poor prognosis. Overexpression of SOCS2 inhibited the migration and invasion of hepatoblastoma cells, while knockdown of SOCS2 expression promoted these malignant phenotypes. In vivo studies revealed overexpression of SOCS2 inhibited the formation of lung metastasis. Up-regulation of SOCS2 in HB cell inhibited EMT and JAK2/STAT5. Conversely, down-regulation of SOCS2 promoted EMT and JAK2/STAT5. The addition of the JAK2 inhibitor Fedratinib partially reversed the effects of si-SOCS2 on HB cells. SOCS2 may inhibit the migration and invasion of HB cells by inhibiting the JAK2/STAT5 signaling pathway. These results may provide guiding significance for the clinical treatment of HB.
Source diversity of Artemia enrichment boosts goldfish (Carassius auratus) performance, β-carotene content, pigmentation, immune-physiological and transcriptomic responses
Authors: Elshafey Ahmed E. , Khalafalla Malik M. , Zaid Attia A. Abou , Mohamed Radi A. , Abdel-Rahim Mohamed M. 
Published: December 2023

AbstractThis study aimed to assess the impact of spirulina and/or canthaxanthin-enriched Artemia on the goldfish (Carassius auratus) growth, pigmentation, blood analysis, immunity, intestine and liver histomorphology, and expression of somatolactin (SL) and growth hormone (GH) genes. Artemia was enriched with spirulina and/or canthaxanthin for 24 h. Goldfish (N = 225, 1.10 ± 0.02 g) were tested in five experimental treatments, three replicates each: (T1) fish fed a commercial diet; (T2) fish fed a commercial diet and un-enriched Artemia (UEA); (T3) fish fed a commercial diet and spirulina-enriched Artemia (SEA); (T4) fish fed a commercial diet and canthaxanthin-enriched Artemia (CEA); and (T5) fish fed a commercial diet and spirulina and canthaxanthin-enriched Artemia (SCA) for 90 days. The results showed that the use of spirulina and/or canthaxanthin increased performance, β-carotene content and polyunsaturated fatty acids of Artemia. For goldfish, T5 showed the highest growth performance, β-carotene concentration and the lowest chromatic deformity. T5 also showed improved hematology profile, serum biochemical, and immunological parameters. Histomorphology of the intestine revealed an increase in villi length and goblet cells number in the anterior and middle intestine, with normal liver structure in T5. SL and GH gene expression in the liver and brain differed significantly among treatments with a significant increase in enriched Artemia treatments compared to T1 and T2. In conclusion, the use of spirulina and/or canthaxanthin improved performance of Artemia. Feeding goldfish spirulina and/or canthaxanthin-enriched Artemia improved performance, β-carotene content, pigmentation, health status and immune-physiological response.
Genome sequence and characterization of a novel Pseudomonas putida phage, MiCath
Authors: Jaryenneh James , Schoeniger Joseph S. , Mageeney Catherine M. 
Published: December 2023

AbstractPseudomonads are ubiquitous bacteria with importance in medicine, soil, agriculture, and biomanufacturing. We report a novel Pseudomonas putida phage, MiCath, which is the first known phage infecting P. putida S12, a strain increasingly used as a synthetic biology chassis. MiCath was isolated from garden soil under a tomato plant using P. putida S12 as a host and was also found to infect four other P. putida strains. MiCath has a ~ 61 kbp double-stranded DNA genome which encodes 97 predicted open reading frames (ORFs); functions could only be predicted for 48 ORFs using comparative genomics. Functions include structural phage proteins, other common phage proteins (e.g., terminase), a queuosine gene cassette, a cas4 exonuclease, and an endosialidase. Restriction digestion analysis suggests the queuosine gene cassette encodes a pathway capable of modification of guanine residues. When compared to other phage genomes, MiCath shares at most 74% nucleotide identity over 2% of the genome with any sequenced phage. Overall, MiCath is a novel phage with no close relatives, encoding many unique gene products.
Predicting the hyperelastic properties of alginate-gelatin hydrogels and 3D bioprinted mesostructures
Authors: Soufivand Anahita Ahmadi , Budday Silvia 
Published: December 2023

AbstractAdditive manufacturing has been widely used in tissue engineering, as 3D bioprinting enables fabricating geometrically complicated replacements for different tissues and organs. It is vital that the replacement mimics the specific properties of native tissue and bears the mechanical loading under its physiological conditions. Computational simulations can help predict and tune the mechanical properties of the printed construct—even before fabrication. In this study, we use the finite element (FE) method to predict the mechanical properties of different hydrogel mesostructures fabricated through various print patterns and validate our results through corresponding experiments. We first quantify the mechanical properties of alginate-gelatin hydrogels used as matrix material through an inverse approach using an FE model and cyclic compression-tension experimental data. Our results show that the fabrication process can significantly affect the material properties so that particular caution needs to be paid when calibrating FE models. We validate our optimized FE model using experimental data and show that it can predict the mechanical properties of different mesostructures, especially under compressive loading. The validated model enables us to tune the mechanical properties of different printed structures before their actual fabrication. The presented methodology can be analogously extended for cell bioprinting applications, other materials, and loading conditions. It can help save time, material, and cost for biofabrication applications in the future.
Pan msr gene deleted strain of Salmonella Typhimurium suffers oxidative stress, depicts macromolecular damage and attenuated virulence
Authors: Sahoo Raj , Chauhan Tapan Kumar Singh , Lalhmangaihzuali Lalhmangaihzuali , Sinha Esha , Qureshi Salauddin , Mahawar Manish 
Published: December 2023

AbstractSalmonella encounters but survives host inflammatory response. To defend host-generated oxidants, Salmonella encodes primary antioxidants and protein repair enzymes. Methionine (Met) residues are highly prone to oxidation and convert into methionine sulfoxide (Met-SO) which compromises protein functions and subsequently cellular survival. However, by reducing Met-SO to Met, methionine sulfoxide reductases (Msrs) enhance cellular survival under stress conditions. Salmonella encodes five Msrs which are specific for particular Met-SO (free/protein bound), and ‘R’/‘S’ types. Earlier studies assessed the effect of deletions of one or two msrs on the stress physiology of S. Typhimurium. We generated a pan msr gene deletion (Δ5msr) strain in S. Typhimurium. The Δ5msr mutant strain shows an initial lag in in vitro growth. However, the Δ5msr mutant strain depicts very high sensitivity (p < 0.0001) to hypochlorous acid (HOCl), chloramine T (ChT) and superoxide-generating oxidant paraquat. Further, the Δ5msr mutant strain shows high levels of malondialdehyde (MDA), protein carbonyls, and protein aggregation. On the other side, the Δ5msr mutant strain exhibits lower levels of free amines. Further, the Δ5msr mutant strain is highly susceptible to neutrophils and shows defective fitness in the spleen and liver of mice. The results of the current study suggest that the deletions of all msrs render S. Typhimurium highly prone to oxidative stress and attenuate its virulence.
Synergistic effect of cryptotanshinone and temozolomide treatment against human glioblastoma cells
Authors: Zhu Songxian , Guo Jingjing , Yu Li , Liu Jun , Chen Jixiang , Xin Jinxin , Zhang Yuqiang , Luo Jie , Duan Chao 
Published: December 2023

AbstractGlioblastoma multiforme (GBM) is a complex disease to treat owing to its profound chemoresistance. Therefore, we evaluated the combined effect and therapeutic efficacy of temozolomide (TMZ), a potent alkylating agent and the current gold standard therapy for GBM, and cryptotanshinone (CTS), which inhibits glioma cell proliferation in GBM cells. Using LN229 and U87-MG human GBM cells in a short-term stimulation in vitro model, the cytotoxic and anti-proliferative effects of single and combined treatment with 4 μM CTS and 200 μM TMZ were investigated. Furthermore, cell viability, DNA damage, apoptosis rate, and signal transducer and activator of transcription 3 (STAT3) protein were measured using cytotoxic assay, comet assay, flow cytometry, and western blotting analysis, respectively. The two drugs’ synergistic interaction was validated using the synergy score. We found that the anti-proliferative effects of combination therapy using the two drugs were greater than that of each agent used alone (CTS or TMZ). Western blot analysis indicated that treatment of GBM cells with CTS combined with TMZ more significantly decreased the expression of MGMT and STAT3, than that with TMZ alone. Combined treatment with CTS and TMZ might be an effective option to overcome the chemoresistance of GBM cells in a long-term treatment strategy.
Clarifying solvent effect during photocatalytic glycerol conversion on TiO2/GQD as selective photocatalyst
Authors: Hassan Sara , El-Hafiz Dalia R. Abd , Abdullah E. S. , Khalil Mostafa M. H. 
Published: December 2023

AbstractNowadays, dealing with the growing chemical and energy demands is important without compromising the environment. So, this work studies photocatalytic glycerol conversion (as biomass derivativ feedstock) into value-added products using an eco-friendly synthesized catalyst. Graphene quantum dots (GQDs) were prepared from available/cheap precursors like glucose via the hydrothermal method and used as a support for TiO2. TiO2/GQDs were characterized via different analytical techniques, revealing very small particle sizes of ~ 3–6 nm with a large surface area of ~ 253 m2/g and a band gap of ~ 2.6 eV. The prepared photocatalyst shows good efficiency during photocatalytic glycerol conversion to dihydroxyacetone (DHA). Different reaction conditions were tested: reaction time, catalyst amount, presence of oxidant (H2O2), and biphasic media (aqueous/organic phases). Comparing a monophasic (H2O) photoreactor with a biphasic reactor containing 90% organic phase (ethyl acetate) and 10% aqueous phase (H2O and/or H2O2) indicates that the presence of H2O2 increases glycerol conversion and liquid selectivity to reach 57% and 91%, respectively after 120 min. However, it still suffers a low DHA/GA ratio (2.7). On the other hand, using a biphasic reactor in the presence of an H2O2 oxidant increases the DHA/GA ratio to ~ 6.6, which was not reached in previous research. The formation of H2O/H2O2 as micro-reactors dispersed in the ethyl acetate phase increased the average light intensity effect of the glycerol/photocatalyst system in the micro-reactors. Unlike previous work, this work presents a facile way to prepare eco-friendly/cheap (noble metal free) photocatalysts for glycerol conversion to ultrapure DHA using a biphasic photoreactor.
Prediction of osteoporosis in patients with rheumatoid arthritis using machine learning
Authors: Lee Chaewon , Joo Gihun , Shin Seunghun , Im Hyeonseung , Moon Ki Won 
Published: December 2023

AbstractOsteoporosis is a serious health concern in patients with rheumatoid arthritis (RA). Machine learning (ML) models have been increasingly incorporated into various clinical practices, including disease classification, risk prediction, and treatment response. However, only a few studies have focused on predicting osteoporosis using ML in patients with RA. We aimed to develop an ML model to predict osteoporosis using a representative Korean RA cohort database. The KORean Observational study Network for Arthritis (KORONA) database, established by the Clinical Research Center for RA in Korea, was used in this study. Among the 5077 patients registered in KORONA, 2374 patients were included in this study. Four representative ML algorithms were used for the prediction: logistic regression (LR), random forest, XGBoost (XGB), and LightGBM. The accuracy, F1 score, and area under the curve (AUC) of each model were measured. The LR model achieved the highest AUC value at 0.750, while the XGB model achieved the highest accuracy at 0.682. Body mass index, age, menopause, waist and hip circumferences, RA surgery, and monthly income were risk factors of osteoporosis. In conclusion, ML algorithms are a useful option for screening for osteoporosis in patients with RA.