bluuebunny/crossref_metadata_2025_split huggingface dataset:
Non-invasive monitoring of microbial triterpenoid production using nonlinear microscopy techniques
Authors: Dianat Mariam , Münchberg Ute , Blank Lars M. , Freier Erik , Ebert Birgitta E. 
Published: March 2023

Introduction: Bioproduction of plant-derived triterpenoids in recombinant microbes is receiving great attention to make these biologically active compounds industrially accessible as nutraceuticals, pharmaceutics, and cosmetic ingredients. So far, there is no direct method for detecting triterpenoids under physiological conditions on a cellular level, information yet highly relevant to rationalizing microbial engineering.Methods: Here, we show in a proof-of-concept study, that triterpenoids can be detected and monitored in living yeast cells by combining coherent anti-Stokes Raman scattering (CARS) and second-harmonic-generation (SHG) microscopy techniques. We applied CARS and SHG microscopy measurements, and for comparison classical Nile Red staining, on immobilized and growing triterpenoid-producing, and non-producing reference Saccharomyces cerevisiae strains.Results and Discussion: We found that the SHG signal in triterpenoid-producing strains is significantly higher than in a non-producing reference strain, correlating with lipophile content as determined by Nile red staining. In growing cultures, both CARS and SHG signals showed changes over time, enabling new insights into the dynamics of triterpenoid production and storage inside cells.
Non-invasive estimation of the parameters of a three-element windkessel model of aortic arch arteries in patients undergoing thoracic endovascular aortic repair
Authors: Tricarico Rosamaria , Berceli Scott A. , Tran-Son-Tay Roger , He Yong 
Published: March 2023

Background: Image-based computational hemodynamic modeling and simulations are important for personalized diagnosis and treatment of cardiovascular diseases. However, the required patient-specific boundary conditions are often not available and need to be estimated.Methods: We propose a pipeline for estimating the parameters of the popular three-element Windkessel (WK3) models (a proximal resistor in series with a parallel combination of a distal resistor and a capacitor) of the aortic arch arteries in patients receiving thoracic endovascular aortic repair of aneurysms. Pre-operative and post-operative 1-week duplex ultrasound scans were performed to obtain blood flow rates, and intra-operative pressure measurements were also performed invasively using a pressure transducer pre- and post-stent graft deployment in arch arteries. The patient-specific WK3 model parameters were derived from the flow rate and pressure waveforms using an optimization algorithm reducing the error between simulated and measured pressure data. The resistors were normalized by total resistance, and the capacitor was normalized by total resistance and heart rate. The normalized WK3 parameters can be combined with readily available vessel diameter, brachial blood pressure, and heart rate data to estimate WK3 parameters of other patients non-invasively.Results: Ten patients were studied. The medians (interquartile range) of the normalized proximal resistor, distal resistor, and capacitor parameters are 0.10 (0.07–0.15), 0.90 (0.84–0.93), and 0.46 (0.33–0.58), respectively, for common carotid artery; 0.03 (0.02–0.04), 0.97 (0.96–0.98), and 1.91 (1.63–2.26) for subclavian artery; 0.18 (0.08–0.41), 0.82 (0.59–0.92), and 0.47 (0.32–0.85) for vertebral artery. The estimated pressure showed fairly high tolerance to patient-specific inlet flow rate waveforms using the WK3 parameters estimated from the medians of the normalized parameters.Conclusion: When patient-specific outflow boundary conditions are not available, our proposed pipeline can be used to estimate the WK3 parameters of arch arteries.
Microwave-assisted cassava pulp hydrolysis as food waste biorefinery for biodegradable polyhydroxybutyrate production
Authors: Prasertsilp Patiya , Pattaragulwanit Kobchai , Kim Beom Soo , Napathorn Suchada Chanprateep 
Published: March 2023

Cassava pulp is one of the most abundant agricultural residues that can cause serious disposal problems. This study aimed to apply a biorefinery approach by examining the feasibility of microwave-assisted cassava pulp hydrolysis to attain sustainable management and efficient use of natural resources. Four factors, namely, the liquid-to-solid ratio (20 mL/g, 10 mL/g, 7.5 mL/g, and 5 mL/g), types of acids (H2SO4and H3PO4), watt power (600 W, 700 W, and 800 W) and time (3, 5 and 8 min), were carefully investigated. The highest fermentable sugar content of 88.1 g/L ± 0.7 g/L (0.88 g fermentable sugars/g dry cassava pulp) was achieved when 20 mL/g cassava pulp was hydrolyzed with 2.5% (v/v) H2SO4under microwave irradiation at 800 W for 8 min. Glucose was a major product (82.0 g/L ± 5.2 g/L). The inhibitor concentration was 5.17 g/L ± 0.01 g/L, and the levulinic acid concentration was 5.15 g/L ± 0.01 g/L. The results indicated that the liquid-to-solid ratio, diluted acid concentration, irradiation watt power and time were important factors in producing fermentable sugars from acid hydrolysis under microwave irradiation. The crude hydrolysate was used for PHB production byCupriavidus necatorstrain A-04. The hydrolysate to nutrients ratio of 30:70 (v/v) yielded a cell dry weight of 7.5 g/L ± 0.1 g/L containing PHB content of 66.8% ± 0.3% (w/w), resulting in a yieldYP/S(g-PHB/g-SPHB) of 0.35 g/g. This study demonstrated that the microwave-assisted cassava pulp hydrolysate developed in this study provided a high amount of glucose (88.1% conversion) and resulted in a low concentration of inhibitors without xylose; this was successfully achieved without pregelatinization, alkaline pretreatment or detoxification.
Bioactive semaphorin 3A promotes sequential formation of sensory nerve and type H vessels during in situ osteogenesis
Authors: Han Xiaoxiao , Ma Yuxuan , Lu Weicheng , Yan Jianfei , Qin Wenpin , He Jiaying , Niu Li-Na , Jiao Kai 
Published: March 2023

Introduction: Sensory nerves and vessels are critical for skeletal development and regeneration, but crosstalk between neurovascular network and mineralization are not clear. The aim of this study was to explore neurovascular changes and identify bioactive regulators during in situ osteogenesis.Method:In situ osteogenesis model was performed in male rats following Achilles tenotomy. At 3, 6 and 9 weeks after surgery, mineralization, blood vessels, sensory innervation, and bioactive regulators expression were evaluated via micro-computed tomography, immunofluorescent staining, histology and reverse transcriptase-polymerase chain reaction analyses.Result: In the process of in situ osteogenesis, the mineral density increased with time, and the locations of minerals, nerves and blood vessels were highly correlated at each time point. The highest density of sensory nerve was observed in the experimental group at the 3rd week, and then gradually decreased with time, but still higher than that in the sham control group. Among many regulatory factors, semaphorin 3A (Sema3A) was highly expressed in experimental model and its expression was temporally sequential and spatially correlated sensory nerve.Conclusion: The present study showes that during in situ osteogenesis, innervation and angiogenesis are highly correlated, and Sema3A is associated with the position and expression of the sensory nerve.
Stepwise use of genomics and transcriptomics technologies increases diagnostic yield in Mendelian disorders
Authors: Colin Estelle , Duffourd Yannis , Chevarin Martin , Tisserant Emilie , Verdez Simon , Paccaud Julien , Bruel Ange-Line , Tran Mau-Them Frédéric , Denommé-Pichon Anne-Sophie , Thevenon Julien , Safraou Hana , Besnard Thomas , Goldenberg Alice , Cogné Benjamin , Isidor Bertrand , Delanne Julian , Sorlin Arthur , Moutton Sébastien , Fradin Mélanie , Dubourg Christèle , Gorce Magali , Bonneau Dominique , El Chehadeh Salima , Debray François-Guillaume , Doco-Fenzy Martine , Uguen Kevin , Chatron Nicolas , Aral Bernard , Marle Nathalie , Kuentz Paul , Boland Anne , Olaso Robert , Deleuze Jean-François , Sanlaville Damien , Callier Patrick , Philippe Christophe , Thauvin-Robinet Christel , Faivre Laurence , Vitobello Antonio 
Published: March 2023

Purpose: Multi-omics offer worthwhile and increasingly accessible technologies to diagnostic laboratories seeking potential second-tier strategies to help patients with unresolved rare diseases, especially patients clinically diagnosed with a rare OMIM (Online Mendelian Inheritance in Man) disease. However, no consensus exists regarding the optimal diagnostic care pathway to adopt after negative results with standard approaches.Methods: In 15 unsolved individuals clinically diagnosed with recognizable OMIM diseases but with negative or inconclusive first-line genetic results, we explored the utility of a multi-step approach using several novel omics technologies to establish a molecular diagnosis. Inclusion criteria included a clinical autosomal recessive disease diagnosis and single heterozygous pathogenic variant in the gene of interest identified by first-line analysis (60%–9/15) or a clinical diagnosis of an X-linked recessive or autosomal dominant disease with no causative variant identified (40%–6/15). We performed a multi-step analysis involving short-read genome sequencing (srGS) and complementary approaches such as mRNA sequencing (mRNA-seq), long-read genome sequencing (lrG), or optical genome mapping (oGM) selected according to the outcome of the GS analysis.Results: SrGS alone or in combination with additional genomic and/or transcriptomic technologies allowed us to resolve 87% of individuals by identifying single nucleotide variants/indels missed by first-line targeted tests, identifying variants affecting transcription, or structural variants sometimes requiring lrGS or oGM for their characterization.Conclusion: Hypothesis-driven implementation of combined omics technologies is particularly effective in identifying molecular etiologies. In this study, we detail our experience of the implementation of genomics and transcriptomics technologies in a pilot cohort of previously investigated patients with a typical clinical diagnosis without molecular etiology.
Visual and rapid identification of Chlamydia trachomatis and Neisseria gonorrhoeae using multiplex loop-mediated isothermal amplification and a gold nanoparticle-based lateral flow biosensor
Authors: Chen Xu , Zhou Qingxue , Yuan Wei , Shi Yuanfang , Dong Shilei , Luo Xinhua 
Published: March 2023

Sexually transmitted chlamydia and gonorrhea infections caused by the bacteria Chlamydia trachomatis and Neisseria gonorrhoeae remain a major public health concern worldwide, particularly in less developed nations. It is crucial to use a point of care (POC) diagnostic method that is quick, specific, sensitive, and user-friendly to treat and control these infections effectively. Here, a novel molecular diagnostic assay, combining multiplex loop-mediated isothermal amplification (mLAMP) with a visual gold nanoparticles-based lateral flow biosensor (AuNPs-LFB) was devised and used for highly specific, sensitive, rapid, visual, and easy identification of C. trachomatis and N. gonorrhoeae. Two unique independent primer pairs were successful designed against the ompA and orf1 genes of C. trachomatis and N. gonorrhoeae, respectively. The optimal mLAMP-AuNPs-LFB reaction conditions were determined to be 67°C for 35 min. The detection procedure, involving crude genomic DNA extraction (~5 min), LAMP amplification (35 min), and visual results interpretation (&lt;2 min), can be completed within 45 min. Our assay has a detection limit of 50 copies per test, and we did not observe any cross-reactivity with any other bacteria in our testing. Hence, our mLAMP-AuNPs-LFB assay can potentially be used for POC testing to detect C. trachomatis and N. gonorrhoeae in clinical settings, particularly in underdeveloped regions.
Altered gut microbiota in the early stage of acute pancreatitis were related to the occurrence of acute respiratory distress syndrome
Authors: Hu Xiaomin , Han Ziying , Zhou Ruilin , Su Wan , Gong Liang , Yang Zihan , Song Xiao , Zhang Shuyang , Shu Huijun , Wu Dong 
Published: March 2023

BackgroundAcute respiratory distress syndrome (ARDS) is the most common cause of organ failure in acute pancreatitis (AP) patients, which associated with high mortality. Specific changes in the gut microbiota have been shown to influence progression of acute pancreatitis. We aimed to determine whether early alterations in the gut microbiota is related to and could predict ARDS occurrence in AP patients.MethodsIn this study, we performed 16S rRNA sequencing analysis in 65 AP patients and 20 healthy volunteers. The AP patients were further divided into two groups: 26 AP-ARDS patients and 39 AP-nonARDS patients based on ARDS occurrence during hospitalization.ResultsOur results showed that the AP-ARDS patients exhibited specific changes in gut microbiota composition and function as compared to subjects of AP-nonARDS group. Higher abundances of Proteobacteria phylum, Enterobacteriaceae family, Escherichia-Shigella genus, and Klebsiella pneumoniae, but lower abundances of Bifidobacterium genus were found in AP-ARDS group compared with AP-nonARDS groups. Random forest modelling analysis revealed that the Escherichia-shigella genus was effective to distinguish AP-ARDS from AP-nonARDS, which could predict ARDS occurrence in AP patients.ConclusionsOur study revealed that alterations of gut microbiota in AP patients on admission were associated with ARDS occurrence after hospitalization, indicating a potential predictive and pathogenic role of gut microbiota in the development of ARDS in AP patients.
Erastin inhibits porcine epidemic diarrhea virus replication in Vero cells
Authors: Zhang Hongliang , Li Yingguang , Yang Ruimei , Xiao Ling , Dong Shaoming , Lin Jiaxu , Liu Gang , Shan Hu 
Published: March 2023

BackgroundPorcine epidemic diarrhea virus (PEDV), an intestinal pathogenic coronavirus, has caused significant economic losses to the swine industry worldwide. At present, there are several treatment methods, but there is still a lack of clinically effective targeted drugs, new antiviral mechanisms and drugs need to be explored.MethodsIn this study, we established a model of erastin versus ferrostatin-1 treatment of Vero cells, and then detected virus proliferation and gene expression by RT-qPCR through PEDV infection experiments.ResultsWe demonstrated for the first time that erastin significantly inhibited the replication of PEDV upon entry into cells; Vero treated with erastin significantly regulated the expression of three genes, NRF2, ACSL4 and GPX4, notably erastin regulated the expression of these three genes negatively correlated with the expression induced by PEDV virus infection.ConclusionsSince NRF2, ACSL4 and GPX4 are classical Ferroptosis genes, this study speculates that erastin may inhibit the replication of PEDV in Vero cells in part through the regulation of ferroptosis pathway, and erastin may be a potential drug for the treatment of PEDV infection.
Implicit cross-situational word learning in children with and without developmental language disorder and its relation to lexical-semantic knowledge
Authors: Broedelet Iris , Boersma Paul , Rispens Judith 
Published: March 2023

IntroductionResearch indicates that statistical learning plays a role in word learning by enabling the learner to track the co-occurrences between words and their visual referents, a process that is named cross-situational word learning. Word learning is problematic for children with developmental language disorder (DLD), and a deficit in statistical learning has been suggested to contribute to the language difficulties in these children. Therefore, we investigate whether children with DLD have more difficulty than TD children with learning novel word–referent pairs based on cross-situational statistics in an implicit task, and whether this ability is related to their lexical-semantic skills. Moreover, we look at the role of variability of the learning environment.MethodsIn our implicit cross-situational word learning task, each trial in the exposure phase was in itself ambiguous: two pictures of unknown objects were shown at the same time and two novel words were played consecutively, without indicating which word referred to which object. However, as every word occurred with its correct referent consistently, the children could learn the word–referent pairs across trials. The children were not explicitly instructed to learn the names of new objects. As an on-line measure of learning, eye-movements were recorded during the exposure phase. After exposure, word–referent knowledge was also tested using multiple choice questions. Several measures of lexical-semantic knowledge were administered to the children with DLD, as well as tasks measuring non-verbal intelligence and phonological processing. Contextual variability (the number of different distractors with which a particular word–referent pair occurs across trials) was manipulated between subjects by constructing two types of exposure conditions: low contextual diversity vs. high contextual diversity.ResultsBoth groups of children performed significantly above chance level on the test phase, but the TD children significantly outperformed the children with DLD. We found no significant effect of contextual diversity. The eye-tracking data revealed some evidence of on-line learning, but no differences between groups. Finally, the regression analyses did not reveal any significant predictors of off-line or on-line cross-situational word learning ability.DiscussionOur results indicate that although children with DLD are able to learn word-referent pairs in an implicit task, they have more difficulty than TD children. Possibly they need more input to achieve the same level.
Feasibility and scalability of a fitness tracker study: Results from a longitudinal analysis of persons with multiple sclerosis
Authors: Sieber Chloé , Haag Christina , Polhemus Ashley , Sylvester Ramona , Kool Jan , Gonzenbach Roman , von Wyl Viktor 
Published: March 2023

BackgroundConsumer-grade fitness trackers offer exciting opportunities to study persons with chronic diseases in greater detail and in their daily-life environment. However, attempts to bring fitness tracker measurement campaigns from tightly controlled clinical environments to home settings are often challenged by deteriorating study compliance or by organizational and resource limitations.ObjectivesBy revisiting the study design and patient-reported experiences of a partly remote study with fitness trackers (BarKA-MS study), we aimed to qualitatively explore the relationship between overall study compliance and scalability. On that account, we aimed to derive lessons learned on strengths, weaknesses, and technical challenges for the conduct of future studies.MethodsThe two-phased BarKA-MS study employed Fitbit Inspire HR and electronic surveys to monitor physical activity in 45 people with multiple sclerosis in a rehabilitation setting and in their natural surroundings at home for up to 8 weeks. We examined and quantified the recruitment and compliance in terms of questionnaire completion and device wear time. Furthermore, we qualitatively evaluated experiences with devices according to participants' survey-collected reports. Finally, we reviewed the BarKA-MS study conduct characteristics for its scalability according to the Intervention Scalability Assessment Tool checklist.ResultsWeekly electronic surveys completion reached 96%. On average, the Fitbit data revealed 99% and 97% valid wear days at the rehabilitation clinic and in the home setting, respectively. Positive experiences with the device were predominant: only 17% of the feedbacks had a negative connotation, mostly pertaining to perceived measurement inaccuracies. Twenty-five major topics and study characteristics relating to compliance were identified. They broadly fell into the three categories: “effectiveness of support measures”, “recruitment and compliance barriers”, and “technical challenges”. The scalability assessment revealed that the highly individualized support measures, which contributed greatly to the high study compliance, may face substantial scalability challenges due to the strong human involvement and limited potential for standardization.ConclusionThe personal interactions and highly individualized participant support positively influenced study compliance and retention. But the major human involvement in these support actions will pose scalability challenges due to resource limitations. Study conductors should anticipate this potential compliance-scalability trade-off already in the design phase.
Geological adaptability of deep CBM fractured horizontal well in SLN block
Authors: Fu Yutong , Yuan Weilin , Xu Zhidan , Zhao Ruosi , Wu Yue , Zheng Haibo , Wang Xianqing , Guo Xudong , Gou Shiyong , Ma Chunlin 
Published: March 2023

The buried depth of the main coal beds in SLN Block is more than 1,500 m, and the gas content of the coal beds is high. However, the coal beds are generally in a high geostress environment, the permeability of the coal beds is generally low, and the development effect of conventional fractured straight wells is poor. Fractured horizontal well is an important technical means to improve the development effect of low permeability coalbed methane, but the investment cost is high. To reduce the investment risk of fractured horizontal wells, it is necessary to find out the gas production capacity and main control factors of the fractured horizontal wells, and determine the area suitable for the development of fractured horizontal wells. In the area with permeability higher than 0.28 md and gas content higher than 12.8 m3/t, the daily gas production capacity of fractured horizontal well is 16,450–21500 m3/d, and the development effect is good. The research results are of great significance to quickly evaluate the adaptability of fractured horizontal wells.