bluuebunny/crossref_metadata_2025_split huggingface dataset:
Improved production of Taxol® precursors in S. cerevisiae using combinatorial in silico design and metabolic engineering
Authors: Malcı Koray , Santibáñez Rodrigo , Jonguitud-Borrego Nestor , Santoyo-Garcia Jorge H. , Kerkhoven Eduard J. , Rios-Solis Leonardo 
Published: November 2023

Abstract
Background
Integrated metabolic engineering approaches that combine system and synthetic biology tools enable the efficient design of microbial cell factories for synthesizing high-value products. In this study, we utilized in silico design algorithms on the yeast genome-scale model to predict genomic modifications that could enhance the production of early-step Taxol® in engineered Saccharomyces cerevisiae cells.

Results
Using constraint-based reconstruction and analysis (COBRA) methods, we narrowed down the solution set of genomic modification candidates. We screened 17 genomic modifications, including nine gene deletions and eight gene overexpressions, through wet-lab studies to determine their impact on taxadiene production, the first metabolite in the Taxol® biosynthetic pathway. Under different cultivation conditions, most single genomic modifications resulted in increased taxadiene production. The strain named KM32, which contained four overexpressed genes (ILV2, TRR1, ADE13, and ECM31) involved in branched-chain amino acid biosynthesis, the thioredoxin system, de novo purine synthesis, and the pantothenate pathway, respectively, exhibited the best performance. KM32 achieved a 50% increase in taxadiene production, reaching 215 mg/L. Furthermore, KM32 produced the highest reported yields of taxa-4(20),11-dien-5α-ol (T5α-ol) at 43.65 mg/L and taxa-4(20),11-dien-5-α-yl acetate (T5αAc) at 26.2 mg/L among early-step Taxol® metabolites in S. cerevisiae.

Conclusions
This study highlights the effectiveness of computational and integrated approaches in identifying promising genomic modifications that can enhance the performance of yeast cell factories. By employing in silico design algorithms and wet-lab screening, we successfully improved taxadiene production in engineered S. cerevisiae strains. The best-performing strain, KM32, achieved substantial increases in taxadiene as well as production of T5α-ol and T5αAc. These findings emphasize the importance of using systematic and integrated strategies to develop efficient yeast cell factories, providing potential implications for the industrial production of high-value isoprenoids like Taxol®.
Evaluating the efficacy and timing of blood purification modalities in early-stage hyperlipidemic acute pancreatitis treatment
Authors: Wang Jianjun , Xia Yang , Cao Yuan , Cai Xianfu , Jiang Shichun , Liao Yougang , Shi Mingsong , Luo Huiwen , Wang Decai 
Published: November 2023

AbstractHypertriglyceridemia-induced acute pancreatitis (HTG-AP) is characterized by a violent cytokine storm-driven inflammation and is associated with a predisposition to severe disease. The treatment strategy for HTG-AP consists mainly of conventional symptomatic and lipid-lowering treatments. For early-stage HTG-AP, blood purification (BP) can rapidly and effectively reduce serum triglyceride and inflammatory cytokine levels, block the development of systemic inflammatory response syndrome, and improve patient outcomes. Currently, the primary modalities for BP in patients with HTG-AP include plasma exchange, hemoperfusion, and hemofiltration. When using BP to treat patients with HTG-AP, a comprehensive analysis incorporating the elevated lipid levels and severity of the patient’s condition contributes to the selection of different treatment modes. Moreover, the timing of the treatment is also imperative. Early intervention is associated with a better prognosis for patients with HTG-AP requiring lipid-lowering treatment.
Development and validation of the systemic lupus erythematous scale amongst the system of quality of life instruments for chronic diseases QLICD-SLE (V2.0)
Authors: Liu Yuxi , Zhang Jiaqi , Xue Honghong , Chen Mingyang , Xie Tong , Wan Chonghua 
Published: November 2023

Abstract
Objective
The present study is aimed to develop and validate a quality of life scale for systemic lupus erythematosus (SLE) patients with Chinese cultural background, QLICD-SLE (V2.0).

Methods
The QLICD-SLE (V2.0) was developed using a systematic approach that involved focus groups, nominal discussions, and pilot testing. A total of 428 SLE patients participated in the scale's assessment. Validity was examined through qualitative analysis, item domain correlation, multidimensional scaling, and factor analysis. Reliability was assessed using Pearson's correlation and Cronbach's alpha coefficients. To evaluate responsiveness, paired T-tests were conducted to compare pre- and post-treatment measurements with the standardised response mean (SRM) being calculated.

Results
Correlation and factor analyses demonstrated strong construct validity. When using SF-36 as criteria, the correlation between various domains of QLICD-SLE and SF-36 ranged from 0.55 to 0.70. Test–retest correlation coefficients exceeded 0.71, and Cronbach’s alpha coefficients for both measurements in each domain were greater than or equal to 0.75. T-test results showed that both the overall score and most facet scores within each domain showed statistically significant changes after treatment (P < 0.05), indicating reasonable responsiveness.

Conclusion
The QLICD-SLE (V2.0) appears to be a valid and reliable instrument for assessing the quality of life in patients with SLE.
Government, governance, and place-based approaches: lessons from and for public policy
Authors: Klepac Bojana , Mowle Amy , Riley Therese , Craike Melinda 
Published: November 2023

AbstractBackgroundPlace-based approaches are increasingly applied to address the determinants of health, many of which are complex problems, to ultimately improve population health outcomes. Through public policy, government actions can affect the effectiveness of place-based approaches by influencing the conceptualisation, development, implementation, governance, and/or evaluation of place-based approaches. Despite the important role of public policy, there has been limited examination of public policy related to place-based approaches. We add to the limited knowledge base by analysing Australian national public policy, to explore: (1) the definitions, conceptualisations, and characteristics of place-based approaches in public policy; (2) the government’s perception and communication of its role in place-based approaches; and (3) the extent to which government policy reflects the necessary conditions for successful place-based governance developed by Marsh and colleagues, namely localised context, embedded learning, and reciprocal accountability.MethodsThis research was underpinned by the Theory of Systems Change and methodologically informed by the READ approach to document analysis. Ritchie and Spencer’s framework method was utilised to analyse the data.ResultsWe identified and reviewed 67 policy documents. In terms of conceptualisation, common characteristics of place-based approaches related to collaboration, including community in decision-making, responsiveness to community needs, and suitability of place-based approaches to address complex problems and socio-economic determinants of health. Three roles of government were identified: funder, partner, and creator of a supportive policy environment. From the three criteria for successful place-based governance,localisedcontextwas the most dominant across the documents andreciprocalaccountabilitythe least.ConclusionsBased on our findings, we drew key implications for public policy and research. There was a disproportionate emphasis on the bottom-up approach across the documents, which presents the risk of diminishing government interest in place-based approaches, potentially burdening communities experiencing disadvantage beyond their capacities. Governments engaged in place-based approaches should work towards a more balanced hybrid approach to place-based approaches that maintain the central functions of government while allowing for successful place-based governance. This could be achieved by promoting consistency in conceptualisations of ‘place-based’, employing an active role in trust building, advancing the creation of a supportive policy environment, and embedding ‘learning’ across place-based approaches.
Phylogenomic assessment of 23 equid alphaherpesvirus 1 isolates obtained from USA-based equids
Authors: Emelogu Ugochi , Lewin Andrew C. , Balasuriya Udeni B. R. , Liu Chin-Chi , Wilkes Rebecca P. , Zhang Jianqiang , Mills Erinn P. , Carter Renee T. 
Published: November 2023

Abstract
Background
Equid alphaherpesvirus 1 (EHV-1) is a global viral pathogen of domestic equids which causes reproductive, respiratory and neurological disease. Few isolates acquired from naturally infected USA-based hosts have been fully sequenced and analyzed to date. An ORF 30 (DNA polymerase) variant (A2254G) has previously been associated with neurological disease in host animals. The purpose of this study was to perform phylogenomic analysis of EHV-1 isolates acquired from USA-based hosts and compare these isolates to previously sequenced global isolates.

Methods
EHV-1 was isolated from 23 naturally infected USA-based equids (6 different states, 15 disease outbreaks) with reproductive (22/23) or neurological disease (1/23). Following virus isolation, EHV-1 DNA was extracted for sequencing using Illumina MiSeq. Following reference-based assembly, whole viral genomes were annotated and assessed. Previously sequenced EHV-1 isolates (n = 114) obtained from global host equids were included in phylogenomic analyses.

Results
The overall average genomic distance was 0.0828% (SE 0.004%) for the 23 newly sequenced USA isolates and 0.0705% (SE 0.003%) when all 137 isolates were included. Clade structure was predominantly based on geographic origin. Numerous nucleotide substitutions (mean [range], 179 [114–297] synonymous and 81 [38–120] non-synonymous substitutions per isolate) were identified throughout the genome of the newly sequenced USA isolates. The previously described ORF 30 A2254G substitution (associated with neurological disease) was found in only one isolate obtained from a host with non-neurological clinical signs (reproductive disease), six additional, unique, non-synonymous ORF 30 substitutions were detected in 22/23 USA isolates. Evidence of recombination was present in most (22/23) of the newly sequenced USA isolates.

Conclusions
Overall, the genomes of the 23 newly sequenced EHV-1 isolates obtained from USA-based hosts were broadly similar to global isolates. The previously described ORF 30 A2254G neurological substitution was infrequently detected in the newly sequenced USA isolates, most of which were obtained from host animals with reproductive disease. Recombination was likely to be partially responsible for genomic diversity in the newly sequenced USA isolates.
The effect of different posterior inclinations of tibial component on tibiofemoral contact pressures after unicompartmental knee arthroplasty
Authors: Yuan Bo , Mo Zhongjun , Zhang Kuan , Zhu Xu , Yan Songhua , Zeng Jizhou 
Published: November 2023

Abstract
Background
Different posterior inclinations of tibial component after unicompartmental knee arthroplasty (UKA) may lead to different biomechanical characteristics of the knee joint. This finite element study was designed to investigate the tibiofemoral contact pressures after UKA with different posterior inclinations of tibial component.

Methods
Finite element model of a healthy knee joint was constructed, and mobile-bearing (MB) UKA models with 5 different posterior inclinations (3°, 5°, 7°, 9° and 11°) of tibial components were simulated. The maximum contact pressures of tibial plateau cartilage in the lateral compartment and polyethylene insert in the medial compartment were calculated based on the ground reaction force and the angle of the knee flexion obtained by 3D motion capture system.

Results
The loading ratio of medial and lateral compartments during standing stance (medial 54.49%, lateral 45.51%) and tibial anterior displacement (134 N, 3.89 mm) of healthy knee was basically consistent with previous experimental data. The maximum contact pressures of the medial meniscus and lateral tibial plateau cartilage of the healthy knee during standing stance were 2.14 MPa and 1.57 MPa, respectively. At the static standing phase, the maximum contact pressures of the polyethylene insert decreased from 17.90 to 17.29 Mpa, and the maximum contact pressures of the tibial plateau cartilage in the lateral compartment increased from 0.81 to 0.92 Mpa following an increase in the posterior inclination of the tibial component. At the first peak of ground reaction force, the maximum contact pressures of polyethylene insert increased from 22.37 to 25.16 MPa, and the maximum contact pressures of tibial plateau cartilage in the lateral compartment increased from 3.03 to 3.33 MPa, with the increase in the posterior inclination of the tibial component. At the second peak of ground reaction force, the maximum contact pressures of polyethylene insert decreased from 2.34 to 2.22 MPa with the increase in posterior inclination of tibial component.

Conclusion
The preoperative and postoperative finite element models of MB UKA were well established. The results showed that the maximum contact pressures of the polyethylene insert did not change significantly with the increase in the posterior inclination of the tibial prosthesis, while the maximum contact pressures of the tibial plateau cartilage of the lateral compartment increased when the posterior inclination of the tibial prosthesis was > 7°. Our results also show that the maximum contact pressures were greater with an excessive inclination angle (11°) of the tibial component, and the pressures of the tibial plateau cartilage in the lateral compartment were more concentrated on the posterior area. This study, therefore, proposes that excessive osteotomy should be avoided.
Choices for cancer prevention for women with a BRCA1 mutation? a personal view
Authors: Narod Steven A. 
Published: November 2023

AbstractWith widespread testing for susceptibility genes, increasing numbers of women are being identified to carry a mutation in one of many genes which renders them susceptible to cancer. The first gene to be identified (in 1994) was BRCA1 which increases a woman’s risk for breast cancer (70%) and ovarian cancer (40%). The prevalence of BRCA1 gene mutations has been studied widely and in many countries, mostly in women affected with cancer. In many settings testing is offered routinely to women with serous ovarian cancer or early-onset or triple-negative breast cancer. It is preferable to identify a mutation in a healthy women prior to the diagnosis of cancer. The basic strategies for prevention include surgical prevention, chemoprevention and screening (early detection). Much progress has been made in the past two decades evaluating the benefits of these three approaches. In this commentary I provide my personal views regarding these various interventions in the context of counselling a newly diagnosed health woman with a BRCA1 mutation.
Combination of serum and peritoneal 1.3-beta-d-glucan can rule out intra-abdominal candidiasis in surgical critically ill patients: a multicenter prospective study
Authors: Novy Emmanuel , Rivière Jérémie , Nguyen Maxime , Arfeuille Gaëlle , Louis Guillaume , Bouhemad Bélaïd , Pottecher Julien , Hecketsweiler Stéphane , Germain Adeline , Laithier François-Xavier , Losser Marie-Reine , Debourgogne Anne , Bernard Yohann , Rousseau Hélène , Baumann Cédric , Luc Amandine , Birckener Julien , Machouart Marie-Claire , Guerci Philippe 
Published: November 2023

Abstract
Background
Intra-abdominal candidiasis (IAC) is difficult to predict in critically ill patients with intra-abdominal infection, leading to the overuse of antifungal treatments. Serum and peritoneal 1.3-beta-d-glucan (sBDG and pBDG) have been proposed to confirm or invalidate the diagnosis of IAC, but clinical studies have reported inconsistent results, notably because of heterogeneous populations with a low IAC prevalence. This study aimed to identify a high-risk IAC population and evaluate pBDG and sBDG in diagnosing IAC.

Methods
This prospective multicenter noninterventional French study included consecutive critically ill patients undergoing abdominal surgery for abdominal sepsis. The primary objective was to establish the IAC prevalence. The secondary objective was to explore whether sBDG and pBDG could be used to diagnose IAC. Wako® beta-glucan test (WT, Fujifilm Wako Chemicals Europe, Neuss, Germany) was used for pBDG measurements. WT and Fungitell® beta-d-glucan assay (FA, Associate of Cape Cod, East Falmouth, USA) were used for sBDG measurements.

Results
Between 1 January 2020 and 31 December 2022, 199 patients were included. Patients were predominantly male (63%), with a median age of 66 [54–72] years. The IAC prevalence was 44% (87/199). The main IAC type was secondary peritonitis. Septic shock occurred in 63% of cases. After multivariate analysis, a nosocomial origin was associated with more IAC cases (P = 0.0399). The median pBDG level was significantly elevated in IAC (448 [107.5–1578.0] pg/ml) compared to non-IAC patients (133 [16.0–831.0] pg/ml), P = 0.0021. For a pBDG threshold of 45 pg/ml, the negative predictive value in assessing IAC was 82.3%. The median sBDG level with WT (n = 42) at day 1 was higher in IAC (5 [3.0–9.0] pg/ml) than in non-IAC patients (3 [3.0–3.0] pg/ml), P = 0.012. Similarly, median sBDG level with FA (n = 140) at day 1 was higher in IAC (104 [38.0–211.0] pg/ml) than in non-IAC patients (50 [23.0–141.0] pg/ml), P = 0.009. Combining a peritonitis score < 3, sBDG < 3.3 pg/ml (WT) and pBDG < 45 pg/ml (WT) yielded a negative predictive value of 100%.

Conclusion
In critically ill patients with intra-abdominal infection requiring surgery, the IAC prevalence was 44%. Combining low sBDG and pBDG with a low peritonitis score effectively excluded IAC and could limit unnecessary antifungal agent exposure.
Trial registration: The study was registered with ClinicalTrials.gov (ID number 03997929, first registered on June 24, 2019).

Graphical abstract
Long noncoding RNA KCNMA1-AS1 promotes osteogenic differentiation of human bone marrow mesenchymal stem cells by activating the SMAD9 signaling pathway
Authors: Mai Zhaoyi , Liu Jingpeng , Jiang Xiao , Gu Wenli , Wang Wei , Li Simin , Schmalz Gerhard , Xiao Hui , Zhao Jianjiang 
Published: November 2023

AbstractThe human bone marrow mesenchymal stem cells (hBMSCs) undergo intense osteogenic differentiation, a crucial bone formation mechanism. Evidence from prior studies suggested an association between long noncoding RNAs (lncRNAs) and the osteogenic differentiation of hBMSCs. However, precise roles and molecular mechanisms are still largely unknown. In this work, we report for the first time that lncRNA KCNMA1 antisense RNA 1 (KCNMA1-AS1) plays a vital role in regulating hBMSCs’ osteogenic differentiation. Here, it was observed that the KCNMA1-AS1 expression levels were significantly upregulated during osteogenic differentiation. In addition, KCNMA1-AS1 overexpression enhanced in vitro osteogenic differentiation of hBMSCs and in vivo bone formation, whereas knockdown of KCNMA1-AS1 resulted in the opposite result. Additionally, the interaction between KCNMA1-AS1 and mothers against decapentaplegic homolog 9 (SMAD9) was confirmed by an RNA pull-down experiment, mass spectrometry, and RIP assay. This interaction regulated the activation of the SMAD9 signaling pathway. Moreover, rescue assays demonstrated that the inhibitor of the SMAD9 signaling pathway reversed the stimulative effects on osteogenic differentiation of hBMSCs by KCNMA1-AS1 overexpression. Altogether, our results stipulate that KCNMA1-AS1 promotes osteogenic differentiation of hBMSCs via activating the SMAD9 signaling pathway and can serve as a biomarker and therapeutic target in treating bone defects.
High-throughput droplet microfluidics screening and genome sequencing analysis for improved amylase-producing Aspergillus oryzae
Authors: Li Qinghua , Lu Jinchang , Liu Jingya , Li Jianghua , Zhang Guoqiang , Du Guocheng , Chen Jian 
Published: November 2023

Abstract
Background
The exceptional protein secretion capacity, intricate post-translational modification processes, and inherent safety features of A. oryzae make it a promising expression system. However, heterologous protein expression levels of existing A. oryzae species cannot meet the requirement for industrial-scale production. Therefore, establishing an efficient screening technology is significant for the development of the A. oryzae expression system.

Results
In this work, a high-throughput screening method suitable for A. oryzae has been established by combining the microfluidic system and flow cytometry. Its screening efficiency can reach 350 droplets per minute. The diameter of the microdroplet was enlarged to 290 µm to adapt to the polar growth of A. oryzae hyphae. Through enrichment and screening from approximately 450,000 droplets within 2 weeks, a high-producing strain with α-amylase increased by 6.6 times was successfully obtained. Furthermore, 29 mutated genes were identified by genome resequencing of high-yield strains, with 15 genes subjected to editing and validation. Two genes may individually influence α-amylase expression in A. oryzae by affecting membrane-associated multicellular processes and regulating the transcription of related genes.

Conclusions
The developed high-throughput screening strategy provides a reference for other filamentous fungi and Streptomyces. Besides, the strains with different excellent characteristics obtained by efficient screening can also provide materials for the analysis of genetic and regulatory mechanisms in the A. oryzae expression system.
Resatorvid alleviates experimental inflammatory TMJOA by restraining chondrocyte pyroptosis and synovial inflammation
Authors: Liu Xin , Li Huimin , Feng Yaping , Guo Huilin , Li Yingjie , Ke Jin , Long Xing 
Published: November 2023

Abstract
Objectives
Innate immunity plays a significant role in the pathogenesis of temporomandibular joint osteoarthritis (TMJOA), which is characterized by synovial inflammation and condylar cartilage degradation. We are urged to investigate the impact of Resatorvid, a preventative drug that inhibits Toll-like receptor 4 (TLR4), on experimental inflammatory TMJOA pathology.

Methods
An intra-articular injection of complete Freund’s adjuvant (CFA) was used to induce an experimental inflammatory mouse TMJOA model, and TLR4 expression was identified by immunofluorescent labeling. Intraperitoneal injections of Resatorvid were administered to CFA-induced TMJOA mice, and the pathology of TMJOA animals with and without Resatorvid treatment was examined by H&E, Safranin-O/Fast Green, and TRAP staining, as well as micro-CT, immunohistochemistry, and immunofluorescence. The impact of Resatorvid on chondrocyte pyroptosis and macrophage inflammation was further investigated using ATDC5 chondrocytes and RAW264.7 macrophages pretreated with relevant antagonists.

Results
CFA-induced TMJOA mice revealed remarkable synovial inflammation, together with a time course of cartilage degradation and bone destruction, with TLR4 elevated in the synovium and condylar cartilage. Prophylactic treatment with Resatorvid mitigated synovial inflammation, cartilage degeneration, and bone destruction in CFA-induced TMJOA mice and downregulated MyD88/NF-κB expression. Ex vivo studies demonstrated that Resatorvid treatment alleviated NOD-like receptor protein 3 (NLRP3)-mediated chondrocyte pyroptosis and degeneration and relieved macrophage inflammation by preventing reactive oxygen species (ROS) production through NLRP3 signaling.

Conclusion
Prophylactic treatment with Resatorvid alleviates TMJOA pathology by inhibiting chondrocyte pyroptosis and degeneration, as well as ROS-induced macrophage inflammation, through TLR4/MyD88/NF-κB/NLRP3.