bluuebunny/crossref_metadata_2025_split huggingface dataset:
Dynamic and self-biodegradable polysaccharide hydrogel stores embryonic stem cell construct under ambient condition
Authors: Yang Kuan , Wei Wei , Gao Li Ting , Zhao Xin Yi , Liu Zhenqi , Li Jianhui , Li Haopeng , Miyatake Hideyuki , Ito Yoshihiro , Chen Yong Mei 
Published: May 2023

The proper microenvironment is critical for the storage and transportation of embryonic stem cells (ESCs). To mimic a dynamic 3D microenvironment as it exists in vivo and consider “off-the-shelf” availability reaching the destination, we proposed an alternative approach that allows for facile storage and transportation of stem cells in the form of ESCs-dynamic hydrogel construct (CDHC) under ambient conditions. To form CDHC, mouse embryonic stem cells (mESCs) were in-situ encapsulated within a polysaccharide-based dynamic and self-biodegradable hydrogel. After storing CDHC in a sterile and hermetic environment for 3 days and then transferring to a sealed vessel with fresh medium for another 3 days, the large and compact colonies retained a 90% survival rate and pluripotency. Furthermore, after transporting and arriving at the destination, the encapsulated stem cell could be automatically released from the self-biodegradable hydrogel. After continuous cultivation of 15 generations of retrieved cells, automatically released from the CDHC, the mESCs underwent 3D encapsulation, storage, transportation, release, and continuous long-term subculture; resumed colony forming capacity and pluripotency were revealed by stem cell markers both in protein and mRNA levels. We believe that the dynamic and self-biodegradable hydrogel provides a simple, cost-effective, and valuable tool for storing and transporting “ready-to-use” CDHC under ambient conditions, facilitating “off-the-shelf” availability and widespread applications.
Lactic acid production from food waste at an anaerobic digestion biorefinery: effect of digestate recirculation and sucrose supplementation
Authors: Bühlmann Christopher H. , Mickan Bede S. , Tait Stephan , Batstone Damien J. , Bahri Parisa A. 
Published: May 2023

Low lactic acid (LA) yields from direct food waste (FW) fermentation restrict this production pathway. However, nitrogen and other nutrients within FW digestate, in combination with sucrose supplementation, may enhance LA production and improve feasibility of fermentation. Therefore, this work aimed to improve LA fermentation from FWs by supplementing nitrogen (0–400 mgN·L−1) as NH4Cl or digestate and dosing sucrose (0–150 g·L−1) as a low-cost carbohydrate. Overall, NH4Cl and digestate led to similar improvements in the rate of LA formation (0.03 ± 0.02 and 0.04 ± 0.02 h−1 for NH4Cl and digestate, respectively), but NH4Cl also improved the final concentration, though effects varied between treatments (5.2 ± 4.6 g·L−1). While digestate altered the community composition and increased diversity, sucrose minimised community diversion from LA, promoted Lactobacillus growth at all dosages, and enhanced the final LA concentration from 25 to 30 g·L−1 to 59–68 g·L−1, depending on nitrogen dosage and source. Overall, the results highlighted the value of digestate as a nutrient source and sucrose as both community controller and means to enhance the LA concentration in future LA biorefinery concepts.
Controlled growth of titanium dioxide nanotubes for doxorubicin loading and studies of in vitro antitumor activity
Authors: Zhang Yunshan , Huang Tuo , Lv Wanwan , Yang Kai , Ouyang Cuiling , Deng Minxin , Yi Rongyuan , Chu Hui , Chen Jian 
Published: May 2023

Titanium dioxide (TiO2) materials are suitable for use as drug carriers due to their natural biocompatibility and nontoxicity. The aim of the study presented in this paper was to investigate the controlled growth of TiO2 nanotubes (TiO2 NTs) of different sizes via an anodization method, in order to delineate whether the size of NTs governs their drug loading and release profile as well as their antitumor efficiency. TiO2 NTs were tailored to sizes ranging from 25 nm to 200 nm according to the anodization voltage employed. The TiO2 NTs obtained by this process were characterized using scanning electron microscopy, transmission electron microscopy, and dynamic light scattering The larger TiO2 NTs exhibited greatly improved doxorubicin (DOX)-loading capacity (up to 37.5 wt%), which contributed to their outstanding cell-killing ability, as evidenced by their lower half-maximal inhibitory concentration (IC50). Comparisons were carried out of cellular uptake and intracellular release rates of DOX for large and small TiO2 NTs loaded with DOX. The results showed that the larger TiO2 NTs represent a promising therapeutic carrier for drug loading and controlled release, which could improve cancer treatment outcomes. Therefore, TiO2 NTs of larger size are useful substances with drug-loading potency that may be used in a wide range of medical applications.
The flavagline FL3 interferes with the association of Annexin A2 with the eIF4F initiation complex and transiently stimulates the translation of annexin A2 mRNA
Authors: Grindheim Ann Kari , Patil Sudarshan S. , Nebigil Canan G. , Désaubry Laurent , Vedeler Anni 
Published: May 2023

Introduction: Annexin A2 (AnxA2) plays a critical role in cell transformation, immune response, and resistance to cancer therapy. Besides functioning as a calcium- and lipidbinding protein, AnxA2 also acts as an mRNA-binding protein, for instance, by interacting with regulatory regions of specific cytoskeleton-associated mRNAs.Methods and Results: Nanomolar concentrations of FL3, an inhibitor of the translation factor eIF4A, transiently increases the expression of AnxA2 in PC12 cells and stimulates shortterm transcription/translation of anxA2 mRNA in the rabbit reticulocyte lysate. AnxA2 regulates the translation of its cognate mRNA by a feed-back mechanism, which can partly be relieved by FL3. Results obtained using the holdup chromatographic retention assay results suggest that AnxA2 interacts transiently with eIF4E (possibly eIF4G) and PABP in an RNA-independent manner while cap pulldown experiments indicate a more stable RNA-dependent interaction. Short-term (2 h) treatment of PC12 cells with FL3 increases the amount of eIF4A in cap pulldown complexes of total lysates, but not of the cytoskeletal fraction. AnxA2 is only present in cap analogue-purified initiation complexes from the cytoskeletal fraction and not total lysates confirming that AnxA2 binds to a specific subpopulation of mRNAs.Discussion: Thus, AnxA2 interacts with PABP1 and subunits of the initiation complex eIF4F, explaining its inhibitory effect on translation by preventing the formation of the full eIF4F complex. This interaction appears to be modulated by FL3. These novel findings shed light on the regulation of translation by AnxA2 and contribute to a better understanding of the mechanism of action of eIF4A inhibitors.
Metformin impairs trophoblast metabolism and differentiation in a dose-dependent manner
Authors: Nashif Sereen K. , Mahr Renee M. , Jena Snehalata , Jo Seokwon , Nelson Alisa B. , Sadowski Danielle , Crawford Peter A. , Puchalska Patrycja , Alejandro Emilyn U. , Gearhart Micah D. , Wernimont Sarah A. 
Published: May 2023

Metformin is a widely prescribed medication whose mechanism of action is not completely defined and whose role in gestational diabetes management remains controversial. In addition to increasing the risk of fetal growth abnormalities and preeclampsia, gestational diabetes is associated with abnormalities in placental development including impairments in trophoblast differentiation. Given that metformin impacts cellular differentiation events in other systems, we assessed metformin’s impact on trophoblast metabolism and differentiation. Using established cell culture models of trophoblast differentiation, oxygen consumption rates and relative metabolite abundance were determined following 200 µM (therapeutic range) and 2000 µM (supra-therapeutic range) metformin treatment using Seahorse and mass-spectrometry approaches. While no differences in oxygen consumption rates or relative metabolite abundance were detected between vehicle and 200 µM metformin-treated cells, 2000 µM metformin impaired oxidative metabolism and increased the abundance of lactate and TCA cycle intermediates, α-ketoglutarate, succinate, and malate. Examining differentiation, treatment with 2000 μM, but not 200 µM metformin, impaired HCG production and expression of multiple trophoblast differentiation markers. Overall, this work suggests that supra-therapeutic concentrations of metformin impair trophoblast metabolism and differentiation whereas metformin concentrations in the therapeutic range do not strongly impact these processes.
Identification of intestinal microbiome associated with lymph-vascular invasion in colorectal cancer patients and predictive label construction
Authors: Chen Chuanbin , Chen Kang , Huang Zigui , Huang Xiaoliang , Wang Zhen , He Fuhai , Qin Mingjian , Long Chenyan , Tang Binzhe , Mo Xianwei , Liu Jungang , Tang Weizhong 
Published: May 2023

ObjectiveTo identify differences between the composition, abundance, and biological function of the intestinal microbiome of patients with and without lymph-vascular invasion (LVI) colorectal cancer (CRC) and to construct predictive labels to support accurate assessment of LVI in CRC.Method134 CRC patients were included, which were divided into two groups according to the presence or absence of LVI, and their intestinal microbiomes were sequenced by 16SrRNA and analyzed for differences. The transcriptome sequencing data of 9 CRC patients were transformed into immune cells abundance matrix by CIBERSORT algorithm, and the correlation among LVI-associated differential intestinal microbiomes, immune cells, immune-related genes and LVI-associated differential GO items and KEGG pathways were analyzed. A random forest (RF) and eXtreme Gradient Boosting (XGB) model were constructed to predict the LVI of CRC patients based on the differential microbiome.ResultThere was no significant difference in α-diversity and β-diversity of intestinal microbiome between CRC patients with and without LVI (P &gt; 0.05). Linear discriminant analysis Effect Size (LEfSe) analysis showed 34 intestinal microbiomes enriched in CRC patients of the LVI group and 5 intestinal microbiomes were significantly enriched in CRC patients of the non-lymph-vascular invasion (NLVI) group. The RF and XGB prediction models constructed with the top 15% of the LVI-associated differential intestinal microbiomes ranked by feature significance had good efficacy.ConclusionsThere are 39 intestinal flora with significantly different species abundance between the LVI and NLVI groups. g:Alistipes.s:Alistipes_indistinctus is closely associated with colorectal cancer vascular invasion. LVI-associated differential intestinal flora may be involved in regulating the infiltration of immune cells in CRC and influencing the expression of immune-related genes. LVI-associated differential intestinal flora may influence the process of vascular invasion in CRC through a number of potential biological functions. RF prediction models and XGB prediction models constructed based on microbial markers of gut flora can be used to predict CRC-LVI conditions.
A 3-year study of Candida infections among patients with malignancy: etiologic agents and antifungal susceptibility profile
Authors: Sharifi Mahdieh , Badiee Parisa , Abastabar Mahdi , Morovati Hamid , Haghani Iman , Noorbakhsh Mahta , Mohammadi Rasoul 
Published: May 2023

ObjectiveOpportunistic fungal infections by Candida species arise among cancer patients due to the weakened immune system following extensive chemotherapy. Prophylaxis with antifungal agents have developed the resistance of Candida spp. to antifungals. Accurate identification of yeasts and susceptibility patterns are main concerns that can directly effect on the treatment of patients.MethodsOver a period of three years, 325 cancer patients suspected to Candida infections were included in the current investigation. The clinical isolates were molecularly identified by polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP). All strains, were examined for in vitro susceptibility to the amphotericin B, itraconazole, fluconazole, and anidulafungin according to the CLSI M27 document.ResultsSeventy-four cancer patients had Candida infections (22.7%). Candida albicans was the most common species (83.8%). Antifungal susceptibility results indicated that 100% of the Candida isolates were sensitive to amphotericin B; however, 17.6%, 9.4%, and 5.4% of clinical isolates were resistant to anidulafungin, fluconazole, and itraconazole, respectively.ConclusionThe findings of the present work shows a warning increase in resistance to echinocandins. Since all fluconazole resistance isolates were obtained from candidemia, we recommend amphotericin B as the first line therapy for this potentially fatal infection.
The clinical significance of macrolide resistance in pediatric Mycoplasma pneumoniae infection during COVID-19 pandemic
Authors: Jiang Ting-ting , Sun Lin , Wang Tian-yi , Qi Hui , Tang He , Wang Ya-cui , Han Qian , Shi Xiao-qing , Bi Jing , Jiao Wei-wei , Shen A-dong 
Published: May 2023

BackgroundMycoplasma pneumoniae (MP) is a commonly occurring pathogen causing community-acquired pneumonia (CAP) in children. The global prevalence of macrolide-resistant MP (MRMP) infection, especially in Asian regions, is increasing rapidly. However, the prevalence of MRMP and its clinical significance during the COVID-19 pandemic is not clear.MethodsThis study enrolled children with molecularly confirmed macrolide-susceptible MP (MSMP) and MRMP CAP from Beijing Children’s Hospital Baoding Hospital, Capital Medical University between August 2021 and July 2022. The clinical characteristics, laboratory findings, chest imaging presentations, and strain genotypes were compared between patients with MSMP and MRMP CAP.ResultsA total of 520 hospitalized children with MP-CAP were enrolled in the study, with a macrolide resistance rate of 92.7%. Patients with MRMP infection exhibited more severe clinical manifestations (such as dyspnea and pleural effusion) and had a longer hospital stay than the MSMP group. Furthermore, abnormal blood test results (including increased LDH and D-dimer) were more common in the MRMP group (P&lt;0.05). Multilocus variable-number tandem-repeat analysis (MLVA) was performed on 304 samples based on four loci (Mpn13-16), and M3562 and M4572 were the major types, accounting for 74.0% and 16.8% of the strains, respectively. The macrolide resistance rate of M3562 strains was up to 95.1%.ConclusionThe prevalence of MRMP strains in hospitalized CAP patients was extremely high in the Baoding area, and patients infected with MRMP strains exhibited more severe clinical features and increased LDH and D-dimer. M3562 was the predominant resistant clone.
Dense agent-based HPC simulation of cell physics and signaling with real-time user interactions
Authors: Merchant Naman , Sampson Adam T. , Boiko Andrei , Falconer Ruth E. 
Published: May 2023

IntroductionDistributed simulations of complex systems to date have focused on scalability and correctness rather than interactive visualization. Interactive visual simulations have particular advantages for exploring emergent behaviors of complex systems. Interpretation of simulations of complex systems such as cancer cell tumors is a challenge and can be greatly assisted by using “built-in” real-time user interaction and subsequent visualization.MethodsWe explore this approach using a multi-scale model which couples a cell physics model with a cell signaling model. This paper presents a novel communication protocol for real-time user interaction and visualization with a large-scale distributed simulation with minimal impact on performance. Specifically, we explore how optimistic synchronization can be used to enable real-time user interaction and visualization in a densely packed parallel agent-based simulation, whilst maintaining scalability and determinism. We also describe the software framework created and the distribution strategy for the models utilized. The key features of the High-Performance Computing (HPC) simulation that were evaluated are scalability, deterministic verification, speed of real-time user interactions, and deadlock avoidance.ResultsWe use two commodity HPC systems, ARCHER (118,080 CPU cores) and ARCHER2 (750,080 CPU cores), where we simulate up to 256 million agents (one million cells) using up to 21,953 computational cores and record a response time overhead of ≃350 ms from the issued user events.DiscussionThe approach is viable and can be used to underpin transformative technologies offering immersive simulations such as Digital Twins. The framework explained in this paper is not limited to the models used and can be adapted to systems biology models that use similar standards (physics models using agent-based interactions, and signaling pathways using SBML) and other interactive distributed simulations.
How social interactions can affect Modern Code Review
Authors: Ciancarini Paolo , Kruglov Artem , Malikova Aygul , Pedrycz Witold , Succi Giancarlo 
Published: May 2023

IntroductionModern Code Review (MCR) is a multistage process where developers evaluate source code written by others to enhance the software quality. Despite the numerous studies conducted on the effects of MCR on software quality, the non-technical issues in the MCR process have not been extensively studied. This study aims to investigate the social problems in the MCR process and to find possible ways to prevent them and improve the overall quality of the MCR process.MethodologyTo achieve the research objectives, we applied the grounded theory research shaped by GQM approach to collect data on the attitudes of developers from different teams toward MCR. We conducted interviews with 25 software developers from 13 companies to obtain the information necessary to investigate how social interactions affect the code reviewing process.ResultsOur findings show that interpersonal relationships within the team can have significant consequences on the MCR process. We also received a list of possible strategies to overcome these problems.DiscussionOur study provides a new perspective on the non-technical issues in the MCR process, which has not been extensively studied before. The findings of this study can help software development teams to address the social problems in the MCR process and improve the overall quality of their software products.ConclusionThis study provides valuable insights into the non-technical issues in the MCR process and the possible ways to prevent them. The findings of this study can help software development teams to improve the MCR process and the quality of their software products. Future research could explore the effectiveness of the identified strategies in addressing the social problems in the MCR process.
Association between corrected QT interval and long-term cardiovascular outcomes in elderly patients who had undergone endovascular therapy for lower extremity arterial disease
Authors: Chang Yao-Ting , Tzeng I-Shiang , Jang Shih-Jung , Liu Kuan-Liang , Hsieh Chien-An , Chou Hsin-Hua , Yeh Kuan-Hung , Huang Hsuan-Li ,   TRENDPAD Study Group
Published: May 2023

BackgroundPopulation-based studies have reported the association between prolonged corrected QT (QTc) intervals and an increased risk of adverse cardiovascular events. Data regarding the association between longer QTc intervals and incident cardiovascular outcomes in patients with lower extremity arterial disease (LEAD) are scarce.ObjectiveTo examine the impact of QTc interval on long-term cardiovascular outcomes in elderly patients with symptomatic LEAD.MethodsThis cohort study extracted data from the Tzu-chi Registry of ENDovascular Intervention for Peripheral Artery Disease (TRENDPAD) and enrolled 504 patients aged ≥ 70 treated with endovascular therapy for atherosclerotic LEAD from July 1, 2005, to December 31, 2019. The main outcomes of interest were all-cause mortality and major adverse cardiovascular events (MACE). Multivariate analysis was conducted using the Cox proportional hazard model to determine independent variables. We performed interaction analysis between corrected QT and other covariates and Kaplan-Meier analysis to compare the outcome of interest among the groups stratified by the tercile of QTc intervals.ResultsA total of 504 patients [235 men (46.6%); mean age, 79.9 ± 6.2 years; mean QTc interval, 459 ± 33 msec] entered the final data analysis. We categorized the baseline patient characteristics according to terciles of QTc intervals. During the median follow-up time of 3.15 (interquartile ranges, 1.65–5.42) years, we noted 264 deaths and 145 MACEs. The 5-year rates of freedom from all-cause mortality (71% vs. 57% vs. 31%, P &lt; 0.001) and MACEs (83% vs. 67% vs. 46%, P &lt; 0.001) were significantly different among the tercile groups. Multivariate analysis showed that a 1-SD increase in the QTc interval increased the risk of all-cause mortality [hazard ratio (HR) 1.49, P &lt; 0.001] and MACEs (HR 1.59, P &lt; 0.001) after adjusting for other covariates. The interaction analysis showed that QTc interval and C-reactive protein levels were most strongly associated with death (HR = 4.88, 95% CI 3.09–7.73, interaction P &lt; 0.001) and MACEs (HR = 7.83, 95% CI 4.14–14.79, interaction P &lt; 0.001).ConclusionsIn elderly patients with symptomatic atherosclerotic LEAD, a prolonged QTc interval is associated with advanced limb ischemia, multiple medical comorbidities, increased risk of MACEs, and all-cause mortality.
Visual analysis based on CiteSpace software: a bibliometric study of atrial myxoma
Authors: Gao Ang , Yang Jinghua , Tian Tongru , Wu Yang , Sun Xiaoting , Qi Na , Tian Nan , Wang Xian , Wang Jisheng 
Published: May 2023

ObjectiveTo use CiteSpace and VOSviewer visual metrology to analyze the research status, frontier hotspots, and trends in research on atrial myxoma.MethodsThe Web of Science core collection database was used to retrieve relevant literature on atrial myxoma from 2001 to 2022. CiteSpace software was used to analyze keywords with a co-occurrence network, co-polymerization class, and burst terms, and a corresponding visual atlas was drawn for analysis.ResultsA total of 893 valid articles were included. The country with the highest number of articles was the United States (n = 186). The organization with the highest number of articles was the Mayo Clinic (n = 15). The author with the highest number of articles was Yuan SM (n = 12). The highest cited author was Reynen K (n = 312). The highest cited journal was Annals of Thoracic Surgery (n = 1,067). The most frequently cited literature was published in the New England Journal of Medicine in 1995, which was cited 233 times. The keywords co-occurrence, copolymerization analysis, and Burst analysis revealed that the main research focuses were surgical methods, case reports, and genetic and molecular level studies on the pathogenesis of myxoma.ConclusionsThis bibliometric analysis revealed that the main research topics and hotspots in atrial myxoma included surgical methods, case reports, genetic and molecular studies.