bluuebunny/crossref_metadata_2025_split huggingface dataset:
Genome‐Scale Metabolic Model's multi‐objective solving algorithm based on the inflexion point of Pareto front including maximum energy utilization and its application in Aspergillus niger DS03043
Authors: Fan Xingcun , Zhou Jingru , Xia Jianye , Yan Xuefeng 
Published: March 2022

AbstractThe solution of Genome‐Scale Metabolic Model (GSMM) directly affects the simulation accuracy of the metabolic process in digital cells. Single‐objective optimization methods, such as flux balance analysis (FBA), which is widely used in solving GSMM, have limitations when simulating actual biological processes, which leads to unrealistic results due to other biological constraints being ignored. A novel multi‐objective differential evolution algorithm based on general FBA (i.e., differential evolution FBA [DEFBA]) is hence proposed to solve GSMM. First, in accordance with the assumption that cells minimize resource consumption and maximize resource utilization, the maximum specific growth rate and the minimum cellular production rate of ATP, NADPH, and NADH are defined as the multi‐objective functions of DEFBA. Second, FBA is used to produce the initial individuals of DEFBA by changing the upper bound of biomass reaction in GSMM. Third, mutation and selection operations help in generating new individuals in the solution space to search the Pareto front. Finally, the optimal solution is selected by analyzing the inflexion point of the Pareto front. In DEFBA, multi‐objective technology and optimal solution judging technology can introduce the biological constraints into the GSMM solving method, such that the solution can be more consistent with the essential biological mechanism. DEFBA is applied to solve Aspergillus niger's GSMM. The improved results show that DEFBA can be an effective general solving algorithm for GSMM.
Effects of π‐conjugation on the charge‐transport properties of hole‐transporting materials featuring diphenylamine‐π‐quinacridone for perovskite solar cells: A theoretical study
Authors: Rashid Md Al Mamunur , Kim Junkyu , Long Dang Xuan , Kwak Kyungwon , Hong Jongin 
Published: March 2022

AbstractDensity functional theory (DFT), time‐dependent DFT, and Marcus theory were used to probe the optoelectronic and charge‐transport properties of compounds obtained by inserting long‐chain aliphatic alkenes or condensed aromatic rings between the planar quinacridone core and the terminal donor diphenylamine moiety of a reference hole‐transporting material (HTM). Compared to the reference HTM, its newly designed derivatives showed lower‐lying highest occupied molecular orbitals that were well matched in energy with the valence band maximum of a representative perovskite absorber. HTMs obtained via the insertion of condensed aromatic rings showed higher hole mobilities than those obtained via the insertion of aliphatic alkenes. Overall, hole mobility was mainly influenced by the charge‐transfer integral, while other factors, such as the hole reorganization energy, hole hopping rate, and centroid distance, had only minor effects.
Simultaneous determination of serum homocysteine, cysteine, and methionine in patients with schizophrenia by liquid chromatography–tandem mass spectrometry
Authors: Li Zhenguo , Liu Mingli , Chen Chunwu , Pan Yongqiang , Cui Xueting , Sun Jian , Zhao Furong , Cao Yunfeng 
Published: March 2022

AbstractSchizophrenia is a debilitating psychiatric disorder affecting approximately 1% of the population worldwide. Disturbances in the homocysteine metabolism are an important factor in the pathophysiology of schizophrenia. In this research, a novel validated liquid chromatography–tandem mass spectrometry (LC–MS/MS) quantification procedure was developed to investigate three significant compounds of homocysteine metabolism: homocysteine, cysteine, and methionine in patients with schizophrenia and healthy controls. Sample preparation involved a reduction with dithiothreitol followed by protein precipitation, and the chromatographic runtime was 2 min. The LC–MS/MS method was validated according to CLSI C62‐A and the Chinese Guidance for Liquid Chromatography and Mass Spectrometry Clinical Application. The performance of the method was excellent with a coefficient of variation for precision in the range of 0.5–6.9%, an accuracy of 90.4–101.6%. In addition, the practical applicability of the method was demonstrated by applying it in the routine sample analysis for a schizophrenic patient. Increased homocysteine levels and decreased cysteine levels were observed in the patient with schizophrenia. These results indicate that the activity of the transsulfuration pathway may play a key role in the pathogenesis of schizophrenia.
Metabolomics analysis reveals Oct4 overexpression drives metabolic reprogramming and enhanced glycolysis and pentose phosphate pathway in lung adenocarcinoma cells
Authors: Tang Yabin , Zhu Liang , Chen Hongzhuan , Meng Shuang 
Published: March 2022

AbstractPoor prognosis in the underlying mechanisms involved in lung adenocarcinoma and its treatment leads to low survival rates in patients. Emerging evidence indicates that cancer is primarily a metabolic disease and metabolic reprogramming is a well‐established hallmark and driving force of cancer. Oct4, acting as an oncogene, is a major regulator of cell pluripotency. It can reprogram the differentiated cells into cancer stem cells (CSCs) and plays an oncogenic role when pathologically hijacked. However, data that Oct4, the genetic reprogramming factor, could induce metabolic reprogramming have been very limited, and the direct evidence in metabolic level whether Oct4 reprograms metabolome is lacking. In the present study, integrated untargeted and targeted metabolomics analyses were utilized to investigate metabolic changes induced by Oct4 overexpression in lung adenocarcinoma cells. The results suggested that elevated expression levels of Oct4 drive metabolic reprogramming. Oct4 overexpression redirects glucose catabolism to glycolysis pathway and to the oxidative pentose phosphate pathway (PPP). This study identifies unique pathways that are candidate therapeutic targets for the treatment of lung adenocarcinoma. This study also aims to improve our understanding of the cancer‐promoting activity of Oct4 and help identify novel diagnostic and therapeutic strategies for cancer treatment.
The effect of physical exercise on circulating brain‐derived neurotrophic factor in healthy subjects: A meta‐analysis of randomized controlled trials
Authors: Wang Ya‐Hai , Zhou Huan‐Huan , Luo Qiang , Cui Sidong 
Published: March 2022

AbstractObjectiveTo investigate how physical exercise (PE) would affect brain‐derived neurotrophic factor (BDNF) in randomized controlled trials (RCTs) of healthy subjects.MethodsSeven databases (PubMed, Web of Science, Cochrane, Embase, PsycINFO, CINAHL, SPORTDiscus) were searched for RCTs assessing the effects of PE on serum and/or plasma BDNF until December 18, 2021. Meta‐analysis was performed by random‐effects method with standardized mean difference (SMD) and 95% confidence intervals (CIs). Subgroup analysis and meta‐regression analysis were conducted to investigate the potential source of heterogeneity. Trim and fill method, and leave‐one‐out cross‐validation were conducted.ResultsEventually, 21 articles, involving 809 participants, were included in the meta‐analysis. Overall, both acute (5 trials, SMD: 1.20, 95% CI: 0.36 to 2.04, p = .005) and long‐term (17 trials, SMD: 0.68, 95% CI: 0.27 to 1.08, p = .001) PE had significant positive effects on BDNF levels. Via subgroup analysis, studies of long‐term PE with larger sample sizes, female participants, participants older than 60 years, and aerobic exercise contributed to a more pronounced improvement on BDNF levels than that found when all studies were combined.ConclusionBoth acute and long‐term PE had significant positive effects on circulating BDNF in healthy subjects. This review suggests that acute exercise and long‐term aerobic exercise are powerful forms of PE to enhance neurotrophic effect, especially for female subjects or subjects over 60 years.
circITCH suppresses cell proliferation and metastasis through miR‐660/TFCP2 pathway in melanoma
Authors: Zhang Jianfei , Cai Yanlin , Sheng Shunliang , Zhao Congling , Jiang Bin 
Published: March 2022

AbstractBackgroundMelanoma is an aggressive disease that is rising in incidence. Advanced melanoma is still a life‐threatening disease. CircRNAs are documented to be involved in melanoma progression. But circITCH role in melanoma remains unclear.Methods and ResultsTo explore the functions of circITCH in melanoma, levels of circITCH in melanoma tissues and paracarcinoma normal tissues were detected. To study the roles of circITCH in melanoma in terms of cell proliferation and migration, in vitro and in vivo experiments were performed. Mechanism study was designed to investigate the potential regulatory effect of circITCH in melanoma. Results revealed that circITCH expression was repressed in melanoma versus adjacent normal tissues. Function study showed that circITCH suppressed melanoma cell proliferation and metastasis. The mechanism study showed that circITCH‐sponged miR‐660 to upregulate TFCP2 and suppress melanoma progression.ConclusionsThe circITCH/miR‐660/TFCP2 axis is involved in melanoma progression hence circITCH can be a diagnostic biomarker as well as a target for treating melanoma.
Persistent COVID‐19 negative report of a physician in Bangladesh living and visiting in Red‐listed country with some special precaution followed
Authors: Nahin Sabrina , Amin Mohammad Ashraful 
Published: March 2022

AbstractCOVID‐19 infections have been widespread in Bangladesh subsequently. We present the example of a 32‐year‐old Bangladeshi physician who worked in a hospital and was previously involved in collecting swabs for COVID‐19 patients. During the pandemic, he also traveled to a red‐listed country and was continuously negative throughout the period.
Nanostructural Analysis of Co‐Re/γ‐Al2O3 Fischer‐Tropsch Catalyst by TEM and XRD
Authors: Dehghan‐Niri Roya , Tsakoumis Nikolaos E. , Voronov Alexey , Holmen Anders , Holmestad Randi , Vullum Per‐Erik , Borg Øyvind , Rytter Erling. , Rønning Magnus. , Walmsley John C. 
Published: March 2022

AbstractA rhenium promoted Fischer‐Tropsch (FT) cobalt catalyst supported on γ‐Al2O3 has been investigated by Transmission Electron Microscopy (TEM) and X‐ray Diffraction (XRD), before and after reduction. Electron diffraction, High Resolution TEM and Electron Energy Loss Spectroscopy were used to confirm the oxidation state. Cobalt aggregate, particle and crystallite sizes have been studied in detail and measured by TEM and XRD. A cobalt particle size of 10.0±2.4 nm obtained from bright field TEM images for the reduced material is consistent with the XRD analysis of the calcined catalyst. After reduction dark field TEM imaging gave a volume‐weighted crystallite size of 7.5±2.5 nm, which is close to the value obtained by XRD. The particles had lost the parallel orientation and physical continuity within the alumina pore structure that were present before reduction. The latter was confirmed by electron tomography. Lamellae identified with the presence of Hexagonal Close Packed cobalt were observed in the predominantly Face Centred Cubic particles.
Cocrystal Formation Precedes the Mechanochemically Acetate‐Assisted C−H Activation with [Cp*RhCl2]2
Authors: Ardila‐Fierro Karen J. , Rubčić Mirta , Hernández José G. 
Published: March 2022

AbstractThis work reports the experimentally studied mechanochemical formation of rhodacycles by ball milling pyridine‐ and quinoline‐derived substrates and [Cp*RhCl2]2 in the presence of NaOAc. Ex‐situ analysis of the mechanochemical reactions using powder X‐ray diffraction (PXRD), solid‐state UV‐vis spectroscopy and ATR‐FTIR spectroscopy revealed the formation of unexpected cocrystals between the substrates and the rhodium dimer prior to the C−H activation step. This sequence of events differs from the generally accepted steps in solution in which cleavage of [Cp*RhCl2]2 is initiated by acetate ions. Additionally, the mechanochemical approach enabled the synthesis of the six‐membered rhodacycle [Cp*Rh(2‐benzilpyridine)Cl], a metal complex repeatedly reported as inaccessible in solution. Altogether, the results of this investigation clarify some of the fundamental aspects of mechanochemical cyclometallations.
Worldwide prevalence of rhinitis in adults: A review of definitions and temporal evolution
Authors: Savouré Marine , Bousquet Jean , Jaakkola Jouni J. K. , Jaakkola Maritta S. , Jacquemin Bénédicte , Nadif Rachel 
Published: March 2022

AbstractIntroductionAlthough rhinitis is among the most common diseases worldwide, rhinitis prevalence in the general adult population is unclear and definitions differ widely.ObjectiveTo summarize the literature on rhinitis prevalence in the general adult population and to assess: (1) the prevalence according to different rhinitis definitions overall and in different regions of the world, and (2) the evolution of rhinitis prevalence over time.MethodsWe conducted an extensive literature review of publications including rhinitis prevalence using Pubmed and Scopus databases up to October 2020. We classified the definitions into three categories: unspecified rhinitis, allergic rhinitis (AR), and nonallergic rhinitis (NAR).ResultsAmong 5878 articles screened, 184 articles were included, presenting 156 different definitions of rhinitis. Rhinitis prevalence ranged from 1% to 63%. The overall median prevalences of unspecified rhinitis, AR and NAR were 29.4%, 18.1% and 12.0%, and they varied according to the geographical location. Rhinitis prevalence tended to increase over time.ConclusionsThis review highlights the great heterogeneity of the definitions. The majority of studies had focused on AR, while only a few epidemiological data exist on NAR. We found geographical variability in rhinitis prevalence. Most of studies reported an increase of rhinitis prevalence over the last decades.
DNA methylation biomarkers in asthma and rhinitis: Are we there yet?
Authors: Legaki Evangelia , Arsenis Christos , Taka Styliani , Papadopoulos Nikolaos G. 
Published: March 2022

AbstractThe study of epigenetics has improved our understanding of mechanisms underpinning gene‐environment interactions and is providing new insights in the pathophysiology of respiratory allergic diseases. We reviewed the literature on DNA methylation patterns across different tissues in asthma and/or rhinitis and attempted to elucidate differentially methylated loci that could be used to characterize asthma or rhinitis. Although nasal and bronchial epithelia are similar in their histological structure and cellular composition, genetic and epigenetic regulation may differ across tissues. Advanced methods have enabled comprehensive, high‐throughput methylation profiling of different tissues (bronchial or nasal epithelial cells, whole blood or isolated mononuclear cells), in subjects with respiratory conditions, aiming to elucidate gene regulation mechanisms and identify new biomarkers. Several genes and CpGs have been suggested as asthma biomarkers, though research on allergic rhinitis is still lacking. The most common differentially methylated loci presented in both blood and nasal samples are ACOT7, EPX, KCNH2, SIGLEC8, TNIK, FOXP1, ATPAF2, ZNF862, ADORA3, ARID3A, IL5RA, METRNL and ZFPM1. Overall, there is substantial variation among studies, (i.e. sample sizes, age groups and disease phenotype). Greater variability of analysis method detailed phenotypic characterization and age stratification should be taken into account in future studies.
Chloroxylon swietenia (Roxb.) DC induces cell death and apoptosis by down‐regulating the NF‐κB pathway in MCF‐7 breast cancer cells: In vitro and in vivo investigations
Authors: Kamble Sonali S. , Choudhari Jasoda , Nimma Ramakrishna , Kumar Totakura Venkata Santosh , Patil Kapil K. , Hese Shrikant V. , Dawane Bhaskar S. , Gacche Rajesh N. 
Published: March 2022

AbstractBackgroundNatural products with targeted bioactivity have gained major attention in the field of cancer research owing to emerging anti‐cancer drug resistance and off target toxicities. Chloroxylon swietenia (Roxb.) DC is recognized as a folklore medicinal plant and has numerous therapeutic benefits in the folklore medicine system, however the anti‐cancer potential of this plant and its mechanism of action is poorly understood.AimsThe aim of the study was to investigate the anti‐breast cancer efficacy of C. swietenia leaves methanol extract (CSLME) against MCF‐7 hormone dependent human breast cancer cell line with possible mechanism of action.Methods and resultsThe anti‐breast cancer activity of CSLME against MCF‐7 cells was assessed by evaluating its efficacy toward cytotoxicity, cell migration, colony formation, DNA fragmentation, apoptosis, cytoskeleton, angiogenesis, cell cycle regulation, and animal toxicity. The preliminary screening of CSLME against MCF‐7 cells revealed the cytotoxicity (IC50 20 μg/ml), inhibited cell migration, colony formation, and angiogenesis. It was observed that CSLME induces apoptosis by nuclear fragmentation and disruption of cytoskeleton by actin derangement. The results of Annexin V‐FITC assay and cell cycle analysis by flow cytometry clearly pointed out the sizable fraction of apoptotic cells, and arrested the cells at G2/M phase of cell cycle. The results of the immunoblotting experiments showed that CSLME activates intrinsic pathway of apoptosis with down regulation of anti‐apoptotic marker like Bcl2, up regulation of pro‐apoptotic markers like Bax & Bad, along with successful cleavage of Caspase‐9 and PARP‐1. Further, western blot analysis revealed the possible down regulation of NF‐κB pathway by CSLME, which may be responsible for anti‐cancer activity in MCF‐7 cells. In vivo animal model studies using NOD‐SCID mice demonstrated impressive anti‐tumor activity with significant reduction in tumor volume of MCF‐7 tumor xenograft. Of note, in‐vivo acute oral toxicity study as per Organization for Economic Cooperation and Development 423 revealed the nontoxic nature of CSLME.ConclusionThe in vitro and in vivo findings clearly outline the potential of CSLME as inhibitor of growth and proliferation of MCF‐7 cells. Mechanistically, CSLME seems to activate intrinsic pathway of apoptosis, arrest cell cycle, target actin cytoskeleton, inhibit growth, colony formation, migration, and angiogenesis, with down regulation of NF‐κB pathway leading to cell death.
Machine‐readable universal data format for bidirectional reflectance distribution function and BiRDview—An open‐source web‐based application for viewing and comparing bidirectional reflectance data
Authors: Lanevski Dmitri , Ferrero Alejandro , Perales Esther , Manoocheri Farshid , Ikonen Erkki 
Published: March 2022

AbstractModern studies of bidirectional reflectance distribution function (BRDF) and its applications using data and machine‐driven science require formatting of BRDF data according to Findable, accessible, interoperable and reusable (FAIR) data principles. As a solution a FAIR universal BRDF file‐format based on Java Script Object Notation (JSON) is proposed. JSON principles as well as file structure are explained and examples are given. Automatic validation of universal BRDF file format is realized with the help of JSON schema. Furthermore, the source code and accompanying documentation are presented in dedicated supporting material files. It is expected that after its wide adoption, the proposed BRDF file format will enhance collaboration between different research groups and benefit machine‐driven science. The uptake is facilitated by introducing a BiRDview—a modern open‐source web‐based application for BRDF visualization.
Rule extraction from decision tree: Transparent expert system of rules
Authors: Boruah Arpita Nath , Biswas Saroj Kr. , Bandyopadhyay Sivaji 
Published: March 2022

AbstractA system which is transparent and has less decision rules is an efficient, user‐convincing system and moreover convenient and manageable to fields like banking, business, and medical. Decision Tree (DT) is a data mining technique which is transparent and produces a set of production rules for decision‐making. However sometimes it creates some unnecessary and redundant rules which diminish its comprehensibility. Thus a system named Transparent Expert System of Rules (TESR) is proposed in this paper to efficiently improve comprehensibility of the DT by reducing the number of rules drastically without compromising accuracy. The proposed system adopts a Sequential Hill Climbing method with a flexible heuristic function to prune the insignificant rules from decision rules generated by DT. Finally, the proposed TESR system produces a transparent and comprehensible rule set for a decision. The proposed TESR performance is evaluated using 10 datasets and is compared with simple DT (ID3, C4.5, and Classification and Regression Trees) and also two of the existing transparent systems with respect to comprehensibility, accuracy, precision, recall, and F‐measures.
Phenoxazine‐Sensitized CO2‐to‐CO Reduction with an Iron Porphyrin Catalyst: A Redox Properties‐Catalytic Performance Study
Authors: Kientz Martin , Lowe Grace , McCarthy Blaine G. , Miyake Garret M. , Bonin Julien , Robert Marc 
Published: March 2022

AbstractWe have evaluated six phenoxazine derivatives as visible light photosensitizers for the photochemical reduction of CO2 to CO with an iron porphyrin catalyst in organic media. The phenoxazine core was functionalized with electron‐donating or ‐withdrawing groups to modify the photophysical properties. Both singlet and triplet excited state potentials of the sensitizers spanned several hundred mV range and the ground state oxidation potentials spanned 250 mV. We observed that no correlation can be established between the production of CO and the excited state potential of the phenoxazine, which determines the driving force for electron transfer to the catalyst. On the contrary, a clear correlation can be made between the oxidation potentials of the phenoxazine and the production of CO. This observation indicates that the process was limited by photosensitizer regeneration and highlights the fact that electron transfers not directly related to the catalyst activation could play a key role in homogeneous photocatalytic systems.
The zebrafish cohesin protein Sgo1 is required for cardiac function and eye development
Authors: Kamel Sarah M. , Broekman Sanne , Tessadori Federico , van Wijk Erwin , Bakkers Jeroen 
Published: March 2022

AbstractBackgroundCohesinopathies is a term that refers to/covers rare genetic diseases caused by mutations in the cohesin complex proteins. The cohesin complex is a multiprotein complex that facilitates different aspects of cell division, gene transcription, DNA damage repair, and chromosome architecture. Shugoshin proteins prevent the cohesin complex from premature dissociation from chromatids during cell division. Patients with a homozygous missense mutation in SGO1, which encodes for Shugoshin1, have problems with normal pacing of the heart and gut.ResultsTo study the role of shugoshin during embryo development, we mutated the zebrafish sgo1 gene. Homozygous sgo1 mutant embryos display various phenotypes related to different organs, including a reduced heart rate accompanied by reduced cardiac function. In addition, sgo1 mutants are vision‐impaired as a consequence of structurally defective and partially non‐functional photoreceptor cells. Furthermore, the sgo1 mutants display reduced food intake and early lethality.ConclusionWe have generated a zebrafish model of Sgo1 that showed its importance during organ development and function.