bluuebunny/crossref_metadata_2025_split huggingface dataset:
In vitro and preclinical evaluation of activities of Origanum vulgare essential oil and its two phenolic compounds on clinical isolates of Candida spp
Authors: Stringaro Annarita , Colone Marisa , Cecchetti Serena , Zeppetella Elisa , Spadaro Francesca , Angiolella Letizia 
Published: July 2022

Abstract
A limited therapeutic arsenal is currently available against Candida infections that show high resistance to antifungal agents. For this reason, there is a great need to prioritize testing therapeutic agents for the treatment of candidiasis. The use of essential oils and their phytoconstituents has been emphasized as a new therapeutic approach. The cell surface hydrophobicity (CSH), polysaccharide content, antimicrobial activity of essential oil from Origanum vulgare L. (OVEO), and its two phenolic compounds carvacrol and thymol were evaluated in four different Candida spp. (Candida albicans and emerging non-albicans Candida (NAC) species such as C. glabrata, C. tropicalis, and C. krusei). The results showed the deep differences between Candida species; for example, C. tropicalis revealed higher resistance than other strains to different natural molecule treatments. The ultrastructural variabilities in the biomembranes and cell walls of these Candida spp. might explain the different biological effects observed after OVEO, carvacrol and thymol treatments. Therefore, to study the biological effects of these natural compounds on Candida strains, the samples were observed by confocal laser scanning microscopy (CLSM) and scanning electron microscopy (SEM). Moreover, the release of cellular materials and their “in vivo” antimicrobial activity on infected G. mellonella larvae were evaluated.
On-line detection of orientation of cellulose nanocrystals in a capillary flow with polarization sensitive optical coherence tomography
Authors: Jäsberg Ari , Puisto Antti , Leppänen Ilona , Koponen Antti I , Alava Mikko J 
Published: July 2022

Abstract
Significant importance in the stiffness of materials, such as filaments and films, made of elongated components, has been attributed to orientation. Thus, the control of orientation during the manufacturing of materials has been the target of process optimization for long time. Measuring orientation during the process allows to better grasp the means to control it. In fact, such on-line tools would enable on-fly process control and optimization improving the flexibility with regards to the raw materials used, and the application requirements. In this article, we will discuss a method based on Polarization Sensitive Optical Coherence Tomography utilized as a light-weight on-line measurement tool of particle (here cellulose nanocrystals) orientation for the purposes of manufacturing next generation products by providing the appropriate interpretation of the retardation images with the help of modelling.
Development and validation of peritoneal metastasis in gastric cancer based on simplified clinicopathological features and serum tumour markers
Authors: Yang Jia , Su Hongtao , Chen Tao , Chen Xinhua , Chen Hao , Li Guoxin , Yu Jiang 
Published: July 2022

Abstract
Background:
Peritoneal metastasis (PM) is not uncommon in patients with gastric cancer(GC), which affects the clinical treatment decisions, but the relevant examination measures are not efficient detection. Our goal is to develop a clinical radiomics nomogram to better predict peritoneal metastases.
Methods:
3480 patients from 2 centers were divided into 1 training, 1 internal validation, and 1 external validation cohorts (1949 in the internal training set and 704 in the validation set, and 827 in the external validation cohorts) with clinicopathologically confirmed GC. We recruited 11 clinical factors including age, sex, smoke or not, tumor size, differentiation, Borrmann type, Location, T stage, serum tumor markers (STMs) comprising carbohydrate antigen 19 − 9 (CA19-9), carbohydrate antigen 72 − 4 (CA72-2), and carcinoembryonic antigen(CEA) to develop the radiomics nomogram. For clinical predictive feature selection and establish clinical models, the Statistical methods of analysis of variance (ANOVA), relief and recursive feature elimination (RFE) and logistic regression analysis were used. To develop combined predictive models, tumor diameters, type, tumor location, T stage and STMs were finally selected. The discriminative ability of the nomogram to predict PM is evaluated by the AUC, decision curve analysis (DCA) was conducted to evaluate the clinical usefulness of the nomogram.
Results:
The AUC of clinical models was 0.762 in the training cohorts, 0.772 in the internal validation cohorts, and 0.758 in the external validation cohort. However, when combined with STMs, the AUC was improved to 0.806,0.839 and 0.801 respectively. DCA analysed that the combined nomogram was of good clinical evaluation value to predict PM in GC.
Conclusions
The present study proposed a clinical nomogram with a combination of clinical risk factors and radiomics features that can potentially be applied in the individualized preoperative prediction of PM in GC patients.
Evaluation of Arsenic Pollution and Anaerobic Arsenic-Metabolizing Bacteria of Lake Van, the World's Largest Soda Lake
Authors: OMEROGLU ESRA ERSOY 
Published: July 2022

Abstract
Arsenic is responsible for water pollution in many places in the World and presents a serious health risk for people. Lake Van is in the position of the world's largest soda lake and there are no studies on seasonal arsenic pollution and arsenic resistant bacteria. So, it was aimed to determine arsenic amount of lake water and sediment, to isolate arsenic metabolizing anaerobic bacteria and their identification and determination of arsenic metabolism. Sampling was done from 7.5 meters to represent the four seasons. Metal contents were determined by using ICP-MS. Pure cultures were obtained using the hungate technique. Growth characteristics of the strains were determined at different conditions as well as at arsenate and arsenite concentrations. Molecular studies were also carried out for various resistance genes. Our results showed that Lake Van’s total arsenic amount changes seasonally. As a result of 16S rRNA sequencing, it was determined that the isolates were the members of 8 different genera had arsC resistance gene. In conclusion; for the sustainability of water resources, it is necessary to prevent chemical and microorganism-based pollution. It is thought that the arsenic resistant bacteria obtained as a result of this study will contribute to the solution of environmental arsenic pollution problems, as they are the first data and provide the necessary basic data for the bioremediation studies of arsenic from contaminated environmental habitat. At the same time, the first data that will contribute to the creation of the seasonal arsenic map of Lake Van are obtained.
Classical music restored fertility status in rat model of premature ovarian failure
Authors: Nazdikbin Nahideh , Ashrafi Mojtaba Alizadeh , Abbasi Hamed , Amjadi Farhad , Geranmayeh Mohammad Hossein , Shirazi Reza , Tamadon Amin , Rahbarghazi Reza , Mahdipour Mahdi 
Published: July 2022

Abstract
Background
The restorative effect of classical music was assessed on the cyclophosphamide-induced animal model of premature ovarian failure (POF).
Methods
Mozart's piano classical music (K.448) was used for up to 4 and 8 weeks. Rats were exposed to music 6 hours every day using a stereo system with a volume of 65–70 dB. Sera and ovarian tissue samples were collected for the evaluation of FSH, LH, and E2 and histopathological examination. At the same time points, samples were taken from the hypothalamus and hippocampus to monitor the expression of Ntrk2, Crh, and Pomc using real-time PCR. Mating trial was performed to evaluate the fertility status of POF rats.
Results
Histopathological examination revealed a significant increase (p < 0.05) in the numbers of morphologically normal follicles at all the developmental stages in POF rats after music therapy compared to the POF group (p < 0.05). Music therapy decreased FSH and LH levels to near-to-normal levels conidied with elevation of E2 (p < 0.05). Ntrk2, Crh, and Pomc expressions were down-regulated in POF rats. Music therapy increasaed the expression of Ntrk2 in the hypothalamus of POF rats (p < 0.05). In contrast, Crh and Pomc failed to reach the detection limit before intervention and four weeks after the intervention however, these genes were expressed eight weeks after music therapy. Fertility status was increased (p < 0.05) in terms of litter size in POF rats after being exposed to music compared to the non-treated POF control group (p < 0.05).
Conclusion
Results showed that music can exert therapeutic effects on POF rats via the alteration of sex-related hormones.
An electric circuit model of the Earth’s polar electrojets and field-aligned currents for the estimation of magnetospheric magnetic field from along-track Swarm magnetic data
Authors: Martinec Zdenek , Velimsky Jakub 
Published: July 2022

Abstract
This study deals with the analysis of Swarm vector magnetic data in order to create a circuit model of electric currents flowing in the Earth's polar ionosphere and the inner magnetosphere. The model is composed of a system of two dimensional electric currents representing the magnetic fields of three-dimensional ionospheric polar electrojets (PEJs), the field-aligned currents (FACs), magnetospheric ring currents (MRCs) and magnetospherically induced electric currents inside the Earth (MICs) for each Swarm track. The aim of this paper is to model PEJ and FAC magnetic fields in terms of electric currents on a track-by-track base, subtract those magnetic fields from along-track Swarm magnetic data and estimate the magnetospheric magnetic field (MMF) in discrete time bins. The proposed method is primarily intended to apply to Swarm signals recorded during magnetic storms. The electric circuit model is set up in three steps. After subtracting the main, lithospheric, Sq ionospheric and oceanic tidal magnetic fields from along-track Swarm magnetic signals, the residuals are grouped in 1-h time bins and adjusted by the magnetic field of a two-circular loop model of MRCs and MICs represented by 3✖2 parameters of the electric circular loops in the magnetosphere and the Earth. The adjustment is carried out for the X and Z magnetic field components only because the Y component contains a large signal due to FACs. In the second step, the modelled MRC-MIC magnetic field is removed from the original residuals and the reduced residuals are adjusted by the magnetic field of a system of two-dimensional electric circuits in the polar ionosphere and FACs. The circuit model is set up according to known geometry of PEJs and FACs. In the final step, the modelled magnetic fields of PEJs and FACs are subtracted from the original residuals and all three magnetic field components are adjusted by the MRC-MIC model, named MMC, in a similar way as in the first step. Reliability of the approach is demonstrated by the scatter plots of model MMC showing a significantly better agreement with Swarm magnetic field residuals than the existing MMFs.
Motion-amplitude-dependent nonlinear VIV model and maximum response over a full bridge span
Authors: Zhang Zhitian 
Published: July 2022

Abstract
Nonlinear vortex-induced vibration (VIV) performances of a bridge section are investigated in terms of motion amplitude (yT) dependent energy-trapping properties. Energy-trapping properties of a model undergoing a full-process from still to a limit cycle oscillation (LCO) state are determined. A van der Pol-type model is used to describe the amplitude-dependent VIV performances. Nonlinear parameter-amplitude relations, ε–yT and ξε–yT , are established. Nonlinear aerodynamic damping during the VIV lock-in range is separated into two parts: the initial damping which varies with the reduced wind speed, and the ε–related part which varies with both the reduced wind speed and the motion amplitude. The initial aerodynamic damping determines the threshold of VIV, while the ε–related part dominates the evolution process and the LCO. The identified nonlinear analytical model is capable of predicting VIV responses at higher mechanical damping ratios. The energy-trapping properties of a section model in time are transformed into nonlinear distribution properties in space along an elongated 3-D elastic bridge span. According to this “time-space” transformation, the convection coefficient, which links the maximum response of a 3-D structure with that of a 2-D sectional model can be determined. Compared with a constant-parameter analytical model, a nonlinear model results in significantly larger convection coefficients. Finally, parameter overflowing phenomena are revealed.
Oxidative Degradation of Dihydrofolate Reductase Increases CD38-Mediated Ferroptosis Susceptibility
Authors: Ma Yingying , Yi Meiqi , Wang Weixuan , Xiaohui Liu , Wang Qingtao , Liu Chongdong , Chen Yuling , Deng Haiteng 
Published: July 2022

Abstract
High expression of CD38 in tissues is a characteristic of aging, resulting in a decline in nicotinamide adenine dinucleotide (NAD) and increasing cellular reactive oxygen species (ROS). However, whether CD38 increases susceptibility to ferroptosis remains largely unexplored. Our previous study showed that CD38 overexpression decreased dihydrofolate reductase (DHFR). In the present study, we confirmed that high expression of CD38 increased ROS levels and induced DHFR degradation, which was prevented by nicotinamide mononucleotide (NMN) replenishment. We further revealed that ROS-mediated sulfonation on Cys7 of DHFR induced its degradation via the proteasome pathway while C7A mutation abolished ROS-induced DHFR degradation. Moreover, oxidative degradation of DHFR was responsible for the increased ferroptosis susceptibility in cells in which CD38 was highly expressed. We also found that CD38 expression was higher in bone-marrow derived macrophages (BMDMs) from aged mice than that from young mice, while DHFR level was lower. Consequently, we demonstrated that BMDMs from aged mice were more susceptible to ferroptosis that can be reverted by NMN replenishment, suggesting that CD38 high expression rendered cells more susceptible to ferroptosis. Taken together, these results indicated that CD38-mediated NAD+ decline promoted DHFR oxidative degradation, thus resulting in increased cellular susceptibility to ferroptosis and suggested that NMN replenishment may protect macrophages from ferroptosis in aged mice.
One-pot preparation of magnetic nitrogen-doped porous carbon from lignin for efficient and selective adsorption of organic pollutants
Authors: Tian Yuxin , Yin Yanbo , Jia Zuoyu , Lou Hongming , Zhou Haifeng 
Published: July 2022

Abstract
Efficient and rapid capture of organic pollutants from wastewater is an urgent problem to be solved by adsorbents. Nitrogen-doped magnetic porous carbon (M-PLAC) with three-dimensional porous structure was synthesized from lignin to adsorb MB and TC in wastewater. M-PLAC had high specific surface area (1252.21 m2/g) and N element content (7.44%). The calculated equilibrium adsorption amount by M-PLAC for MB and TC was 645.52 and 1251.09 mg/g, respectively. The adsorption of MB and TC on M-PLAC conformed to the pseudo-second-order kinetic model, demonstrating that the adsorption process was attributed to chemisorption. The excellent adsorption performance was a synergistic effect among various adsorption mechanisms. The removal of MB and TC by M-PLAC showed fast and efficient characteristics, and exhibited high selectivity for TC in binary system. In addition, M-PLAC was suitable for a variety of complex water environments and had good regeneration performance, demonstrating potential advantages in practical wastewater treatment.
ACCT: Automatic Cell Counting with Trainable Weka Segmentation
Authors: Kataras Theodore J. , Jang Tyler J. , Koury Jeffery , Singh Hina , Kaul Marcus 
Published: July 2022

Abstract
Counting cells is a cornerstone of tracking disease progression in neuroscience. A common approach for this process is having trained researchers individually select and count cells within an image, which is not only difficult to standardize but also very time-consuming. While tools exist to automatically count cells in images, the accuracy and accessibility of such tools can be improved. Thus, we introduce a novel tool ACCT: Automatic Cell Counting with Trainable Weka Segmentation which allows for flexible automatic cell counting via object segmentation after user-driven training. ACCT is demonstrated with a comparative analysis of publicly available images of neurons and an in-house dataset of immunofluorescence-stained microglia cells. For comparison, both datasets were manually counted to demonstrate the applicability of ACCT as an accessible means to automatically quantify cells in a precise manner without the need for computing clusters or advanced data preparation.
Molecular and Physiological Mechanisms of Tea (Camellia sinensis (L.) O. Kuntze) Leaf and Root in Response to Nitrogen Deficiency
Authors: Lin Zheng-He , Chen Chang-Song , Zhao Shui-Qing , Liu Yuan , Zhong Qiu-Sheng , Ruan Qi-Chun , Chen Zhi-Hui , You Xiao-Mei , Shan Rui-Yang , Li Xin-Lei , Zhang Ya-Zhen 
Published: July 2022

Abstract
Background: As an economically important crop, tea is strongly nitrogen-dependent. However, the physiological and molecular mechanisms underlying the response of N deficiency in tea are not fully understood. Tea cultivar “Chunlv” [Camellia sinensis (L.) O. Kuntze] were cultured with nutrient solution with 0 mM (N-deficiency) or 3 (control) mM NH4NO3 in 6 L pottery pots containing clean river sands. Results: N deficiency significantly decreased N content and biomass,Chl content, NR, NiR and GOGAT activity, but increased the content of total flavonoids in tea leaves. N deficiency delayed the sprouting time of tea buds. By using RNA-seq technique and subsequent bioinformatics analysis, 3050 up-regulated and 2688 down-regulated DEGs were isolated in tea leaf in response to N deficiency. However, only 1025 genes were up-regulated and 744 down-regulated in roots. GO term enrichment analysis showed that 205 DEGs in tea leaves were enriched in seven GO terms and 152 DEGs in tea roots were enriched in 11 GO items based on P < 0.05. In tea leaves, most of GO-enriched DEGs were involved in chlorophyll a/b binding activities, photosynthetic performance and transport activities in tea leaves. But most of DEGs in tea roots were involved in the metabolism of carbohydrate and plant hormone with regard to the GO terms of biological processes. It is worth mentioning that N deficiency significantly increased the expression level of phosphate transporter genes, which indicated that N deficiency might impair phosphorus metabolism in tea leaves. Furthermore, some DEGs, such as NATs, probable anion transporter 3 and high affinity nitrate transporter 2.7, might be of great potential on improving the tolerance of N deficiency in tea plants and further study could work on this area in the future. Conclusions: These results increased our knowledge about physiological and molecular mechanisms of tea plant in response to N limited condition.
ABX-1431 inhibits the development of endometrial adenocarcinoma and reverses progesterone resistance by regulating the MGLL-ROS/AKR1C1 pathway
Authors: Jiang Jie , Qiu Chunping , Ma Xiaohong , Xia Min , Guo Kui , Wei Lina , Sun Rui , Liu Yao 
Published: July 2022

Abstract
Endometrial cancer is a common gynecological malignancy. With the delay of female fertility, conservative treatment with progesterone has been an important option for patients trying to preserve reproductive function. However, the progesterone resistance becomes a huge challenge and it is urgent to clarify the mechanism so as to propose a potential target and inhibit the development of endometrial adenocarcinoma and progesterone resistance. MGLL, an important factor involved in lipid mobilization, is overexpressed in many tumors, however the biological function of MGLL in the development of endometrial adenocarcinoma and the process of progesterone resistance still remains unclear. In this study, we first found MGLL was highly expressed in endometrial adenocarcinoma specimens by bioinformatics analysis, RT-PCR and immunohistochemistry and then we found the expression was further increased in progesterone resistant samples. Through in vitro and in vivo experiments, we demonstrated that overexpression of MGLL promoted tumor proliferation, metastasis and the occurrence of progestogen resistance, knockdown MGLL inhibited tumor proliferation, metastasis and reversed progestogen resistance. In addition, knockdown of MGLL can sensitize endometrial adenocarcinoma cells to progesterone by affecting ROS generation and reducing the expression of AKR1C1. Finally, it was verified that ABX-1431, MGLL inhibitor, reversed progesterone resistance and enhanced the sensitivity of endometrial adenocarcinoma to progesterone both in vitro and in vivo. In conclusion, the high expression of MGLL is involved in the occurrence and development of endometrial adenocarcinoma and progesterone resistance. Targeted inhibition of MGLL by inhibitors may be an effective method for the treatment of progesterone resistance in endometrial adenocarcinoma.
Metabolome-wide association study on physical activity
Authors: Kojouri Maedeh , Pinto Rui , Mustafa Rima , Huang Jian , Gao He , Elliott Paul , Tzoulaki Ioanna , Dehghan Abbas 
Published: July 2022

Abstract
Background - The underlying mechanisms linking physical activity to better health are not fully understood. Here we examined the associations between physical activity and small circulatory molecules, the metabolome, to highlight relevant biological pathways.Methods - We examined plasma metabolites associated with self-reported physical activity among 2,217 participants from the Airwave Health Monitoring Study. Metabolic profiling was conducted by the Metabolon platform using liquid chromatography-mass spectrometry (LC/GC-MS), measuring 828 known metabolites. We replicated our findings in an independent subset of the study (n=2,971) using untargeted LC-MS. Mendelian randomisation was carried out to investigate potential causal associations between physical activity, body mass index, and metabolites.Results - Higher vigorous physical activity was (P<0.05/828=6.03×10-5) associated with circulatory levels of 28 metabolites adjusted for age, sex and body mass index. The association was inverse for one amino acid (glutamate), and six diacylglycerol lipids and direct for ten amino acids (3-4-hydroxyphenyllactate, phenyl lactate (PLA), alpha-hydroxy isovalerate, tiglylcarnitine, alpha-hydroxyisocaproate, 2-hydroxy-3-methylvalerate, isobutyrylcarnitine, imidazole lactate, methionine sulfone, indole lactate), nine plasmalogen lipids, one fatty acid lipid (pristanate) and one energy tricarboxylic acid cycle metabolite (fumarate). In the replication panel, we found 23 untargeted LC-MS features annotated to the identified metabolites, of which we found nominal associations with the same direction of effect for three features annotated to 1-(1-enyl-palmitoyl)-2-oleoyl-GPC (P-16:0/18:1), 1-(1-enyl-palmitoyl)-2-linoleoyl-GPC (P-16:0/18:2), 1-stearoyl-2-dihomo-linolenoyl-GPC (18:0/20:3n3 or 6). Using Mendelian randomisation, we showed a potential causal relationship between body mass index and three identified metabolites. Conclusions - Circulatory metabolites are associated with physical activity and may play a role in mediating its health effects.