bluuebunny/crossref_metadata_2025_split huggingface dataset:
Centrifugation does not remove bacteria from the fat fraction of human milk
Authors: Stinson Lisa F. , Ma Jie , Rea Alethea , Dymock Michael , Geddes Donna T. 
Published: January 2021

AbstractAnalysis of the human milk microbiome is complicated by the presence of a variable quantity of fat. The fat fraction of human milk is typically discarded prior to analysis. It is assumed that all cells are pelleted out of human milk by high speed centrifugation; however, studies of bovine milk have reported that bacteria may remain trapped within the fat fraction. Here, the bacterial DNA profiles of the fat fraction and cell pellet of human milk (n = 10) were analysed. Human and bacterial DNA was consistently recovered from the fat fraction of human milk (average of 12.4% and 32.7%, respectively). Two low-abundanceStaphylococcusspecies (< 0.5% relative abundance) was significantly more abundant in the cell pellet compared to the fat fraction (P < 0.04), and three low-abundance species (< 5% relative abundance) were recovered from one fraction only. However, inclusion of fat reduced the efficiency of DNA extraction by 39%. Culture-based methods were used to quantify the distribution of an exogenously added strain ofStaphylococcus aureusin human milk fractions.S. aureuswas consistently recovered from the fat fraction (average 28.9%). Bacterial DNA profiles generated from skim milk or cell pellets are not representative of the entire human milk microbiome. These data have critical implications for the design of future work in this field.
Human whole genome sequencing in South Africa
Authors: Glanzmann Brigitte , Jooste Tracey , Ghoor Samira , Gordon Richard , Mia Rizwana , Mao Jun , Li Hao , Charls Patrick , Douman Craig , Kotze Maritha J. , Peeters Armand V. , Loots Glaudina , Esser Monika , Tiemessen Caroline T. , Wilkinson Robert J. , Louw Johan , Gray Glenda , Warren Robin M. , Möller Marlo , Kinnear Craig 
Published: January 2021

AbstractThe advent and evolution of next generation sequencing has considerably impacted genomic research. Until recently, South African researchers were unable to access affordable platforms capable of human whole genome sequencing locally and DNA samples had to be exported. Here we report the whole genome sequences of the first six human DNA samples sequenced and analysed at the South African Medical Research Council’s Genomics Centre. We demonstrate that the data obtained is of high quality, with an average sequencing depth of 36.41, and that the output is comparable to data generated internationally on a similar platform. The Genomics Centre creates an environment where African researchers are able to access world class facilities, increasing local capacity to sequence whole genomes as well as store and analyse the data.
Adiabatic mode transformation in width-graded nano-gratings enabling multiwavelength light localization
Authors: Shayegannia Moein , Montazeri Arthur O. , Dixon Katelyn , Prinja Rajiv , Kazemi-Zanjani Nastaran , Kherani Nazir P. 
Published: January 2021

AbstractWe delineate the four principal surface plasmon polariton coupling and interaction mechanisms in subwavelength gratings, and demonstrate their significant roles in shaping the optical response of plasmonic gratings. Within the framework of width-graded metal–insulator-metal nano-gratings, electromagnetic field confinement and wave guiding result in multiwavelength light localization provided conditions of adiabatic mode transformation are satisfied. The field is enhanced further through fine tuning of the groove-width (w), groove-depth (L) and groove-to-groove-separation (d). By juxtaposing the resonance modes of width-graded and non-graded gratings and defining the adiabaticity condition, we demonstrate the criticality of w and d in achieving adiabatic mode transformation among the grooves. We observe that the resonant wavelength of a graded grating corresponds to the properties of a single groove when the grooves are adiabatically coupled. We show that L plays an important function in defining the span of localized wavelengths. Specifically, we show that multiwavelength resonant modes with intensity enhancement exceeding three orders of magnitude are possible with w < 30 nm and 300 nm < d < 900 nm for a range of fixed values of L. This study presents a novel paradigm of deep-subwavelength adiabatically-coupled width-graded gratings—illustrating its versatility in design, hence its viability for applications ranging from surface enhanced Raman spectroscopy to multispectral imaging.
Development of air pressure mirroring particle dispersion method for producing high-density tungsten medical radiation shielding film
Authors: Kim Seon-Chil 
Published: January 2021

AbstractRadiation shielding films used in medical institutions are manufactured by mixing polymer materials with eco-friendly shielding materials. However, it is not easy to distribute the shielding material particles uniformly during the process. The uniform distribution of the shielding material particles is key to the reproducibility of the shielding performance of the films. Therefore, in this study, an air pressure mirroring particle dispersion method was developed to maintain a uniform distribution of the shielding material by dispersing the shielding material on a curved reflector through an air nozzle. The particle distribution state, density, and shielding performance of the cross-section and surface of the shielding films developed using the single-sided dispersion, double-dispersion, and air pressure mirroring particle dispersion methods were evaluated. Compared to the conventional single-sided distribution method, the shielding film produced by the air pressure mirroring particle dispersion method increased the particle packing by 41.5%, density by 12.9%, shielding material content by 22.2%, and shielding performance by 21.4%. Thus, the proposed dispersion method enables better shielding performance through uniform dispersion of shielding material, which is the most important parameter in the manufacture of low-dose shielding films.
Contralesional functional network reorganization of the insular cortex in diffuse low-grade glioma patients
Authors: Fang Shengyu , Zhou Chunyao , Wang Yinyan , Jiang Tao 
Published: January 2021

AbstractDiffuse low-grade gliomas (DLGGs) growing on the insular lobe induce contralesional hemispheric insular lobe compensation of damaged functioning by increasing cortical volumes. However, it remains unclear how functional networks are altered in patients with insular lobe DLGGs during functional compensation. Thirty-five patients with insular DLGGs were classified into the left (insL, n = 16) and right groups (insR, n = 19), and 33 healthy subjects were included in the control group. Resting state functional magnetic resonance imaging was used to generate functional connectivity (FC), and network topological properties were evaluated using graph theoretical analysis based on FC matrices. Network-based statistics were applied to compare differences in the FC matrices. A false discovery rate was applied to correct the topological properties. There was no difference in the FC of edges between the control and insL groups; however, the nodal shortest path length of the right insular lobe was significantly increased in the insL group compared to the control group. Additionally, FC was increased in the functional edges originating from the left insular lobe in the insR group compared to the control group. Moreover, there were no differences in topological properties between the insR and control groups. The contralesional insular lobe is crucial for network alterations. The detailed patterns of network alterations were different depending on the affected hemisphere. The observed network alterations might be associated with functional network reorganization and functional compensation.
Two-port access for laparoscopic surgery for endometrial cancer using conventional laparoscopic instruments
Authors: Huang Kuan-Ju , Li Ying-Xuan , Sheu Bor-Ching , Chang Wen-Chun 
Published: January 2021

AbstractMinimally invasive surgery is the first-line management for endometrial cancer. The role of 2-port access laparoscopy (TPA) has been underestimated. Compared to conventional laparoscopic surgery (CL), TPA is associated with smaller total incision size and less postoperative pain. Compared to single-incision laparoscopic surgery, no specific instruments and surgical techniques are needed. This study primarily evaluated the surgical and pathologic outcomes of TPA with conventional instruments, and additionally evaluated the surgeon’s learning curve. Consecutive patients who underwent TPA and CL for endometrial cancer between 2015 and 2019 were included. Baseline characteristics were recorded. In total, 148 patients (TPA, 89; CL, 59) were identified. The baseline characteristics were similar, except for a greater proportion of patients in the CL group receiving para-aortic lymph node dissection (5.62% vs. 35.59%, P < 0.01). The mean operation time was significantly less in the TPA group (152.09 vs. 187.15 min; P < 0.01). Both the groups had comparable 5-year progression-free survival (TPA, 86.68%) and 5-year overall survival rates (TPA, 93.24%). Analysis of the learning curve showed that the operation time decreased after 3–4 procedures. TPA using conventional laparoscopic instruments for endometrial cancer is feasible and is easily accessible to patients and surgeons.
Transport of environmental natural organic matter coated silver nanoparticle across cell membrane based on membrane etching treatment and inhibitors
Authors: Zhong Laijin , Chen Sisi , Tang Zhijie , Guo Xuewen , Hu Xin , Zheng Weijuan , Lian Hong-zhen 
Published: January 2021

AbstractEnvironmental natural organic matters (NOMs) have great effects on the physicochemical properties of engineering nanoparticles, which may impact the transport of nanoparticles across plasma membrane and the cytotoxicity. Therefore, the kinetics, uptake pathway and mass of transporting into A549 cell membrane of silver nanoparticles (AgNPs) coated with citric acid (CA), tartaric acid (TA) and fulvic acid (FA) were investigated, respectively. CA, FA and TA enhanced the colloidal stability of AgNPs in culture medium and have greatly changed the surface plasmon resonance spectrum of AgNPs due to the absorption of CA, FA and TA on surface of AgNPs. Internalizing model showed that velocity of CA-, TA- and FA-nAg transporting into A549 cell were 5.82-, 1.69- and 0.29-fold higher than those of the control group, respectively. Intracellular mass of Ag was dependent on mass of AgNPs delivered to cell from suspension, which obeyed Logistic model and was affected by NOMs that CA- and TA-nAg showed a large promotion on intracellular mass of Ag. The lipid raft/caveolae-mediated endocytosis (LME) of A549 cell uptake of AgNPs were susceptible to CA, TA and FA that uptake of CA-, TA- and FA-nAg showed lower degree of dependent on LME than that of the control (uncoated AgNPs). Actin-involved uptake pathway and macropinocytosis would have less contribution to uptake of FA-nAg. Overall, transmembrane transport of NOMs-coated AgNPs differs greatly from that of the pristine AgNPs.
Non-invasive skin sampling of tryptophan/kynurenine ratio in vitro towards a skin cancer biomarker
Authors: Jankovskaja Skaidre , Engblom Johan , Rezeli Melinda , Marko-Varga György , Ruzgas Tautgirdas , Björklund Sebastian 
Published: January 2021

AbstractThe tryptophan to kynurenine ratio (Trp/Kyn) has been proposed as a cancer biomarker. Non-invasive topical sampling of Trp/Kyn can therefore serve as a promising concept for skin cancer diagnostics. By performing in vitro pig skin permeability studies, we conclude that non-invasive topical sampling of Trp and Kyn is feasible. We explore the influence of different experimental conditions, which are relevant for the clinical in vivo setting, such as pH variations, sampling time, and microbial degradation of Trp and Kyn. The permeabilities of Trp and Kyn are overall similar. However, the permeated Trp/Kyn ratio is generally higher than unity due to endogenous Trp, which should be taken into account to obtain a non-biased Trp/Kyn ratio accurately reflecting systemic concentrations. Additionally, prolonged sampling time is associated with bacterial Trp and Kyn degradation and should be considered in a clinical setting. Finally, the experimental results are supported by the four permeation pathways model, predicting that the hydrophilic Trp and Kyn molecules mainly permeate through lipid defects (i.e., the porous pathway). However, the hydrophobic indole ring of Trp is suggested to result in a small but noticeable relative increase of Trp diffusion via pathways across the SC lipid lamellae, while the shunt pathway is proposed to slightly favor permeation of Kyn relative to Trp.
Novel FXR agonist nelumal A suppresses colitis and inflammation-related colorectal carcinogenesis
Authors: Miyazaki Tsuneyuki , Shirakami Yohei , Mizutani Taku , Maruta Akinori , Ideta Takayasu , Kubota Masaya , Sakai Hiroyasu , Ibuka Takashi , Genovese Salvatore , Fiorito Serena , Taddeo Vito Alessandro , Epifano Francesco , Tanaka Takuji , Shimizu Masahito 
Published: January 2021

AbstractFXR is a member of the nuclear receptor superfamily and bile acids are endogenous ligands of FXR. FXR activation has recently been reported to inhibit intestinal inflammation and tumour development. This study aimed to investigate whether the novel FXR agonist nelumal A, the active compound of the plant Ligularia nelumbifolia, can prevent colitis and colorectal carcinogenesis. In a mouse colitis model, dextran sodium sulfate-induced colonic mucosal ulcer and the inflammation grade in the colon significantly reduced in mice fed diets containing nelumal A. In an azoxymethane/dextran sodium sulfate-induced mouse inflammation-related colorectal carcinogenesis model, the mice showed decreased incidence of colonic mucosal ulcers and adenocarcinomas in nelumal A-treated group. Administration of nelumal A also induced tight junctions, antioxidant enzymes, and FXR target gene expression in the intestine, while it decreased the gene expression of bile acid synthesis in the liver. These findings suggest that nelumal A effectively attenuates colonic inflammation and suppresses colitis-related carcinogenesis, presumably through reduction of bile acid synthesis and oxidative damage. This agent may be potentially useful for treatment of inflammatory bowel diseases as well as their related colorectal cancer chemoprevention.
Bedload transport in rivers, size matters but so does shape
Authors: Cassel Mathieu , Lavé Jérôme , Recking Alain , Malavoi Jean-René , Piégay Hervé 
Published: January 2021

AbstractBedload transport modelling in rivers takes into account the size and density of pebbles to estimate particle mobility, but does not formally consider particle shape. To address this issue and to compare the relative roles of the density and shape of particles, we performed original sediment transport experiments in an annular flume using molded artificial pebbles equipped with a radio frequency identification tracking system. The particles were designed with four distinct shapes and four different densities while having the same volume, and their speeds and distances traveled under constant hydraulic conditions were analyzed. The results show that particle shape has more influence than particle density on the resting time between particle displacement and the mean traveling distance. For all densities investigated, the particle shape systematically induced differences in travel distance that were strongly correlated (R2 = 0.94) with the Sneed and Folks shape index. Such shape influences, although often mentioned, are here quantified for the first time, demonstrating why and how they can be included in bedload transport models.
Increasing AFM colloidal probe accuracy by optical tweezers
Authors: Witko Tomasz , Baster Zbigniew , Rajfur Zenon , Sofińska Kamila , Barbasz Jakub 
Published: January 2021

AbstractA precise determination of the cantilever spring constant is the critical point of all colloidal probe experiments. Existing methods are based on approximations considering only cantilever geometry and do not take into account properties of any object or substance attached to the cantilever. Neglecting the influence of the colloidal sphere on the cantilever characteristics introduces significant uncertainty in a spring constant determination and affects all further considerations. In this work we propose a new method of spring constant calibration for ‘colloidal probe’ type cantilevers based on the direct measurement of force constant. The Optical Tweezers based calibration method will help to increase the accuracy and repeatability of the AFM colloidal probe experiments.
Association between endometriosis and risk of systemic lupus erythematosus
Authors: Fan Yu-Hsi , Leong Pui-Ying , Chiou Jeng-Yuan , Wang Yu-Hsun , Ku Ming-Hsiang , Wei James Cheng-Chung 
Published: January 2021

AbstractTo examine the association between endometriosis and the risk of systemic lupus erythematosus (SLE), this nationwide, population-based, retrospective cohort study was conducted based on National Health Insurance Research Database in Taiwan. Endometriosis (N = 16,758) and non-endometriosis (N = 16,758) groups were identified by matching baseline characteristics and comorbidities. Student’s t-tests and the Kaplan–Meier estimator were utilized to estimate the hazard ratio (HR) and cumulative probability of SLE in the two groups. The endometriosis group showed a significantly higher incidence density rate (0.3 vs. 0.1 per 1000 person-years) and hazard ratio in SLE group (adjusted HR [aHR], 2.37; 95% confidence interval [CI] 1.35–4.14) compared to the non-endometriosis group. Subgroup analysis revealed that patients with endometriosis between 30 and 45 years of age, or were non-steroidal anti-inflammatory drug users, or were hormonal medications-free participants, had higher risks of SLE. For patients with endometriosis, surgical intervention did not significantly impact on the risk of SLE. Our results demonstrated an increased risk of SLE in patients with endometriosis. Clinicians should be aware of this association when managing patients with endometriosis or SLE.
Outer membrane vesicles containing OmpA induce mitochondrial fragmentation to promote pathogenesis of Acinetobacter baumannii
Authors: Tiku Varnesh , Kofoed Eric M. , Yan Donghong , Kang Jing , Xu Min , Reichelt Mike , Dikic Ivan , Tan Man-Wah 
Published: January 2021

AbstractAcinetobacter baumannii is a highly antibiotic resistant Gram-negative bacterium that causes life-threatening infections in humans with a very high mortality rate. A. baumannii is an extracellular pathogen with poorly understood virulence mechanisms. Here we report that A. baumannii employs the release of outer membrane vesicles (OMVs) containing the outer membrane protein A (OmpAAb) to promote bacterial pathogenesis and dissemination. OMVs containing OmpAAb are taken up by mammalian cells where they activate the host GTPase dynamin-related protein 1 (DRP1). OmpAAb mediated activation of DRP1 enhances its accumulation on mitochondria that causes mitochondrial fragmentation, elevation in reactive oxygen species (ROS) production and cell death. Loss of DRP1 rescues these phenotypes. Our data show that OmpAAb is sufficient to induce mitochondrial fragmentation and cytotoxicity since its expression in E. coli transfers its pathogenic properties to E. coli. A. baumannii infection in mice also induces mitochondrial damage in alveolar macrophages in an OmpAAb dependent manner. We finally show that OmpAAb is also required for systemic dissemination in the mouse lung infection model. In this study we uncover the mechanism of OmpAAb as a virulence factor in A. baumannii infections and further establish the host cell factor required for its pathogenic effects.
4-chlorophenol removal by air lift packed bed bioreactor and its modeling by kinetics and numerical model (artificial neural network)
Authors: Azizi Elahe , Abbasi Fariba , Baghapour Mohammad Ali , Shirdareh Mohammad Reza , Shooshtarian Mohammad Reza 
Published: January 2021

Abstract4-chlorophenol (4-CP) is a hazardous contaminant that is hardly removed by some technologies. This study investigated the biodegradation, and physical 4-CP removal by a mixed microbial consortium in the Airlift packed bed bioreactor (ALPBB) and modeling by an artificial neural network (ANN) for first the time. The removal efficiency of ALPBB was investigated at 4-CP(1-1000 mg/L) and hydraulic retention time (HRT)(6-96 hr) by HPLC. The results showed that removal efficiency decreased from 85 at 1 to 0.03% at 1000 mg/L, with increasing 4-CP concentration and HRT decreasing. BOD5/COD increased with increasing exposure time and concentration decreasing, from 0.05 at 1000 to 0.96 at 1 mg/L. With time increasing, the correlation between COD and 4-CP removal increased (R2 = 0.5, HRT = 96 h). There was a positive correlation between the removal of 4-CP and SCOD by curve fitting was R2 = 0.93 and 0.96, respectively. Moreover, the kinetics of 4-CP removal follows the first-order and pseudo-first-order equation at 1 mg/L and other concentrations, respectively. 4-CP removal modeling has shown that the 2:3:1 and 2:4:1 were the best structures (MSE: physical = 0.126 and biological = 0.9)(R2allphysical = 0.999 and R2testphysical = 0.999) and (R2allbiological = 0.71, and R2testbiological = 0.997) for 4-CP removal. Also, the output obtained by the ANN prediction of 4-CP was correlated to the actual data (R2physical = 0.9997 and R2biological = 0.59). Based on the results, ALPBB with up-flow submerged aeration is a suitable option for the lower concentration of 4-CP, but it had less efficiency at high concentrations. So, physical removal of 4-CP was predominant in biological treatment. Therefore, the modification of this reactor for 4-CP removal is suggested at high concentrations.
α-MSH-induced activation of spinal MC1R but not MC4R enhances colorectal motility in anaesthetised rats
Authors: Ueda Hiromi H. , Naitou Kiyotada , Nakamori Hiroyuki , Horii Kazuhiro , Shiina Takahiko , Masatani Tatsunori , Shiraishi Mitsuya , Shimizu Yasutake 
Published: January 2021

AbstractThe central nervous system is involved in regulation of defaecation. It is generally considered that supraspinal regions control the spinal defaecation centre. However, signal transmission from supraspinal regions to the spinal defaecation centre is still unclear. In this study, we investigated the regulatory role of an anorexigenic neuropeptide, α-MSH, in the spinal defaecation centre in rats. Intrathecal administration of α-MSH to the L6-S1 spinal cord enhanced colorectal motility. The prokinetic effect of α-MSH was abolished by severing the pelvic nerves. In contrast, severing the colonic nerves or thoracic cord transection at the T4 level had no impact on the effect of α-MSH. RT-PCR analysis revealed MC1R mRNA and MC4R mRNA expression in the L6-S1 spinal cord. Intrathecally administered MC1R agonists, BMS470539 and SHU9119, mimicked the α-MSH effect, but a MC4R agonist, THIQ, had no effect. These results demonstrate that α-MSH binds to MC1R in the spinal defaecation centre and activates pelvic nerves, leading to enhancement of colorectal motility. This is, to our knowledge, the first report showing the functional role of α-MSH in the spinal cord. In conclusion, our findings suggest that α-MSH is a candidate for a neurotransmitter from supraspinal regions to the spinal defaecation centre.