bluuebunny/crossref_metadata_2025 huggingface dataset:
Fine-scale genetic structure in the critically endangered red-fronted macaw in the absence of geographic and ecological barriers
Authors: Blanco Guillermo , Morinha Francisco , Roques Séverine , Hiraldo Fernando , Rojas Abraham , Tella José L.
Published: January 2021

Behavioural and socio-cultural traits are recognized in the restriction of gene flow in species with high cognitive capacity and complex societies. This isolation by social barriers has been generally overlooked in threatened species by assuming disrupted gene flow due to population fragmentation and decline. We examine the genetic structure and ecology of the global population of the Critically Endangered red-fronted macaw (Ara rubrogenys), an endemic species to the inter-Andean valleys of Bolivia. We found a fine-scale genetic structuring in four genetic clusters. Genetic diversity was higher in wild compared to captive-bred macaws, but similar to that of captive wild-caught macaws. We found no clear evidence of severe genetic erosion in the population in recent decades, but it was patent in historic times, overlapping with drastic human habitat transformation and macaw persecution over millennia. We found no evidence of geographical and ecological barriers, owing to the high dispersal ability, nesting and foraging habits between genetic clusters. The lack of genetic intermixing despite long-distance foraging and seasonal movements suggests recruitment in natal colonies and other social factors reinforcing philopatry-related genetic structure. Conservation efforts should be specifically focussed on major threats in each genetic cluster as independent conservation units, and also considered in ex-situ management.
BMP signaling suppresses Gemc1 expression and ependymal differentiation of mouse telencephalic progenitors
Authors: Omiya Hanae , Yamaguchi Shima , Watanabe Tomoyuki , Kuniya Takaaki , Harada Yujin , Kawaguchi Daichi , Gotoh Yukiko
Published: January 2021

The lateral ventricles of the adult mammalian brain are lined by a single layer of multiciliated ependymal cells, which generate a flow of cerebrospinal fluid through directional beating of their cilia as well as regulate neurogenesis through interaction with adult neural stem cells. Ependymal cells are derived from a subset of embryonic neural stem-progenitor cells (NPCs, also known as radial glial cells) that becomes postmitotic during the late embryonic stage of development. Members of the Geminin family of transcriptional regulators including GemC1 and Mcidas play key roles in the differentiation of ependymal cells, but it remains largely unclear what extracellular signals regulate these factors and ependymal differentiation during embryonic and early-postnatal development. We now show that the levels of Smad1/5/8 phosphorylation and Id1/4 protein expression—both of which are downstream events of bone morphogenetic protein (BMP) signaling—decline in cells of the ventricular-subventricular zone in the mouse lateral ganglionic eminence in association with ependymal differentiation. Exposure of postnatal NPC cultures to BMP ligands or to a BMP receptor inhibitor suppressed and promoted the emergence of multiciliated ependymal cells, respectively. Moreover, treatment of embryonic NPC cultures with BMP ligands reduced the expression level of the ependymal marker Foxj1 and suppressed the emergence of ependymal-like cells. Finally, BMP ligands reduced the expression levels of Gemc1 and Mcidas in postnatal NPC cultures, whereas the BMP receptor inhibitor increased them. Our results thus implicate BMP signaling in suppression of ependymal differentiation from NPCs through regulation of Gemc1 and Mcidas expression during embryonic and early-postnatal stages of mouse telencephalic development.
Potential diagnostic value of pleural fluid cytokines levels for tuberculous pleural effusion
Authors: Dalil Roofchayee Neda , Marjani Majid , Dezfuli Neda K. , Tabarsi Payam , Moniri Afshin , Varahram Mohammad , Adcock Ian M. , Mortaz Esmaeil
Published: January 2021

Patients with tuberculous pleural effusion (TPE) or malignant pleural effusions (MPE) frequently have similar pleural fluid profiles. New biomarkers for the differential diagnosis of TPE are required. We determined whether cytokine profiles in the PE of patients could aid the differential diagnosis of TPE. 30 patients with TPE, 30 patients with MPE, 14 patients with empyema (EMP) and 14 patients with parapneumonic effusion (PPE) were enrolled between Dec 2018 and 2019. The levels of interleukin (IL)-6, IL-18, IL-27, CXCL8, CCL-1 and IP-10 were determined in PE by ELISA along with measurements of adenosine deaminase (ADA). The best predictors of TPE were combined ADA.IL-27 [optimal cut-off value = 42.68 (103 U ng/l2), sensitivity 100%, specificity 98.28%], ADA [cut off value 27.5 (IU/l), sensitivity 90%, specificity 96.5%] and IL-27 [cut-off value = 2363 (pg/ml), sensitivity 96.7%, specificity 98.3%, p ≤ 0.0001]. A high level of IL-6 [cut-off value = 3260 (pg/ml), sensitivity 100%, specificity 67.2%], CXCL8 [cut-off value = 144.5 (pg/ml), sensitivity 93.3%, specificity 58.6%], CCL1 [cut-off value = 54 (pg/ml), sensitivity 100%, specificity 70.7%] and IP-10 [cut-off value = 891.9 (pg/ml), sensitivity 83.3%, specificity 48.3%] were also predictive of TPE. High ADA.IL-27, ADA and IL-27 levels differentiate between TPE and non-TPE with improved specificity and diagnostic accuracy and may be useful clinically.
Criteria for identifying residual tumours after neoadjuvant chemotherapy of breast cancers: a magnetic resonance imaging study
Authors: Kim Yunju , Sim Sung Hoon , Park Boram , Chae In Hye , Han Jai Hong , Jung So-Youn , Lee Seeyoun , Kwon Youngmi , Park In Hae , Ko Kyounglan , Lee Chan Wha , Lee Keun Seok , Kang Han-Sung , Lee Eun Sook
Published: January 2021

We investigated magnetic resonance imaging (MRI) criteria identifying residual tumours in patients with triple-negative and human epidermal growth factor receptor type 2-positive (HER2+) breast cancer following neoadjuvant chemotherapy. Retrospectively, 290 patients were included who had undergone neoadjuvant chemotherapy and definitive surgery. Clinicopathological features, as well as lesion size and lesion-to-background parenchymal signal enhancement ratio (SER) in early- and late-phase MRIs, were analysed. Receiver operating characteristic (ROC) analyses evaluated diagnostic performances. Maximal MRI values showing over 90% sensitivity and negative predictive value (NPV) were set as cut-off points. Identified MRI criteria were prospectively applied to 13 patients with hormone receptor-negative (HR-) tumours. The lesion size in HR-HER2-tumours had the highest area under the ROC curve value (0.92), whereas this parameter in HR + HER2 + tumours was generally low (≤ 0.75). For HR-tumours, both sensitivity and NPV exceeded the 90% threshold for early size > 0.2 cm (HR-HER2-) or > 0.1 cm (HR-HER2 +), late size > 0.4 cm, and early SER > 1.3. In the prospective pilot cohort, the criteria size and early SER did not find false negative cases, but one case was false negative with late SER. Distinguishing residual tumours based on MRI is feasible in selected triple-negative and HER2 + breast cancer patients.
Experimental and computational study on roles of WOx promoting strong metal support promoter interaction in Pt catalysts during glycerol hydrogenolysis
Authors: Saelee Tinnakorn , Limsoonthakul Poonnapa , Aphichoksiri Phakaorn , Rittiruam Meena , Lerdpongsiripaisarn Mongkol , Miyake Takanori , Yamashita Hiromi , Mori Kohsuke , Kuwahara Yasutaka , Praserthdam Supareak , Praserthdam Piyasan
Published: January 2021

Biodiesel is of high interest due to increased demand for energy with the concern regarding more sustainable production processes. However, an inevitable by-product is glycerol. Hence, the conversion of this by-product to higher-value chemicals, especially 1,3-propanediol (1,3-PDO) via glycerol hydrogenolysis reaction, is one of the most effective pathways towards a profitable process. In general, this process is catalyzed by a highly active Pt-based catalyst supported on γ-Al2O3. However, its low 1,3-PDO selectivity and stability due to surface deactivation of such catalysts remained. This led to the surface modification by WOx to improve both the selectivity by means of the increased Brønsted acidity and the stability in terms of Pt leaching-resistance. Hence, we applied experimental and density functional theory (DFT)-based techniques to study the fundamentals of how WOx modified the catalytic performance in the Pt/γ-Al2O3 catalyst and provided design guidelines. The effects of WOx promoter on improved activity were due to the shifting of the total density of states towards the antibonding region evident by the total density of states (TDOS) profile. On the improved 1,3-PDO selectivity, the main reason was the increasing number of Brønsted acid sites due to the added WOx promoter. Interestingly, the stability improvement was due to the strong metal-support interaction (SMSI) that occurred in the catalyst, like typical high leaching-resistant catalysts. Also, the observed strong metal-support-promoter interaction (SMSPI) is an additional effect preventing leaching. The SMSPI stemmed from additional bonding between the WOx species and the Pt active site, which significantly strengthened Pt adsorption to support and a high electron transfer from both Pt and Al2O3 to WOx promoter. This suggested that the promising promoter for our reaction performed in the liquid phase would improve the stability if SMSI occurred, where the special case of the WOx promoter would even highly improve the stability through SMSPI. Nevertheless, various promoters that can promote SMSPI need investigations.
Uncovering multi-faceted taxonomic and functional diversity of soil bacteriomes in tropical Southeast Asian countries
Authors: Likhitrattanapisal Somsak , Siriarchawatana Paopit , Seesang Mintra , Chunhametha Suwanee , Boonsin Worawongsin , Phithakrotchanakoon Chitwadee , Kitikhun Supattra , Eurwilaichitr Lily , Ingsriswang Supawadee
Published: January 2021

Environmental microbiomes encompass massive biodiversity and genetic information with a wide-ranging potential for industrial and agricultural applications. Knowledge of the relationship between microbiomes and environmental factors is crucial for translating that information into practical uses. In this study, the integrated data of Southeast Asian soil bacteriomes were used as models to assess the variation in taxonomic and functional diversity of bacterial communities. Our results demonstrated that there were differences in soil bacteriomes across different geographic locality with different soil characteristics: soil class and pH level. Such differences were observed in taxonomic diversity, interspecific association patterns, and functional diversity of soil bacteriomes. The bacterial-mediated biogeochemical cycles of nitrogen, sulfur, carbon, and phosphorus illustrated the functional relationship of soil bacteriome and soil characteristics, as well as an influence from bacterial interspecific interaction. The insights from this study reveal the importance of microbiome data integration for future microbiome research.
Comprehensive study of antimicrobial susceptibility pattern and extended spectrum beta-lactamase (ESBL) prevalence in bacteria isolated from urine samples
Authors: Gharavi Mohammad Javad , Zarei Javad , Roshani-Asl Parisa , Yazdanyar Zahra , Sharif Masoud , Rashidi Niloufar
Published: January 2021

Nowadays, increasing extended-spectrum β-lactamase (ESBL)-producing bacteria have become a global concern because of inducing resistance toward most of the antimicrobial classes and making the treatment difficult. In order to achieve an appropriate treatment option, identification of the prevalent species which generate ESBL as well as their antibiotic susceptibility pattern is essential worldwide. Hence, this study aimed to investigate the prevalence of ESBL-producing bacteria and assess their drug susceptibility in Fardis Town, Iran. A total of 21,604 urine samples collected from patients suspected to have urinary tract infection (UTI) were processed in the current study. The antimicrobial susceptibility of the isolates was tested by the disk diffusion method. The ESBL producing bacteria were determined by Double Disc Synergy Test (DDST) procedure. Bacterial growth was detected in 1408 (6.52%) cases. The most common bacterial strains causing UTI were found E. coli (72.16%), followed by K. pneumoniae (10.3%) and S. agalactiae (5.7%). Overall, 398 (28.26%) were ESBL producer. The highest ESBL production was observed in E. coli, followed by Klebsiella species. ESBL producers revealed a higher level of antibiotic resistance compared with non-ESBLs. In conclusion, ESBL production in uropathogens was relatively high. Carbapenems and Aminoglycosides were confirmed as the most effective treatment options for these bacteria.
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

Analysis 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

The 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

We 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

Radiation 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

Diffuse 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

Minimally 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

Environmental 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

The 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

FXR 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

Bedload 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

A 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

To 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

Acinetobacter 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

4-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

The 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.
Bioinformatic mapping of a more precise Aspergillus niger degradome
Authors: Dong Zixing , Yang Shuangshuang , Lee Byong H.
Published: January 2021

Aspergillus niger has the ability to produce a large variety of proteases, which are of particular importance for protein digestion, intracellular protein turnover, cell signaling, flavour development, extracellular matrix remodeling and microbial defense. However, the A. niger degradome (the full repertoire of peptidases encoded by the A. niger genome) available is not accurate and comprehensive. Herein, we have utilized annotations of A. niger proteases in AspGD, JGI, and version 12.2 MEROPS database to compile an index of at least 232 putative proteases that are distributed into the 71 families/subfamilies and 26 clans of the 6 known catalytic classes, which represents ~ 1.64% of the 14,165 putative A. niger protein content. The composition of the A. niger degradome comprises ~ 7.3% aspartic, ~ 2.2% glutamic, ~ 6.0% threonine, ~ 17.7% cysteine, ~ 31.0% serine, and ~ 35.8% metallopeptidases. One hundred and two proteases have been reassigned into the above six classes, while the active sites and/or metal-binding residues of 110 proteases were recharacterized. The probable physiological functions and active site architectures of these peptidases were also investigated. This work provides a more precise overview of the complete degradome of A. niger, which will no doubt constitute a valuable resource and starting point for further experimental studies on the biochemical characterization and physiological roles of these proteases.
Topoisomerase IV tracks behind the replication fork and the SeqA complex during DNA replication in Escherichia coli
Authors: Helgesen Emily , Sætre Frank , Skarstad Kirsten
Published: January 2021

Topoisomerase IV (TopoIV) is a vital bacterial enzyme which disentangles newly replicated DNA and enables segregation of daughter chromosomes. In bacteria, DNA replication and segregation are concurrent processes. This means that TopoIV must continually remove inter-DNA linkages during replication. There exists a short time lag of about 10–20 min between replication and segregation in which the daughter chromosomes are intertwined. Exactly where TopoIV binds during the cell cycle has been the subject of much debate. We show here that TopoIV localizes to the origin proximal side of the fork trailing protein SeqA and follows the movement pattern of the replication machinery in the cell.
Ammonium and organic carbon co-removal under feammox-coupled-with-heterotrophy condition as an efficient approach for nitrogen treatment
Authors: Le Chung Phuong , Nguyen Hai Thi , Nguyen Toi Duy , Nguyen Quyen Huynh Minh , Pham Hai The , Dinh Hang Thuy
Published: January 2021

Nitrification is the rate limiting step in the nitrogen removal processes since nitrifiers have high oxygen demand, but poorly compete with aerobic heterotrophs. In a laboratory-scaled system, we investigated a process of ammonium oxidation under ferric-iron reducing condition (feammox) in the presence of organic carbon using influents with high NH4+ and COD contents, and ferrihydrite as the only electron acceptor. Batch incubations testing influents with different NH4+ and COD concentrations revealed that the [COD]/[NH4+] ratio of 1.4 and the influent redox potential ranging from − 20 to + 20 mV led to the highest removal efficiencies, i.e. 98.3% for NH4+ and 58.8% for COD. N2 was detected as the only product of NH4+ conversion, whereas NO2− and NO3− were not detected. While operating continuously with influent having a [COD]/[NH4+] ratio of 1.4, the system efficiently removed NH4+ (> 91%) and COD (> 54%) within 6 day retention time. Fluorescence in situ hybridization analyses using Cy3-labeled 16S rRNA oligonucleotide probes revealed that gamma-proteobacteria dominated in the microbial community attaching to the matrix bed of the system. The iron-reduction dependent NH4+ and COD co-removal with a thorough conversion of NH4+ to N2 demonstrated in this study would be a novel approach for nitrogen treatment.
Transcriptomics analysis for the identification of potential age-related genes and cells associated with three major urogenital cancers
Authors: Cao Jinlong , Li Jianpeng , Yang Xin , Li Pan , Yao Zhiqiang , Han Dali , Ying Lijun , Wang Lijie , Tian Junqiang
Published: January 2021

Age is one of the most important risk factors of the occurrence for tumor patients. The majority of patients with urogenital cancers are the elderly, whose clinical characteristics are greatly affected by age and ageing. Our study aimed to explore age-related genes, cells, and biological changes in three common urogenital cancers via integrative bioinformatics analysis. First, mRNA (count format) and clinical data for bladder cancer, prostate cancer and renal cell carcinoma were downloaded from the Cancer Genome Atlas (TCGA). Through the comparison of clinicopathological characteristics, genes expression and cells infiltration between the old group and the young group, it was found that the clinical characteristics, genes and cells in the tumor microenvironment of different ages were quite different. And 4 key cells, 14 hub genes and some potential pathways were identified and considered as important factors. More importantly, we analyzed the differential landscape of the genes and cells from different perspectives, and confirmed its importance. In conclusion, we identified genes and cell types associated with age-related changes in the tumour microenvironment in urogenital cancer patients. These genes and cell types may play a critical role in the age-associated differences in clinicopathological characteristics among urogenital cancers, thus providing a link between ageing and cancer occurrence. The findings of this study may pave the way for the development of age-tailored approaches to treat cancer and other age-related diseases.
Neural representations of own-voice in the human auditory cortex
Authors: Hosaka Taishi , Kimura Marino , Yotsumoto Yuko
Published: January 2021

We have a keen sensitivity when it comes to the perception of our own voices. We can detect not only the differences between ourselves and others, but also slight modifications of our own voices. Here, we examined the neural correlates underlying such sensitive perception of one’s own voice. In the experiments, we modified the subjects’ own voices by using five types of filters. The subjects rated the similarity of the presented voices to their own. We compared BOLD (Blood Oxygen Level Dependent) signals between the voices that subjects rated as least similar to their own voice and those they rated as most similar. The contrast revealed that the bilateral superior temporal gyrus exhibited greater activities while listening to the voice least similar to their own voice and lesser activation while listening to the voice most similar to their own. Our results suggest that the superior temporal gyrus is involved in neural sharpening for the own-voice. The lesser degree of activations observed by the voices that were similar to the own-voice indicates that these areas not only respond to the differences between self and others, but also respond to the finer details of own-voices.
Prediction of pharmacological activities from chemical structures with graph convolutional neural networks
Authors: Sakai Miyuki , Nagayasu Kazuki , Shibui Norihiro , Andoh Chihiro , Takayama Kaito , Shirakawa Hisashi , Kaneko Shuji
Published: January 2021

Many therapeutic drugs are compounds that can be represented by simple chemical structures, which contain important determinants of affinity at the site of action. Recently, graph convolutional neural network (GCN) models have exhibited excellent results in classifying the activity of such compounds. For models that make quantitative predictions of activity, more complex information has been utilized, such as the three-dimensional structures of compounds and the amino acid sequences of their respective target proteins. As another approach, we hypothesized that if sufficient experimental data were available and there were enough nodes in hidden layers, a simple compound representation would quantitatively predict activity with satisfactory accuracy. In this study, we report that GCN models constructed solely from the two-dimensional structural information of compounds demonstrated a high degree of activity predictability against 127 diverse targets from the ChEMBL database. Using the information entropy as a metric, we also show that the structural diversity had less effect on the prediction performance. Finally, we report that virtual screening using the constructed model identified a new serotonin transporter inhibitor with activity comparable to that of a marketed drug in vitro and exhibited antidepressant effects in behavioural studies.
Quantification of narrow band UVB radiation doses in phototherapy using diacetylene based film dosimeters
Authors: Mittal Apoorva , Kumar Manoj , Gopishankar N. , Kumar Pratik , Verma Akhilesh K.
Published: January 2021

Narrow band ultraviolet B (NB UVB) radiation doses are administered during phototherapy for various dermatological ailments. Precise quantification of these doses is vital because the absorbed irradiation can cause adverse photochemical reactions which can lead to potential phototherapeutic side effects. The paper presents development of diacetylene based dosimeter for the determination of therapeutic NB UVB doses during phototherapy. The amide terminated diacetylene analogues have been synthesized by tailoring them with different functional groups. The synthesized diacetylene monomers have been introduced in a polyvinyl alcohol binder solution to obtain a film dosimeter. The influence of different headgroups on the colorimetric response to UV radiation has been studied. Among all the synthesized diacetylene analogues, the naphthylamine substituted diacetylene exhibited excellent color transition from white to blue color at 100 mJ cm−2 NB UVB radiation dose. The developed amide films can be easily pasted on multiple sites of the patient’s skin to monitor doses during phototherapy simultaneously at different anatomical regions. The digital image processing of the scanned images of the irradiated films facilitates rapid dose measurement which enables facile implementation of the developed film dosimeters and promising application in routine clinical dosimetry.
Increased red cell distribution width predicts severity of drug-induced liver injury: a retrospective study
Authors: Li Xu , Xu Hongqin , Gao Pujun
Published: January 2021

We used a retrospective study design to evaluated the predictive value of red cell distribution width (RDW) for drug-induced liver injury (DILI) severity in Chinese patients with liver biopsy to assist with early DILI management. We included 164 DILI patients with complete laboratory information and medical history. We compared outcomes of 36 patients with severe DILI with outcomes of a control group of 128 patients with mild-to-moderate DILI. Multivariate analyses of risk factors for severe liver injury in Chinese patients with DILI revealed an estimated adjusted odds ratio (AOR) (95% CI) of 4.938 (1.088–22.412) in patients with drinking. Risk for serious liver injury was also increased significantly in patients with dyslipidemia [AOR (95% CI) 3.926 (1.282–12.026)], higher serum total bile acid (TBA) levels [AOR (95% CI) 1.014 (1.009–1.020)] and higher RDW [AOR (95% CI) 1.582 (1.261–1.986)]. The result for area under the curve of 0.905 for TBA levels indicated this variable had high diagnostic performance for predicting DILI severity. Based on an area under the curve value of 0.855, RDW also had superior diagnostic performance in prediction of DILI severity. This performance was not significantly different compared with TBA and was superior compared with other variables, which had area under values ranging from poor to failure (0.527–0.714).The risk for severe DILI was associated with drinking, dyslipidemia, higher TBA levels and RDW values. This study found that RDW and TBA levels were predictors of DILI severity in Chinese patients.