bluuebunny/crossref_metadata_2025_split huggingface dataset:
Nutritional profile of rodent diets impacts experimental reproducibility in microbiome preclinical research
Authors: Tuck C. J. , De Palma G. , Takami K. , Brant B. , Caminero A. , Reed D. E. , Muir J. G. , Gibson P. R. , Winterborn A. , Verdu E. F. , Bercik P. , Vanner S. 
Published: October 2020

AbstractThe lack of reproducibility of animal experimental results between laboratories, particularly in studies investigating the microbiota, has raised concern among the scientific community. Factors such as environment, stress and sex have been identified as contributors, whereas dietary composition has received less attention. This study firstly evaluated the use of commercially available rodent diets across research institutions, with 28 different diets reported by 45 survey respondents. Secondly, highly variable ingredient, FODMAP (Fermentable Oligo-, Di-, Mono-saccharides And Polyols) and gluten content was found between different commercially available rodent diets. Finally, 40 mice were randomized to four groups, each receiving a different commercially available rodent diet, and the dietary impact on cecal microbiota, short- and branched-chain fatty acid profiles was evaluated. The gut microbiota composition differed significantly between diets and sexes, with significantly different clusters in β-diversity. Total BCFA were highest (p = 0.01) and SCFA were lowest (p = 0.03) in mice fed a diet lower in FODMAPs and gluten. These results suggest that nutritional composition of commercially available rodent diets impact gut microbiota profiles and fermentation patterns, with major implications for the reproducibility of results across laboratories. However, further studies are required to elucidate the specific dietary factors driving these changes.
MLH1 single-nucleotide variant in circulating tumor DNA predicts overall survival of patients with hepatocellular carcinoma
Authors: Kim Soon Sun , Eun Jung Woo , Choi Ji-Hye , Woo Hyun Goo , Cho Hyo Jung , Ahn Hye Ri , Suh Chul Won , Baek Geum Ok , Cho Sung Won , Cheong Jae Youn 
Published: October 2020

AbstractLiquid biopsy can provide a strong basis for precision medicine. We aimed to identify novel single-nucleotide variants (SNVs) in circulating tumor DNA (ctDNA) in patients with hepatocellular carcinoma (HCC). Deep sequencing of plasma-derived ctDNA from 59 patients with HCC was performed using a panel of 2924 SNVs in 69 genes. In 55.9% of the patients, at least one somatic mutation was detected. Among 25 SNVs in 12 genes, four frequently observed SNVs, MLH1 (13%), STK11 (13%), PTEN (9%), and CTNNB1 (4%), were validated using droplet digital polymerase chain reaction with ctDNA from 62 patients with HCC. Three candidate SNVs were detected in 35.5% of the patients, with a frequency of 19% for MLH1 chr3:37025749T>A, 11% for STK11 chr19:1223126C>G, and 8% for PTEN chr10:87864461C>G. The MLH1 and STK11 SNVs were also confirmed in HCC tissues. The presence of the MLH1 SNV, in combination with an increased ctDNA level, predicted poor overall survival among 107 patients. MLH1 chr3:37025749T>A SNV detection in ctDNA is feasible, and thus, ctDNA can be used to detect somatic mutations in HCC. Furthermore, the presence or absence of the MLH1 SNV in ctDNA, combined with the ctDNA level, can predict the prognosis of patients with HCC.
Large-scale biometry with interpretable neural network regression on UK Biobank body MRI
Authors: Langner Taro , Strand Robin , Ahlström Håkan , Kullberg Joel 
Published: October 2020

AbstractIn a large-scale medical examination, the UK Biobank study has successfully imaged more than 32,000 volunteer participants with magnetic resonance imaging (MRI). Each scan is linked to extensive metadata, providing a comprehensive medical survey of imaged anatomy and related health states. Despite its potential for research, this vast amount of data presents a challenge to established methods of evaluation, which often rely on manual input. To date, the range of reference values for cardiovascular and metabolic risk factors is therefore incomplete. In this work, neural networks were trained for image-based regression to infer various biological metrics from the neck-to-knee body MRI automatically. The approach requires no manual intervention or direct access to reference segmentations for training. The examined fields span 64 variables derived from anthropometric measurements, dual-energy X-ray absorptiometry (DXA), atlas-based segmentations, and dedicated liver scans. With the ResNet50, the standardized framework achieves a close fit to the target values (median R$$^2 > 0.97$$

2

>
0.97

) in cross-validation. Interpretation of aggregated saliency maps suggests that the network correctly targets specific body regions and limbs, and learned to emulate different modalities. On several body composition metrics, the quality of the predictions is within the range of variability observed between established gold standard techniques.
Development of TiO2-coated YSZ/silica nanofiber membranes with excellent photocatalytic degradation ability for water purification
Authors: Huh Jin Young , Lee Jongman , Bukhari Syed Zaighum Abbas , Ha Jang-Hoon , Song In-Hyuck 
Published: October 2020

AbstractNumerous reports have elucidated that TiO2 nanoparticles (TiO2-NPs) exhibit respectable photocatalytic degradation capacities due to their high specific surface areas. However, the current recovery process leads to a loss of TiO2-NPs; therefore, there is a need to immobilize TiO2-NPs on the substrate used. Herein, TiO2-coated yttria-stabilized zirconia/silica nanofiber (TiO2-coated YSZ/silica NF) was prepared by coating TiO2 on the surface of YSZ/silica NF using a sol–gel process. The TiO2 coating layer on the nanofiber surface improved the separation ability of the membrane as well as the photocatalytic degradation ability. The pore size of the TiO2-coated YSZ/silica NF membrane was less than that of the pristine YSZ/silica NF membrane, and it rejected over 99.6% of the 0.5 μm polymeric particles. In addition, the TiO2-coated YSZ/silica NF membrane showed excellent adsorption/degradation of humic acid (HA, 88.2%), methylene blue (MB, 92.4%), and tetracycline (TC, 99.5%). Six recycling tests were performed to evaluate the reusability of the TiO2-coated YSZ/silica NF membrane. The adsorption/degradation efficiency for HA, MB, and TC decreased by 3.7%, 2.8%, and 2.2%, respectively. We thus verified the high separation ability, excellent photocatalytic degradation ability, and excellent reusability of the TiO2-coated YSZ/silica NF membranes.
Multiple early introductions of SARS-CoV-2 into a global travel hub in the Middle East
Authors: Tayoun Ahmad Abou , Loney Tom , Khansaheb Hamda , Ramaswamy Sathishkumar , Harilal Divinlal , Deesi Zulfa Omar , Varghese Rupa Murthy , Al Suwaidi Hanan , Alkhajeh Abdulmajeed , AlDabal Laila Mohamed , Uddin Mohammed , Hamoudi Rifat , Halwani Rabih , Senok Abiola , Hamid Qutayba , Nowotny Norbert , Alsheikh-Ali Alawi 
Published: October 2020

AbstractInternational travel played a significant role in the early global spread of SARS-CoV-2. Understanding transmission patterns from different regions of the world will further inform global dynamics of the pandemic. Using data from Dubai in the United Arab Emirates (UAE), a major international travel hub in the Middle East, we establish SARS-CoV-2 full genome sequences from the index and early COVID-19 patients in the UAE. The genome sequences are analysed in the context of virus introductions, chain of transmissions, and possible links to earlier strains from other regions of the world. Phylogenetic analysis showed multiple spatiotemporal introductions of SARS-CoV-2 into the UAE from Asia, Europe, and the Middle East during the early phase of the pandemic. We also provide evidence for early community-based transmission and catalogue new mutations in SARS-CoV-2 strains in the UAE. Our findings contribute to the understanding of the global transmission network of SARS-CoV-2.
Phosphatidylinositol-specific phospholipase C enhances epidermal penetration by Staphylococcus aureus
Authors: Nakamura Yoshikazu , Kanemaru Kaori , Shoji Madoka , Totoki Kengo , Nakamura Karen , Nakaminami Hidemasa , Nakase Keisuke , Noguchi Norihisa , Fukami Kiyoko 
Published: October 2020

AbstractStaphylococcus aureus(S. aureus) commonly colonizes the human skin and nostrils. However, it is also associated with a wide variety of diseases.S. aureusis frequently isolated from the skin of patients with atopic dermatitis (AD), and is linked to increased disease severity.S. aureusimpairs the skin barrier and triggers inflammation through the secretion of various virulence factors.S. aureussecretes phosphatidylinositol-specific phospholipase C (PI-PLC), which hydrolyses phosphatidylinositol and cleaves glycosylphosphatidylinositol-anchored proteins. However, the role ofS. aureusPI-PLC in the pathogenesis of skin diseases, including AD, remains unclear. In this study, we sought to determine the role ofS. aureusPI-PLC in the pathogenesis of skin diseases. PI-PLC was observed to enhance the invasion and persistence ofS. aureusin keratinocytes. Besides, PI-PLC promoted the penetration ofS. aureusthrough the epidermal barrier in a mouse model of AD and the human organotypic epidermal equivalent. Furthermore, the loss of PI-PLC attenuated epidermal hyperplasia and the infiltration of Gr-1+cells and CD4+cells induced byS. aureusinfection in the mouse model of AD. Collectively, these results indicate that PI-PLC eases the entry ofS. aureusinto the dermis and aggravates acanthosis and immune cell infiltration in infected skin.
Transient photothermal inactivation of Escherichia coli stained with visible dyes by using a nanosecond pulsed laser
Authors: Kohmura Yuji , Igami Natsuho , Tatsuno Ichiro , Hasegawa Tadao , Matsumoto Takahiro 
Published: October 2020

AbstractEfficient inactivation ofEscherichia coli(E. coli) under visible (532 nm) pulsed light irradiation was achieved by fusion of a visible light-absorbing dye withE. coli. Inactivation experiments showed that 3-log inactivation ofE. coliwas obtained within 20 min under a 50 kJ/cm2dose. This treatment time and dose magnitude were 10 times faster and 100 times lower, respectively, than the values previously obtained by using a visible femtosecond laser. The mechanism of bacterial death was modeled based on a transient photothermal evaporation effect, where a quantitative evaluation of the temperature increase was given based on the heat transfer equation. As a result of this theoretical analysis, the maximum temperature of the bacteria was correlated with the absorption ratio, pulse energy, and surface-to-volume ratio. An increase in the surface-to-volume ratio with the decreasing size of organic structures leads to the possibility of efficient inactivation of viruses and bacteria under low-dose and non-harmful-visible pulsed light irradiation. Hence, this method can be applied in many fields, such as the instantaneous inactivation of pathogenic viruses and bacteria in a safe and simple manner without damaging large organic structures.
The albumin–bilirubin score as a predictor of outcomes in Japanese patients with PBC: an analysis using time-dependent ROC
Authors: Ito Takanori , Ishigami Masatoshi , Morooka Hikaru , Yamamoto Kenta , Imai Norihiro , Ishizu Yoji , Honda Takashi , Nishimura Daisaku , Tada Toshifumi , Yasuda Satoshi , Toyoda Hidenori , Kumada Takashi , Fujishiro Mitsuhiro 
Published: October 2020

AbstractThe albumin–bilirubin (ALBI) score is calculated using only serum albumin and bilirubin levels, and was developed as a simple method to assess hepatic function. In this study, a total of 409 patients with primary biliary cholangitis (PBC) were enrolled between March 1990 and October 2018. The predictive performances of the ALBI score and other well-established prognostic scores were compared using time-dependent receiver operating characteristic (ROC) analysis. During the follow-up period, 60 patients died, 45 due to liver-related diseases and 15 due to non-liver-related diseases, and 16 patients underwent liver transplantation. Time-dependent ROC analysis showed that the ALBI score has higher the areas under the ROC curves (AUROCs) than the Child–Pugh (C–P) score at each time point; AUROCs at 3, 5, and 10 years after the start of follow-up were 0.94, 0.91, and 0.90 for the ALBI score, and 0.89, 0.88, and 0.82 for the C–P score, respectively. The ALBI score showed the highest AUROCs within 2 years after the start of observation; beyond 2 years, however, the Mayo score had better prognostic ability for mortality and liver transplantation. The ALBI score/grade, derived from objective blood tests, and the Mayo score were superior prognostic tools in PBC patients.
Development of humanized tri-specific nanobodies with potent neutralization for SARS-CoV-2
Authors: Dong Jianbo , Huang Betty , Wang Bo , Titong Allison , Gallolu Kankanamalage Sachith , Jia Zhejun , Wright Meredith , Parthasarathy Pannaga , Liu Yue 
Published: October 2020

AbstractSARS-CoV-2 is a newly emergent coronavirus, which has adversely impacted human health and has led to the COVID-19 pandemic. There is an unmet need to develop therapies against SARS-CoV-2 due to its severity and lack of treatment options. A promising approach to combat COVID-19 is through the neutralization of SARS-CoV-2 by therapeutic antibodies. Previously, we described a strategy to rapidly identify and generate llama nanobodies (VHH) from naïve and synthetic humanized VHH phage libraries that specifically bind the S1 SARS-CoV-2 spike protein, and block the interaction with the human ACE2 receptor. In this study we used computer-aided design to construct multi-specific VHH antibodies fused to human IgG1 Fc domains based on the epitope predictions for leading VHHs. The resulting tri-specific VHH-Fc antibodies show more potent S1 binding, S1/ACE2 blocking, and SARS-CoV-2 pseudovirus neutralization than the bi-specific VHH-Fcs or combination of individual monoclonal VHH-Fcs. Furthermore, protein stability analysis of the VHH-Fcs shows favorable developability features, which enable them to be quickly and successfully developed into therapeutics against COVID-19.
Disclosing crystal nucleation mechanism in lithium disilicate glass through molecular dynamics simulations and free-energy calculations
Authors: Lodesani Federica , Menziani Maria Cristina , Maeda Kei , Takato Yoichi , Urata Shingo , Pedone Alfonso 
Published: October 2020

AbstractUnraveling detailed mechanism of crystal nucleation from amorphous materials is challenging for both experimental and theoretical approaches. In this study, we have examined two methods to understand the initial stage of crystal precipitation from lithium disilicate glasses using molecular dynamics simulations. One of the methods is a modified exploring method to find structurally similar crystalline clusters in the glass models, enabling us to find three different embryos, such as Li2Si2O5 (LS2), Li2SiO3 (LS) and Li3PO4 (LP), in the 33Li2O·66SiO2·1P2O5 glass (LS2P1), in which P2O5 is added as a nucleating agent. Interestingly, LS2 and LP crystals were found inside the LS2P1 glass while LS crystal appeared on the glass surface, which agrees with experimental observations. The other method is free energy calculation using a subnano-scale spherical crystal embedded in the glass model. This method, which we called Free-Energy Seeding Method (FESM), allows us to evaluate free energy change as a function of crystal radius and to identify critical size of the crystal precipitation. The free energy profiles for LS and LS2 crystal nuclei in the LS2 glass models possess maximum energy at a critical radius as expected by classical nucleation theory. Furthermore, the critical radius and the energy barrier height agree well with recent experimental investigation, proving the applicability of this method to design glass–ceramics by atomistic modeling.
A nationwide assessment of plastic pollution in the Danish realm using citizen science
Authors: Syberg Kristian , Palmqvist Annemette , Khan Farhan R. , Strand Jakob , Vollertsen Jes , Clausen Lauge Peter Westergaard , Feld Louise , Hartmann Nanna B. , Oturai Nikoline , Møller Søren , Nielsen Torkel Gissel , Shashoua Yvonne , Hansen Steffen Foss 
Published: October 2020

AbstractPlastic pollution is considered one of today’s major environmental problems. Current land-based monitoring programs typically rely on beach litter data and seldom include plastic pollution further inland. We initiated a citizen science project known as the Mass Experiment inviting schools throughout The Danish Realm (Denmark, Greenland and the Faeroe Islands) to collect litter samples of and document plastic pollution in 8 different nature types. In total approximately 57,000 students (6–19 years) collected 374,082 plastic items in 94 out of 98 Danish municipalities over three weeks during fall 2019. The Mass Experiment was the first scientific survey of plastic litter to cover an entire country. Here we show how citizen science, conducted by students, can be used to fill important knowledge gaps in plastic pollution research, increase public awareness, establish large scale clean-up activities and subsequently provide information to political decision-makers aiming for a more sustainable future.
Artificial modulation of cell width significantly affects the division time of Escherichia coli
Authors: Liang Baihui , Quan Baogang , Li Junjie , Loton Chantal , Bredeche Marie-Florence , Lindner Ariel B. , Xu Luping 
Published: October 2020

AbstractBacterial cells have characteristic spatial and temporal scales. For instance, Escherichia coli, the typical rod-shaped bacteria, always maintains a relatively constant cell width and cell division time. However, whether the external physical perturbation of cell width has an impact on cell division time remains largely unexplored. In this work, we developed two microchannel chips, namely straight channels and ‘necked’ channels, to precisely regulate the width of E. coli cells and to investigate the correlation between cell width and division time of the cells. Our results show that, in the straight channels, the wide cells divide much slower than narrow cells. In the ‘necked’ channels, the cell division is remarkably promoted compared to that in straight channels with the same width. Besides, fluorescence time-lapse microscopy imaging of FtsZ dynamics shows that the cell pre-constriction time is more sensitive to cell width perturbation than cell constriction time. Finally, we revealed a significant anticorrelation between the death rate and the division rate of cell populations with different widths. Our work provides new insights into the correlation between the geometrical property and division time of E. coli cells and sheds new light on the future study of spatial–temporal correlation in cell physiology.
Ion irradiation induced phase transformation in gold nanocrystalline films
Authors: Suri Pranav K. , Nathaniel James E. , Li Nan , Baldwin Jon K. , Wang Yongqiang , Hattar Khalid , Taheri Mitra L. 
Published: October 2020

AbstractGold is a noble metal typically stable as a solid in a face-centered cubic (FCC) structure under ambient conditions; however, under particular circumstances aberrant allotropes have been synthesized. In this work, we document the phase transformation of 25 nm thick nanocrystalline (NC) free-standing gold thin-film via in situ ion irradiation studied using atomic-resolution transmission electron microscopy (TEM). Utilizing precession electron diffraction (PED) techniques, crystallographic orientation and the radiation-induced relative strains were measured and furthermore used to determine that a combination of surface and radiation-induced strains lead to an FCC to hexagonal close packed (HCP) crystallographic phase transformation upon a 10 dpa radiation dose of Au4+ ions. Contrary to previous studies, HCP phase in nanostructures of gold was stabilized and did not transform back to FCC due to a combination of size effects and defects imparted by damage cascades.
Toxic oligomers of the amyloidogenic HypF-N protein form pores in mitochondrial membranes
Authors: Farrugia Maria Ylenia , Caruana Mario , Ghio Stephanie , Camilleri Angelique , Farrugia Claude , Cauchi Ruben J. , Cappelli Sara , Chiti Fabrizio , Vassallo Neville 
Published: October 2020

AbstractStudies on the amyloidogenic N-terminal domain of the E. coli HypF protein (HypF-N) have contributed significantly to a detailed understanding of the pathogenic mechanisms in neurodegenerative diseases characterised by the formation of misfolded oligomers, by proteins such as amyloid-β, α-synuclein and tau. Given that both cell membranes and mitochondria are increasingly recognised as key targets of oligomer toxicity, we investigated the damaging effects of aggregates of HypF-N on mitochondrial membranes. Essentially, we found that HypF-N oligomers characterised by high surface hydrophobicity (type A) were able to trigger a robust permeabilisation of mito-mimetic liposomes possessing cardiolipin-rich membranes and dysfunction of isolated mitochondria, as demonstrated by a combination of mitochondrial shrinking, lowering of mitochondrial membrane potential and cytochrome c release. Furthermore, using single-channel electrophysiology recordings we obtained evidence that the type A aggregates induced currents reflecting formation of ion-conducting pores in mito-mimetic planar phospholipid bilayers, with multi-level conductances ranging in the hundreds of pS at negative membrane voltages. Conversely, HypF-N oligomers with low surface hydrophobicity (type B) could not permeabilise or porate mitochondrial membranes. These results suggest an inherent toxicity of membrane-active aggregates of amyloid-forming proteins to mitochondria, and that targeting of oligomer-mitochondrial membrane interactions might therefore afford protection against such damage.
Self-competence increases the willingness to pay for social influence
Authors: Hertz Uri , Tyropoulou Evangelia , Traberg Cecilie , Bahrami Bahador 
Published: October 2020

AbstractTheoretical works in social psychology and neuroscientific evidence have proposed that social rewards have intrinsic value, suggesting that people place a high premium on the ability to influence others. To test this hypothesis, we asked whether, and under what conditions, people are willing to forgo monetary reward for the sake of influencing others’ decisions. In four experiments, online and lab-based participants competed with a rival for influence over a client. The majority of participants sacrificed some of their financial reward to increase their chance of being selected over their rival within the experiment. Willingness to pay was affected by the participant’s current level of influence and performance, as participants were most likely to pay to promote their competence after having given good advice that had been ignored by the client using a situation where monetary incentives fail to explain human motivations, our experiments highlight the intrinsic value of social influence.