bluuebunny/crossref_metadata_2025_split huggingface dataset:
Prebiotic effects of yeast mannan, which selectively promotes Bacteroides thetaiotaomicron and Bacteroides ovatus in a human colonic microbiota model
Authors: Oba Shunsuke , Sunagawa Tadahiro , Tanihiro Reiko , Awashima Kyoko , Sugiyama Hiroshi , Odani Tetsuji , Nakamura Yasunori , Kondo Akihiko , Sasaki Daisuke , Sasaki Kengo 
Published: October 2020

AbstractYeast mannan (YM) is an indigestible water-soluble polysaccharide of the yeast cell wall, with a notable prebiotic effect on the intestinal microbiota. We previously reported that YM increased Bacteroides thetaiotaomicron abundance in in vitro rat faeces fermentation, concluding that its effects on human colonic microbiota should be investigated. In this study, we show the effects of YM on human colonic microbiota and its metabolites using an in vitro human faeces fermentation system. Bacterial 16S rRNA gene sequence analysis showed that YM administration did not change the microbial diversity or composition. Quantitative real-time PCR analysis revealed that YM administration significantly increased the relative abundance of Bacteroides ovatus and B. thetaiotaomicron. Moreover, a positive correlation was observed between the relative ratio (with or without YM administration) of B. thetaiotaomicron and B. ovatus (r = 0.92), suggesting that these bacteria utilise YM in a coordinated manner. In addition, YM administration increased the production of acetate, propionate, and total short-chain fatty acids. These results demonstrate the potential of YM as a novel prebiotic that selectively increases B. thetaiotaomicron and B. ovatus and improves the intestinal environment. The findings also provide insights that might be useful for the development of novel functional foods.
In vivo measurement of shear modulus of the human cornea using optical coherence elastography
Authors: Ramier Antoine , Eltony Amira M. , Chen YiTong , Clouser Fatima , Birkenfeld Judith S. , Watts Amy , Yun Seok-Hyun 
Published: October 2020

AbstractCorneal stiffness plays a critical role in shaping the cornea with respect to intraocular pressure and physical interventions. However, it remains difficult to measure the mechanical properties noninvasively. Here, we report the first measurement of shear modulus in human corneas in vivo using optical coherence elastography (OCE) based on surface elastic waves. In a pilot study of 12 healthy subjects aged between 25 and 67, the Rayleigh-wave speed was 7.86 ± 0.75 m/s, corresponding to a shear modulus of 72 ± 14 kPa. Our data reveal two unexpected trends: no correlation was found between the wave speed and IOP between 13–18 mmHg, and shear modulus decreases with age (− 0.32 ± 0.17 m/s per decade). We propose that shear stiffness is governed by the interfibrillar matrix, whereas tensile strength is dominated by collagen fibrils. Rayleigh-wave OCE may prove useful for clinical diagnosis, refractive surgeries, and treatment monitoring.
Analysis of gene expression from systemic lupus erythematosus synovium reveals myeloid cell-driven pathogenesis of lupus arthritis
Authors: Hubbard Erika L. , Catalina Michelle D. , Heuer Sarah , Bachali Prathyusha , Robl Robert , Geraci Nicholas S. , Grammer Amrie C. , Lipsky Peter E. 
Published: October 2020

AbstractArthritis is a common manifestation of systemic lupus erythematosus (SLE) yet understanding of the underlying pathogenic mechanisms remains incomplete. We, therefore, interrogated gene expression profiles of SLE synovium to gain insight into the nature of lupus arthritis (LA), using osteoarthritis (OA) and rheumatoid arthritis (RA) as comparators. Knee synovia from SLE, OA, and RA patients were analyzed for differentially expressed genes (DEGs) and also by Weighted Gene Co-expression Network Analysis (WGCNA) to identify modules of highly co-expressed genes. Genes upregulated and/or co-expressed in LA revealed numerous immune/inflammatory cells dominated by a myeloid phenotype, in which pathogenic macrophages, myeloid-lineage cells, and their secreted products perpetuate inflammation, whereas OA was characterized by fibroblasts and RA of lymphocytes. Genes governing trafficking of immune cells into the synovium by chemokines were identified, but not in situ generation of germinal centers (GCs). Gene Set Variation Analysis (GSVA) confirmed activation of specific immune cell types in LA. Numerous therapies were predicted to target LA, including TNF, NFκB, MAPK, and CDK inhibitors. Detailed gene expression analysis identified a unique pattern of cellular components and physiologic pathways operative in LA, as well as drugs potentially able to target this common manifestation of SLE.
Detection of REEs with lightweight UAV-based hyperspectral imaging
Authors: Booysen René , Jackisch Robert , Lorenz Sandra , Zimmermann Robert , Kirsch Moritz , Nex Paul A. M. , Gloaguen Richard 
Published: October 2020

AbstractRare earth elements (REEs) supply is important to ensure the energy transition, e-mobility and ultimately to achieve the sustainable development goals of the United Nations. Conventional exploration techniques usually rely on substantial geological field work including dense in-situ sampling with long delays until provision of analytical results. However, this approach is limited by land accessibility, financial status, climate and public opposition. Efficient and innovative methods are required to mitigate these limitations. The use of lightweight unmanned aerial vehicles (UAVs) provides a unique opportunity to conduct rapid and non-invasive exploration even in socially sensitive areas and in relatively inaccessible locations. We employ drones with hyperspectral sensors to detect REEs at the earth’s surface and thus contribute to a rapidly evolving field at the cutting edge of exploration technologies. We showcase for the first time the direct mapping of REEs with lightweight hyperspectral UAV platforms. Our solution has the advantage of quick turn-around times (< 1 d), low detection limits (< 200 ppm for Nd) and is ideally suited to support exploration campaigns. This procedure was successfully tested and validated in two areas: Marinkas Quellen, Namibia, and Siilinjärvi, Finland. This strategy should invigorate the use of drones in exploration and for the monitoring of mining activities.
The physical origin of rate promoting vibrations in enzymes revealed by structural rigidity
Authors: Chalopin Yann 
Published: October 2020

AbstractEnzymes are the most efficient catalysts known to date. However, decades of research have failed to fully explain the catalytic power of enzymes, and most of the current attempts to uncloak the details of atomic motions at active sites remain incomplete. Here, a straightforward manner for understanding the interplay between the complex or irregular enzyme topology and dynamical effects at catalytic sites is introduced, by revealing how fast localized vibrations form spontaneously in the stiffest parts of the scaffold. While shedding light on a physical mechanism that allowed the selection of the picosecond (ps) timescale to increase the catalytic proficiency, this approach exposes the functional importance of localized motions as a by-product of the stability-function tradeoff in enzyme evolution. From this framework of analysis—directly accessible from available diffraction data—experimental strategies for engineering the catalytic rate in enzymatic proteins are proposed.
Uncertainty quantification based cloud parameterization sensitivity analysis in the NCAR community atmosphere model
Authors: Pathak Raju , Sahany Sandeep , Mishra Saroj K. 
Published: October 2020

AbstractUsing uncertainty quantification techniques, we carry out a sensitivity analysis of a large number (17) of parameters used in the NCAR CAM5 cloud parameterization schemes. The LLNL PSUADE software is used to identify the most sensitive parameters by performing sensitivity analysis. Using Morris One-At-a-Time (MOAT) method, we find that the simulations of global annual mean total precipitation, convective, large-scale precipitation, cloud fractions (total, low, mid, and high), shortwave cloud forcing, longwave cloud forcing, sensible heat flux, and latent heat flux are very sensitive to the threshold-relative-humidity-for-stratiform-low-clouds ($$rhminl)$$

r
h
m
i
n
l
)

and the auto-conversion-size-threshold-for-ice-to-snow $$\left( {dcs} \right).$$

dcs

.

The seasonal and regime specific dependence of some parameters in the simulation of precipitation is also found for the global monsoons and storm track regions. Through sensitivity analysis, we find that the Somali jet strength and the tropical easterly jet associated with the south Asian summer monsoon (SASM) show a systematic dependence on $$dcs$$

dcs

and $$rhminl$$

rhminl

. The timing of the withdrawal of SASM over India shows a monotonic increase (delayed withdrawal) with an increase in $$dcs$$

dcs

. Overall, we find that $$rhminl$$

rhminl

, $$dcs$$

dcs

, $$ai,$$

a
i
,

and $$as$$

as

are the most sensitive cloud parameters and thus are of high priority in the model tuning process, in order to reduce uncertainty in the simulation of past, present, and future climate.
Role of the paramagnetic donor-like defects in the high n-type conductivity of the hydrogenated ZnO microparticles
Authors: Savchenko Dariya , Vasin Andrii , Kuz Oleksandr , Verovsky Igor , Prokhorov Andrey , Nazarov Alexey , Lančok Jan , Kalabukhova Ekaterina 
Published: October 2020

AbstractThe magnetic and electronic properties of the hydrogenated highly conductive zinc oxide (ZnO) microparticles were investigated by electron paramagnetic resonance (EPR) and contactless microwave (MW) conductivity techniques in the wide temperature range. The EPR spectra simulation allowed us to resolve four overlapping EPR signals in ZnO microparticles. The Lorentzian EPR line with isotropic g-factor 1.9623(5) was related to the singly ionized oxygen vacancy. Another Lorentzian line with g|| = 1.9581(5), g⊥ = 1.9562(5) was attributed to the zinc interstitial shallow donor center, while EPR signal with g|| = 1.9567(5), g⊥ = 1.9556(5) and Gaussian lineshape was assigned to the hydrogen interstitial shallow effective-mass-like donor. The EPR signal with g|| = 1.9538(5), g⊥ = 1.9556(5) and Lorentzian lineshape was tentatively attributed to the shallow donor center. The charge transport properties in ZnO microparticles have been investigated by the contactless MW conductivity technique at T = 5–296 K. Two conduction mechanisms, including ionization of electrons from the shallow donors to the conduction band and hopping conduction process, have been distinguished. The hopping conduction process follows Mott’s variable-range hopping T−1/4 law at T = 10–100 K. The evaluated values of the average hopping distance (15.86 Å), and hopping energy (1.822 meV at 40 K) enable us to estimate the donor concentration in the investigated ZnO microparticles as ~ 1018 cm−3.
Vertical transmission of hepatitis E virus in pregnant rhesus macaques
Authors: Yu Wenhai , Hao Xianhui , Li Yi , Yang Chenchen , Li Yunlong , He Zhanlong , Huang Fen 
Published: October 2020

AbstractHepatitis E virus (HEV) is the major pathogen of viral hepatitis. HEV causes high mortality in pregnant women. Its infection during pregnancy usually leads to fulminant hepatic failure, spontaneous abortions, premature delivery, or stillbirth. Vertical transmission of HEV has been reported, but the pathogenesis during pregnancy remains largely elusive. Pregnant rhesus macaques were infected with HEV to explore the pathogenesis of genotype 4 HEV infection during pregnancy. Active HEV infections were established with shedding viruses in the feces and blood, and elevated liver enzymes. Notably, higher viral titers and longer durations of HEV infection were found in HEV-infected pregnant rhesus macaques than in non-pregnant macaques. Premature delivery and fetal death occurred in one of the HEV-infected pregnant rhesus macaques. HEV RNA was detected in the liver, spleen, kidneys, and intestines of the dead fetus. This result strongly indicated vertical HEV transmission from mother to fetus. Maternal-transferred antibodies were observed in one of the babies with poor protection. The expressions of interferon-stimulated genes (ISGs) related to HEV infection were completely different between pregnant and non-pregnant rhesus macaques. During pregnancy, impaired innate immune responses, reduced progesterone levels, and shifts in immune states may aggravate HEV infection and result in adverse pregnancy outcomes.
Generalized enzymatic mechanism of catalysis by tetrameric l-asparaginases from mesophilic bacteria
Authors: Strzelczyk Pawel , Zhang Di , Dyba Marzena , Wlodawer Alexander , Lubkowski Jacek 
Published: October 2020

AbstractThe mechanism of catalysis by the l-glutaminase-asparaginase from Pseudomonas 7A (PGA) was investigated using structural, mass spectrometry, and kinetic data. We had previously proposed mechanism of hydrolysis of l-Asn by the type II l-asparaginase from E. coli (EcAII), but that work was limited to just one enzyme. Based on results presented in this report, we postulate that all homotetrameric l-asparaginases from mesophilic bacteria utilize a common ping-pong mechanism of catalysis consisting of two subsequent nucleophilic substitutions. Several new structures of non-covalent complexes of PGA with different substrates, as well as structures of covalent acyl-enzyme intermediates of PGA with canonical substrates (l-Asp and l-Glu) and an opportunistic ligand, a citrate anion, were determined. The results of kinetic experiments monitored by high-resolution LC/MS, when combined with new structural data, clearly show that the reaction catalyzed by l-glutaminase-asparaginases proceeds through formation of a covalent intermediate, as observed previously for EcAII. Additionally, by showing that the same mechanism applies to l-Asn and l-Gln, we postulate that it is common for all these structurally related enzymes.
Associations of second-hand smoke exposure with hand eczema and atopic dermatitis among college students in China
Authors: Jing Danrong , Li Juan , Tao Juan , Wang Xiaohui , Shan Shijun , Kang Xiaojing , Wu Bin , Zhang Yichi , Xiao Yi , Chen Xiang , Shen Minxue 
Published: October 2020

AbstractSmoking has been identified as a risk factor for atopic dermatitis and hand eczema, but less is known about the association of exposure to second-hand smoke (SHS) with hand eczema. The study aimed to investigate the association of SHS exposure with hand eczema and atopic dermatitis in a group of adolescents. We conducted a cross-sectional study among first-year college students. SHS exposure was measured by a self-administered questionnaire. Skin diseases were diagnosed by dermatologists in the field survey. Mixed models were used to estimate the associations. A total of 20,129 participants that underwent skin examination and a questionnaire survey were included in the analyses. The prevalence rates of atopic dermatitis and hand eczema were 3.86% and 3.35%, respectively. Crude and adjusted estimates consistently showed that exposure to SHS was significantly associated with atopic dermatitis and hand eczema in a dose–response manner. Attention deficit/hyperactivity disorder mediated minimal or no effect of SHS on hand eczema and atopic dermatitis. Subgroup analysis by type of hand eczema, and sensitivity analysis by excluding data with center effect showed consistent results. Exposure to SHS is an independent but modifiable risk factor for hand eczema and atopic dermatitis in adolescents.
In vivo bactericidal effect of colistin–linezolid combination in a murine model of MDR and XDR Acinetobacter baumannii pneumonia
Authors: Ma Xiao-Lin , Guo Yong-Zhong , Wu Yan-Min , Gong Wei-Tao , Sun Jie , Huang Zhen 
Published: October 2020

AbstractRecently, paradoxical combinations of colistin with anti-Gram-positive bacterial agents were introduced as a treatment alternative for multidrug-resistant Acinetobacter baumannii (MDRAB) infection. We assessed the therapeutic efficacy of the colistin–linezolid combination regimen in vitro and in a murine model of Acinetobacter baumannii pneumonia. A multidrug-resistant clinical strain (MDRAB31) and an extensively drug-resistant clinical strain (XDRAB78) were used in this study. The survival rates of mice and bacterial counts in lung tissue were used to assess the effects of colistin–linezolid combination. The survival rates of colistin–linezolid combination groups significantly increased compared with colistin groups for MDRAB31 (72% versus 32%, P = 0.03) and for XDRAB78 (92% versus 68%, P = 0.031). The colistin–linezolid combination groups significantly reduced the bacterial counts in lung tissue compared with colistin groups for MDRAB31 and for XDRAB78 (P < 0.05). The colistin–linezolid combination had a bactericidal and synergistic effect compared with colistin alone in time-kill assay and in murine model of pneumonia. Our data demonstrated the synergistic effect of colistin–linezolid combination regimen as a treatment alternative for the severe pulmonary infection caused by MDRAB and XDRAB.
Structural insights into metal-metalloid glasses from mass spectrometry
Authors: Baksi Ananya , Bag Soumabha , Kruk Robert , Nandam Sree Harsha , Hahn Horst 
Published: October 2020

AbstractDespite being studied for nearly 50 years, smallest chemically stable moieties in the metallic glass (MG) could not be found experimentally. Herein, we demonstrate a novel experimental approach based on electrochemical etching of amorphous alloys in inert solvent (acetonitrile) in the presence of a high voltage (1 kV) followed by detection of the ions using electrolytic spray ionization mass spectrometry (ESI MS). The experiment shows stable signals corresponding to Pd, PdSi and PdSi2ions, which emerges due to the electrochemical etching of the Pd80Si20metallic glass electrode. These fragments are observed from the controlled dissolution of the Pd80Si20melt-spun ribbon (MSR) electrode. Annealed electrode releases different fragments in the same experimental condition. These specific species are expected to be the smallest and most stable chemical units from the metallic glass which survived the chemical dissolution and complexation (with acetonitrile) process. Theoretically, these units can be produced from the cluster based models for the MG. Similar treatment on Pd40Ni40P20MSR resulted several complex peaks consisting of Pd, Ni and P in various combinations suggesting this can be adopted for any metal-metalloid glass.
Impact of volatile organic compounds on chromium containing atmospheric particulate: insights from molecular dynamics simulations
Authors: Shah Dhawal , Karibayev Mirat , Adotey Enoch Kwasi , Amouei Torkmahalleh Mehdi 
Published: October 2020

AbstractThe effect of volatile organic compounds (VOCs) on chromium-containing atmospheric particles remains obscured because of difficulties in experimental measurements. Moreover, several ambiguities exist in the literature related to accurate measurements of atmospheric chromium concentration to evaluate its toxicity. We investigated the interaction energies and diffusivity for several VOCs in chromium (III)-containing atmospheric particles using classical molecular dynamics simulations. We analyzed xylene, toluene, ascorbic acid, carbon tetrachloride, styrene, methyl ethyl ketone, naphthalene, and anthracene in Cr(III) solutions, with and without air, to compare their effects on solution chemistry. The interaction energy between Cr(III) and water changed from 48 to 180% for different VOCs, with the highest change with anthracene and the lowest change with naphthalene. The results revealed no direct interactions between Cr(III) particles and the analyzed volatile organic compounds, except ascorbic acid. Interactions of Cr(III) and ascorbic acid differ significantly between the solution phase and the particulate phase. The diffusion of Cr(III) and all the VOCs also were observed in a similar order of magnitude (~ 10−5 cm2/s). The results can further assist in exploring the variation in chromium chemistry and reaction rates in the atmospheric particles in the presence of VOCs.
Recombinant thrombomodulin alleviates oxidative stress without compromising host resistance to infection in rats infected with methicillin-resistant Staphylococcus aureus
Authors: Ito Takashi , Shrestha Binita , Kakihana Yasuyuki , Maruyama Ikuro 
Published: October 2020

AbstractRecombinant thrombomodulin (rTM) has been used for treatment of sepsis-associated disseminated intravascular coagulation. Recent studies have suggested that anticoagulant therapy might dampen the protective role of immunothrombosis. We examined if rTM might worsen infectious diseases. Male Sprague–Dawley rats with jugular-vein catheterization were divided into three groups: no anticoagulation; rTM pretreatment; rTM treatment at 6 h. Live methicillin-resistant Staphylococcus aureus (MRSA) was inoculated into the tail vein of rats. rTM was administered into the jugular-vein catheter before or 6 h after MRSA inoculation, while an equal volume of saline was administered in the no-anticoagulation group. Blood samples were collected from the jugular-vein catheter before, 6 h and 12 h after MRSA inoculation. Tissue samples were collected from anesthetized rats when moribund or 18 h after MRSA inoculation. The survival rate of rats in the no-anticoagulation group, rTM pretreatment group, and rTM treatment at 6-h group was 50%, 25%, and 75%, respectively. Bacterial burden in blood, lung, liver, and spleen was neither increased nor decreased in rats treated with rTM. The ratio of bacteria found in the extravascular space to those in the intravascular space was increased in rats treated with rTM although the statistical power for this was low because of the small sample size. Metabolomics analysis revealed that rTM treatment alleviated oxidative stress, as evidenced by the decrease in levels of oxidized glutathione with reference to reduced glutathione. rTM did not promote bacterial propagation but alleviated oxidative stress in our rat model of bloodstream infection with MRSA. Further large-scale studies are needed to confirm these findings.
Evaluation of the RAS signaling network in response to MEK inhibition using organoids derived from a familial adenomatous polyposis patient
Authors: Osumi Hiroki , Muroi Atsushi , Sakahara Mizuho , Kawachi Hiroshi , Okamoto Takuya , Natsume Yasuko , Yamanaka Hitomi , Takano Hiroshi , Kusama Daisuke , Shinozaki Eiji , Ooki Akira , Yamaguchi Kensei , Ueno Masashi , Takeuchi Kengo , Noda Tetsuo , Nagayama Satoshi , Koshikawa Naohiko , Yao Ryoji 
Published: October 2020

AbstractRAS signaling is a promising target for colorectal cancer (CRC) therapy, and a variety of selective inhibitors have been developed. However, their use has often failed to demonstrate a significant benefit in CRC patients. Here, we used patient-derived organoids (PDOs) derived from a familial adenomatous polyposis (FAP) patient to analyze the response to chemotherapeutic agents targeting EGFR, BRAF and MEK. We found that PDOs carrying KRAS mutations were resistant to MEK inhibition, while those harboring the BRAF class 3 mutation were hypersensitive. We used a systematic approach to examine the phosphorylation of RAS effectors using reverse-phase protein array (RPPA) and found increased phosphorylation of MEK induced by binimetinib. A high basal level of ERK phosphorylation and its rebound activation after MEK inhibition were detected in KRAS-mutant PDOs. Notably, the phosphorylation of EGFR and AKT was more closely correlated with that of MEK than that of ERK. Transcriptome analysis identified MYC-mediated transcription and IFN signaling as significantly correlated gene sets in MEK inhibition. Our experiments demonstrated that RPPA analysis of PDOs, in combination with the genome and transcriptome, is a useful preclinical research platform to understand RAS signaling and provides clues for the development of chemotherapeutic strategies.