bluuebunny/crossref_metadata_2025_split huggingface dataset:
Ketogenesis Impact on Liver Metabolism Revealed by Proteomics of Lysine β-hydroxybutyrylation
Authors: Koronowski Kevin B. , Greco Carolina M. , Huang He , Kim Jin-Kwang , Fribourgh Jennifer L. , Crosby Priya , Partch Carrie L. , Qiao Feng , Zhao Yingming , Sassone-Corsi Paolo 
Published: January 2021

SUMMARYKetone bodies are evolutionarily conserved metabolites that function as energy substrates, signaling molecules and epigenetic regulators. β-hydroxybutyrate (β-OHB) is utilized in lysine β-hydroxybutyrylation (Kbhb) of histones, which associates with starvation-responsive genes, effectively coupling ketogenic metabolism with gene expression. The emerging diversity of the lysine acylation landscape prompted us to investigate the full proteomic impact of Kbhb. Global protein Kbhb is induced in a tissue-specific manner by a variety of interventions that evoke β-OHB. Mass spectrometry analysis of the β-hydroxybutyrylome in mouse liver revealed 891 sites of Kbhb within 267 proteins enriched for fatty acid, amino acid, detoxification and 1-carbon metabolic pathways. Kbhb of S-adenosyl-L-homocysteine hydrolase (AHCY), a rate-limiting enzyme of the methionine cycle, results in inhibition of enzymatic activity. Our results illuminate the role of Kbhb on hepatic metabolism under ketogenic conditions and demonstrate the functional consequence of this modification on a central metabolic enzyme.
BMP-treated human embryonic stem cells transcriptionally resemble amnion cells in the monkey embryo
Authors: Chhabra Sapna , Warmflash Aryeh 
Published: January 2021

AbstractHuman embryonic stem cells (hESCs) possess an immense potential to generate clinically relevant cell types and unveil mechanisms underlying early human development. However, using hESCs for discovery or translation requires accurately identifying differentiated cell types through comparison with their in vivo counterparts. Here, we set out to determine the identity of much debated BMP-treated hESCs by comparing their transcriptome to the recently published single cell transcriptomes of early human embryos in the study Xiang et al 2019. Our analyses reveal several discrepancies in the published human embryo dataset, including misclassification of putative amnion, intermediate and inner cell mass cells. These misclassifications primarily resulted from similarities in pseudogene expression, highlighting the need to carefully consider gene lists when making comparisons between cell types. In the absence of a relevant human dataset, we utilized the recently published single cell transcriptome of the early post implantation monkey embryo to discern the identity of BMP-treated hESCs. Our results suggest that BMP-treated hESCs are transcriptionally more similar to amnion cells than trophectoderm cells in the monkey embryo. Together with prior studies, this result indicates that hESCs possess a unique ability to form mature trophectoderm subtypes via an amnion-like transcriptional state.
Simulation of sugar kelp (Saccharina latissima) breeding guided by practices to prioritize accelerated research gains
Authors: Huang Mao , Robbins Kelly R , Li Yaoguang , Umanzor Schery , Marty-Rivera Michael , Bailey David , Yarish Charles , Lindell Scott , Jannink Jean-Luc 
Published: January 2021

AbstractThe domestication process of sugar kelp in the Northeast U.S. was initiated by selective breeding two years ago. In this study, we will demonstrate how obstacles for accelerated genetic gain can be assessed using simulation approaches that inform resource allocation decisions in our research. Thus far, we have used 140 wild sporophytes (SPs) that were sampled from the northern Gulf of Maine (GOM) to southern New England (SNE). From these SPs, we sampled gametophytes (GPs) and made and evaluated over 600 progeny SPs from crosses among the GPs. The biphasic life cycle of kelp gives a great advantage in selective breeding as we can potentially select both on the SPs and GPs. However, several obstacles exist, such as the amount of time it takes to complete a breeding cycle, the number of GPs that can be maintained in the lab, and whether positive selection can be conducted on farm tested SPs. Using the GOM population characteristics for heritability and effective population size, we simulated a founder population of 1000 individuals and evaluated the impact of overcoming these obstacles on genetic gain. Our results showed that key factors to improve current genetic gain rely mainly on our ability to induce reproduction of the best farm-tested SPs, and to accelerate the clonal vegetative growth of released GPs so that enough GP biomass is ready for making crosses by the next growing season. Overcoming these challenges could improve rates of genetic gain more than two-fold. Future research should focus on conditions favorable for inducing spring and early summer reproduction, and increasing the amount of GP tissue available in time to make fall crosses.
CloudBrain: Online neural computation in the cloud
Authors: Larsen Leon Bonde , Karnøe Stagsted Rasmus , Strohmer Beck , Christensen Anders Lyhne 
Published: January 2021

AbstractNeuromorphic computing currently relies heavily on complicated hardware design to implement asynchronous, parallel and very large-scale brain simulations. This dependency slows down the migration of biological insights into technology. It typically takes several years from idea to finished hardware and once developed the hardware is not broadly available to the community. In this contribution, we present the CloudBrain research platform, an alternative based on modern cloud computing and event stream processing technology. Typical neuromorphic design goals, such as small form factor and low power consumption, are traded for 1) no constraints on the model elements, 2) access to all events and parameters during and after the simulation, 3) online reconfiguration of the network, and 4) real-time simulation. We explain principles for how neuron, synapse and network models can be implemented and we demonstrate that our implementation can be used to control a physical robot in real-time. CloudBrain is open source and can run on commodity hardware or in the cloud, thus providing the community a new platform with a different set of features supporting research into, for example, neuron models, structural plasticity and three-factor learning.
Mechanisms of far-red light-mediated dampening of defense againstBotrytis cinereain tomato leaves
Authors: Courbier Sarah , Snoek Basten L. , Kajala Kaisa , Van Wees Saskia C.M. , Pierik Ronald 
Published: January 2021

AbstractPlants detect neighboring competitors through a decrease in the ratio between red and far-red light (R:FR). This decreased R:FR is perceived by phytochrome photoreceptors and triggers shade avoidance responses such as shoot elongation and upward leaf movement (hyponasty). In addition to promoting elongation growth, low R:FR perception enhances plant susceptibility to pathogens: the growth-defense trade-off. Although increased susceptibility in low R:FR has been studied for over a decade, the associated timing of molecular events is still unknown. Here, we studied the chronology of FR-induced susceptibility events in tomato plants pre-exposed to either white light (WL) or WL supplemented with FR light (WL+FR) prior to inoculation with the necrotrophic fungusBotrytis cinerea(B.c.). We monitored the leaf transcriptional changes over a 30-hr time course upon infection and followed up with functional studies to identify mechanisms. We found that FR-induced susceptibility in tomato is linked to a general dampening ofB.c.-responsive gene expression, and a delay in both pathogen recognition and jasmonic acid-mediated defense gene expression. In addition, we found that the supplemental FR-induced ethylene emissions affect plant immune responses under WL+FR conditions. This study increases our understanding of the growth-immunity trade-off, while simultaneously providing leads to improve tomato resistance against pathogens in dense cropping systems.One-sentence summaryLow Red:Far-red ratio enhances tomato susceptibility towards the necrotrophic fungusBotrytis cinereavia delayed early pathogen detection and dampening of jasmonic acid-mediated defense activation.
A structural basis for inhibition of the complement initiator protease C1r by Lyme disease spirochetes
Authors: Garrigues Ryan J. , Powell Pierce Alexandra D. , Hammel Michal , Skare Jon T. , Garcia Brandon L. 
Published: January 2021

AbstractComplement evasion is a hallmark of extracellular microbial pathogens such asBorreliella burgdorferi, the causative agent of Lyme disease. Lyme disease spirochetes express nearly a dozen outer surface lipoproteins that bind complement components and interfere with their native activities. Among these, BBK32 is unique in its selective inhibition of the classical pathway. BBK32 blocks activation of this pathway by selectively binding and inhibiting the C1r serine protease of first component of complement, C1. To understand the structural basis for BBK32-mediated C1r inhibition, we performed co-crystallography and size exclusion chromatography-coupled small angle x-ray scattering experiments, which revealed a molecular model of BBK32-C in complex with activated human C1r. Structure-guided site-directed mutagenesis was combined with surface plasmon resonance binding experiments and assays of complement function to validate the predicted molecular interface. The studies reported here, for the first time, provide a structural basis for classical pathway-specific inhibition by a human pathogen.
Rapid Identification of Water‐Conducting Fractures Using a Trace Methane Gas Measurement
Authors: Niwa Ph.D Masakazu , Amano Ph.D Kenji , Takeuchi Ph.D Ryuji , Shimada Ph.D Koji 
Published: January 2021

AbstractIdentification of water‐conducting fractures is important for the safety assessment of underground projects in crystalline rocks at geological disposal sites. We applied a portable methane gas analyzer by wavelength‐scanned cavity ring‐down spectroscopy to detect the water‐conducting fractures in the underground tunnel of the Mizunami Underground Research Laboratory, central Japan. The tunnel is excavated in granite with CH4‐rich groundwater. Two approaches were taken to obtain the profile of CH4 concentration along the gallery walls: (1) “Scan by walking” at the speed of 0.5 m/s and (2) monitoring for 30 s at 0.5 or 1 m intervals. In the Scan by walking approach, the peaks of the CH4 concentration corresponded well with the occurrence of high water flow rate fractures. Thus, this method is useful for rapid identification of major water‐conducting fractures. Monitoring at constant intervals takes more time than the Scan by walking approach; however, this method can largely detect occurrences of fractures with low fluid fluxes.
Exploring the effects of for‐profit and nonprofit size congruency: An exchange perspective on cause‐related marketing
Authors: Hamby Anne , Jones Niusha , Yu Guohong 
Published: January 2021

AbstractPrior research on cause‐related marketing (CM) shows that congruencies between for‐profit and nonprofit organizational missions and target markets affect consumers' perceptions of the partnership fit, and their subsequent response to CM promotions. The current work explores how congruencies between for‐profit and nonprofit sizes influence consumers' perceptions of the partnership fit, and subsequently, their attitudes toward CM efforts. Study 1 shows that consumers perceive a low degree of organizational partnership fit between a small for‐profit and large nonprofit (relative to other partnership configurations). Study 2 shows the nature of donated resources can affect organizational partnership fit perceptions, such that donations of needed goods (vs. money) can improve consumers' perceptions of partnership fit between a small for‐profit and large nonprofit. Study 3 shows that organizational cause congruency and organizational size both independently contribute to perceptions of organizational partnership fit.
Five decades of the Journal of Consumer Affairs: A bibliometric analysis
Authors: Baker H. Kent , Kumar Satish , Pandey Nitesh 
Published: January 2021

AbstractThis study presents a retrospective of the Journal of Consumer Affairs (JCA) using bibliographic analysis between 1967 and 2019. The results indicate that both the number of JCA's publications and citations grew markedly over time. The dominant contributors to the journal are authors affiliated with U.S. institutions. Trends show increasing organizational diversity and collaboration among authors. The journal's central themes are consumer perception, consumer behavior, financial behavior, consumer spending patterns, financial literacy, consumer decision‐making processes, and marketing practices. Statistically significant relationships exist between the following article attributes and citations based on our negative binomial regression analysis. Age has a negative association with citations, but the direction of association turns positive when considering non‐linearity. A positive association exists between the number of authors, references, and U.S. affiliation. A negative relationship exists with article order, non‐academic author, top institution affiliation (FT100), funding, lead article, title length, and conceptual article.
Inhibition of persimmon tannin extract on guinea pig skin pigmentation
Authors: Sun Wanting , Chen Xuanhong , Nan Xijun , Zhang Jun , Dong Leichao , Ji Wei , Sheng Guihua , Zhou Quancheng 
Published: January 2021

AbstractBackgroundIn daily life, excessive exposure to ultraviolet light can lead to pigmentation.AimsThis study is to determine the mechanism of persimmon tannin extract in inhibiting pigmentation, to investigate whether the effect of persimmon tannin extract is superior to that of arbutin, and to detect the optimal concentration.MethodsIn this study, the guinea pig pigmentation model was established by ultraviolet B (UVB) irradiation. With arbutin as a positive control, Masson‐Fontana silver staining was used to observe the effects of persimmon tannin extract on melanin distribution in guinea pigs' skin tissue. Then, the tyrosinase activity was measured, and an Enzyme‐linked immunosorbent assay was used to investigate the contents of antioxidant enzymes, inflammatory factors, and signaling pathway inhibitors in guinea pigs' skin tissue.ResultsThe results showed that compared with the model group, superoxide dismutase, catalase, glutathione peroxidase, DKK1 content of Wnt/‐catenin signaling pathway inhibitors levels, and inhibitory tyrosinase activity were increased by 24.3%, 33.3%, 59.3%, 36.81%, and 17.16%, respectively. Meanwhile, the interleukin‐6 and interleukin‐8 expression were reduced by approximately 22.2% and 54%. The results also showed that persimmon tannin extract could significantly reduce melanin density. The differences in experimental results were statistically significant (P < .01).ConclusionsCompared with the arbutin group, the medium‐dose group (persimmon tannin extract of 20%) had a more significant effect on inhibiting pigmentation. Persimmon tannin could serve as a promising agent for preventing skin pigmentation. It is expected to provide ideas for the development of deep‐processed persimmon products related to functional foods and cosmetics.
Effects of dietary cellobiose on the intestinal microbiota and excretion of nitrogen metabolites in healthy adult dogs
Authors: Paßlack Nadine , Kohn Barbara , Vahjen Wilfried , Zentek Jürgen 
Published: January 2021

AbstractIn order to evaluate the potential prebiotic effects of cellobiose, 10 healthy adult research beagle dogs received a complete diet containing 0, 0.5 and 1 g cellobiose/kg bodyweight (BW)/day. At the end of each feeding period, faeces, urine and blood of the dogs were collected. The results demonstrated a significant increase of faecal lactate concentrations, indicating a bacterial fermentation of cellobiose in the canine intestine. Along with this, a dose‐dependent linear increase of the relative abundance of Lactobacillaceae in the faeces of the dogs was observed (p = 0.014). In addition, a dose‐dependent increase (p < 0.05) of Alloprevotella, Bacteroides and Prevotella, and a linear decrease for unidentified Lachnospiraceae (p = 0.011) was observed when cellobiose was added to the diet, although the relative abundance of these genera was low (<1%) among all groups. The faecal pH was not affected by dietary cellobiose. Cellobiose seemed to modulate the excretion of nitrogen metabolites, as lower concentrations of phenol (p = 0.034) and 4‐ethylphenol (p = 0.002) in the plasma of the dogs were measured during the supplementation periods. Urinary phenols and indoles, however, were not affected by the dietary supplementation of cellobiose. In conclusion, cellobiose seems to be fermented by the intestinal microbiota of dogs. Although no effect on the faecal pH was detected, the observed increase of microbial lactate production might lower the pH in the large intestine and consecutively modulate the intestinal absorption of nitrogen metabolites. Also, the observed changes of some bacterial genera might have been mediated by increased intestinal lactate concentrations or a higher relative abundance of lactobacilli. Whether these results could be considered as a prebiotic effect and used as a dietetic strategy in diseased animals to improve gut function or hepatic and renal nitrogen metabolism should be evaluated in future studies.
Evaluation of origanum oil, hydrolysable tannins and tea saponin in mitigating ruminant methane: In vitro and in vivo methods
Authors: Zhang Fangyu , Li Baihao , Ban Zhibin , Liang Hao , Li Lijia , Zhao Wei , Yan Xiaogang 
Published: January 2021

AbstractThe objective of this study was to investigate the effects of origanum oil (ORO), hydrolysable tannins (HYT) and tea saponin (TES) on methane (CH4) emission, rumen fermentation, productive performance and gas exchange in sheep by using in vitro and in vivo methods. The ORO, HYT and TES additive levels were normalized per kg dry matter (DM) in both in vitro and in vivo experiments: ORO‐0, 10, 20 and 40 ml/kg; HYT‐0, 15, 30 and 60 g/kg; and TES‐0, 15, 30 and 60 g/kg, respectively. During in vitro incubation, 40 ml/kg ORO linearly decreased CH4 emission (p < 0.05); 20 and 40 ml/kg ORO cubically decreased carbon dioxide (CO2) production (p < 0.05), and rumen pH was cubically raised with the increasing ORO additive level (p < 0.01). The 60 g/kg HYT cubically decreased CH4 production (p < 0.05). The pH of 60 g/kg HYT was higher than that of 15 and 30 g/kg (p < 0.01); the pH of 20 g/kg TES was higher than that of 5 g/kg (p < 0.05). In the in vivo experiments, 40 ml/kg ORO inhibited dry matter intake (p < 0.01) cubically and reduced average daily gain (ADG) and feed conversion ratio (FCR) cubically (p < 0.05), and 20 or 40 ml/kg ORO linearly decreased CH4 production based on per day or metabolic weight (W0.75) (p < 0.05). Both 30 and 60 g/kg HYT linearly inhibited CH4 emission on the bases of per day and W0.75 (p < 0.05). The 20 g/kg TES improved the apparent digestibility of crude protein (p < 0.05), 10 and 20 g/kg of TES decreased CH4 emission (p < 0.05), and 5 g/kg of TES reduced O2 consumption and CO2 production (p < 0.05). In conclusion, these three plant extracts all showed the abilities on mitigating CH4 emission of sheep with appropriate additive ranges.
Antibiofilm activity of chitosan/epsilon‐poly‐L‐lysine hydrogels in a porcine ex vivo skin wound polymicrobial biofilm model
Authors: Pati Brooke A. , Kurata Wendy E. , Horseman Timothy S. , Pierce Lisa M. 
Published: January 2021

AbstractAs antibiotic resistance continues to increase globally, there is an urgency for novel, non‐antibiotic approaches to control chronic drug‐resistant infections, particularly those associated with polymicrobial biofilm formation in chronic wounds. Also needed are clinically relevant polymicrobial biofilm models that can be utilized to assess the efficacy of innovative therapeutics against mature biofilms. We successfully developed a highly reproducible porcine ex vivo skin wound polymicrobial biofilm model using clinical isolates of multidrug‐resistant Pseudomonas aeruginosa, methicillin‐resistant Staphylococcus aureus, and Candida albicans. This ex vivo biofilm model was then used to assess the antimicrobial and antibiofilm properties of an easily fabricated chitosan hydrogel incorporating the natural antimicrobial peptide epsilon‐poly‐L‐lysine. Antimicrobial activity was evaluated against planktonic cultures in vitro and against mature biofilms ex vivo. The antibiofilm efficiency of the hydrogels was especially pronounced against Pseudomonas aeruginosa, whose counts were reduced by 99.98% after 2 hours in vitro and by 99.94% after treatment for 24 hours when applied to 24 hour ex vivo polymicrobial wound biofilms. The activity of the hydrogels was lower against Staphylococcus aureus and ineffective against Candida albicans. Gram, Hucker‐Twort staining of paraffin sections revealed balanced polymicrobial communities in mature 48 hour untreated biofilms. Treatment of 48 or 72 hour biofilms for 2 or 3 days with hydrogels that were applied within 5 hours after inoculation resulted in an impressive 96% and 97% reduction in biofilm thickness compared to untreated biofilms, respectively (P < .001). Likewise, topical gel treatment for 24 hours reduced biofilm thickness by 84% and 70%, respectively, when applied to mature biofilms at 24 and 48 hours after inoculation (P < .001). Thus, this ex vivo wound biofilm model provides a useful means to assess the efficacy of novel treatments to prevent and eradicate polymicrobial biofilms consisting of multidrug‐resistant Pseudomonas aeruginosa, methicillin‐resistant Staphylococcus aureus, and Candida albicans.