bluuebunny/crossref_metadata_2025_split huggingface dataset:
Cellular senescence contributes to radiation-induced hyposalivation by affecting the stem/progenitor cell niche
Authors: Peng Xiaohong , Wu Yi , Brouwer Uilke , van Vliet Thijmen , Wang Boshi , Demaria Marco , Barazzuol Lara , Coppes Rob P. 
Published: October 2020

AbstractRadiotherapy for head and neck cancer is associated with impairment of salivary gland function and consequent xerostomia, which has a devastating effect on the quality of life of the patients. The mechanism of radiation-induced salivary gland damage is not completely understood. Cellular senescence is a permanent state of cell cycle arrest accompanied by a secretory phenotype which contributes to inflammation and tissue deterioration. Genotoxic stresses, including radiation-induced DNA damage, are known to induce a senescence response. Here, we show that radiation induces cellular senescence preferentially in the salivary gland stem/progenitor cell niche of mouse models and patients. Similarly, salivary gland-derived organoids show increased expression of senescence markers and pro-inflammatory senescence-associated secretory phenotype (SASP) factors after radiation exposure. Clearance of senescent cells by selective removal of p16Ink4a-positive cells by the drug ganciclovir or the senolytic drug ABT263 lead to increased stem cell self-renewal capacity as measured by organoid formation efficiency. Additionally, pharmacological treatment with ABT263 in mice irradiated to the salivary glands mitigates tissue degeneration, thus preserving salivation. Our data suggest that senescence in the salivary gland stem/progenitor cell niche contributes to radiation-induced hyposalivation. Pharmacological targeting of senescent cells may represent a therapeutic strategy to prevent radiotherapy-induced xerostomia.
Photobase effect for just-in-time delivery in photocatalytic hydrogen generation
Authors: Fang Jiawen , Debnath Tushar , Bhattacharyya Santanu , Döblinger Markus , Feldmann Jochen , Stolarczyk Jacek K. 
Published: October 2020

AbstractCarbon dots (CDs) are a promising nanomaterial for photocatalytic applications. However, the mechanism of the photocatalytic processes remains the subject of a debate due to the complex internal structure of the CDs, comprising crystalline and molecular units embedded in an amorphous matrix, rendering the analysis of the charge and energy transfer pathways between the constituent parts very challenging. Here we propose that the photobasic effect, that is the abstraction of a proton from water upon excitation by light, facilitates the photoexcited electron transfer to the proton. We show that the controlled inclusion in CDs of a model photobase, acridine, resembling the molecular moieties found in photocatalytically active CDs, strongly increases hydrogen generation. Ultrafast spectroscopy measurements reveal proton transfer within 30 ps of the excitation. This way, we use a model system to show that the photobasic effect may be contributing to the photocatalytic H2 generation of carbon nanomaterials and suggest that it may be tuned to achieve further improvements. The study demonstrates the critical role of the understanding the dynamics of the CDs in the design of next generation photocatalysts.
A strategy to incorporate prior knowledge into correlation network cutoff selection
Authors: Benedetti Elisa , Pučić-Baković Maja , Keser Toma , Gerstner Nathalie , Büyüközkan Mustafa , Štambuk Tamara , Selman Maurice H. J. , Rudan Igor , Polašek Ozren , Hayward Caroline , Al-Amin Hassen , Suhre Karsten , Kastenmüller Gabi , Lauc Gordan , Krumsiek Jan 
Published: October 2020

AbstractCorrelation networks are frequently used to statistically extract biological interactions between omics markers. Network edge selection is typically based on the statistical significance of the correlation coefficients. This procedure, however, is not guaranteed to capture biological mechanisms. We here propose an alternative approach for network reconstruction: a cutoff selection algorithm that maximizes the overlap of the inferred network with available prior knowledge. We first evaluate the approach on IgG glycomics data, for which the biochemical pathway is known and well-characterized. Importantly, even in the case of incomplete or incorrect prior knowledge, the optimal network is close to the true optimum. We then demonstrate the generalizability of the approach with applications to untargeted metabolomics and transcriptomics data. For the transcriptomics case, we demonstrate that the optimized network is superior to statistical networks in systematically retrieving interactions that were not included in the biological reference used for optimization.
Plant species determine tidal wetland methane response to sea level rise
Authors: Mueller Peter , Mozdzer Thomas J. , Langley J. Adam , Aoki Lillian R. , Noyce Genevieve L. , Megonigal J. Patrick 
Published: October 2020

AbstractBlue carbon (C) ecosystems are among the most effective C sinks of the biosphere, but methane (CH4) emissions can offset their climate cooling effect. Drivers of CH4 emissions from blue C ecosystems and effects of global change are poorly understood. Here we test for the effects of sea level rise (SLR) and its interactions with elevated atmospheric CO2, eutrophication, and plant community composition on CH4 emissions from an estuarine tidal wetland. Changes in CH4 emissions with SLR are primarily mediated by shifts in plant community composition and associated plant traits that determine both the direction and magnitude of SLR effects on CH4 emissions. We furthermore show strong stimulation of CH4 emissions by elevated atmospheric CO2, whereas effects of eutrophication are not significant. Overall, our findings demonstrate a high sensitivity of CH4 emissions to global change with important implications for modeling greenhouse-gas dynamics of blue C ecosystems.
Self-reliance crowds out group cooperation and increases wealth inequality
Authors: Gross Jörg , Veistola Sonja , De Dreu Carsten K. W. , Van Dijk Eric 
Published: October 2020

AbstractHumans establish public goods to provide for shared needs like safety or healthcare. Yet, public goods rely on cooperation which can break down because of free-riding incentives. Previous research extensively investigated how groups solve this free-rider problem but ignored another challenge to public goods provision. Namely, some individuals do not need public goods to solve the problems they share with others. We investigate how such self-reliance influences cooperation by confronting groups in a laboratory experiment with a safety problem that could be solved either cooperatively or individually. We show that self-reliance leads to a decline in cooperation. Moreover, asymmetries in self-reliance undermine social welfare and increase wealth inequality between group members. Less dependent group members often choose to solve the shared problem individually, while more dependent members frequently fail to solve the problem, leaving them increasingly poor. While self-reliance circumvents the free-rider problem, it complicates the governing of the commons.
Rationally designed transition metal hydroxide nanosheet arrays on graphene for artificial CO2 reduction
Authors: Lu Kang-Qiang , Li Yue-Hua , Zhang Fan , Qi Ming-Yu , Chen Xue , Tang Zi-Rong , Yamada Yoichi M. A. , Anpo Masakazu , Conte Marco , Xu Yi-Jun 
Published: October 2020

AbstractThe performance of transition metal hydroxides, as cocatalysts for CO2 photoreduction, is significantly limited by their inherent weaknesses of poor conductivity and stacked structure. Herein, we report the rational assembly of a series of transition metal hydroxides on graphene to act as a cocatalyst ensemble for efficient CO2 photoreduction. In particular, with the Ru-dye as visible light photosensitizer, hierarchical Ni(OH)2 nanosheet arrays-graphene (Ni(OH)2-GR) composites exhibit superior photoactivity and selectivity, which remarkably surpass other counterparts and most of analogous hybrid photocatalyst system. The origin of such superior performance of Ni(OH)2-GR is attributed to its appropriate synergy on the enhanced adsorption of CO2, increased active sites for CO2 reduction and improved charge carriers separation/transfer. This work is anticipated to spur rationally designing efficient earth-abundant transition metal hydroxides-based cocatalysts on graphene and other two-dimension platforms for artificial reduction of CO2 to solar chemicals and fuels.
Fermentative production of Vitamin E tocotrienols in Saccharomyces cerevisiae under cold-shock-triggered temperature control
Authors: Shen Bin , Zhou Pingping , Jiao Xue , Yao Zhen , Ye Lidan , Yu Hongwei 
Published: October 2020

AbstractThe diverse physiological functions of tocotrienols have listed them as valuable supplementations to α-tocopherol-dominated Vitamin E products. To make tocotrienols more readily available, tocotrienols-producing S. cerevisiae has been constructed by combining the heterologous genes from photosynthetic organisms with the endogenous shikimate pathway and mevalonate pathway. After identification and elimination of metabolic bottlenecks and enhancement of precursors supply, the engineered yeast can produce tocotrienols at yield of up to 7.6 mg/g dry cell weight (DCW). In particular, proper truncation of the N-terminal transit peptide from the plant-sourced enzymes is crucial. To further solve the conflict between cell growth and tocotrienols accumulation so as to enable high-density fermentation, a cold-shock-triggered temperature control system is designed for efficient control of two-stage fermentation, leading to production of 320 mg/L tocotrienols. The success in high-density fermentation of tocotrienols by engineered yeast sheds light on the potential of fermentative production of vitamin E tocochromanols.
Fungal oxylipins direct programmed developmental switches in filamentous fungi
Authors: Niu Mengyao , Steffan Breanne N. , Fischer Gregory J. , Venkatesh Nandhitha , Raffa Nicholas L. , Wettstein Molly A. , Bok Jin Woo , Greco Claudio , Zhao Can , Berthier Erwin , Oliw Ernst , Beebe David , Bromley Michael , Keller Nancy P. 
Published: October 2020

AbstractFilamentous fungi differentiate along complex developmental programs directed by abiotic and biotic signals. Currently, intrinsic signals that govern fungal development remain largely unknown. Here we show that an endogenously produced and secreted fungal oxylipin, 5,8-diHODE, induces fungal cellular differentiation, including lateral branching in pathogenic Aspergillus fumigatus and Aspergillus flavus, and appressorium formation in the rice blast pathogen Magnaporthe grisea. The Aspergillus branching response is specific to a subset of oxylipins and is signaled through G-protein coupled receptors. RNA-Seq profiling shows differential expression of many transcription factors in response to 5,8-diHODE. Screening of null mutants of 33 of those transcription factors identifies three transcriptional regulators that appear to mediate the Aspergillus branching response; one of the mutants is locked in a hypo-branching phenotype, while the other two mutants display a hyper-branching phenotype. Our work reveals an endogenous signal that triggers crucial developmental processes in filamentous fungi, and opens new avenues for research on the morphogenesis of filamentous fungi.
Topological analysis reveals state transitions in human gut and marine bacterial communities
Authors: Chang William K. , VanInsberghe David , Kelly Libusha 
Published: October 2020

AbstractMicrobiome dynamics influence the health and functioning of human physiology and the environment and are driven in part by interactions between large numbers of microbial taxa, making large-scale prediction and modeling a challenge. Here, using topological data analysis, we identify states and dynamical features relevant to macroscopic processes. We show that gut disease processes and marine geochemical events are associated with transitions between community states, defined as topological features of the data density. We find a reproducible two-state succession during recovery from cholera in the gut microbiomes of multiple patients, evidence of dynamic stability in the gut microbiome of a healthy human after experiencing diarrhea during travel, and periodic state transitions in a marine Prochlorococcus community driven by water column cycling. Our approach bridges small-scale fluctuations in microbiome composition and large-scale changes in phenotype without details of underlying mechanisms, and provides an assessment of microbiome stability and its relation to human and environmental health.
Dynamic disorder phonon scattering mediated by Cu atomic hopping and diffusion in Cu3SbSe3
Authors: Wang Chen , Wu Yixuan , Pei Yanzhong , Chen Yue 
Published: October 2020

AbstractCu3SbSe3 that exhibits distinct liquid-like sublattice due to the heterogeneous bonding environment has emerged as a promising low cost superionic semiconductor with intrinsic ultralow thermal conductivity. However, the relationship between atomic dynamics resulting in liquid-like diffusion and anomalous phonon transport properties remains poorly understood. Herein, combing ab initio molecular dynamics with temperature-dependent Raman measurements, we have performed a thorough investigation on the lattice dynamics of Cu3SbSe3. Superionic transition is unveiled for both structurally inequivalent Cu atoms at elevated temperatures, while the Se-formed tetrahedral framework can simultaneously maintain. An intermediate state of Cu3SbSe3 through the mixture of quasi-1D/2D Cu nearest-neighbor vacancy hopping is discovered below the superionic transition temperature. Our results also manifest that phonons predominately involved with Cu contributions along diffusion channels have been strongly scattered during the superionic transition, whereas the liquid-like diffusion of Cu is too slow to completely breakdown the propagation of all transverse phonon modes. The insight provided by this work into the atomic dynamics and phonon scattering relationship may pave the way for further phonon engineering of Cu3SbSe3 and related superionic materials.
Subthalamic deep brain stimulation improves sleep and excessive sweating in Parkinson’s disease
Authors: Bjerknes Silje , Skogseid Inger Marie , Hauge Tuva Jin , Dietrichs Espen , Toft Mathias 
Published: October 2020

AbstractParkinson’s disease (PD) is a complex multisystem disorder with motor and non-motor symptoms (NMS). NMS may have an even greater impact on quality of life than motor symptoms. Subthalamic nucleus deep brain stimulation (STN-DBS) has been shown to improve motor fluctuations and quality of life, whereas the effects on different NMS have been less examined. Sleep disturbances and autonomic dysfunction are among the most prevalent NMS. We here report the efficacy of STN-DBS on sleep disturbances and autonomic dysfunction. In the parent trial, 60 patients were included in a single-center randomized prospective study, with MDS-UPDRS III and PDQ-39 as primary endpoints at 12 months of STN-DBS. Preplanned assessments at baseline and postoperatively at 3 and 12 months also included Parkinson’s Disease Sleep Scale (PDSS); Scopa-Aut; and MDS-UPDRS I, II, and IV. We found that STN-DBS had a significant and lasting positive effect on overall sleep quality, nocturnal motor symptoms and restlessness, and daytime dozing. Several aspects of autonomic dysfunction were also improved at 3 months postoperatively, although at 12 months only thermoregulation (sudomotor symptoms) remained significantly improved. We could not identify preoperative factors that predicted improvement in PDSS or Scopa-Aut. There was a close relationship between improved autonomic symptoms and improved quality of life after 1 year. NMS and especially sleep and autonomic dysfunction deserve more focus to improve patient outcomes further.
Engineering a fidelity-variant live-attenuated vaccine for chikungunya virus
Authors: Weiss Christopher M. , Liu Hongwei , Riemersma Kasen K. , Ball Erin E. , Coffey Lark L. 
Published: October 2020

AbstractChikungunya virus (CHIKV), which causes a febrile illness characterized by severe and prolonged polyarthralgia/polyarthritis, is responsible for a global disease burden of millions of cases each year with autochthonous transmission in over 100 countries and territories worldwide. There is currently no approved treatment or vaccine for CHIKV. One live-attenuated vaccine (LAV) developed by the United States Army progressed to Phase II human clinical trials but was withdrawn when 8% of volunteers developed joint pain associated with vaccination. Attenuation of the Army’s CHIKV LAV strain 181 clone 25 (CHIKV-181/25) relies on two mutations in the envelope 2 (E2) glycoprotein responsible for cell binding and entry, making it particularly prone to reversion, a common concern for replication-competent vaccines. High error rates associated with RNA virus replication have posed a challenge for LAV development where stable incorporation of attenuating elements is necessary for establishing safety in pre-clinical models. Herein, we incorporate two replicase mutations into CHIKV-181/25 which modulate CHIKV replication fidelity combined with additional attenuating features that cannot be eliminated by point mutation. The mutations were stably incorporated in the LAV and did not increase virulence in mice. Two fidelity-variant CHIKV LAVs generated neutralizing antibodies and were protective from CHIKV disease in adult mice. Unexpectedly, our fidelity-variant candidates were more mutable than CHIKV-181/25 and exhibited restricted replication in mice and Aedes mosquitoes, a possible consequence of hypermutation. Our data demonstrate safety and efficacy but highlight a further need to evaluate fidelity-altering phenotypes before use as a LAV given the potential for virulent reversion.
In vivo estrogenicity of p-phenoxyphenol and p-pentyloxyphenol
Authors: Wang Yue , Xiao Han , Yang Lei , Jia Xiaojing , Guo Xuan , Zhang Zhaobin 
Published: October 2020

Abstractp-Alkoxyphenols (AOPs) are a class of ethers that are widely used in industrial and agricultural productions and daily necessities.p-Phenoxyphenol (PhOP) andp-pentyloxyphenol (PeOP) belong to this class and have been reported to be estrogenic in vitro. However, their in vivo estrogenic activities have rarely been of concern. In this study, we performed an immature mouse uterotrophic assay and studied the estrogenic effects of these two compounds in mice. The results revealed that the uterine weights of the animals treated with PhOP significantly increased at doses of 30 and 300 mg kg-1bw day-1for 3 days (P < 0.05), while no significant uterotrophic effects were observed in the mice treated with PeOP. Using next-generation transcriptome sequencing (RNA-seq), we also analyzed the gene expression in the uterine tissue of mice treated with PhOP and PeOP. The observed gene regulation patterns of the PhOP- and PeOP-treated specimens were similar to those of the 17β-estradiol (E2)-treated specimens. In particular, some estrogen-responsive genes, such as theSprr2gene family,Apoa1,Prap1, andAhsg, displayed a regulation trend similar to that of E2. In addition, molecule docking analysis revealed that both PhOP and PeOP could be well docked into the active site of hERα, with potential of mean force (PMF) values of − 58.68 and − 52.67 kcal mol-1for PhOP and PeOP, respectively. The results of this study indicate that PhOP exhibits relatively strong in vivo estrogenic activity, which could be of future concern.
The comparative risk of acute kidney injury of vancomycin relative to other common antibiotics
Authors: Gaggl Martina , Pate Virginia , Stürmer Til , Kshirsagar Abhijit V. , Layton J. Bradley 
Published: October 2020

AbstractThe glycopeptide antibiotic vancomycin is a mainstay in the treatment of Gram-positive infection. While its association with acute kidney injury (AKI) has waxed and waned, recent data suggest nephrotoxicity, even as mono-therapy. Our study aimed to evaluate the 2-week risk of AKI after at least 3 days of intravenous vancomycin mono-therapy initiated within 5 days of hospitalization compared to other intravenous antibiotics used for similar indications. We used a new user-active comparator study design and identified patients with a first hospitalization during which they received vancomycin or comparator, from commercial claims based in the United States. We estimated incidence rates, hazard ratios using adjusted cox-regression models, and standardized mortality/morbidity ratio weighted cox-regression models. In the 32,997 patients vancomycin was used in 17% of patients and 129 cases of AKI were observed. Overall incidence of AKI was 9.3 (95% CI 0.78–1.22) per 100 person-years. The adjusted hazard ratio for vancomycin versus all other comparators was 0.74 (95% CI 0.45–1.21). Separate models for respective comparators resulted in hazard ratios below the null, except for vancomycin vs. cefazolin. Intravenous vancomycin mono-therapy does not increase the risk of AKI compared to other intravenous antibiotics used for similar indication in this cohort of hospitalized patients.
De novo transcriptome analysis of the critically endangered alpine Himalayan herb Nardostachys jatamansi reveals the biosynthesis pathway genes of tissue-specific secondary metabolites
Authors: Dhiman Nisha , Kumar Anil , Kumar Dinesh , Bhattacharya Amita 
Published: October 2020

AbstractThe study is the first report on de novo transcriptome analysis of Nardostachys jatamansi, a critically endangered medicinal plant of alpine Himalayas. Illumina GAIIx sequencing of plants collected during end of vegetative growth (August) yielded 48,411 unigenes. 74.45% of these were annotated using UNIPROT. GO enrichment analysis, KEGG pathways and PPI network indicated simultaneous utilization of leaf photosynthates for flowering, rhizome fortification, stress response and tissue-specific secondary metabolites biosynthesis. Among the secondary metabolite biosynthesis genes, terpenoids were predominant. UPLC-PDA analysis of in vitro plants revealed temperature-dependent, tissue-specific differential distribution of various phenolics. Thus, as compared to 25 °C, the phenolic contents of both leaves (gallic acid and rutin) and roots (p-coumaric acid and cinnamic acid) were higher at 15 °C. These phenolics accounted for the therapeutic properties reported in the plant. In qRT-PCR of in vitro plants, secondary metabolite biosynthesis pathway genes showed higher expression at 15 °C and 14 h/10 h photoperiod (conditions representing end of vegetative growth period). This provided cues for in vitro modulation of identified secondary metabolites. Such modulation of secondary metabolites in in vitro systems can eliminate the need for uprooting N. jatamansi from wild. Hence, the study is a step towards effective conservation of the plant.
Using a theory of mind to find best responses to memory-one strategies
Authors: Glynatsi Nikoleta E. , Knight Vincent A. 
Published: October 2020

AbstractMemory-one strategies are a set of Iterated Prisoner’s Dilemma strategies that have been praised for their mathematical tractability and performance against single opponents. This manuscript investigates best response memory-one strategies with a theory of mind for their opponents. The results add to the literature that has shown that extortionate play is not always optimal by showing that optimal play is often not extortionate. They also provide evidence that memory-one strategies suffer from their limited memory in multi agent interactions and can be out performed by optimised strategies with longer memory. We have developed a theory that has allowed to explore the entire space of memory-one strategies. The framework presented is suitable to study memory-one strategies in the Prisoner’s Dilemma, but also in evolutionary processes such as the Moran process. Furthermore, results on the stability of defection in populations of memory-one strategies are also obtained.