bluuebunny/crossref_metadata_2025_split huggingface dataset:
Duration of cold exposure defines the rate of reactivation of a perennial FLC orthologue via H3K27me3 accumulation
Authors: Nishio Haruki , Iwayama Koji , Kudoh Hiroshi 
Published: September 2020

AbstractVernalisation is the process in which long-term cold exposure makes plants competent to flower. In vernalisation of Arabidopsis thaliana, a floral repressor, AtFLC, undergoes epigenetic silencing. Although the silencing of AtFLC is maintained under warm conditions after a sufficient duration of cold, FLC orthologues are reactivated under the same conditions in perennial plants, such as A. halleri. In contrast to the abundant knowledge on cold requirements in AtFLC silencing, it has remained unknown how cold duration affects the reactivation of perennial FLC. Here, we analysed the dynamics of A. halleri FLC (AhgFLC) mRNA, H3K4me3, and H3K27me3 over 8 weeks and 14 weeks cold followed by warm conditions. We showed that the minimum levels of AhgFLC mRNA and H3K4me3 were similar between 8 and 14 weeks vernalisation; however, the maximum level of H3K27me3 was higher after 14 weeks than after 8 weeks vernalisation. Combined with mathematical modelling, we showed that H3K27me3 prevents a rapid increase in AhgFLC expression in response to warm temperatures after vernalisation, which controls AhgFT expression and the initiation of flowering. Thus, the duration of cold defines the rate of AhgFLC reactivation via the buffering function of H3K27me3 against temperature increase.
Collective dynamics of repeated inference in variational autoencoder rapidly find cluster structure
Authors: Nagano Yoshihiro , Karakida Ryo , Okada Masato 
Published: September 2020

AbstractDeep neural networks are good at extracting low-dimensional subspaces (latent spaces) that represent the essential features inside a high-dimensional dataset. Deep generative models represented by variational autoencoders (VAEs) can generate and infer high-quality datasets, such as images. In particular, VAEs can eliminate the noise contained in an image by repeating the mapping between latent and data space. To clarify the mechanism of such denoising, we numerically analyzed how the activity pattern of trained networks changes in the latent space during inference. We considered the time development of the activity pattern for specific data as one trajectory in the latent space and investigated the collective behavior of these inference trajectories for many data. Our study revealed that when a cluster structure exists in the dataset, the trajectory rapidly approaches the center of the cluster. This behavior was qualitatively consistent with the concept retrieval reported in associative memory models. Additionally, the larger the noise contained in the data, the closer the trajectory was to a more global cluster. It was demonstrated that by increasing the number of the latent variables, the trend of the approach a cluster center can be enhanced, and the generalization ability of the VAE can be improved.
Malpighamoeba infection compromises fluid secretion and P-glycoprotein detoxification in Malpighian tubules
Authors: Rossi Marta , Ott Swidbert R. , Niven Jeremy E. 
Published: September 2020

AbstractMalpighian tubules, analogous to vertebrate nephrons, play a key role in insect osmoregulation and detoxification. Tubules can become infected with a protozoan, Malpighamoeba, which damages their epithelial cells, potentially compromising their function. Here we used a modified Ramsay assay to quantify the impact of Malpighamoeba infection on fluid secretion and P-glycoprotein-dependent detoxification by desert locust Malpighian tubules. Infected tubules have a greater surface area and a higher fluid secretion rate than uninfected tubules. Infection also impairs P-glycoprotein-dependent detoxification by reducing the net rhodamine extrusion per surface area. However, due to the increased surface area and fluid secretion rate, infected tubules have similar total net extrusion per tubule to uninfected tubules. Increased fluid secretion rate of infected tubules likely exposes locusts to greater water stress and increased energy costs. Coupled with reduced efficiency of P-glycoprotein detoxification per surface area, Malpighamoeba infection is likely to reduce insect survival in natural environments.
Re-establishment of the epigenetic state and rescue of kinome deregulation in Ts65Dn mice upon treatment with green tea extract and environmental enrichment
Authors: De Toma I. , Ortega M. , Catuara-Solarz S. , Sierra C. , Sabidó E. , Dierssen M. 
Published: September 2020

AbstractDown syndrome (DS) is the main genetic cause of intellectual disability due to triplication of human chromosome 21 (HSA21). Although there is no treatment for intellectual disability, environmental enrichment (EE) and the administration of green tea extracts containing epigallocatechin-3-gallate (EGCG) improve cognition in mouse models and individuals with DS. Using proteome, and phosphoproteome analysis in the hippocampi of a DS mouse model (Ts65Dn), we investigated the possible mechanisms underlying the effects of green tea extracts, EE and their combination. Our results revealed disturbances in cognitive-related (synaptic proteins, neuronal projection, neuron development, microtubule), GTPase/kinase activity and chromatin proteins. Green tea extracts, EE, and their combination restored more than 70% of the phosphoprotein deregulation in Ts65Dn, and induced possible compensatory effects. Our downstream analyses indicate that re-establishment of a proper epigenetic state and rescue of the kinome deregulation may contribute to the cognitive rescue induced by green tea extracts.
Quantifying machine influence over human forecasters
Authors: Abeliuk Andrés , Benjamin Daniel M. , Morstatter Fred , Galstyan Aram 
Published: September 2020

AbstractCrowdsourcing human forecasts and machine learning models each show promise in predicting future geopolitical outcomes. Crowdsourcing increases accuracy by pooling knowledge, which mitigates individual errors. On the other hand, advances in machine learning have led to machine models that increase accuracy due to their ability to parameterize and adapt to changing environments. To capitalize on the unique advantages of each method, recent efforts have shown improvements by “hybridizing” forecasts—pairing human forecasters with machine models. This study analyzes the effectiveness of such a hybrid system. In a perfect world, independent reasoning by the forecasters combined with the analytic capabilities of the machine models should complement each other to arrive at an ultimately more accurate forecast. However, well-documented biases describe how humans often mistrust and under-utilize such models in their forecasts. In this work, we present a model that can be used to estimate the trust that humans assign to a machine. We use forecasts made in the absence of machine models as prior beliefs to quantify the weights placed on the models. Our model can be used to uncover other aspects of forecasters’ decision-making processes. We find that forecasters trust the model rarely, in a pattern that suggests they treat machine models similarly to expert advisors, but only the best forecasters trust the models when they can be expected to perform well. We also find that forecasters tend to choose models that conform to their prior beliefs as opposed to anchoring on the model forecast. Our results suggest machine models can improve the judgment of a human pool but highlight the importance of accounting for trust and cognitive biases involved in the human judgment process.
Early prophylaxis of central venous catheter-related thrombosis using 1% chlorhexidine gluconate and chlorhexidine-gel-impregnated dressings: a retrospective cohort study
Authors: Yamashita Tomoko , Takamori Ayako , Nakagawachi Akira , Tanigawa Yoshinori , Hamada Yohei , Aoki Yosuke , Sakaguchi Yoshiro 
Published: September 2020

AbstractTo determine the prophylactic effect of using combined 1% alcoholic chlorhexidine gluconate and chlorhexidine gel-impregnated dressings (CGCD) on catheter-related thrombosis (CRT) in critically ill patients. This retrospective cohort study was performed in an intensive care unit from November 2009 to August 2014. The CRT incidence diagnosed with ultrasound examination was compared between patients applying CGCD and combined 10% aqueous povidone-iodine and standard transparent dressings (PITD) after central venous catheter insertion into the internal jugular vein for ≥ 48 h. CRT was stratified into early (within 7 days) and late (days 8–14) thromboses. Multivariate analyses using logistic regression models clarified the relationships between early- and late-CRT risks and skin antiseptic and catheter site dressing combinations. CRT occurred in 74 of 134 patients (55%), including 52 with early CRT and 22 with late CRT. Patients receiving CGCD had a significantly lower incidence of early CRT than those receiving PITD (odds ratio = 0.18; 95% confidence interval = 0.07–0.45, p  < .001). No significant association was evident between using CGCD and late CRT (p  = .514). Compared to PITD, CGCD reduced the CRT risk over 7 days in critically ill patients.UMIN Clinical Trials Registry: UMIN000037492.
Systematic experimental investigation of the obstacle effect during non-competitive and extremely competitive evacuations
Authors: Feliciani Claudio , Zuriguel Iker , Garcimartín Angel , Maza Diego , Nishinari Katsuhiro 
Published: September 2020

AbstractAlthough some experimental evidence showed that an obstacle placed in front of a door allows making people’s evacuations faster, the efficacy of such a solution has been debated for over 15 years. Researchers are split between those who found the obstacle beneficial and those who could not find a significant difference without it. One of the reasons for the several conclusions lies in the variety of the experiments performed so far, both in terms of competitiveness among participants, geometrical configuration and number of participants. In this work, two unique datasets relative to evacuations with/without obstacle and comprising low and high competitiveness are analyzed using state-of-the-art definitions for crowd dynamics. In particular, the so-called congestion level is employed to measure the smoothness of collective motion. Results for extreme conditions show that, on the overall, the obstacle does not reduce density and congestion level and it could rather slightly increase it. From this perspective, the obstacle was found simply shifting the dangerous spots from the area in front of the exit to the regions between the obstacle and the wall. On the other side, it was however confirmed, that the obstacle can stabilize longitudinal crowd waves, thus reducing the risk of trampling, which could be as important (in terms of safety) as improving the evacuation time. However, under urgent, competitive, but non-extreme conditions, the obstacle generally had a positive effect, helping channeling the flow of pedestrians through the exit while facilitating their interactions.
Giant controllable gigahertz to terahertz nonlinearities in superlattices
Authors: Pereira M. F. , Anfertev V. , Shevchenko Y. , Vaks V. 
Published: September 2020

AbstractOptical nonlinearities are of perpetual importance, notably connected with emerging new materials. However, they are difficult to exploit in the gigahertz–terahertz (GHz–THz) range at room temperature and using low excitation power. Here, we present a clear-cut theoretical and experimental demonstration of real time, low power, room temperature control of GHz–THz nonlinearities. The nonlinear susceptibility concept, successful in most materials, cannot be used here and we show in contrast, a complex interplay between applied powers, voltages and asymmetric current flow, delivering giant control and enhancement of the nonlinearities. Semiconductor superlattices are used as nonlinear sources and as mixers for heterodyne detection, unlocking their dual potential as compact, room temperature, controllable sources and detectors. The low input powers and voltages applied are within the range of compact devices, enabling the practical extension of nonlinear optics concepts to the GHz–THz range, under controlled conditions and following a predictive design tool.
Identification of hybridization and introgression between Cinnamomum kanehirae Hayata and C. camphora (L.) Presl using genotyping-by-sequencing
Authors: Wu Chia-Chen , Chang Shu-Hwa , Tung Chih-Wei , Ho Cheng-Kuen , Gogorcena Yolanda , Chu Fang-Hua 
Published: September 2020

AbstractCinnamomum kanehirae Hayata and C. camphora (L.) Presl are important tree species in eastern Asia. The wood of C. kanehirae is in increasing demand for culturing Antrodia cinnamomea, a medicinal fungus that naturally grows inside the trunk of C. kanehirae. Putative hybrids between C. kanehirae and C. camphora were previously reported but with no scientific evidence, leading to confusion or misplanting. First, to identify the female parent of putative hybrids, the maternal inheritance InDel (insertion/deletion) markers were developed by using low-coverage sequencing. SNPs were developed by using genotyping-by-sequencing (GBS) approach in C. kanehirae, C. camphora and putative hybrids. The results indicated that the female parent of the studied hybrids was C. camphora. Eight hundred and forty of the 529,006 high-density SNPs were selected and used for analysis. Hybrids were classified as F1 (C. kanehirae × C. camphora), F2 and backcrosses. Hybridization has occurred in the human-developed area of eastern and southwestern Taiwan, and the introgression was bidirectional. For producing pure wood, buffering zones should be established around seed orchards to avoid cross-species pollination and to preserve the genetic purity of C. kanehirae. The DNA markers developed in this study will also be valuable for further wood identification, breeding and evolutionary research.
Dietary fatty acid intake and gut microbiota determine circulating endocannabinoidome signaling beyond the effect of body fat
Authors: Castonguay-Paradis Sophie , Lacroix Sébastien , Rochefort Gabrielle , Parent Lydiane , Perron Julie , Martin Cyril , Lamarche Benoît , Raymond Frédéric , Flamand Nicolas , Di Marzo Vincenzo , Veilleux Alain 
Published: September 2020

AbstractThe endocannabinoidome encompasses several fatty acid (FA)-derived mediators, including the endocannabinoid anandamide (AEA) and 2-arachidonoyl-glycerol (2-AG), which served as targets for anti-obesity drug development, and their congener N-acyl-ethanolamines (NAEs) and 2-monoacyl-glycerols (2‑MAGs), which are involved in food intake and energy metabolism. Body weight and fat distribution have been suggested as determinants of peripheral endocannabinoid levels. We aimed at investigating factors, beyond body fat composition, that are associated with circulating NAE and 2-MAG levels in a heterogeneous human population. Plasma NAEs and 2-MAGs were measured using LC–MS/MS in a cross-sectional sample of healthy men and women (n = 195) covering a wide range of BMI and individuals before and after a 2-day Mediterranean diet (n = 21). Circulating levels of all 2-MAGs and NAEs, other than N-oleoyl-ethanolamine (OEA), correlated with body fat mass and visceral adipose tissue (0.26 < r < 0.54). NAE levels were elevated in individuals with elevated fat mass, while 2-MAGs were increased in individuals with predominantly visceral body fat distribution. Dietary intakes of specific FAs were associated with 2-AG and omega-3-FA-derived NAEs or 2-MAGs, irrespective of the body fat distribution. Some gut bacterial families (e.g. Veillonellaceae, Peptostreptococcaceae and Akkermansiaceae) were associated with variations in most NAEs or omega-3-FA-derived 2‑MAGs, independently of fat mass and dietary FA intake. Finally, a 2-day Mediterranean diet intervention increased circulating levels of NAEs and 2-MAGs in agreement with changes in FA intake (p < 0.01). Self-reported intake and short-term dietary intervention increased in oleic acid and EPA and DHA intake as well as certain gut microbiota taxa are associated to circulating NAEs and 2‑MAGs independently of adiposity measures, thus highlighting the potential importance of these variables in determining endocannabinoidome signaling in humans.
Harnessing endogenous repair mechanisms for targeted gene knock-in of bovine embryos
Authors: Owen Joseph R. , Hennig Sadie L. , McNabb Bret R. , Lin Jason C. , Young Amy E. , Murray James D. , Ross Pablo J. , Van Eenennaam Alison L. 
Published: September 2020

AbstractIntroducing useful traits into livestock breeding programs through gene knock-ins has proven challenging. Typically, targeted insertions have been performed in cell lines, followed by somatic cell nuclear transfer cloning, which can be inefficient. An alternative is to introduce genome editing reagents and a homologous recombination (HR) donor template into embryos to trigger homology directed repair (HDR). However, the HR pathway is primarily restricted to actively dividing cells (S/G2-phase) and its efficiency for the introduction of large DNA sequences in zygotes is low. The homology-mediated end joining (HMEJ) approach has been shown to improve knock-in efficiency in non-dividing cells and to harness HDR after direct injection of embryos. The knock-in efficiency for a 1.8 kb gene was contrasted when combining microinjection of a gRNA/Cas9 ribonucleoprotein complex with a traditional HR donor template or an HMEJ template in bovine zygotes. The HMEJ template resulted in a significantly higher rate of gene knock-in as compared to the HR template (37.0% and 13.8%; P < 0.05). Additionally, more than a third of the knock-in embryos (36.9%) were non-mosaic. This approach will facilitate the one-step introduction of gene constructs at a specific location of the bovine genome and contribute to the next generation of elite cattle.
Putative morphology of Neoehrlichia mikurensis in salivary glands of Ixodes ricinus
Authors: Ondruš Jaroslav , Kulich Pavel , Sychra Oldřich , Široký Pavel 
Published: September 2020

AbstractNeoehrlichia mikurensis is an emerging tick-borne intracellular pathogen causing neoehrlichiosis. Its putative morphology was described in mammalian, but not in tick cells. In this study, we aim to show the presumptive morphology of N. mikurensis in salivary glands of engorged females of Ixodes ricinus. To accomplish this, we collected I. ricinus ticks in a locality with a high N. mikurensis prevalence, allowed them to feed in the artificial in vitro feeding system, dissected salivary glands and screened them by PCR for N. mikurensis and related bacteria. Ultrathin sections of salivary glands positive for N. mikurensis but negative for other pathogens were prepared and examined by transmission electron microscopy. We observed two individual organisms strongly resembling N. mikurensis in mammalian cells as described previously. Both bacteria were of ovoid shape between 0.5–0.8 μm surrounded by the inner cytoplasmic and the rippled outer membrane separated by an irregular electron-lucent periplasmic space. Detection of N. mikurensis in salivary glands of I. ricinus suggests that this bacterium uses the “salivary pathway of transmission” to infect mammals.
Activity-dependent compensation of cell size is vulnerable to targeted deletion of ion channels
Authors: Gorur-Shandilya Srinivas , Marder Eve , O’Leary Timothy 
Published: September 2020

AbstractIn many species, excitable cells preserve their physiological properties despite significant variation in physical size across time and in a population. For example, neurons in crustacean central pattern generators generate similar firing patterns despite several-fold increases in size between juveniles and adults. This presents a biophysical problem because the electrical properties of cells are highly sensitive to membrane area and channel density. It is not known whether specific mechanisms exist to sense membrane area and adjust channel expression to keep a consistent channel density, or whether regulation mechanisms that sense activity alone are capable of compensating cell size. We show that destabilising effects of growth can be specifically compensated by feedback mechanism that senses average calcium influx and jointly regulate multiple conductances. However, we further show that this class of growth-compensating regulation schemes is necessarily sensitive to perturbations that alter the expression of subsets of ion channel types. Targeted perturbations of specific ion channels can trigger a pathological response of the regulation mechanism and a failure of homeostasis. Our findings suggest that physiological regulation mechanisms that confer robustness to growth may be specifically vulnerable to deletions or mutations that affect subsets of ion channels.
miR-369-3p modulates inducible nitric oxide synthase and is involved in regulation of chronic inflammatory response
Authors: Scalavino Viviana , Liso Marina , Cavalcanti Elisabetta , Gigante Isabella , Lippolis Antonio , Mastronardi Mauro , Chieppa Marcello , Serino Grazia 
Published: September 2020

AbstractDendritic cells are the most important antigen-presenting cells that link the innate and acquired immune system. In our previous study, we identified that the upregulation of miR-369-3p suppresses the LPS-induced inflammatory response, reducing C/EBP-β, TNFα and IL-6 production. With the aim of gaining further insight into the biological function of miR-369-3p during acute inflammatory response, in the present study we identified novel gene targets of miR-369-3p and demonstrated the suppressive ability of these genes on the inflammatory dendritic cells. Bioinformatic analyses revealed that iNOS is a potential target of miR-369-3p. We demonstrated that the ectopic induction of miR-369-3p markedly reduced iNOS mRNA and protein as well as NO production. Moreover, we found that the upregulation of miR-369-3p decreased the release of TNFα, IL-6, IL-12, IL-1α, IL-1β in response to LPS, and increased the production of anti-inflammatory cytokines such as IL-10 and IL-1RA. In addition, LPS-induced nuclear translocation of NF-kB was inhibited by miR-369-3p. Levels of miR-369-3p were decreased in human inflamed regions of human intestine obtained from IBD patients. Our results provide novel additional information on miR-369-3p as a potential core of the signaling regulating the inflammatory response. These findings suggest that miR-369-3p should be considered as a potential target for the future development of new molecular therapeutic approaches.