bluuebunny/crossref_metadata_2025_split huggingface dataset:
The rational use of causal inference to guide reinforcement learning strengthens with age
Authors: Cohen Alexandra O. , Nussenbaum Kate , Dorfman Hayley M. , Gershman Samuel J. , Hartley Catherine A. 
Published: October 2020

AbstractBeliefs about the controllability of positive or negative events in the environment can shape learning throughout the lifespan. Previous research has shown that adults’ learning is modulated by beliefs about the causal structure of the environment such that they update their value estimates to a lesser extent when the outcomes can be attributed to hidden causes. This study examined whether external causes similarly influenced outcome attributions and learning across development. Ninety participants, ages 7 to 25 years, completed a reinforcement learning task in which they chose between two options with fixed reward probabilities. Choices were made in three distinct environments in which different hidden agents occasionally intervened to generate positive, negative, or random outcomes. Participants’ beliefs about hidden-agent intervention aligned with the true probabilities of the positive, negative, or random outcome manipulation in each of the three environments. Computational modeling of the learning data revealed that while the choices made by both adults (ages 18–25) and adolescents (ages 13–17) were best fit by Bayesian reinforcement learning models that incorporate beliefs about hidden-agent intervention, those of children (ages 7–12) were best fit by a one learning rate model that updates value estimates based on choice outcomes alone. Together, these results suggest that while children demonstrate explicit awareness of the causal structure of the task environment, they do not implicitly use beliefs about the causal structure of the environment to guide reinforcement learning in the same manner as adolescents and adults.
Validation and feasibility of liver T1 mapping using free breathing MOLLI sequence in children and young adults
Authors: Cho Yeon Jin , Kim Woo Sun , Choi Young Hun , Lee Seul Bi , Lee SeungHyun , Cheon Jung-Eun , Paek MunYoung , Woo SeungTae 
Published: October 2020

AbstractWe investigated the feasibility of free-breathing modified Look-Locker inversion recovery (MOLLI) sequence for measuring hepatic T1 values in children and young adults. To investigate the accuracy and the reproducibility of the T1 maps, a phantom study was performed with 12 different gadoterate meglumine concentrations and the T1 relaxation times of phantoms measured with the MOLLI sequence were compared against those measured with three different sequences: spin-echo inversion recovery, variable flip angle (VFA), and VFA with B1 correction. To evaluate the feasibility of free-breathing MOLLI sequence, hepatic T1 relaxation times obtained by free-breathing and breath-hold technique in twenty patients were compared. The phantom study revealed the excellent accuracy and reproducibility of MOLLI. In twenty patients, the mean value of hepatic T1 values obtained by free-breathing (606.7 ± 64.5 ms) and breath-hold (609.8 ± 64.0 ms) techniques showed no significant difference (p > 0.05). The Bland–Altman plot between the free-breathing and breath-hold revealed that the mean difference of T1 values was − 3.0 ms (− 0.5%). Therefore, T1 relaxation times obtained by MOLLI were comparable to the values obtained using the standard inversion recovery method. The hepatic T1 relaxation times measured by MOLLI technique with free-breathing were comparable to those obtained with breath-hold in children and young adults.
Rotational coherence of encapsulated ortho and para water in fullerene-C60 revealed by time-domain terahertz spectroscopy
Authors: Zhukov Sergey S. , Balos Vasileios , Hoffman Gabriela , Alom Shamim , Belyanchikov Mikhail , Nebioglu Mehmet , Roh Seulki , Pronin Artem , Bacanu George R. , Abramov Pavel , Wolf Martin , Dressel Martin , Levitt Malcolm H. , Whitby Richard J. , Gorshunov Boris , Sajadi Mohsen 
Published: October 2020

AbstractWe resolve the real-time coherent rotational motion of isolated water molecules encapsulated in fullerene-C60 cages by time-domain terahertz (THz) spectroscopy. We employ single-cycle THz pulses to excite the low-frequency rotational motion of water and measure the subsequent coherent emission of electromagnetic waves by water molecules. At temperatures below ~ 100 K, C60 lattice vibrational damping is mitigated and the quantum dynamics of confined water are resolved with a markedly long rotational coherence, extended beyond 10 ps. The observed rotational transitions agree well with low-frequency rotational dynamics of single water molecules in the gas phase. However, some additional spectral features with their major contribution at ~2.26 THz are also observed which may indicate interaction between water rotation and the C60 lattice phonons. We also resolve the real-time change of the emission pattern of water after a sudden cooling to 4 K, signifying the conversion of ortho-water to para-water over the course of 10s hours. The observed long coherent rotational dynamics of isolated water molecules confined in C60 makes this system an attractive candidate for future quantum technology.
Nano- to microscale three-dimensional morphology relevant to transport properties in reactive porous composite paint films
Authors: Liu Xiaoyang , Di Tullio Valeria , Lin Yu-Chung , De Andrade Vincent , Zhao Chonghang , Lin Cheng-Hung , Wagner Molly , Zumbulyadis Nicholas , Dybowski Cecil , Centeno Silvia A. , Chen-Wiegart Yu-chen Karen 
Published: October 2020

AbstractThe quantitative evaluation of the three-dimensional (3D) morphology of porous composite materials is important for understanding mass transport phenomena, which further impact their functionalities and durability. Reactive porous paint materials are composites in nature and widely used in arts and technological applications. In artistic oil paintings, ambient moisture and water and organic solvents used in conservation treatments are known to trigger multiple physical and chemical degradation processes; however, there is no complete physical model that can quantitatively describe their transport in the paint films. In the present study, model oil paints with lead white (2PbCO3·Pb(OH)2) and zinc white (ZnO) pigments, which are frequently found in artistic oil paintings and are associated with the widespread heavy metal soap deterioration, were studied using synchrotron X-ray nano-tomography and unilateral nuclear magnetic resonance. This study aims to establish a relationship among the paints’ compositions, the 3D morphological properties and degradation. This connection is crucial for establishing reliable models that can predict transport properties of solvents used in conservation treatments and of species involved in deterioration reactions, such as soap formation.
Discerning the thermodynamic feasibility of the spontaneous coexistence of multiple functional vegetation groups
Authors: Richardson Meredith , Kumar Praveen 
Published: October 2020

AbstractCan the Second Law of Thermodynamics explain why ecosystems naturally organize into a complex structure composed of multiple vegetation species and functional groups? Ecosystem structure, which refers to the number and type of plant functional groups, is the result of self-organization, or the spontaneous emergence of order from random fluctuations. By considering ecosystems as open thermodynamic systems, we model and study these fluctuations of throughput signatures on short timescales to determine the drivers and characteristics of ecosystem structure. This diagnostic approach allows us to use fluxes of energy and entropy to calculate an ecosystem’s estimated work and understand the thermodynamic behavior of the system. We use a multi-layer canopy-root-soil model to calculate the energy and entropy fluxes of different scenarios for field sites across various climates. At each site, scenarios comprised of native individual plant functional groups and a coexisting multi-group composition scenario including all functional groups observed at the site are compared. Ecosystem-scale calculations demonstrate that entropy fluxes and work efficiency—the work performed for the amount of radiation entering the ecosystem—are greatest in the multi-group scenario when its leaf area is significantly larger than each of its individual functional groups. Thus, we conclude that ecosystems self-organize towards the vegetation structure with the greatest outgoing entropy flux and work efficiency, resulting in the coexistence of multiple functional groups and performing the maximum amount of work within the constraints of locally available energy, water, and nutrients.
The trans-kingdom battle between donor and recipient gut microbiome influences fecal microbiota transplantation outcome
Authors: Kazemian Negin , Ramezankhani Milad , Sehgal Aarushi , Khalid Faizan Muhammad , Kalkhoran Amir Hossein Zeinali , Narayan Apurva , Wong Gane Ka-Shu , Kao Dina , Pakpour Sepideh 
Published: October 2020

AbstractFundamental restoration ecology and community ecology theories can help us better understand the underlying mechanisms of fecal microbiota transplantation (FMT) and to better design future microbial therapeutics for recurrent Clostridioides difficile infections (rCDI) and other dysbiosis-related conditions. In this study, stool samples were collected from donors and rCDI patients one week prior to FMT (pre-FMT), as well as from patients one week following FMT (post-FMT). Using metagenomic sequencing and machine learning, our results suggested that FMT outcome is not only dependent on the ecological structure of the recipients, but also the interactions between the donor and recipient microbiomes at the taxonomical and functional levels. We observed that the presence of specific bacteria in donors (Clostridioides spp., Desulfovibrio spp., Odoribacter spp. and Oscillibacter spp.) and the absence of fungi (Yarrowia spp.) and bacteria (Wigglesworthia spp.) in recipients prior to FMT could predict FMT success. Our results also suggested a series of interlocked mechanisms for FMT success, including the repair of the disturbed gut ecosystem by transient colonization of nexus species followed by secondary succession of bile acid metabolizers, sporulators, and short chain fatty acid producers.
Stratified layer analysis reveals intrinsic leptin stimulates cryptal mesenchymal cells for controlling mucosal inflammation
Authors: Matsumura Seiichi , Kurashima Yosuke , Murasaki Sayuri , Morimoto Masako , Arai Fujimi , Saito Yukari , Katayama Nana , Kim Dayoung , Inagaki Yutaka , Kudo Takahiro , Ernst Peter B. , Shimizu Toshiaki , Kiyono Hiroshi 
Published: October 2020

AbstractMesenchymal cells in the crypt play indispensable roles in the maintenance of intestinal epithelial homeostasis through their contribution to the preservation of stem cells. However, the acquisition properties of the production of stem cell niche factors by the mesenchymal cells have not been well elucidated, due to technical limitations regarding the isolation and subsequent molecular and cellular analyses of cryptal mesenchymal cells. To evaluate the function of mesenchymal cells located at the large intestinal crypt, we established a novel method through which cells are harvested according to the histologic layers of mouse colon, and we compared cellular properties between microenvironmental niches, the luminal mucosa and crypts. The gene expression pattern in the cryptal mesenchymal cells showed that receptors of the hormone/cytokine leptin were highly expressed, and we found a decrease in Wnt2b expression under conditions of leptin receptor deficiency, which also induced a delay in cryptal epithelial proliferation. Our novel stratified layer isolation strategies thus revealed new microenvironmental characteristics of colonic mesenchymal cells, including the intrinsic involvement of leptin in the control of mucosal homeostasis.
Needle-injectable microcomposite cryogel scaffolds with antimicrobial properties
Authors: Joshi Navare Kasturi , Colombani Thibault , Rezaeeyazdi Mahboobeh , Bassous Nicole , Rana Devyesh , Webster Thomas , Memic Adnan , Bencherif Sidi A. 
Published: October 2020

AbstractPorous three-dimensional hydrogel scaffolds have an exquisite ability to promote tissue repair. However, because of their high water content and invasive nature during surgical implantation, hydrogels are at an increased risk of bacterial infection. Recently, we have developed elastic biomimetic cryogels, an advanced type of polymeric hydrogel, that are syringe-deliverable through hypodermic needles. These needle-injectable cryogels have unique properties, including large and interconnected pores, mechanical robustness, and shape-memory. Like hydrogels, cryogels are also susceptible to colonization by microbial pathogens. To that end, our minimally invasive cryogels have been engineered to address this challenge. Specifically, we hybridized the cryogels with calcium peroxide microparticles to controllably produce bactericidal hydrogen peroxide. Our novel microcomposite cryogels exhibit antimicrobial properties and inhibit antibiotic-resistant bacteria (MRSA and Pseudomonas aeruginosa), the most common cause of biomaterial implant failure in modern medicine. Moreover, the cryogels showed negligible cytotoxicity toward murine fibroblasts and prevented activation of primary bone marrow-derived dendritic cells ex vivo. Finally, in vivo data suggested tissue integration, biodegradation, and minimal host inflammatory responses when the antimicrobial cryogels, even when purposely contaminated with bacteria, were subcutaneously injected in mice. Collectively, these needle-injectable microcomposite cryogels show great promise for biomedical applications, especially in tissue engineering and regenerative medicine.
Progressive seawater acidification on the Great Barrier Reef continental shelf
Authors: Fabricius Katharina E. , Neill Craig , Van Ooijen Erik , Smith Joy N. , Tilbrook Bronte 
Published: October 2020

AbstractCoral reefs are highly sensitive to ocean acidification due to rising atmospheric CO2 concentrations. We present 10 years of data (2009–2019) on the long-term trends and sources of variation in the carbon chemistry from two fixed stations in the Australian Great Barrier Reef. Data from the subtropical mid-shelf GBRWIS comprised 3-h instrument records, and those from the tropical coastal NRSYON were monthly seawater samples. Both stations recorded significant variation in seawater CO2 fugacity (fCO2), attributable to seasonal, daytime, temperature and salinity fluctuations. Superimposed over this variation, fCO2 progressively increased by > 2.0 ± 0.3 µatm year−1 at both stations. Seawater temperature and salinity also increased throughout the decade, whereas seawater pH and the saturation state of aragonite declined. The decadal upward fCO2 trend remained significant in temperature- and salinity-normalised data. Indeed, annual fCO2 minima are now higher than estimated fCO2 maxima in the early 1960s, with mean fCO2 now ~ 28% higher than 60 years ago. Our data indicate that carbonate dissolution from the seafloor is currently unable to buffer the Great Barrier Reef against ocean acidification. This is of great concern for the thousands of coral reefs and other diverse marine ecosystems located in this vast continental shelf system.
Experimental and computation assessment of thermomechanical effects during auxetic foam fabrication
Authors: Critchley Richard , Smy Victoria , Corni Ilaria , Wharton Julian A. , Walsh Frank C. , Wood Robert J. K. , Stokes Keith R. 
Published: October 2020

AbstractAuxetic foams continue to interest researchers owing to their unique and enhanced properties. Existing studies attest to the importance of fabrication mechanisms and parameters. However, disparity in thermo-mechanical parameters has left much debate as to which factors dominate fabrication output quality. This paper provides experimental, computational, and statistical insights into the mechanisms that enable auxetic foams to be produced, using key parameters reported within the literature: porosity; heating time; and volumetric compression ratio. To advance the considerations on manufacturing parameter dominance, both study design and scale have been optimised to enable statistical inferences to be drawn. Whilst being unusual for a manufacturing domain, such additional analysis provides more conclusive evidence of auxetic properties and highlights the supremacy of volumetric compression ratio in predicting Poisson’s ratio outcomes in the manufacture process. Furthermore statistical results are exploited to formulate key recommendations for those wishing to maximise/optimise auxetic foam production.
Fruit volatilome profiling through GC × GC-ToF-MS and gene expression analyses reveal differences amongst peach cultivars in their response to cold storage
Authors: Muto Antonella , Müller Carsten T. , Bruno Leonardo , McGregor Laura , Ferrante Antonio , Chiappetta Adriana Ada Ceverista , Bitonti Maria Beatrice , Rogers Hilary J. , Spadafora Natasha Damiana 
Published: October 2020

AbstractPeaches have a short shelf life and require chilling during storage and transport. Peach aroma is important for consumer preference and determined by underlying metabolic pathways and gene expression. Differences in aroma (profiles of volatile organic compounds, VOCs) have been widely reported across cultivars and in response to cold storage. However, few studies used intact peaches, or used equilibrium sampling methods subject to saturation. We analysed VOC profiles using TD-GC × GC-ToF-MS and expression of 12 key VOC pathway genes of intact fruit from six cultivars (three peaches, three nectarines) before and after storage at 1 °C for 7 days including 36 h shelf life storage at 20 °C. Two dimensional GC (GC × GC) significantly enhances discrimination of thermal desorption gas chromatography time-of-flight mass spectrometry (TD-GC-ToF-MS) and detected a total of 115 VOCs. A subset of 15 VOCs from analysis with Random Forest discriminated between cultivars. Another 16 VOCs correlated strongly with expression profiles of eleven key genes in the lipoxygenase pathway, and both expression profiles and VOCs discriminated amongst cultivars, peach versus nectarines and between treatments. The cultivar-specific response to cold storage underlines the need to understand more fully the genetic basis for VOC changes across cultivars.
Transcriptome analysis of chicken intraepithelial lymphocyte natural killer cells infected with very virulent infectious bursal disease virus
Authors: Boo Sook Yee , Tan Sheau Wei , Alitheen Noorjahan Banu , Ho Chai Ling , Omar Abdul Rahman , Yeap Swee Keong 
Published: October 2020

AbstractThe infectious bursal disease (IBD) is an acute immunosuppressive viral disease that significantly affects the economics of the poultry industry. The IBD virus (IBDV) was known to infect B lymphocytes and activate macrophage and T lymphocytes, but there are limited studies on the impact of IBDV infection on chicken intraepithelial lymphocyte natural killer (IEL-NK) cells. This study employed an mRNA sequencing approach to investigate the early regulation of gene expression patterns in chicken IEL-NK cells after infection with very virulent IBDV strain UPM0081. A total of 12,141 genes were expressed in uninfected chicken IEL-NK cells, and most of the genes with high expression were involved in the metabolic pathway, whereas most of the low expressed genes were involved in the cytokine-cytokine receptor pathway. A total of 1,266 genes were differentially expressed (DE) at 3 day-post-infection (dpi), and these DE genes were involved in inflammation, antiviral response and interferon stimulation. The innate immune response was activated as several genes involved in inflammation, antiviral response and recruitment of NK cells to the infected area were up-regulated. This is the first study to examine the whole transcriptome profile of chicken NK cells towards IBDV infection and provides better insight into the early immune response of chicken NK cells.
Silencing of sinusoidal DDR1 reduces murine liver metastasis by colon carcinoma
Authors: Romayor Irene , Badiola Iker , Benedicto Aitor , Márquez Joana , Herrero Alba , Arteta Beatriz , Olaso Elvira 
Published: October 2020

AbstractLiver metastasis depends on the collagenous microenvironment generated by hepatic sinusoidal cells (SCs). DDR1 is an atypical collagen receptor linked to tumor progression, but whether SCs express DDR1 and its implication in liver metastasis remain unknown. Freshly isolated hepatic stellate cells (HSCs), Kupffer cells (KCs), and liver sinusoidal endothelial cells (LSECs), that conform the SCs, expressed functional DDR1. HSCs expressed the largest amounts. C26 colon carcinoma secretomes increased DDR1 phosphorylation in HSCs and KCs by collagen I. Inhibition of kinase activity by DDR1-IN-1 or mRNA silencing of DDR1 reduced HSCs secretion of MMP2/9 and chemoattractant and proliferative factors for LSECs and C26 cells. DDR1-IN-1 did not modify MMP2/9 in KCs or LSECs secretomes, but decreased the enhancement of C26 migration and proliferation induced by their secretomes. Gene array showed that DDR1 silencing downregulated HSCs genes for collagens, MMPs, interleukins and chemokines. Silencing of DDR1 before tumor inoculation reduced hepatic C26 metastasis in mice. Silenced livers bore less tumor foci than controls. Metastatic foci in DDR1 silenced mice were smaller and contained an altered stroma with fewer SCs, proliferating cells, collagen and MMPs than foci in control mice. In conclusion, hepatic DDR1 promotes C26 liver metastasis and favors the pro-metastatic response of SCs to the tumor.
A systems genomics approach to uncover the molecular properties of cancer genes
Authors: Grassmann Felix , Pawitan Yudi , Czene Kamila 
Published: October 2020

AbstractGenes involved in cancer are under constant evolutionary pressure, potentially resulting in diverse molecular properties. In this study, we explore 23 omic features from publicly available databases to define the molecular profile of different classes of cancer genes. Cancer genes were grouped according to mutational landscape (germline and somatically mutated genes), role in cancer initiation (cancer driver genes) or cancer survival (survival genes), as well as being implicated by genome-wide association studies (GWAS genes). For each gene, we also computed feature scores based on all omic features, effectively summarizing how closely a gene resembles cancer genes of the respective class. In general, cancer genes are longer, have a lower GC content, have more isoforms with shorter exons, are expressed in more tissues and have more transcription factor binding sites than non-cancer genes. We found that germline genes more closely resemble single tissue GWAS genes while somatic genes are more similar to pleiotropic cancer GWAS genes. As a proof-of-principle, we utilized aggregated feature scores to prioritize genes in breast cancer GWAS loci and found that top ranking genes were enriched in cancer related pathways. In conclusion, we have identified multiple omic features associated with different classes of cancer genes, which can assist prioritization of genes in cancer gene discovery.