bluuebunny/crossref_metadata_2025_split huggingface dataset:
3‐D Modeling of Induced Seismicity Along Multiple Faults: Magnitude, Rate, and Location in a Poroelasticity System
Authors: Chang K. W. , Yoon H. 
Published: October 2018

AbstractUnderstanding of the potential to injection‐induced seismicity along faults requires the response of fault zone system to spatiotemporal perturbations in pore pressure and stress. In this study, three‐dimensional (3‐D) model system consisting of the caprock, reservoir, and basement is intersected by vertical strike‐slip faults. We examine the full poroelastic behavior of the formation and perform the mechanical analysis along each fault zone using the Coulomb stress change. The magnitude, rate, and location of potential earthquakes are predicted using the spatial distribution of stresses and pore pressure over time. Rapid diffusion of pore pressure into conductive faults initiates failure, but the majority of induced seismicity occurs at deep fault zones due to poroelastic stabilization near the injection interval. Less permeable faults can be destabilized by either delayed pore pressure diffusion or poroelastic stressing. A two‐dimensional (2‐D) horizontal model, representing the interface between the reservoir and the basement, limits diffusion of pore pressure and deformation of the formation in the vertical direction that may overestimate or underestimate the potential of earthquakes along the fault. Our numerical results suggest that the 3‐D modeling of faulting system including poroelastic coupling can reduce the uncertainty in the seismic hazard prediction by considering the hydraulic and mechanical interaction between faults and bounding formations.
Opportunities to Prevent Alcoholic Liver Cirrhosis in High-Risk Populations: A Systematic Review With Meta-Analysis
Authors: Askgaard Gro , Kjær Mette S. , Tolstrup Janne S. 
Published: October 2018

BACKGROUND:
Alcoholic liver cirrhosis is preventable and caused by heavy drinking. Few in the general population may be at risk and interventions targeting individuals at high risk may be a more feasible opportunity for prevention than interventions targeting the whole population.

METHODS:
We conducted a systematic review to identify opportunities to prevent alcoholic liver cirrhosis in high-risk populations. Following MOOSE guidelines, we included observational studies published between 1980 and 2017. Prospective studies of alcohol-problem cohorts were included to investigate whether alcohol-problem cohorts qualify as high-risk populations for alcoholic liver cirrhosis. Studies on the alcohol amount consumed by alcoholic liver cirrhosis patients were included to compare with the amount consumed by the general population. Moreover, studies on alcohol-related healthcare contacts prior to alcoholic liver cirrhosis diagnosis were included to identify opportunities to offer prevention interventions. Of 7198 screened references, 38 studies (N = 120,928) were included.

RESULTS:
Alcohol-problem cohorts qualified as high-risk populations with an incidence of alcoholic liver cirrhosis ranging from 7 to 16% after 8–12 years. The alcohol amount consumed by alcoholic liver cirrhosis patients was high compared to the general population. For example, 45% (95%CI 34, 56) of alcoholic liver cirrhosis patients were drinking >110 g alcohol/day. Finally, there were opportunities to reach alcoholic liver cirrhosis patients prior to diagnosis; 40–61% of alcoholic liver cirrhosis patients had a previous alcohol-related healthcare contact.

CONCLUSIONS:
We conclude that alcohol-problem cohorts are high-risk populations for alcoholic liver cirrhosis and there seems to be opportunities to reach later alcoholic liver cirrhosis cases with preventive interventions in healthcare settings.
Oxygen loss from seagrass roots coincides with colonisation of sulphide-oxidising cable bacteria and reduces sulphide stress
Authors: Martin Belinda C , Bougoure Jeremy , Ryan Megan H , Bennett William W , Colmer Timothy D , Joyce Natalie K , Olsen Ylva S , Kendrick Gary A 
Published: October 2018

Abstract
Seagrasses thrive in anoxic sediments where sulphide can accumulate to phytotoxic levels. So how do seagrasses persist in this environment? Here, we propose that radial oxygen loss (ROL) from actively growing root tips protects seagrasses from sulphide intrusion not only by abiotically oxidising sulphides in the rhizosphere of young roots, but also by influencing the abundance and spatial distribution of sulphate-reducing and sulphide-oxidising bacteria. We used a novel multifaceted approach combining imaging techniques (confocal fluorescence in situ hybridisation, oxygen planar optodes, and sulphide diffusive gradients in thin films) with microbial community profiling to build a complete picture of the microenvironment of growing roots of the seagrasses Halophila ovalis and Zostera muelleri. ROL was restricted to young root tips, indicating that seagrasses will have limited ability to influence sulphide oxidation in bulk sediments. On the microscale, however, ROL corresponded with decreased abundance of potential sulphate-reducing bacteria and decreased sulphide concentrations in the rhizosphere surrounding young roots. Furthermore, roots leaking oxygen had a higher abundance of sulphide-oxidising cable bacteria; which is the first direct observation of these bacteria on seagrass roots. Thus, ROL may enhance both abiotic and bacterial sulphide oxidation and restrict bacterial sulphide production around vulnerable roots, thereby helping seagrasses to colonise sulphide-rich anoxic sediments.
Homeostasis of protein and mRNA concentrations in growing cells
Authors: Lin Jie , Amir Ariel 
Published: October 2018

AbstractMany experiments show that the numbers of mRNA and protein are proportional to the cell volume in growing cells. However, models of stochastic gene expression often assume constant transcription rate per gene and constant translation rate per mRNA, which are incompatible with these experiments. Here, we construct a minimal gene expression model to fill this gap. Assuming ribosomes and RNA polymerases are limiting in gene expression, we show that the numbers of proteins and mRNAs both grow exponentially during the cell cycle and that the concentrations of all mRNAs and proteins achieve cellular homeostasis; the competition between genes for the RNA polymerases makes the transcription rate independent of the genome number. Furthermore, by extending the model to situations in which DNA (mRNA) can be saturated by RNA polymerases (ribosomes) and becomes limiting, we predict a transition from exponential to linear growth of cell volume as the protein-to-DNA ratio increases.
Reference-point centering and range-adaptation enhance human reinforcement learning at the cost of irrational preferences
Authors: Bavard Sophie , Lebreton Maël , Khamassi Mehdi , Coricelli Giorgio , Palminteri Stefano 
Published: October 2018

AbstractIn economics and perceptual decision-making contextual effects are well documented, where decision weights are adjusted as a function of the distribution of stimuli. Yet, in reinforcement learning literature whether and how contextual information pertaining to decision states is integrated in learning algorithms has received comparably little attention. Here, we investigate reinforcement learning behavior and its computational substrates in a task where we orthogonally manipulate outcome valence and magnitude, resulting in systematic variations in state-values. Model comparison indicates that subjects’ behavior is best accounted for by an algorithm which includes both reference point-dependence and range-adaptation—two crucial features of state-dependent valuation. In addition, we find that state-dependent outcome valuation progressively emerges, is favored by increasing outcome information and correlated with explicit understanding of the task structure. Finally, our data clearly show that, while being locally adaptive (for instance in negative valence and small magnitude contexts), state-dependent valuation comes at the cost of seemingly irrational choices, when options are extrapolated out from their original contexts.
Cell specific delivery of modified mRNA expressing therapeutic proteins to leukocytes
Authors: Veiga Nuphar , Goldsmith Meir , Granot Yasmin , Rosenblum Daniel , Dammes Niels , Kedmi Ranit , Ramishetti Srinivas , Peer Dan 
Published: October 2018

AbstractTherapeutic alteration of gene expression in vivo can be achieved by delivering nucleic acids (e.g., mRNA, siRNA) using nanoparticles. Recent progress in modified messenger RNA (mmRNA) synthesis facilitated the development of lipid nanoparticles (LNPs) loaded with mmRNA as a promising tool for in vivo protein expression. Although progress have been made with mmRNA-LNPs based protein expression in hepatocytes, cell specificity is still a major challenge. Moreover, selective protein expression is essential for an improved therapeutic effect, due to the heterogeneous nature of diseases. Here, we present a precision protein expression strategy in Ly6c+ inflammatory leukocytes in inflammatory bowel disease (IBD) induced mice. We demonstrate a therapeutic effect in an IBD model by targeted expression of the interleukin 10 in Ly6c+ inflammatory leukocytes. A selective mmRNA expression strategy has tremendous therapeutic potential in IBD and can ultimately become a novel therapeutic modality in many other diseases.
Transforming food waste: how immobilized enzymes can valorize waste streams into revenue streams
Authors: Andler Stephanie M. , Goddard Julie M. 
Published: October 2018

AbstractFood processing generates byproduct and waste streams rich in lipids, carbohydrates, and proteins, which contribute to its negative environmental impact. However, these compounds hold significant economic potential if transformed into revenue streams such as biofuels and ingredients. Indeed, the high protein, sugar, and fat content of many food waste streams makes them ideal feedstocks for enzymatic valorization. Compared to synthetic catalysts, enzymes have higher specificity, lower energy requirement, and improved environmental sustainability in performing chemical transformations, yet their poor stability and recovery limits their performance in their native state. This review article surveys the current state-of-the-art in enzyme stabilization & immobilization technologies, summarizes opportunities in enzyme-catalyzed valorization of waste streams with emphasis on streams rich in mono- and disaccharides, polysaccharides, lipids, and proteins, and highlights challenges and opportunities in designing commercially translatable immobilized enzyme systems towards the ultimate goals of sustainable food production and reduced food waste.
Killer immunoglobulin-like receptor genotype did not correlate with response to anti-PD-1 antibody treatment in a Japanese cohort
Authors: Ishida Yoshihiro , Nakashima Chisa , Kojima Hiroto , Tanaka Hidenori , Fujimura Taku , Matsushita Shigeto , Yamamoto Yuki , Yoshino Koji , Fujisawa Yasuhiro , Otsuka Atsushi , Kabashima Kenji 
Published: October 2018

AbstractImmune checkpoint blockade (ICB) induces a remarkable response in patients with certain cancers. However, the response rate is not yet satisfactory. Biomarkers that help physicians identify patients who would benefit from ICB need to be developed. Killer immunoglobulin-like receptors (KIRs) are a class of receptors that are mainly expressed by natural killer cells. KIR genotypes have been shown to influence the outcomes of patients with neuroblastoma and hematopoietic malignancies. KIRs may thus influence the clinical outcomes of melanoma patients receiving nivolumab. We aimed to identify the KIR genotype, or KIR/KIR-ligand combinations, which influence the outcomes of melanoma patients receiving nivolumab. We genotyped 112 melanoma patients who were treated with nivolumab for KIR and human leukocyte antigen. The clinical records of the patients were analyzed to determine if they showed a response to nivolumab, and whether or not they experienced adverse events. Our analysis showed that no KIR gene was associated with a response to nivolumab. The KIR/KIR-ligand combination did not correlate with a response to nivolumab. KIR genes were not predictive of experiencing adverse events of grade 2 or greater. We conclude that the KIR genotype or KIR/KIR-ligand genotype do not show predictive value in melanoma patients receiving nivolumab.
Topological assessment of metabolic networks reveals evolutionary information
Authors: Machicao Jeaneth , Filho Humberto A. , Lahr Daniel J. G. , Buckeridge Marcos , Bruno Odemir M. 
Published: October 2018

AbstractEvolutionary information was inferred from the topology of metabolic networks corresponding to 17 plant species belonging to major plant lineages Chlorophytes, Bryophytes, Lycophytes and Angiosperms. The plant metabolic networks were built using the substrate-product network modeling based on the metabolic reactions available on the PlantCyc database (version 9.5), from which their local topological properties such as degree, in-degree, out-degree, clustering coefficient, hub-score, authority-score, local efficiency, betweenness and eigencentrality were measured. The topological measurements corresponding to each metabolite within the networks were considered as a set of metabolic characters to compound a feature vector representing each plant. Our results revealed that some local topological characters are able to discern among plant kinships, since similar phylogenies were found when comparing dendrograms obtained by topological metrics to the one obtained by DNA sequences of chloroplast genes. Furthermore, we also found that even a smaller number of metabolic characters is able to separate among major clades with high bootstrap support (BS > 95), while for some suborders a bigger content has been required.
Selection and validation of suitable reference genes for qPCR gene expression analysis in goats and sheep under Peste des petits ruminants virus (PPRV), lineage IV infection
Authors: Sahu Amit Ranjan , Wani Sajad Ahmad , Saxena Shikha , Rajak Kaushal Kishor , Chaudhary Dheeraj , Sahoo Aditya Prasad , Khanduri Alok , Pandey Aruna , Mondal Piyali , Malla Waseem Akram , Khan Raja Ishaq Nabi , Tiwari Ashok Kumar , Mishra Bina , Muthuchelvan D. , Mishra Bishnu Prasad , Singh Raj Kumar , Gandham Ravi Kumar 
Published: October 2018

AbstractIdentification of suitable candidate reference genes is an important prerequisite for validating the gene expression data obtained from downstream analysis of RNA sequencing using quantitative real time PCR (qRT-PCR). Though existence of a universal reference gene is myth, commonly used reference genes can be assessed for expression stability to confer their suitability to be used as candidate reference genes in gene expression studies. In this study, we evaluated the expression stability of ten most commonly used reference genes (GAPDH, ACTB, HSP90, HMBS, 18S rRNA, B2M, POLR2A, HPRT1, ACAC, YWHAZ) in fourteen different Peste des petits ruminants virus (PPRV) infected tissues of goats and sheep. RefFinder and RankAggreg software were used to deduce comprehensive ranking of reference genes. Our results suggested HMBS and B2M in goats and HMBS and HPRT1 in sheep can be used as suitable endogenous controls in gene expression studies of PPRV infection irrespective of tissues and condition as a whole, thus eliminating the use of tissue specific/ condition specific endogenous controls. We report for the first time suitable reference genes for gene expression studies in PPRV infected tissues. The reference genes determined here can be useful for future studies on gene expression in sheep and goat infected with PPRV, thus saving extra efforts and time of repeating the reference gene determination and validation.
Signals of stream fish homogenization revealed by AI-based clusters
Authors: Cheng Su-Ting , Tsai Wen-Ping , Yu Tzu-Chun , Herricks Edwin E. , Chang Fi-John 
Published: October 2018

AbstractRisks of stream fish homogenization are attributable to multiple variables operating at various spatial and temporal scales. However, understanding the mechanisms of homogenization requires not only watershed-scale, but also exhaustive fish community structure shifts representing detailed local functional relationships essential to homogenization potentials. Here, we demonstrate the idea of applying AI-based clusters to reveal nonlinear responses of homogenization risks among heterogeneous hydro-chemo-bio variables in space and time. Results found that species introduction, dam isolation, and the potential of climate-mediated disruptions in hydrologic cycles producing degradation in water quality triggered shifts of community assembly and resulting structures producing detrimental conditions for endemic fishes. The AI-based clustering approach suggests that endemic species conservation should focus on alleviation of low flows, control of species introduction, limiting generalist expansion, and enhancing the hydrological connectivity fragmented by dams. Likewise, it can be applied in other geographical and environmental settings for finding homogenization mitigation strategies.
The Beta-adrenergic agonist, Ractopamine, increases skeletal muscle expression of Asparagine Synthetase as part of an integrated stress response gene program
Authors: Brown David , Ryan Kevin , Daniel Zoe , Mareko Molebeledi , Talbot Richard , Moreton Joanna , Giles Tom C. B. , Emes Richard , Hodgman Charlie , Parr Tim , Brameld John M. 
Published: October 2018

AbstractSynthetic beta-adrenergic agonists (BA) have broad biomedical and agricultural application for increasing lean body mass, yet a poor understanding of the biology underpinning these agents is limiting further drug discovery potential. Growing female pigs (77 ± 7 kg) were administered the BA, Ractopamine (20 ppm in feed), or the recombinant growth hormone (GH), Reporcin (10 mg/48 hrs injected) for 1, 3, 7, 13 (n = 10 per treatment, per time point) or 27 days (n = 15 per treatment). Using RNA-sequencing and inferred pathway analysis, we examined temporal changes to the Longissimus Dorsi skeletal muscle transcriptome (n = 3 per treatment, per time point) relative to a feed-only control cohort. Gene expression changes were affirmed by quantitative-PCR on all samples (n = 164). RNA-sequencing analysis revealed that BA treatment had greater effects than GH, and that asparagine synthetase (Asns) was the 5th most significantly increased gene by BA at day 3. ASNS protein expression was dramatically increased by BA treatment at day 7 (p < 0.05). The most significantly increased gene at day 3 was activating transcription factor 5 (Atf5), a transcription factor known to regulate ASNS gene expression. Gene and protein expression of Atf4, another known regulator of Asns expression, was not changed by BA treatment. Expression of more than 20 known Atf4 target genes were increased by BA treatment, suggesting that BA treatment induces an integrated stress response (ISR) in skeletal muscle of pigs. In support of this, mRNA expression of sestrin-2 (Sesn2) and cyclin-dependant kinase 1 alpha (Cdkn1a), two key stress-responsive genes and negative regulators of cellular growth, were also strongly increased from day 3 of BA treatment. Finally, tRNA charging was the most significantly enriched pathway induced by BA treatment, suggesting alterations to the translational capacity/efficiency of the muscle. BA-mediated changes to the skeletal muscle transcriptome are highly indicative of an integrated stress response (ISR), particularly genes relating to amino acid biosynthesis and protein translational capacity.
Integrative taxonomy reveals hidden species within a common fungal parasite of ladybirds
Authors: Haelewaters Danny , De Kesel André , Pfister Donald H. 
Published: October 2018

AbstractOur understanding of fungal diversity is far from complete. Species descriptions generally focus on morphological features, but this approach may underestimate true diversity. Using the morphological species concept,Hesperomyces virescens(Ascomycota, Laboulbeniales) is a single species with global distribution and wide host range. Since its description 120 years ago, this fungal parasite has been reported from 30 species of ladybird hosts on all continents except Antarctica. These host usage patterns suggest thatH. virescenscould be made up of many different species, each adapted to individual host species. Using sequence data from three gene regions, we found evidence for distinct clades withinHesperomyces virescens, each clade corresponding to isolates from a single host species. We propose that these lineages represent separate species, driven by adaptation to different ladybird hosts. Our combined morphometric, molecular phylogenetic and ecological data provide support for a unified species concept and an integrative taxonomy approach.
Comparative cochlear transcriptomics of echolocating bats provides new insights into different nervous activities of CF bat species
Authors: Wang Hui , Zhao Hanbo , Huang Xiaobin , Sun Keping , Feng Jiang 
Published: October 2018

AbstractThe molecular mechanisms used by echolocating bats to deal with different ultrasonic signals remain to be revealed. Here, we utilised RNA-Seq data to conduct comparative cochlear transcriptomics to assess the variation of gene expression among bats with three types of echolocation: constant-frequency (CF) bats, frequency-modulated (FM) bats and click bats. Our results suggest larger differences in gene expression between CF and click bats than between CF and FM bats and small differences between FM and click bats. We identified 426 and 1,504 differentially expressed genes (DEGs) by the different methods as functionally important for CF bats, in that they showed consistent upregulation in the cochlea of two CF bats, relative to the levels in click and FM bats. Subsequently, downstream GO and KEGG enrichment analyses indicated that both the 426 and 1,504 gene sets were associated with changes in nervous activities in the cochleae of CF bats. In addition, another set of 1,764 DEGs were identified to have crucial hearing related physiological functions for laryngeally echolocating bats. Our study provides a comprehensive overview of the genetic basis of differences among echolocating bats, revealing different nervous system activities during auditory perception in the cochlea particularly in CF bats.
Autologous cell lines from circulating colon cancer cells captured from sequential liquid biopsies as model to study therapy-driven tumor changes
Authors: Soler Alexandra , Cayrefourcq Laure , Mazard Thibault , Babayan Anna , Lamy Pierre-Jean , Assou Said , Assenat Eric , Pantel Klaus , Alix-Panabières Catherine 
Published: October 2018

AbstractCirculating tumor cells (CTCs) are important clinical indicators for prognosis and treatment efficacy. However, CTC investigation is hampered by their low number, making the establishment of permanent CTC lines very challenging. We derived and characterized nine CTC lines using blood samples from a patient with metastatic colorectal cancer collected before and after chemotherapy and targeted therapy, and during cancer progression. These cell lines displayed an intermediate epithelial/mesenchymal phenotype, stem-cell like characteristics, angiogenesis potential, an osteomimetic signature and the capacity to escape from the immune system. Moreover, they showed changes in mRNA and protein expression (e.g., DEFA6, ABCB1 and GAL), whereas analysis of chromosomal copy number aberrations revealed no significant variation over time. These data indicate that although CTC lines derived from sequential blood samples during therapy have common traits, treatment-resistant CTC clones with distinct phenotypic characteristics are selected over time.