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Additional file 10 of Deficiency of exchange protein directly activated by cAMP (EPAC)-1 in mice augments glucose intolerance, inflammation, and gut dysbiosis associated with Western diet

Preeti Dinesh Virwani, Lin Cai, Patrick Ka Kit Yeung, Gordon Qian, Yingxian Chen, Lei Zhou, Jason Wing Hon Wong, Yu Wang, Joshua Wing Kei Ho, Kui Kai Lau, Pei-Yuan Qian & Sookja Kim Chung
Additional file 10: Table S8. Gene coverage of various functional KEGG genes detected through shotgun sequencing.

Additional file 11 of Deficiency of exchange protein directly activated by cAMP (EPAC)-1 in mice augments glucose intolerance, inflammation, and gut dysbiosis associated with Western diet

Preeti Dinesh Virwani, Lin Cai, Patrick Ka Kit Yeung, Gordon Qian, Yingxian Chen, Lei Zhou, Jason Wing Hon Wong, Yu Wang, Joshua Wing Kei Ho, Kui Kai Lau, Pei-Yuan Qian & Sookja Kim Chung
Additional file 11: Table S9. KEGG orthology IDs.

Additional file 6 of Deficiency of exchange protein directly activated by cAMP (EPAC)-1 in mice augments glucose intolerance, inflammation, and gut dysbiosis associated with Western diet

Preeti Dinesh Virwani, Lin Cai, Patrick Ka Kit Yeung, Gordon Qian, Yingxian Chen, Lei Zhou, Jason Wing Hon Wong, Yu Wang, Joshua Wing Kei Ho, Kui Kai Lau, Pei-Yuan Qian & Sookja Kim Chung
Additional file 6: Table S5. Relative abundance of families detected through 16S rRNA gene sequencing using fecal DNA.

Additional file 8 of Deficiency of exchange protein directly activated by cAMP (EPAC)-1 in mice augments glucose intolerance, inflammation, and gut dysbiosis associated with Western diet

Preeti Dinesh Virwani, Lin Cai, Patrick Ka Kit Yeung, Gordon Qian, Yingxian Chen, Lei Zhou, Jason Wing Hon Wong, Yu Wang, Joshua Wing Kei Ho, Kui Kai Lau, Pei-Yuan Qian & Sookja Kim Chung
Additional file 8: Fig. S1. Characterization of baseline GM of WT, Epac1–/–, and Epac2–/– mice at the class and order levels. Fig. S2. Characterization of baseline GM of WT, Epac1–/–, and Epac2–/– mice at the family and genus levels. Fig. S3. GM alterations at the class and order levels in the WT, Epac1–/– and Epac2–/– mice induced by an 8-week WD. Fig. S4. GM alterations at the family level in the WT, Epac1–/– and Epac2–/–...

Deficiency of exchange protein directly activated by cAMP (EPAC)-1 in mice augments glucose intolerance, inflammation, and gut dysbiosis associated with Western diet

Preeti Dinesh Virwani, Lin Cai, Patrick Ka Kit Yeung, Gordon Qian, Yingxian Chen, Lei Zhou, Jason Wing Hon Wong, Yu Wang, Joshua Wing Kei Ho, Kui Kai Lau, Pei-Yuan Qian & Sookja Kim Chung
Abstract Background Gut microbiota (GM) dysregulation, known as dysbiosis, has been proposed as a crucial driver of obesity associated with “Western” diet (WD) consumption. Gut dysbiosis is associated with increased gut permeability, inflammation, and insulin resistance. However, host metabolic pathways implicated in the pathophysiology of gut dysbiosis are still elusive. Exchange protein directly activated by cAMP (Epac) plays a critical role in cell-cell junction formation and insulin secretion. Here, we used homozygous Epac1-knockout (Epac1–/–), Epac2-knockout...

Deficiency of exchange protein directly activated by cAMP (EPAC)-1 in mice augments glucose intolerance, inflammation, and gut dysbiosis associated with Western diet

Preeti Dinesh Virwani, Lin Cai, Patrick Ka Kit Yeung, Gordon Qian, Yingxian Chen, Lei Zhou, Jason Wing Hon Wong, Yu Wang, Joshua Wing Kei Ho, Kui Kai Lau, Pei-Yuan Qian & Sookja Kim Chung
Abstract Background Gut microbiota (GM) dysregulation, known as dysbiosis, has been proposed as a crucial driver of obesity associated with “Western” diet (WD) consumption. Gut dysbiosis is associated with increased gut permeability, inflammation, and insulin resistance. However, host metabolic pathways implicated in the pathophysiology of gut dysbiosis are still elusive. Exchange protein directly activated by cAMP (Epac) plays a critical role in cell-cell junction formation and insulin secretion. Here, we used homozygous Epac1-knockout (Epac1–/–), Epac2-knockout...

Supplementary document for Anomalous π Modes by Floquet Engineering in Optical Lattices with Long-range Coupling - 6137074.pdf

Shengjie Wu, Wange Song, Zhiyuan Lin, Chen Chen, Shining Zhu & Tao Li
Detailed theoretical calculation and experimental proposal

Additional file 4 of Repetitive mild TBI causes pTau aggregation in nigra without altering preexisting fibril induced Parkinson’s-like pathology burden

Vedad Delic, Joshua H. Karp, Maynard Guzman, Gabriel R. Arismendi, Katherine J. Stalnaker, Julia A. Burton, Kathleen E. Murray, Joshua P. Stamos, Kevin D. Beck, Arpine Sokratian, Andrew B. West & Bruce A. Citron
Additional file 4. Figure 2S. Figure 4S. S100beta serum levels were measured with the 3 most frequently cited commercially available antibodies using western blot approaches. S100beta was detected only in the brain homogenate with two antibodies A,B while the third antibody did not detect S100beta (C). White arrow indicates location of the faint 10 kDa band in brain homogenate controls.

sj-pdf-1-ajs-10.1177_03635465221130448 – Supplemental material for Double-Limb Graft Versus Single-Limb Graft Medial Patellofemoral Ligament Reconstruction for Recurrent Patellar Dislocation: A Meta-analysis of Randomized Controlled Trials and Cohort Studies

Long Pang, Kefan Mou, Yinghao Li, Tao Li, Jian Li, Jing Zhu & Xin Tang
Supplemental material, sj-pdf-1-ajs-10.1177_03635465221130448 for Double-Limb Graft Versus Single-Limb Graft Medial Patellofemoral Ligament Reconstruction for Recurrent Patellar Dislocation: A Meta-analysis of Randomized Controlled Trials and Cohort Studies by Long Pang, Kefan Mou, Yinghao Li, Tao Li, Jian Li, Jing Zhu and Xin Tang in The American Journal of Sports Medicine

Double-Limb Graft Versus Single-Limb Graft Medial Patellofemoral Ligament Reconstruction for Recurrent Patellar Dislocation: A Meta-analysis of Randomized Controlled Trials and Cohort Studies

Long Pang, Kefan Mou, Yinghao Li, Tao Li, Jian Li, Jing Zhu & Xin Tang
Background:The medial patellofemoral ligament (MPFL) is the most important stabilizer of lateral dislocation of the patella. Single-limb (SL) and double-limb (DL) graft MPFL reconstructions have been increasingly used to treat recurrent patellar dislocations, but the clinical efficacy of SL versus DL graft MPFL reconstructions remains controversial owing to the inconsistent conclusions of previous studies.Purpose:This study aimed to compare the clinical outcomes of SL and DL graft MPFL reconstructions for patients with recurrent patellar dislocation by...

sj-pdf-1-imr-10.1177_03000605221147201 - Supplemental material for Comparative analysis of three common imaging modalities for nasolabial cysts

Shengyang Liu, Dingqian Hao, Liang Yu, Hui Ma, Hui Zhao, Shujuan Sun, Peng Yu, Hongzhi Ji, Li Shi, Yuzhu Wan & Aiping Chen
Supplemental material, sj-pdf-1-imr-10.1177_03000605221147201 for Comparative analysis of three common imaging modalities for nasolabial cysts by Shengyang Liu, Dingqian Hao, Liang Yu, Hui Ma, Hui Zhao, Shujuan Sun, Peng Yu, Hongzhi Ji, Li Shi, Yuzhu Wan and Aiping Chen in Journal of International Medical Research

Petrogenesis and geochronology of the bronze fox porphyry Cu-Au deposit: Implications for the geodynamic evolution of the Gurvansaykhan Island arc, southern Mongolia

Bayaraa Ganbat, Xiaoyong Yang, Yu Wang, Dashdorjgochoo Odgerel, Mohamed Faisal, Dorjgochoo Sanchir, Amgaa Tsolmon, Enkhtur Munkhtur & Chao Sun
A diversity of Devonian-Carboniferous volcanic arcs and granitoid intrusions are exposed in the Gurvansaykhan arc terrane of southern Mongolia. Several giant porphyry Cu-Au-Mo deposits are associated with intrusions within these arcs. The Bronze Fox deposit located in the central part of the Gurvansaykhan arc terrane is an example of a potentially economic deposit with affinity of adakite-like granitoid porphyry (i.e. 428 Mt grading 0.26% to 0.30% Cu for up to 2,437 Mlb of copper and...

Advances in pharmacology, biosynthesis, and metabolic engineering of Scutellaria-specialized metabolites

Xinyi Yang, Sihao Zheng, Xiaotong Wang, Jing Wang, Syed Basit Ali shah, Yu Wang, Ranran Gao & Zhichao Xu
Scutellaria Linn., which belongs to the family Lamiaceae, is a commonly used medicinal plant for heat clearing and detoxification. In particular, the roots of S. baicalensis and the entire herb of S. barbata have been widely used in traditional medicine for thousands of years. The main active components of Scutellaria, including: baicalein, wogonin, norwogonin, scutellarein, and their glycosides have potential or existing drug usage. However, the wild resources of Scutellaria plants have been overexploited, and...

Identification of Escherichia coli β-glucuronidase inhibitors from Polygonum cuspidatum Siebold & Zucc.

Jing-Xin Li, Yu Wang, Ying Hao, Xiao-Kui Huo, Cheng-Peng Sun, Xiao-Xia Zhao, Jin-Cheng Wang, Jian-Bin Zhang, Jing Ning, Xiang-Ge Tian, Chao Wang, Wen-Yu Zhao, Xia Lv, Ya-Chen Li & Xiao-Chi Ma
Abstract Gut bacterial β-glucuronidase (GUS) can reactivate xenobiotics that exert enterohepatic circulation- triggered gastrointestinal tract toxicity. GUS inhibitors can alleviate drug-induced enteropathy and improve treatment outcomes. We evaluated the inhibitory effect of Polygonum cuspidatum Siebold & Zucc. and its major constituents against Escherichia coli GUS (EcGUS), and characterized the inhibitory mechanism of each of the components. Trans-resveratrol 4’-O-β-D-glucopyranoside (HZ-1) and (-)-epicatechin gallate (HZ-2) isolated from P. cuspidatum were identified as the key components and potent...

Individual differences in coping styles and associations with social structure in wild baboons (Papio anubis)

Alexander J. Pritchard, Alecia J. Carter & Ryne A. Palombit
The patterning of interactions between individuals over time form the foundation for relationships, which are the basis for social group structure. The emergent social structure scaling from interactions might, therefore, be influenced by individual differences in how individuals respond to stressors and uncertainty, which are often intrinsic aspects of social dynamics. During a 17-month study of wild olive baboons, Papio anubis, in Laikipia, Kenya, we measured individual differences in coping style and stress reactivity by...

Data from: Evolution alters post-invasion temporal dynamics in experimental communities.

Cara Faillace & Peter Morin
1. The causes and consequences of temporal variation in the abundance of organisms constitute central themes in ecological inquiry. Rapid evolution can occur over ecological time scales, potentially resulting in altered temporal variation in abundance and complicating inferences about the consequences of temporal variation. 2. We assessed whether evolution altered the temporal variability in species’ abundances in simple assemblages of species. We then compared experimental results to predictions from two-species models to better understand our...

Data from: Protection of large predators in a marine reserve alters size-dependent prey mortality

Rebecca L. Selden, Steven D. Gaines, Scott L. Hamilton & Robert R. Warner
Where predator–prey interactions are size-dependent, reductions in predator size owing to fishing has the potential to disrupt the ecological role of top predators in marine ecosystems. In southern California kelp forests, we investigated the size-dependence of the interaction between herbivorous sea urchins and one of their predators, California sheephead (Semicossyphus pulcher). Empirical tests examined how differences in predator size structure between reserve and fished areas affected size-specific urchin mortality. Sites inside marine reserves had greater...

Data from: Evidence that implicit assumptions of ‘no evolution’ of disease vectors in changing environments can be violated on a rapid timescale

Andrea Egizi, Nina H. Fefferman & Dina M. Fonseca
Projected impacts of climate change on vector-borne disease dynamics must consider many variables relevant to hosts, vectors and pathogens, including how altered environmental characteristics might affect the spatial distributions of vector species. However, many predictive models for vector distributions consider their habitat requirements to be fixed over relevant time-scales, when they may actually be capable of rapid evolutionary change and even adaptation. We examine the genetic signature of a spatial expansion by an invasive vector...

Data from: Vicariance divergence and gene flow among islet populations of an endemic lizard

Anna Runemark, Jody Hey, Bengt Hansson & Erik I. Svensson
Allopatry and allopatric speciation can arise through two different mechanisms: vicariance or colonization through dispersal. Distinguishing between these different allopatric mechanisms is difficult and one of the major challenges in biogeographical research. Here, we address whether allopatric isolation in an endemic island lizard is the result of vicariance or dispersal. We estimated the amount and direction of gene flow during the divergence of isolated islet populations and subspecies of the endemic Skyros wall lizard Podarcis...

Data from: Complex phylogeographic patterns in the freshwater alga Synura provide new insights on ubiquity versus endemism in microbial eukaryotes

Sung Min Boo, Han Soon Kim, Woongghi Shin, Ga Hun Boo, Sung Mi Cho, Bok Yeon Cho, Jee-Hwan Kim, Jin Hee Kim, Eun Chan Yang, Peter A Siver, Alexander P Wolfe, Debashish Bhattacharya, Robert A Andersen & Hwan Su Yoon
The global distribution, abundance, and diversity of microscopic freshwater algae demonstrate an ability to overcome significant barriers such as dry land and oceans by exploiting a range of biotic and abiotic colonization vectors. If these vectors are considered unlimited and colonization occurs in proportion to population size, then globally ubiquitous distributions are predicted to arise. This model contrasts with observations that many freshwater microalgal taxa possess true biogeographies. Here, using a concatenated multi-gene dataset, we...

Data from: Using seedling and pericarp tissues to determine maternal parentage of dispersed valley oak recruits

Peter E. Smouse, Victoria L. Sork, Douglas G. Scofield & Delphine Grivet
The spatial pattern of established seedlings yields valuable information about variation in fecundity, dispersal, and spatial structure of distributed recruits, but separating maternal and paternal contributions in monoecious species has been hampered by the “2 parent” problem. It is now possible to determine the maternal parentage of established recruits with genetic assay of maternally derived tissues of the seed or fruit, but the DNA of weathered maternal tissues often yields unreliable genotypes, reducing the practical...

Data from: Host conservatism or host specialization? Patterns of fungal diversification are influenced by host plant specificity in Ophiognomonia (Gnomoniaceae, Diaporthales)

Donald M. Walker, Amy Y. Rossman, Lisa A. Castlebury & Lena Struwe
In this study evolutionary host plant patterns at ranks from order to species were analysed using spatial evolutionary and ecological vicariance analysis (SEEVA), based on a multigene phylogeny of 45 ascomycete fungal species. The objective was to understand speciation events and host associations in Ophiognomonia (Gnomoniaceae). Species of this genus are perithecial fungi that occur as endophytes, pathogens, and latent saprobes on plants in the families of Betulaceae, Fagaceae, Juglandaceae, Lauraceae, Malvaceae, Platanaceae, Rosaceae, Salicaceae,...

Data from: Cryptic introductions and the interpretation of island biodiversity

Julian D. Avery, Dina M. Fonseca, Pascal Campagne & Julie L. Lockwood
Species with cryptic origins (i.e. those that cannot be reliably classed as native or non-native) present a particular challenge to our understanding of the generation and maintenance of biodiversity. Such species may be especially common on islands given that some islands have had a relatively recent history of human settlement. It is likely that select island species considered native might have achieved their current distributions via direct or indirect human actions. As an example, we...

Data from: Identifying loci under selection against gene flow in isolation with migration models

Vitor C. Sousa, Miguel Carneiro, Nuno Ferrand & Jody Hey
When divergence occurs in the presence of gene flow, there can arise an interesting dynamic in which selection against gene flow, at sites associated with population-specific adaptations or genetic incompatibilities, can cause net gene flow to vary across the genome. Loci linked to sites under selection may experience reduced gene flow and may experience genetic bottlenecks by the action of nearby selective sweeps. Data from histories such as these may be poorly fitted by conventional...

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