Miracle-dz/UniFAR-FTUs huggingface dataset:
Filtering across Spatial Scales: Phylogeny, Biogeography and Community Structure in Bumble Bees

Despite the expansion of phylogenetic community analysis to understand community assembly, few studies have used these methods on mobile organisms and it has been suggested the local scales that are typically considered may be too small to represent the community as perceived by organisms with high mobility. Mobility is believed to allow species to mediate competitive interactions quickly and thus highly mobile species may appear randomly assembled in local communities. At larger scales, however, biogeographical processes could cause communities to be either phylogenetically clustered or even. Using phylogenetic community analysis we examined patterns of relatedness and trait similarity in communities of bumble bees (Bombus) across spatial scales comparing: local communities to regional pools, regional communities to continental pools and the continental community to a global species pool. Species composition and data on tongue lengths, a key foraging trait, were used to test patterns of relatedness and trait similarity across scales. Although expected to exhibit limiting similarity, local communities were clustered both phenotypically and phylogenetically. Larger spatial scales were also found to have more phylogenetic clustering but less trait clustering. While patterns of relatedness in mobile species have previously been suggested to exhibit less structure in local communities and to be less clustered than immobile species, we suggest that mobility may actually allow communities to have more similar species that can simply limit direct competition through mobility.
Front‐Page News: The Effect of News Positioning on Financial Markets

This paper estimates the effect of news positioning on the speed of price discovery, using exogenous variation in prominent (“front‐page”) positioning of news articles on the Bloomberg terminal. Front‐page articles see 240% higher trading volume and 176% larger absolute excess returns during the first 10 minutes after publication than equally important non‐front‐page articles. Overall, the information in front‐page articles is fully incorporated into prices within an hour of publication. The response to non‐front‐page information of similar importance eventually converges but takes more than two days to be fully reflected in prices.This article is protected by copyright. All rights reserved
RE-AIM in Clinical, Community, and Corporate Settings: Perspectives, Strategies, and Recommendations to Enhance Public Health Impact

The RE-AIM Framework is a planning and evaluation model that has been used in a variety of settings to address various programmatic, environmental, and policy innovations for improving population health. In addition to the broad application and diverse use of the framework, there are lessons learned and recommendations for the future use of the framework across clinical, community, and corporate settings. The purposes of this article are to: (A) provide a brief overview of the RE-AIM Framework and its pragmatic use for planning and evaluation; (B) offer recommendations to facilitate the application of RE-AIM in clinical, community, and corporate settings; and (C) share perspectives and lessons learned about employing RE-AIM dimensions in the planning, implementation, and evaluation phases within these different settings. In this article, we demonstrate how the RE-AIM concepts and elements within each dimension can be applied by researchers and practitioners in diverse settings, among diverse populations and for diverse health topics.
The Dynamic International Optimal Hedge Ratio

Instead of modeling asset price and currency risks separately, this paper derives the international hedge portfolio, hedging asset price and currency risk simultaneously for estimating the dynamic international optimal hedge ratio. The model estimation is specified in a multivariate GARCH setting with vector error correction terms and estimated for the commodity and stock markets of the U.S., the U.K., and Japan.
Controlling Decoding for More Abstractive Summaries with Copy-Based Networks

Attention-based neural abstractive summarization systems equipped with copy mechanisms have shown promising results. Despite this success, it has been noticed that such a system generates a summary by mostly, if not entirely, copying over phrases, sentences, and sometimes multiple consecutive sentences from an input paragraph, effectively performing extractive summarization. In this paper, we verify this behavior using the latest neural abstractive summarization system - a pointer-generator network. We propose a simple baseline method that allows us to control the amount of copying without retraining. Experiments indicate that the method provides a strong baseline for abstractive systems looking to obtain high ROUGE scores while minimizing overlap with the source article, substantially reducing the n-gram overlap with the original article while keeping within 2 points of the original model's ROUGE score.
Effectiveness and Safety of Biolimus A9™-Eluting stEnt in Patients with AcUTe Coronary sYndrome; A Multicenter, Observational Study (BEAUTY Study)

Purpose This study sought to determine the 1-year clinical effectiveness and safety of a biodegradable, polymer-containing Biolimus A9™-eluting stent (BES) in Korean patients with acute coronary syndrome (ACS). Materials and Methods A total of 1000 ACS patients with 1251 lesions who underwent implantation of BESs at 22 centers in Korea were enrolled between May 2011 and July 2013. We assessed major adverse cardiac events (MACE) defined as the composite of cardiac death, non-fatal myocardial infarction (MI), and clinical-driven target vessel revascularization at 12 months. Results Patient mean age was 62.6±11.4 years. 72.8% of the patients were male, 28.5% had diabetes, 32.8% had multi-vessel disease (MVD), and 47.9% presented with acute MI (AMI). The mean global registry of acute coronary events risk score of all patients was 103.0±27.6. The number of stents per patient was 1.3±0.6. The incidences of MACE and definite stent thrombosis at 12 months were 3.9% and 0.2%, respectively. On multivariate Cox-regression analysis, age ≥65 years was identified as an independent predictors of 1-year MACE (hazard ratio=2.474; 95% confidence interval=1.202−5.091). Subgroup analyses revealed no significant differences in the incidence of MACE between patients with and without diabetes (4.3% vs. 3.7%, p=0.667), between those who presented with and without AMI (4.4% vs. 3.4%, p=0.403), and between those with and without MVD (4.6% vs. 3.5%, p=0.387). Conclusion Our study demonstrated excellent 1-year clinical outcomes of BES implantation in patients at low-risk for ACS.
Amyloid Assembly Endows Gad m 1 with Biomineralization Properties

Acid proteins capable of nucleating Ca2+ and displaying aggregation capacity play key roles in the formation of calcium carbonate biominerals. The helix-loop helix EF-hands are the most common Ca2+-binding motifs in proteins. Calcium is bound by the loop region. These motifs are found in many proteins that are regulated by calcium. Gad m 1, an Atlantic cod β-parvalbumin isoform, is a monomeric EF-hand protein that acts as a Ca2+ buffer in fish muscle; the neutral and acid apo-forms of this protein can form amyloids. Since Ca2+-nucleating proteins have a propensity to form extended β-strand structures, we wondered whether amyloid assemblies of an EF-hand protein were able to influence calcium carbonate crystallization in vitro. Here, we used the Gad m 1 chain as a model to generate monomeric and amyloid assemblies and to analyze their effect on calcite formation in vitro. We found that only amyloid assemblies alter calcite morphology.
Administration of Non-Absorbable Antibiotics to Pregnant Mice to Perturb the Maternal Gut Microbiota Is Associated with Alterations in Offspring Behavior

There is increasing evidence that the gut microbiota plays a major role in host health and disease. In this study, we examined whether perturbation of the maternal gut microbiota during pregnancy, induced by administration of non-absorbable antibiotics to pregnant dams, influences the behavior of offspring. Terminal restriction fragment length polymorphism analyses of fecal bacterial composition showed that the relative abundance of the bacterial order Lactobacillales was lower in offspring born from antibiotic-treated dams (20.7±3.4%) than in control offspring (42.1±6.2%) at P24, while the relative abundance of the bacterial family Clostridium subcluster XIVa was higher in offspring born from antibiotic-treated dams (34.2±5.0%) than in control offspring (16.4±3.3%). Offspring born from antibiotic-treated dams exhibited low locomotor activity in both familiar and novel environments, and preferred to explore in the peripheral area of an unfamiliar field at postnatal week 4. At postnatal weeks 7–8, no difference was observed in the level of locomotor activity between control offspring and offspring from antibiotic-treated dams, while the tendency for the offspring from antibiotic-treated dams to be less engaged in exploring the inside area was still observed. The behavioral phenotypes of the offspring from antibiotic-treated dams at postnatal week 4 could be rescued to a considerable extent through fostering of these offspring by normal dams from postnatal day 1. Although the detailed underlying mechanisms are not fully elucidated, the present results suggest that administration of non-absorbable antibiotics to pregnant dams to perturb the maternal gut microbiota during pregnancy leads to alterations in the behavior of their offspring.
Projected Near-Future Levels of Temperature and pCO2 Reduce Coral Fertilization Success

Increases in atmospheric carbon dioxide (pCO2) are projected to contribute to a 1.1–6.4°C rise in global average surface temperatures and a 0.14–0.35 reduction in the average pH of the global surface ocean by 2100. If realized, these changes are expected to have negative consequences for reef-building corals including increased frequency and severity of coral bleaching and reduced rates of calcification and reef accretion. Much less is known regarding the independent and combined effects of temperature and pCO2 on critical early life history processes such as fertilization. Here we show that increases in temperature (+3°C) and pCO2 (+400 µatm) projected for this century negatively impact fertilization success of a common Indo-Pacific coral species, Acropora tenuis. While maximum fertilization did not differ among treatments, the sperm concentration required to obtain 50% of maximum fertilization increased 6- to 8- fold with the addition of a single factor (temperature or CO2) and nearly 50- fold when both factors interact. Our results indicate that near-future changes in temperature and pCO2 narrow the range of sperm concentrations that are capable of yielding high fertilization success in A. tenuis. Increased sperm limitation, in conjunction with adult population decline, may have severe consequences for coral reproductive success. Impaired sexual reproduction will further challenge corals by inhibiting population recovery and adaptation potential.
Developmental Regulation of Diacylglycerol Acyltransferase Family Gene Expression in Tung Tree Tissues

Diacylglycerol acyltransferases (DGAT) catalyze the final and rate-limiting step of triacylglycerol (TAG) biosynthesis in eukaryotic organisms. DGAT genes have been identified in numerous organisms. Multiple isoforms of DGAT are present in eukaryotes. We previously cloned DGAT1 and DGAT2 genes of tung tree (Vernicia fordii), whose novel seed TAGs are useful in a wide range of industrial applications. The objective of this study was to understand the developmental regulation of DGAT family gene expression in tung tree. To this end, we first cloned a tung tree gene encoding DGAT3, a putatively soluble form of DGAT that possesses 11 completely conserved amino acid residues shared among 27 DGAT3s from 19 plant species. Unlike DGAT1 and DGAT2 subfamilies, DGAT3 is absent from animals. We then used TaqMan and SYBR Green quantitative real-time PCR, along with northern and western blotting, to study the expression patterns of the three DGAT genes in tung tree tissues. Expression results demonstrate that 1) all three isoforms of DGAT genes are expressed in developing seeds, leaves and flowers; 2) DGAT2 is the major DGAT mRNA in tung seeds, whose expression profile is well-coordinated with the oil profile in developing tung seeds; and 3) DGAT3 is the major form of DGAT mRNA in tung leaves, flowers and immature seeds prior to active tung oil biosynthesis. These results suggest that DGAT2 is probably the major TAG biosynthetic isoform in tung seeds and that DGAT3 gene likely plays a significant role in TAG metabolism in other tissues. Therefore, DGAT2 should be a primary target for tung oil engineering in transgenic organisms.
A flexible authorization mechanism for relational data management systems

In this article, we present an authorization model that can be used to express a number of discretionary access control policies for relational data management systems. The model permits both positive and negative authorizations and supports exceptions at the same time. The model is flexible in that the users can specify, for each authorization they grant, whether the authorization can allow for exceptions or whether it must be strongly obeyed. It provides authorization management for groups with exceptions at any level of the group hierarchy, and temporary suspension of authorizations. The model supports ownership together with decentralized administration of authorizations. Administrative privileges can also be restricted so that owners retain control over their tables.
Increasing recovery time between injuries improves cognitive outcome after repetitive mild concussive brain injuries in mice.

BACKGROUND Although previous evidence suggests that the cognitive effects of concussions are cumulative, the effect of time interval between repeat concussions is largely unknown. OBJECTIVE To determine the effect of time interval between repeat concussions on the cognitive function of mice. METHODS We used a weight-drop model of concussion to subject anesthetized mice to 1, 3, 5, or 10 concussions, each a day apart. Additional mice were subjected to 5 concussions at varying time intervals: daily, weekly, and monthly. Morris water maze performance was measured 24 hours, 1 month, and 1 year after final injury. RESULTS After 1 concussion, injured and sham-injured mice performed similarly in the Morris water maze. As the number of concussions increased, injured mice performed worse than sham-injured mice. Mice sustaining 5 concussions either 1 day or 1 week apart performed worse than sham-injured mice. When 5 concussions were delivered at 1-month time intervals, no difference in Morris water maze performance was observed between injured and sham-injured mice. After a 1-month recovery period, mice that sustained 5 concussions at daily and weekly time intervals continued to perform worse than sham-injured mice. One year after the final injury, mice sustaining 5 concussions at a daily time interval still performed worse than sham-injured mice. CONCLUSION When delivered within a period of vulnerability, the cognitive effects of multiple concussions are cumulative, persistent, and may be permanent. Increasing the time interval between concussions attenuates the effects on cognition. When multiple concussions are sustained by mice daily, the effects on cognition are long term.
Increased Cell Proliferation and Mucocyte Density in the Sea Anemone Aiptasia pallida Recovering from Bleaching

Recovery of coral after bleaching episodes is a critical period for the health of the reef ecosystem. While events such as symbiont (genus Symbiodinium) shifting/shuffling or tissue apoptosis have been demonstrated to occur following bleaching, little is known concerning tissue recovery or cell proliferation. Here, we studied the sea anemone Aiptasia pallida exposed to a transient elevation of water temperature combined with high illumination (33°C and 1900 µmolphotons.m−2.s−1 for 30h). Following such treatment bleached anemones showed a significant reduction of their Symbiodinium density. Cell proliferation in the ectodermis and gastrodermis was determined by assessing the densities of cells labeled with a thymidine analogue (EdU). Cell proliferation significantly increased during the first day following stress in both tissue types. This increased cell proliferation returned to pre-stress values after one week. Although cell proliferation was higher in the ectodermis in absence of stress, it was relatively more pronounced in the gastrodermis of stressed anemones. In addition, the ratio of ectodermal mucocytes significantly increased three weeks after induced stress. These results suggest that thermal/photic stress coupled with the loss of the symbionts is able to enhance cell proliferation in both gastrodermis and ectodermis of cnidarians. While new cells formed in the gastrodermis are likely to host new Symbiodinium, the fate of new cells in the ectodermis was only partially revealed. Some new ectodermal cells may, in part, contribute to the increased number of mucocytes which could eventually help strengthen the heterotrophic state until restoration of the symbiosis.
Herbivory and Body Size: Allometries of Diet Quality and Gastrointestinal Physiology, and Implications for Herbivore Ecology and Dinosaur Gigantism

Digestive physiology has played a prominent role in explanations for terrestrial herbivore body size evolution and size-driven diversification and niche differentiation. This is based on the association of increasing body mass (BM) with diets of lower quality, and with putative mechanisms by which a higher BM could translate into a higher digestive efficiency. Such concepts, however, often do not match empirical data. Here, we review concepts and data on terrestrial herbivore BM, diet quality, digestive physiology and metabolism, and in doing so give examples for problems in using allometric analyses and extrapolations. A digestive advantage of larger BM is not corroborated by conceptual or empirical approaches. We suggest that explanatory models should shift from physiological to ecological scenarios based on the association of forage quality and biomass availability, and the association between BM and feeding selectivity. These associations mostly (but not exclusively) allow large herbivores to use low quality forage only, whereas they allow small herbivores the use of any forage they can physically manage. Examples of small herbivores able to subsist on lower quality diets are rare but exist. We speculate that this could be explained by evolutionary adaptations to the ecological opportunity of selective feeding in smaller animals, rather than by a physiologic or metabolic necessity linked to BM. For gigantic herbivores such as sauropod dinosaurs, other factors than digestive physiology appear more promising candidates to explain evolutionary drives towards extreme BM.
Hybrid Multi-scale Simulations of Fracture of Silicon Single Crystals

We report a novel multi-paradigm multi-scale approach based on a combination of the first principles ReaxFF force field with an empirical Tersoff potential. Our hybrid multi-scale simulation model is computationally efficient and capable of treating thousands of atoms with QM accuracy, extending our ability to simulate the dynamical behavior of a wider range of chemically complex materials such as silicon, silica and metal-organic compounds. We exemplify our method in a study focused on fracture dynamics in silicon under mode I tensile and mode II shear loading. Under mode I loading, we observe a jump in the crack speed as the critical fracture load reached, which is also seen in experiments. We show that this threshold crack speed may be due to a localized phase transformation of the silicon lattice from 6-membered rings to a 5-7 double ring at the tip of the crack. Study of a shear mode II crack shows it tends to branch at an angle of approximately 45 degrees from the original path once the crack speed approaches 38% of the Rayleigh-wave speed. Our studies illustrate the significance of the properties of an ensemble of chemical bonds under large deformation, an aspect neglected in most existing fracture theories.
Cbfβ governs osteoblast−adipocyte lineage commitment through enhancing β-catenin signaling and suppressing adipogenesis gene expression

Significance Age-associated increased marrow adiposity is often coupled with increased bone loss, presenting a significant age-associated osteoporosis health problem. Here, we examined the mechanisms underlying how transcription factors regulate mesenchymal stem cell lineage determination and showed that Cbfβ plays a critical role in stimulating osteogenesis and inhibiting adipogenesis through activating Wnt10b/β-catenin signaling and inhibiting adipogenesis regulatory gene (c/ebpα) expression. The insights resulting from this study will fill an important knowledge gap and may facilitate the development of novel bone loss therapeutics that minimize the adverse side effects on bone homeostasis. The mechanism underlying how transcription factors regulate mesenchymal stem cell lineage commitment remains unclear. To determine the role of core-binding factor subunit beta (Cbfβ) in osteoblast lineage commitment, we generated three mouse models by deleting Cbfβ at different osteoblast lineage stages. We demonstrated that the Cbfβf/fPrx1-Cre, Cbfβf/fCol2α1-Cre, and Cbfβf/fOsx-Cre mice exhibited severe osteoporosis with substantial accumulation of marrow adipocytes resembling aged bone from enhanced adipogenesis, indicating that mesenchymal stem cells and osteoblasts can be programed and reprogramed, respectively, into adipocytes. Consistently, Cbfβ-deficient calvarial cells and bone marrow mesenchymal stem cells displayed strong adipogenic potential, with 5- to ∼70-fold increased adipocyte gene expression, which can be rescued by Cbfβ overexpression. Canonical Wnt signaling was impeded in the Cbfβ-deficient cells, with ∼80% decrease of Wnt10b expression. Accordingly, ChIP and luciferase assays demonstrated that Cbfβ/RUNX2 binds to Wnt10b promoter driving Wnt10b expression. Furthermore, Wnt3a suppressed adipogenesis but did not rescue osteoblastogenesis in Cbfβ-deficient cells. Notably, mixing culture of Cbfβ-deficient with normal cells demonstrates that Cbfβ functions not only through WNT paracrine pathway but also through endogenous signaling. Further analysis shows that Cbfβ/RUNX2 inhibits c/ebpα expression at transcriptional level. Our results show that, besides its osteogenic role, Cbfβ governs osteoblast−adipocyte lineage commitment both cell nonautonomously through enhancing β-catenin signaling and cell autonomously through suppressing adipogenesis gene expression to maintain osteoblast lineage commitment, indicating Cbfβ may be a therapeutic target for osteoporosis.