bluuebunny/crossref_metadata_2025_split huggingface dataset:
Edge-of-field runoff prediction by a hybrid modeling approach using causal inference
Authors: Hu Yao , Fitzpatrick Lindsay , Fry Lauren M , Mason Lacey , Read Laura K , Goering Dustin C 
Published: June 2021

Abstract
Unforeseen runoff events cause nutrient losses that affect crop production, revenue, and contribute to deteriorated water quality, leading to harmful algal blooms and hypoxia in receiving water bodies in the Great Lakes region. To mitigate the negative impacts caused by runoff events, we developed a hybrid modeling approach by combining physics-based and statistical models to predict the occurrence and level of severity of daily runoff events, supporting agricultural producers to avoid nutrient application before significant runoff events. We chose to use the National Oceanic and Atmospheric Administration’s National Water Model (NWM) as the physical model given its flexible architecture design, technical robustness, model resolution, data availability, and wide application scale. For the statistical model, we developed a data-driven tool built from Directed Information and eXtreme Gradient Boosting (XGBoost) to estimate the occurrence and the level of severity of daily edge-of-eld (EOF) runoff events. This data-driven tool ingests a large variety of variables from NWM operational runs and translates them into the EOF runoff predictions on a daily scale in the Great Lakes region. Without calibrating the large-scale NWM for the local runoff prediction, the results show large improvements in the prediction of the occurrence and level of severity of daily EOF runoff using the hybrid physical-statistical modeling approach. Ultimately, the hybrid approach, when integrated into runoff risk decision support tools, is expected to provide dual benefits to agricultural producers and water quality, retaining more nutrients on their fields and lowering nutrient loads to water bodies during runoff events.
The evolutionary origin of near-death experiences: a systematic investigation
Authors: Peinkhofer Costanza , Martial Charlotte , Cassol Helena , Laureys Steven , Kondziella Daniel 
Published: June 2021

AbstractNear-death experiences are known from all parts of the world, various times and numerous cultural backgrounds. This universality suggests that near-death experiences may have a biological origin and purpose. Adhering to a preregistered protocol, we investigate the hypothesis that thanatosis, aka death-feigning, a last-resort defense mechanism in animals, is the evolutionary origin of near-death experiences. We first show that thanatosis is a highly preserved survival strategy occurring at all major nodes in a cladogram ranging from insects to humans. We then show that humans under attack by animal, human and ‘modern’ predators can experience both thanatosis and near-death experiences, and we further show that the phenomenology and the effects of the two overlap. In summary, we build a line of evidence suggesting that thanatosis is the evolutionary foundation of near-death experiences and that their shared biological purpose is the benefit of survival. We propose that the acquisition of language enabled humans to transform these events from relatively stereotyped death-feigning under predatory attacks into the rich perceptions that form near-death experiences and extend to non-predatory situations.
Hilbert’s Tenth Problem for Complex Meromorphic Functions in Several Variables
Authors: Pheidas Thanases , Vidaux Xavier 
Published: June 2021

Abstract
We prove that Hilbert’s Tenth Problem for meromorphic functions and for entire functions in several variables is unsolvable over the language of rings, together with constant symbols for two of the variables and a predicate for a place. This is the first result in the literature, which proves unsolvability of a diophantine problem for the ring of complex analytic functions in a number of variables. The proof rests upon an interplay between analytic geometry, analysis, number theory, and logic.
KIC 9406652: A laboratory for tilted disks in cataclysmic variable stars. II. Modeling of the orbital light curves
Authors: Kimura Mariko , Osaki Yoji 
Published: June 2021

Abstract
KIC 9406652, one of the recently identified IW And-type dwarf novae, is the best target for studying the tilted disk in cataclysmic variable stars. In a previous paper by Kimura et al. (2020b, PASJ, 72, 94), we analyzed its Kepler light curves and found that its orbital light curves during the brightening stage were dominated by the reflection effect of the secondary star and varied with the orientation of the tilted disk; the amplitude was maximized at the minimum of the super-orbital signal and the phase of the light maximum shifted to an earlier one with the advance of the super-orbital phase. We argued in that work that this was direct evidence of the retrogradely precessing tilted disk as the secondary star acts like a reflecting object. In order to confirm this interpretation, we have performed numerical modeling of orbital light curves in this paper. We have succeeded in reproducing the main characteristics of the observed orbital light curves by a simple model in which the secondary star is irradiated by the tilted disk. We have also constrained the inclination angle, i, of the binary system and the tilt angle, θ, of the disk purely from photometric considerations. The best-fitting parameter set is found to be i ∼ 45° and $\theta \sim {2{_{.}^{\circ}}0}$, respectively. The orbital inclination thus estimated is consistent with that obtained from the spectroscopic considerations within the uncertainty limit. On the other hand, the tilt angle of the disk could be underestimated by using only the semi-amplitude of super-orbital signals.
Deciphering controversial results of cell proliferation on TiO2 nanotubes using machine learning
Authors: Shen Ziao , Wang Si , Shen Zhenyu , Tang Yufei , Xu Junbin , Lin Changjian , Chen Xun , Huang Qiaoling 
Published: June 2021

Abstract
With the rapid development of biomedical sciences, contradictory results on the relationships between biological responses and material properties emerge continuously, adding to the challenge of interpreting the incomprehensible interfacial process. In the present paper, we use cell proliferation on titanium dioxide nanotubes (TNTs) as a case study and apply machine learning methodologies to decipher contradictory results in the literature. The gradient boosting decision tree model demonstrates that cell density has a higher impact on cell proliferation than other obtainable experimental features in most publications. Together with the variation of other essential features, the controversy of cell proliferation trends on various TNTs is understandable. By traversing all combinational experimental features and the corresponding forecast using an exhausted grid search strategy, we find that adjusting cell density and sterilization methods can simultaneously induce opposite cell proliferation trends on various TNTs diameter, which is further validated by experiments. This case study reveals that machine learning is a burgeoning tool in deciphering controversial results in biomedical researches, opening up an avenue to explore the structure–property relationships of biomaterials.
Effects of lipid and starch supplementation as water intake mitigation techniques on performance and efficiency of nursing Holstein calves
Authors: Macias Franco A , da Silva A E M , de Moura F H , Norris A B , Van Den Broek K , Valcheck M , de Mello A , Fonseca M 
Published: June 2021

Abstract
Exploring alternative supplementation sources capable of maximizing feed and water efficiency in nursing Holstein calves is often ignored. The goals herein involve investigating the effects of two isoenergetic supplements on a nonmedicated milk replacer diet on total water intake, milk water intake, fresh water intake, feed intake parameters, and performance of Holstein nursing bull calves. Twenty-three animals (body weight [BW] = 94.67 ± 12.07 kg, age = 67 days old) were randomly assigned to one of three treatments for 68 days: control (CON; ad libitum milk replacer, n = 7), carbohydrate supplement (CHO; corn starch on top of ad libitum milk replacer-based diet, n = 8), or lipid supplement (FAT; menhaden fish oil on top of ad libitum milk replacer-based diet, n = 8). The isoenergetic supplementation consisted of 3% menhaden fish oil addition on DM basis for FAT. This was matched energetically with corn starch for the CHO group resulting in a 7% composition in DM basis. All animals were provided free access to mineral mix and 120 g daily dried microbrewer’s spent grains (BG). Data were analyzed with the GLMMIX procedure of SAS in a completely randomized design with the diets as a fixed effect. Dry matter intake (DMI) adjusted by average daily gain (ADG; DMI/ADG) resulted in significantly lower values for supplemented groups with CON = 2.48, CHO = 2.38, and FAT = 2.27 kg/kg (ADG) (P = 0.033). Energy intake values were lower for CON when analyzing metabolizable energy intake (P &lt; 0.0001), net energy intake for maintenance (P &lt; 0.0001), and net energy intake for gain (P &lt; 0.0001), followed by CHO, and then FAT. Total water intake (P &lt; 0.0001), milk water intake (P &lt; 0.0001), and fresh water intake (P &lt; 0.0001) all resulted in CHO consuming 0.5 L or less water than the other two treatments. Energy requirements as digestible energy (P &lt; 0.0001), metabolizable energy (P &lt; 0.0001), net energy for maintenance (P &lt; 0.0001), and net energy for gain (P &lt; 0.0001) were lower for CHO, followed by CON, and then FAT having the highest requirements. Similar results were observed for residual feed (RFI; P = 0.006) and residual water intakes (RTWI; P = 0.902). Ultimately, no performance differences were detected with regards to BW (CON = 146.71, CHO = 146.25, and FAT = 150.48 kg; P &gt; 0.1). These results indicate that lipid-based and starch-based supplementation can potentially increase feed efficiency and decrease voluntary water intake without adversely affecting performance.
Host microbe interactions in the primate gut: Implications for human origins
Authors: Gomez Andres , Torralba Manlito , Nelson Karen E. , Stumpf Rebecca , Blekhman Ran , Petrzelkova Klara 
Published: June 2021

The breadth of microbiome research produced in the last decade has evidenced the vast diversity of human‐associated microbial systems, correlating specific microbial states to a myriad of host phenotypes. However, there is still a significant gap in our understanding of how humans and their residing microbes communicate, in light of environmental change and host evolution. By employing a meta‐OMIC approach (metatranscriptomics, metagenomics and metabolomics) in stool samples of wild western lowland gorillas (G.g.gorilla) and BaAka hunter‐gatherers (H.sapiens), and non‐invasive screening of host‐derived signals from fecal samples, we sought to characterize gene expression profiles in the tissue lining up the host distal gut, in the context of host‐specific bacterial composition, function and diets. The data show that despite the limited amount of host signals generated from fecal samples, unique gene regulation profiles distinguishing the colonic tissue of the 2 primate species correlate strongly with the abundance of particular metabolites and bacterial taxa; specifically, while increased expression of genes involved in metabolism and cell architecture characterizing the distal gut tissue of gorillas corresponded with higher abundance of phenolic metabolites; differential expression of immune‐associated genes in human colonic tissue showed associations with lipid‐derived metabolites and bacteria typically associated with the processing of simpler polysaccharides. As such, we discuss how diet‐derived metabolites and the gut microbiome converged to impact genes involved nutrition and immunity in the host along evolutionary timescales, and examine the pivotal role that diet could have had in human speciation and evolution, through a microbiome lens. Likewise, we show how studies of this nature could lay the foundations to understand mechanistic insights of gene regulation by the microbiome to impact diverse host phenotypes.Support or Funding InformationKONTAKT (American Science Information Agency, Czech‐American Scientific cooperation)This abstract is from the Experimental Biology 2018 Meeting. There is no full text article associated with this abstract published in The FASEB Journal.
The gut microbiome connection to Parkinson's disease
Authors: Mazmanian Sarkis K. 
Published: June 2021

The intestinal microbiota influence neurodevelopment, modulate behavior, and contribute to neurological disorders. However, a functional link between gut bacteria and neurodegenerative diseases remains unexplored. Synucleinopathies are characterized by aggregation of the protein a–synuclein (aSyn), often resulting in motor dysfunction as exemplified by Parkinson's disease (PD). Using mice that overexpress aSyn, we report herein that gut microbiota are required for motor deficits, microglia activation, and aSyn pathology. Antibiotic treatment ameliorates, while microbial re‐colonization promotes, pathophysiology in adult animals, suggesting that postnatal signaling between the gut and the brain modulates disease. Indeed, oral administration of specific microbial metabolites to germ‐free mice promotes neuroinflammation and motor symptoms. Remarkably, colonization of aSyn‐overexpressing mice with microbiota from PD‐affected patients enhances physical impairments compared to microbiota transplants from healthy human donors. These findings reveal that gut bacteria regulate movement disorders in mice and suggest that alterations in the human microbiome represent a risk factor for PD.Support or Funding InformationNational Institutes of HealthThis abstract is from the Experimental Biology 2018 Meeting. There is no full text article associated with this abstract published in The FASEB Journal.
Structural and Functional Studies of the Streptococcal Fibrillar Adhesin CshA
Authors: Back Catherine , Higman‐Davies Victoria , Sztukowska Maryta , Till Marisa , Crump Matthew , Lamont Richard , Jenkinson Howard , Nobbs Angela , Race Paul 
Published: June 2021

Adherence of bacteria to biotic or abiotic surfaces is a prerequisite for host colonization and represents an important step in microbial pathogenicity. This attachment is facilitated by bacterial adhesins at the cell surface. Due to their size and often elaborate multi‐domain architectures, these polypeptides represent challenging targets for detailed structural and functional characterization. The multifunctional fibrillar adhesin CshA, which mediates binding to both host molecules and other microorganisms, is an important determinant of colonization by Streptococcus gordonii, an oral commensal and opportunistic human pathogen. CshA has a low sequence identity to other proteins, indicating potentially novel structural characteristics.Our studies indicate that the N‐terminal region of CshA forms a functional head of the fibril, with a disordered portion at the tip. The C‐terminal region comprises 17 repeat blocks, each of ~99 aa residues (three incomplete), which form a long, flexible stalk, presenting the potential binding domain distal from the bacterial cell surface. In this study we present a structural analysis of CshA, derived from a combination of X‐ray crystallography, NMR, SAXS, and complementary biophysical methods. The data suggest that CshA has a novel structure not previously reported for bacterial cell surface adhesins.CshA binds the high‐molecular‐weight glycoprotein fibronectin (Fn) via the N‐terminal non‐repetitive region, and this protein‐protein interaction has been proposed to promote S. gordonii colonization at multiple sites within the host. However, the molecular details of how these two proteins interact had not previously been investigated. In vitro binding studies support a hitherto unreported two‐state ‘catch‐clamp’ mechanism of Fn binding by CshA. The disordered N‐terminal domain of CshA acts to ‘catch’ Fn, via formation of a rapidly assembled but also readily dissociable pre‐complex, enabling its neighbouring ligand binding domain to tightly ‘clamp’ the two polypeptides together. This study presents a new paradigm for target binding by a bacterial adhesin, the identification of which will inform future efforts towards the development of anti‐adhesive agents that target S. gordonii and related streptococci.Support or Funding InformationThis work was supported in part by National Institutes of Health grants DE016690 (to H. F. J. and R. J. L.) and DE012505 (to R. J. L.), Biotechnology and Biological Sciences Research Council Grant BB/I006478/1 (to P. R. R.), and Royal Society University Research Fellowship Award UF080534 (to P. R. R.). The content is solely the responsibility of the authors and does not necessarily represent the official views of the National Institutes of Health.This abstract is from the Experimental Biology 2018 Meeting. There is no full text article associated with this abstract published in The FASEB Journal.
Chemical tools to investigate gene regulation by histone sumoylation
Authors: Chatterjee Champak 
Published: June 2021

Histone modification by the small ubiquitin‐like modifier protein (SUMO) has been observed from yeast to humans. However, little is known regarding the precise biochemical roles of histone sumoylation, or its interplay with other key histone modifications such as methylation and acetylation. Efforts to investigate histone sumoylation are limited by the low abundance and transient nature of this modification in cells. Therefore, we developed and applied several facile chemical strategies to generate site‐specifically sumoylated histones in sufficient amounts for biochemical studies. Chemically sumoylated histones were reconstituted in nucleosomes and employed in a series of biochemical assays with the LSD1‐CoREST complex. Results from these experiments revealed an unprecedented relationship between histone sumoylation, methylation and acetylation and provided the first mechanistic clues toward gene regulation by SUMO.Support or Funding InformationR01 GM110430This abstract is from the Experimental Biology 2018 Meeting. There is no full text article associated with this abstract published in The FASEB Journal.
Semi‐Synthetic Glycosaminoglycan Ethers Decrease Receptors for Advanced Glycation End‐Products and Increase AXL Receptor in the Lung from Secondhand Smoke Treated Mice
Authors: Ostergar Adam , Egbert Kaleb , Clark Christian , Hall Parker , Davis Taylor , Hirschi Kelsey M. , Arroyo Juan A. , Reynolds Paul R. 
Published: June 2021

Tobacco exposure is one of the top three global health risks leading to the development of chronic obstructive pulmonary disease (COPD). Although there is extensive research into the effects of cigarette smoke, the effect of secondhand smoke (SHS) in the lung remains limited. SHS induces Receptors for advanced glycation end‐products (RAGE) and an inflammatory response that leads to the development of COPD characteristics. Semi‐synthetic glycosaminoglycan ethers (SAGEs) are sulfated polysaccharides derived from hyaluronic acid (HA) that inhibit RAGE signaling. The growth arrest‐specific 6 (Gas6) protein is known to induce dynamic cellular responses and is correlated with cell function. Gas6 binds to the AXL tyrosine kinase receptor and AXL‐mediated signaling is implicated in proliferation and migratory mechanisms in several tissues. This project's purpose was to study the correlation between RAGE, AXL, and Gas6 during SHS exposure in the lung. C57/Bl6 mice were exposed to SHS alone or SHS + SAGEs for 4 weeks and compared to control animals exposed to room air (RA). At the time of necropsy lungs were extracted, frozen for mRNA studies or embedded for immunohistological analysis. Compared to controls we observed: 1) increased RAGE mRNA expression in SHS‐exposed lungs which was decreased by SAGEs; 2) no difference in Gas6 or AXL expression in SHS lungs and expression was significantly increased with SAGEs; 3) increased RAGE protein expression in SHS lungs that was decreased by SAGEs; and 4) decreased AXL protein in SHS animals and increased AXL protein in animals treated with SAGEs. Our results suggest that there is a direct correlation between RAGE and AXL during SHS exposure. These studies provide insight into tobacco‐mediated effects in the lung and clarify possible avenues for alleviating complications that could arise during SHS exposure such as those observed during COPD.Support or Funding InformationThis work was supported by a grant from the Flight Attendant's Medical Research Institute (FAMRI, PRR and JAA) and a BYU Mentoring Environment Grant (JAA and PRR).This abstract is from the Experimental Biology 2018 Meeting. There is no full text article associated with this abstract published in The FASEB Journal.
Role of Farnesoid X Receptor Activation in Counteracting Tumor‐promoting Functions of Cancer‐Associated Fibroblasts in Breast Cancers
Authors: BARONE INES , Vircillo Valentina , Giordano Cinzia , Tarallo Roberta , Rinaldi Antonio , Bruno Giuseppina , Gyorffy Balazs , Bonofiglio Daniela , Andò Sebastiano , Catalano Stefania 
Published: June 2021

Cancer‐associated fibroblasts (CAFs), the principal components of the tumor microenvironment, play multiple roles in breast cancer onset and progression. While their significance is widely accepted, treatment options to target CAFs in clinical practice have not yet been well established. The nuclear receptor superfamily encompasses a druggable class of molecules, expressed in various stroma and parenchymal cell types, with the interesting therapeutic potential to modulate also the reactive microenvironment. Previously, we have demonstrated that activation of the nuclear Farnesoid X Receptor (FXR) in mammary epithelial cancer cells was associated with a reduction of cell proliferation, migration, and invasion ‘in vitro’ and tumor growth ‘in vivo’. To extend these observations, here, we propose to assess the function of FXR in CAFs and evaluate whether this receptor may affect their tumor‐promoting features.Our results evidenced, for the first time, FXR mRNA and protein expression in CAFs isolated from biopsies of primary human breast tumors. Treatment with the FXR agonist GW4064 treatment was able to significantly decrease CAF motility, stress fiber formation and their contractility. RNA sequencing highlighted cell movement and migration of cells among the most down‐regulated functions and identified signalings known to govern cell cytoskeleton organization and migration (i.e. ILK‐actin cytoskeletal‐Rho signalings) among the most down‐regulated ingenuity canonical pathways in response to GW4064 treatment. Accordingly, decreased expression and activation of proteins and/or downstream effectors of these pathways were observed in GW4064‐treated CAFs. Moreover, FXR activation reduced expression of different secreted factors, that act as mediators of tumor‐stroma interaction. Indeed, coculture experiments revealed a significant inhibition in growth and motility of breast cancer cells treated with conditioned‐media derived from GW4064‐treated CAFs compared to vehicle‐treated CAFs. All this sounds to fit with the clinical relevance that increased FXR levels in bulk tumors are associated with a statistically significant longer survival of patients.In conclusion, FXR ligands, by targeting both breast cancer epithelial cells and tumor associated stroma, may represent emerging pharmacological tools to be exploited for the future management of breast cancer.Support or Funding InformationMy First AIRC Grant #16899 to IBThis abstract is from the Experimental Biology 2018 Meeting. There is no full text article associated with this abstract published in The FASEB Journal.