bluuebunny/crossref_metadata_2025_split huggingface dataset:
Using molecular diet analysis to inform invasive species management: A case study of introduced rats consuming endemic New Zealand frogs
Authors: Egeter Bastian , Roe Cailín , Peixoto Sara , Puppo Pamela , Easton Luke J. , Pinto Joana , Bishop Phillip J. , Robertson Bruce C. 
Published: April 2019

AbstractThe decline of amphibians has been of international concern for more than two decades, and the global spread of introduced fauna is a major factor in this decline. Conservation management decisions to implement control of introduced fauna are often based on diet studies. One of the most common metrics to report in diet studies is Frequency of Occurrence (FO), but this can be difficult to interpret, as it does not include a temporal perspective. Here, we examine the potential for FO data derived from molecular diet analysis to inform invasive species management, using invasive ship rats (Rattus rattus) and endemic frogs (Leiopelma spp.) in New Zealand as a case study. Only two endemic frog species persist on the mainland. One of these, Leiopelma archeyi, is Critically Endangered (IUCN 2017) and ranked as the world's most evolutionarily distinct and globally endangered amphibian (EDGE, 2018). Ship rat stomach contents were collected by kill‐trapping and subjected to three methods of diet analysis (one morphological and two DNA‐based). A new primer pair was developed targeting all anuran species that exhibits good coverage, high taxonomic resolution, and reasonable specificity. Incorporating a temporal parameter allowed us to calculate the minimum number of ingestion events per rat per night, providing a more intuitive metric than the more commonly reported FO. We are not aware of other DNA‐based diet studies that have incorporated a temporal parameter into FO data. The usefulness of such a metric will depend on the study system, in particular the feeding ecology of the predator. Ship rats are consuming both species of native frogs present on mainland New Zealand, and this study provides the first detections of remains of these species in mammalian stomach contents.
Fluvial incision and coarse gravel redistribution across the modern Dead Sea shelf as a result of base‐level fall
Authors: Eyal Haggai , Dente Elad , Haviv Itai , Enzel Yehouda , Dunne Thomas , Lensky Nadav G. 
Published: April 2019

AbstractGlobal eustatic lowstands can expose vast areas of continental shelves, and occasionally the shelf edge and the continental slope. The degree of fluvial connectivity to receding shores influences the redistribution of sediments across these emerging landscapes. Shelf and slope emergence in the Dead Sea since the middle of the 20th century, offers a rare opportunity to examine evolution of stream connectivity in response to continuous base‐level decline. We characterize the connectivity evolution of two streams, using high‐resolution time series of aerial imagery and elevation models, field mapping, and grain‐size analyses. Our rich spatiotemporal dataset of evolving channel geomorphology, sediment transport conditions, and sediment redistribution, allows calculating potential coarse sediment mobility in response to base level decline. Following shelf emergence, alluvial fans first prograded onto the low‐gradient shelf under unfavourable conditions for transporting coarse sediment to the regressing shoreline. Then, with shelf and slope emergence, the two adjacent streams evolved differently. The smaller, more arid watershed still maintains its highstand delta progradation on the shelf and is practically disconnected from the receding lake. The larger catchment, heading in wetter environments and having a narrower shelf, has incised the shelf and renewed and gradually intensified the sediment transport from the highstand to the lowstand delta. Sediment mobilization to lowstand shorelines is controlled by the evolution of the channel profile and by the average speed of gravel transport (10s‐100s m yr‐1). These findings from the Dead Sea are relevant to fluvial processes operating on continental shelves during glacial maxima. Streams would have commonly stored high proportions of their coarse sediment on the continental shelves rather than efficiently connecting with the lowstand level. Additionally, differences in sediment routing patterns should exist among nearby streams, primarily due to continental margin geometry and watershed hydrology. © 2019 John Wiley & Sons, Ltd.
Citizen Science and Gamification
Authors: Kreitmair Karola V. , Magnus David C. 
Published: April 2019

AbstractAccording to the mainstream conception of research involving human participants, researchers have been trained scientists acting within institutions and have been the individuals doing the studying, while participants, who are nonscientist members of the public, have been the individuals being studied. The relationship between the public and scientists is evolving, however, giving rise to several new concepts, including crowdsourcing and citizen science. In addition, the practice of gamification has been applied to research protocols. The role of gamified, crowdsourced citizen scientist is new in the domain of scientific research and does not fit into the existing taxonomy of researchers and participants. We delineate and explicate this role and show that, while traditional roles are governed by well‐established norms and regulations, individuals engaged in gamified, crowdsourced citizen science—gamers—fall through the cracks of research protections and regulations. We consider the issues this raises, including exploitation and the absence of responsibility and accountability. Finally, we offer suggestions for how the current lack of appropriate norms may be rectified.
Impact of the spatial variability of daily precipitation on hydrological projections: A comparison of GCM‐ and RCM‐driven cases in the Han River basin, Korea
Authors: Lee Moon‐Hwan , Im Eun‐Soon , Bae Deg‐Hyo 
Published: April 2019

AbstractIn this study, we investigate the impact of the spatial variability of daily precipitation on hydrological projections based on a comparative assessment of streamflow simulations driven by a global climate model (GCM) and two regional climate models (RCMs). A total of 12 different climate input datasets, that is, the raw and bias‐corrected GCM and raw and bias‐corrected two RCMs for the reference and future periods, are fed to a semidistributed hydrological model to assess whether the bias correction using quantile mapping and dynamical downscaling using RCMs can improve streamflow simulation in the Han River basin, Korea. A statistical analysis of the daily precipitation demonstrates that the precipitation simulated by the GCM fails to capture the large variability of the observed daily precipitation, in which the spatial autocorrelation decreases sharply within a relatively short distance. However, the spatial variability of precipitation simulated by the two RCMs shows better agreement with the observations. After applying bias correction to the raw GCM and raw RCMs outputs, only a slight change is observed in the spatial variability, whereas an improvement is observed in the precipitation intensity. Intensified precipitation but with the same spatial variability of the raw output from the bias‐corrected GCM does not improve the heterogeneous runoff distributions, which in turn regulate unrealistically high peak downstream streamflow. GCM‐simulated precipitation with a large bias correction that is necessary to compensate for the poor performance in present climate simulation appears to distort streamflow patterns in the future projection, which leads to misleading projections of climate change impacts on hydrological extremes.
Bulk density optimization to determine subsurface hydraulic properties in Rocky Mountain catchments using the GEOtop model
Authors: Fullhart Andrew T. , Kelleners Thijs J. , Chandler Dave G. , McNamara James P. , Seyfried Mark S. 
Published: April 2019

AbstractIntegrated watershed models can be used to calculate streamflow generation in snow‐dominated mountainous catchments. Parameterization of water flow is often complicated by the lack of information on subsurface hydraulic properties. In this study, bulk density optimization was used to determine hydraulic parameters for the upper and lower regolith in the GEOtop model. The methodology was tested in two small catchments in the Dry Creek Watershed in Idaho and the Libby Creek Watershed in Wyoming. Modelling efficiencies for profile‐average soil–water content for the two catchments were between 0.52 and 0.64. Modelling efficiencies for stream discharge (cumulative stream discharge) were 0.45 (0.91) and 0.54 (0.94) for the Idaho and Wyoming catchments, respectively. The calculated hydraulic properties suggest that lateral flow across the upper–lower regolith interface is an important driver of streamflow in both the Idaho and Wyoming watersheds. The overall calibration procedure is computationally efficient because only two bulk density values are optimized. The two‐parameter calibration procedure was complicated by uncertainty in hydraulic conductivity anisotropy. Different upper regolith hydraulic conductivity anisotropy factors had to be tested in order to describe streamflow in both catchments.
Does the world need faunists? Based on rotifer (Rotifera) occurrence reflections on the role of faunistic research in ecology
Authors: Ejsmont‐Karabin Jolanta 
Published: April 2019

AbstractMost faunistic studies of large‐scale patterns concern terrestrial vertebrates, whereas smaller organisms, and in particular, freshwater invertebrates like rotifers receive less attention. As a result, the “rotiferologists” effect”, that is sampling intensity, is among the most influential factors observed, globally or locally, on species richness.Because there are many more small, isolated patches of habitats available to the specialist species, greater specialization has occurred in those forms than in ubiquitous species. This rule also applies to rotifers. Results show that: (a) the total number of rotifer species observed in a lake depends on both the number of samples collected and the type and number of lake habitats involved; and (b) the originality (variability) of rotifer fauna in particular lakes is more pronounced with the more species found in a lake.The important purpose of faunistic studies is the registration of indigenous species. The inflow of alien species is currently one of the greatest threats to the preservation of natural fauna. However, if we do not recognize the composition of natural communities, we will not be able to recognize the invaders. The second most important goal is to enable tracking of long‐term changes in species diversity of rotifer fauna. Rotifers seem to be sensitive enough to climate change and pollution of the aquatic environment. Thus, for the reasons described above, faunistics will be still necessary.
Isolation and characterization of a novel scFv antibody fragments specific for Hsp70 as a tumor biomarker
Authors: Vostakolaei Mehdi Asghari , Molavi Ommoleila , Hejazi Mohammad Saeid , Kordi Shirafkan , Rahmati Saman , Barzegari Abolfazl , Abdolalizadeh Jalal 
Published: April 2019

AbstractMany studies have shown that more than 50% of tumors express heat shock protein 70 kDa (Hsp70) at the plasma membrane surface while not seen in normal cells, therefore it is a promising therapeutic target in human cancers. Hence, we used phage display technology to produce a single‐chain fragment variable (scFv) antibody against human Hsp70. For this, a target peptide from human Hsp70 was designed using bioinformatics studies and was chemically synthesized. Then, the selection was performed using four rounds of biopanning with a stepwise decreased amount of the target peptide. Fourteen positive scFv clones were selected using monoclonal phage enzyme‐linked immunosorbent assay screening, which was further characterized by means of the polymerase chain reaction and DNA sequencing. Among them, the G6 clone was selected to express scFv into the Escherichia coli. Expression and purification of the scFv shown by sodium dodecyl sulfate‐polyacrylamide gel electrophoresis and confirmed by Western blot analysis. In silico analysis confirmed specific binding of the scFv to Hsp70 in CDR regions. The specificity of the scFv measured by surface plasmon resonance and immunofluorescence of the A549 human lung carcinoma cell line confirmed the in vitro function of the scFv. Based upon these findings, we propose a novel anti‐human Hsp70 scFv as potential immunotherapy agents that may be translated into preclinical/clinical applications.
A noncoding RNA LINC00504 interacts with c‐Myc to regulate tumor metabolism in colon cancer
Authors: Feng Jinfeng , Ma Jun , Liu Shaoqun , Wang Jianfa , Chen Yi 
Published: April 2019

AbstractAccumulating evidence has shown a critical role of long‐non‐coding RNAs (lncRNAs) during multiple tumor progression. However, the potential functions of LINC00504 in colon cancer as well as its mechanisms remain obscure. By lncRNA profiling, we identified LINC00504 as a novel oncogenic lncRNA in colon cancer. The lncRNA LINC00504 was markedly upregulated in colon cancer cell lines and specimens. LINC00504 increases viability and migration of colon cells in vitro. Furthermore, LINC00504 also enhances colon cancer xenograft tumors in vivo. We noted that LINC00504 regulates metabolism at a transcriptional level which influences multiple metabolic pathways, such as glucose metabolism, pentose phosphate pathway, and tricarboxylic acid cycle. Mechanistic study showed that LINC00504 could interact with c‐Myc to promote chromatin recruitment of c‐Myc and enhance its transactivation activity. Collectively, our results showed that LINC00504 serves as an important transcriptional regulator for c‐Myc in colon cancer cells. LINC00504 can reprogram central metabolism in colon cancer cells implying that LINC00504 may serve as a potential target for therapeutic intervention.
Generation of a nitric oxide signaling pathway in mesenchymal stem cells promotes endothelial lineage commitment
Authors: Bandara Nadeeka , Gurusinghe Saliya , Kong Anne , Mitchell Geraldine , Wang Le‐Xin , Lim Shiang Y. , Strappe Padraig 
Published: April 2019

AbstractEnhancing differentiation of mesenchymal stem cells (MSCs) to endothelial cells may improve their ability to vascularize tissue and promote wound healing. This study describes a novel role for nitric oxide (NO) in reprogramming MSCs towards an endothelial lineage and highlights the role of Wnt signaling and epigenetic modification by NO. Rat MSCs were transduced with lentiviral vectors expressing endothelial nitric oxide synthase (pLV‐eNOS) and a mutated caveolin gene (pLV‐CAV‐1F92A) to enhance NO generation resulting in increased in vitro capillary tubule formation and endothelial marker gene expression. An exogenous source of NO could also stimulate CD31 expression in MSCs. NO was associated with an arterial‐specific endothelial gene expression profile of Notch1, Dll4, and Hey2 and significantly reduced expression of venous markers. Wnt signaling associated with NO was evident through increased gene expression of Wnt3a and β‐catenin protein, and expression of the endothelial marker Pecam‐1 could be significantly reduced by treatment with the Wnt signaling inhibitor Dkk‐1. The role of NO as an epigenetic modifier was evident with reduced gene expression of the methyltransferase, DNMT1, and bisulfite sequencing of the endothelial Flt1 promoter region in NO‐producing MSCs showed significant demethylation compared to control cells. Finally, subcutaneous implantation of NO‐producing MSCs seeded in a biomaterial scaffold (NovoSorb®) resulted in survival of transplanted cells and the formation of blood vessels. In summary, this study describes, NO as a potent endothelial programming factor which acts as an epigenetic modifier in MSCs and may provide a novel platform for vascular regenerative therapy.
Frontline Science: TLR3 activation inhibits food allergy in mice by inducing IFN-γ+ Foxp3+ regulatory T cells
Authors: Hong Jing-Yi , Li Shan-Shan , Hu Tian-Yong , Liu Zhi-Qiang , Yu Dian , Yu Hai-Qiong , Guan Li , Wu Gao-Hui , Zeng Hao-Tao , Liu Zhi-Gang , Yang Ping-Chang 
Published: April 2019

Abstract
The pathologic feature of food allergy (FA) is the aberrant Th2-biased immune response in the intestine. Regulatory T cells (Tregs) play an important role in the suppression of aberrant immune response. The activities of the TLRs regulate multiple cell functions. This study aims to investigate the role of TLR3 activation in the regulation of Th2-biased immune response in the intestine by the generation of inducible Tregs (iTregs). In this study, polyinosinic polycytidylic acid (polyI:C) was used as an activator of TLR3. An FA mouse model was developed to establish the Th2-biased inflammation in the intestine. The effects of TLR3 activation on the generation of iTreg were tested in the culture and in mice. We observed that exposure to polyI:C induced IFN-γ+ Foxp3+ iTregs in mouse intestine and in the culture. The IFN-γ+ Foxp3+ iTregs showed immune suppressive functions. Exposure to polyI:C increased T-bet levels in CD4+ T cells. The T-bet formed a complex with GATA3 to dissociate Foxp3 from GATA3/Foxp3 complex in CD4+ T cells. The Foxp3 thus gained the opportunity to move to TGF-β promoter to generate iTregs. Administration with polyI:C prevented the development of FA and inhibited existing FA. In conclusion, activation of TLR3 induces IFN-γ+ Foxp3+ Tregs, which can prevent FA development and inhibit existing FA in mice.
Top‐down mass spectrometry of intact phosphorylated β‐casein: Correlation between the precursor charge state and internal fragments
Authors: Chen Jianzhong , Shiyanov Pavel , Green Kari B. 
Published: April 2019

AbstractPhosphorylated proteins play essential roles in many cellular processes, and identification and characterization of the relevant phosphoproteins can help to understand underlying mechanisms. Herein, we report a collision‐induced dissociation top‐down approach for characterizing phosphoproteins on a quadrupole time‐of‐flight mass spectrometer. β‐casein, a protein with two major isoforms and five phosphorylatable serine residues, was used as a model. Peaks corresponding to intact β‐casein ions with charged states up to 36+ were detected. Tandem mass spectrometry was performed on β‐casein ions of different charge states (12+, and 15+ to 28+) in order to determine the effects of charge state on dissociation of this protein. Most of the abundant fragments corresponded to y, b ions, and internal fragments caused by cleavage of the N‐terminal amide bond adjacent to proline residues (Xxx‐Pro). The abundance of internal fragments increased with the charge state of the protein precursor ion; these internal fragments predominantly arose from one or two Xxx‐Pro cleavage events and were difficult to accurately assign. The presence of abundant sodium adducts of β‐casein further complicated the spectra. Our results suggest that when interpreting top‐down mass spectra of phosphoproteins and other proteins, researchers should consider the potential formation of internal fragments and sodium adducts for reliable characterization.
Herpesviral infections and antimicrobial protection for Alzheimer's disease: Implications for prevention and treatment
Authors: Qin Qingsong , Li Yun 
Published: April 2019

AbstractAccumulating evidence suggests that infections by herpesviruses might be closely linked to Alzheimer's disease (AD). Pathological hallmarks of AD brains include senile plaques induced by amyloid β peptide (Aβ) in the extracellular space and intracellular neurofibrillary tangles (NFTs) consisting of phosphorylated tau protein. The prevailing hypothesis for the mechanism of AD is amyloid cascade reaction. Recent studies revealed that infections by herpesviruses induce the similar pathological hallmarks of AD, including Aβ production, phosphorylation of tau (P‐tau), oxidative stress, neuroinflammation, etc. Aβ peptide is regarded as one of the antimicrobial peptides, which inhibits HSV‐1 replication. In the elderly, reactivation of herpesviruses might act as an initiator for amyloid cascade reaction in vulnerable individuals, triggering the neurofibrillary formation of phosphorylated tau and inducing oxidative stress and neuroinflammation, which can further contribute to the accumulation of Aβ and P‐tau by impairing mitochondria and autophagosome. Epidemiological studies have shown AD susceptibility genes, such as APOE‐ε4 allele, are highly linked to infections by herpesviruses. Interestingly, anti‐herpesviral therapy significantly reduced the risk of AD in a large population study. Given that herpesviruses are arguably the most prevalent opportunistic pathogens and often reactivate in the elderly, it is reasonable to argue reactivation of herpesviruses might be major culprits for initiating AD in individuals carrying AD susceptibility genes. In this review, we summarize epidemiological and molecular evidence that support for a hypothesis of herpesviral infections and antimicrobial protection in the development of AD, and discuss the implications for future prevention and treatment of the disease.
RW‐2018—Research Workshop: The Effect of Nutrition on Epigenetic Status, Growth, and Health
Authors: Skinner Michael , Lumey L. H. , Fleming Tom P. , Sapienza Carmen , Hoyo Cathrine , Aronica Lucia , Thompson Jeff , Nichol Peter F. 
Published: April 2019

AbstractThe goal of the 2018 American Society for Parenteral and Enteral Nutrition (ASPEN) Research Workshop was to explore the influence of nutrition and dietary exposure to xenobiotics on the epigenome during critical periods in development and how these exposures influence both disease incidence and severity transgenerationally. A growing compendium of research indicates that the incidence and severity of common and costly human diseases may be influenced by dietary exposures and deficiencies that modify the epigenome. The greatest periods of vulnerability to these exposures are the periconception period and early childhood. Xenobiotics in the food chain, protein malnutrition, and methyl donor deficiencies could have a profound bearing on the risk of developing heart disease, diabetes, obesity, hypertension, and mental illness over multiple generations. The financial impact and the life burden of these diseases are enormous. These and other aspects of nutrition, epigenetics, and health are explored in this research workshop.