bluuebunny/crossref_metadata_2025_split huggingface dataset:
Genetic Monitoring and Molecular Phylogeny for Cymothoid Isopod Invasion in Egyptian Lake Qarun Fishes by Using adopted taxonomic marker (COI)
Authors: Hassan Mohammed A. 
Published: April 2019

AbstractDifferent types of aquatic ecosystem is abundant by a lot of crustaceans. There are species adapted to maximum of temperature, pressure and salinity. Isopods are a marine parasitic organism and commonly live in warmer seas. They are feeding on blood. Several species settle in the buccal cavity of fish. Parasite became a morbidity case in lake Qarun, GAFRD (General Authority for fish resources development, Fish Statistics yearbook, 2015). DNA barcoding gene (COI gene) was used to make the genetic characterization for the invasive species of Cymothoidae, Cymothoidae sp and recorded in the Genbank. Constructing a phylogeny depending on the degree of similarity between the new record (LC138010.1) and the other records of Cymothoidae species in the Genebank then the environmental conditions were compared according to the analysis of the constructed tree. Suez canal is the primary resource for the fingers of mullet which transferred to Qarun Lake (salinity, 49 ppt). Ballast water have an environmental effect by transferring the alien species in the Suez Gulf which have a warm weather. This study suggests that the Cymothoidae is expanded invasive species came from its habitat regions to a closed lakes which have a similar condition of water environment, temperature and depth to live and to be a morbidity in Lake Quran. Ballast water is a risky way to transfer the invasive species to Suez Canal then New Suez Canal poses and lead to biodiversity risks. Using eDNA techniques to diagnose the invasive species is very important unit which must be established in general authorities of fish resources and development in Egypt and other countries which invaded by different alien species.
Odor Coding of Nestmate Recognition in the Eusocial AntCamponotus floridanus
Authors: Ferguson S.T. , Park K.Y. , Ruff A. , Bakis I. , Zwiebel L.J. 
Published: April 2019

AbstractBackgroundIn eusocial ants, aggressive behaviors require a sophisticated ability to detect and discriminate between chemical signatures such as cuticular hydrocarbons that distinguish nestmate friends from non-nestmate foes. It has been suggested that a mismatch between a chemical signature (label) and the internal, neuronal representation of the colony odor (template) leads to the recognition of and subsequent aggression between non-nestmates. While several studies have demonstrated that ant chemosensory systems, most notably olfaction, are largely responsible for the decoding of these chemical signatures, a definitive demonstration that odorant receptors are responsible for the detection and processing of the pheromonal signals that regulate nestmate recognition has thus far been lacking. To address this, we have developed an aggression-based bioassay incorporating a suite of highly selective odorant receptor modulators to characterize the role of olfaction in nestmate recognition in the formicine antCamponotus floridanus.ResultsValidation of our aggression-based behavioral assay was carried out by demonstrating an antennal requirement for nestmate recognition. In order to adapt this bioassay for the volatile delivery of Orco modulators, electroantennography was used to show that both a volatilized Orco antagonist (VUANT1) and an Orco agonist (VUAA4) eliminated or otherwise interfered with the electrophysiological responses to the hydrocarbon decane, respectively. Volatilize administration of these compounds to adult workers significantly reduced aggression between non-nestmates without altering aggression levels between nestmates but did not alter aggressive responses towards a mechanical stimulus.ConclusionsOur studies provide direct evidence that the antennae (as olfactory appendages) and odorant receptors (at the molecular level) are necessary for mediating aggression towards non-nestmates. Furthermore, our observations support a hypothesis in which rejection of non-nestmates depends on the precise detection and decoding of chemical signatures present on non-nestmates as opposed to the absence of any information or the active acceptance of familiar signatures. In addition to describing a novel approach to assess olfactory signaling in genetically intractable insect systems, these studies contribute to a long-standing interest in odor coding and the molecular neuroethology of nestmate recognition.
Phenological matching drives wheat pest range shift under climate change
Authors: Wu Yuqing , Gong Zhongjun , Bebber Daniel P. , Miao Jin , Zhao Zhonghua , Jiang Yuying , Xiao Shihe , Zhang Guoyan , Yu Dazhao , Fang Jichao , Lu Xinmin , Lei Chaoliang , Ding Jianqing , Wang Qiang , Jiang Yueli , Li Tong , Lian Hongmei , Li Huiling , Duan Yun , Huang Jianrong , Jing Donglin , He Yunzhuan , Zhang Zhi , Zhang Yunhui , Chen Julian , Qiao Hongbo , Huang Wenjiang 
Published: April 2019

AbstractShifting geographical ranges of crop pests and pathogens in response to climate change pose a threat to food security (1, 2). The orange wheat blossom midge (Sitodiplosis mosellana Géhin) is responsible for significant yield losses in China (3), the world’s largest wheat producer. Here we report that rising temperatures in the North China Plain have resulted in a mean northward range shift of 3.3° (58.8 km per decade) from the 1950s to 2010s, which accelerated to 91.3 km per decade after 1985 when the highly toxic pesticide hexachlorocyclohexane (HCH) was banned (4). Phenological matching between wheat midge adult emergence and wheat heading in this new expanded range has resulted in greater damage to wheat production. Around $286.5 million worth of insecticides were applied to around 19 million hectares in an attempt to minimize wheat midge damage to crops between 1985 and 2016. Despite use of these pesticides, wheat midge caused losses of greater than 0.95 million metric tons of grain during this period. Our results demonstrate the potential for indirect negative impacts of climate change on crop production and food security, and constitute the first large scale example of plant pest range shift due to global warming.
Convolutional Neural Networks for Decoding of Covert Attention Focus and Saliency Maps for EEG Feature Visualization
Authors: Farahat Amr , Reichert Christoph , Sweeney-Reed Catherine M. , Hinrichs Hermann 
Published: April 2019

ABSTRACTObjectiveConvolutional neural networks (CNNs) have proven successful as function approximators and have therefore been used for classification problems including electroencephalography (EEG) signal decoding for brain-computer interfaces (BCI). Artificial neural networks, however, are considered black boxes, because they usually have thousands of parameters, making interpretation of their internal processes challenging. Here we systematically evaluate the use of CNNs for EEG signal decoding and investigate a method for visualizing the CNN model decision process.ApproachWe developed a CNN model to decode the covert focus of attention from EEG event-related potentials during object selection. We compared the CNN and the commonly used linear discriminant analysis (LDA) classifier performance, applied to datasets with different dimensionality, and analyzed transfer learning capacity. Moreover, we validated the impact of single model components by systematically altering the model. Furthermore, we investigated the use of saliency maps as a tool for visualizing the spatial and temporal features driving the model output.Main resultsThe CNN model and the LDA classifier achieved comparable accuracy on the lower-dimensional dataset, but CNN exceeded LDA performance significantly on the higher-dimensional dataset (without hypothesis-driven preprocessing), achieving an average decoding accuracy of 90.7% (chance level = 8.3%). Parallel convolutions, tanh or ELU activation functions, and dropout regularization proved valuable for model performance, whereas the sequential convolutions, ReLU activation function, and batch normalization components, reduced accuracy or yielded no significant difference. Saliency maps revealed meaningful features, displaying the typical spatial distribution and latency of the P300 component expected during this task.SignificanceFollowing systematic evaluation, we provide recommendations for when and how to use CNN models in EEG decoding. Moreover, we propose a new approach for investigating the neural correlates of a cognitive task by training CNN models on raw high-dimensional EEG data and utilizing saliency maps for relevant feature extraction.
PD-L1:CD80 Heterodimer Triggers CD28 While Repressing Both PD-1 and CTLA4 Pathways
Authors: Zhao Yunlong , Lin Chia-Hao , Lee Calvin , Xu Xiaozheng , Huang Zhe , Xiao Changchun , Bui Jack , Lu Li-Fan , Hui Enfu 
Published: April 2019

ABSTRACTCombined immunotherapy with anti-PD-1/PD-L1 and anti-CTLA4 has resulted in superior clinical responses compared to single agent therapy. The underlying mechanisms for this synergy have yet to be elucidated and investigations have largely focused on cellular interactions. Herein, we report a molecular crosstalk in which the PD-1 ligand PD-L1 and the CTLA4 ligand CD80 heterodimerize incis. This heterodimerization blocks both PD-L1:PD-1 and CD80:CTLA4 interactions, but preserves the ability of CD80 to activate the T cell costimulatory receptor CD28. Remarkably, PD-L1 expression on antigen presenting cells (APCs) protects CD80 from CTLA4 mediatedtrans-endocytosis, and the therapeutic PD-L1 blockade antibody atezolizumab paradoxically downregulates CD80 on APCs, presumably reducing its co-stimulatory ability. Importantly, this effect can be negated by co-blockade of CTLA4 with ipilimumab. Our study reveals an unexpected immune stimulatory role ofcis-acting PD-L1 and a mechanism of anti-PD-L1/anti-CTLA4 crosstalk, providing a therapeutic rationale for combination blockade of PD-L1 and CTLA4.
TLR7-agonist and antineoplastic MEK1/2-inhibitor combination unlocks interferon responses from macrophages
Authors: Yang Lei , Ding Jeak Ling 
Published: April 2019

AbstractType I interferons are a family of pleiotropic cytokines that exert anti-tumor actions directly on tumor cells and indirectly on the tumor immune microenvironment (TIME). Hitherto, therapeutic strategies aiming to garner the efficacies of interferon responses are still limited. Here we show a novel strategy that elicits an interferon signature response while targeting both tumor cells using antineoplastic mitogen-activated protein kinase (MAPK) kinase 1/2 (MEK1/2) inhibitor and the TIME using toll-like receptor 7 (TLR7)-based immune adjuvant. The combination of MEK1/2 inhibitor and TLR7 agonist unlocked an interferon signature response unexpectedly in macrophages, which was otherwise tightly constrained by TLR7 agonist alone. Deficiency of interferon regulatory factor 1 (Irf1) completely abrogated the responses and prevented the reprogramming of activated macrophages, subduing them in an immunosuppressive state. In a murine melanoma model, combination therapy with TLR7 agonist and MEK1/2 inhibitor synergistically extended survival in wild-type but notIrf1-deficient mice. Specifically, we identified interferon response genes as favorable prognosis markers for cutaneous melanoma patients. Our findings demonstrate a novel strategy for combination therapy that targets both tumor cells and the immunosuppressive TIME through additive effects of monotherapies and synergistic interferon responses.
Kidney osteoclast factors and matrix metalloproteinase expression in a mice model of diet-induced obesity and diabetes
Authors: dos Santos-Macedo Francine , Martins-Gregorio Bianca , Paes-de-Almeida Elan Cardozo , de Souza Mendonça Leonardo , de Souza Azevedo Rebeca , Fernandes-Santos Caroline 
Published: April 2019

ABSTRACTThe role of RANKL/RANK/OPG system on bone remodeling is well known, and there is evidence that it is also important to cardiovascular and kidney pathology, although the underlying mechanisms are not elucidated so far. Thus, we investigated in a mice model of diet-induced obesity and diabetes if renal histopathological changes are associated with the expression of RANKL/RANK/OPG system and matrix metalloproteinases (MMPs). Three months old C57BL/6 mice were fed with control (AIN93M) or high-fat high sucrose (HFHS) diets for 21 weeks (CEUA/UFF #647/15). The HFHS group showed weight gain (+35%, P=0.0001), increased epididymal, inguinal and retroperitoneal fat pad weight (+121 %, P = 0.0006; +287 %, P = 0.0007 and; +286 %, P < 0.0001, respectively), and hyperglycemia (+43%, P=0.02). The kidney of some HFHS fed mice displayed mononuclear inflammatory cell infiltrate (40%), perivascular fibrosis (20%), and focal tubule mineralization (20%). Glomeruli hypertrophy was not detected. Unexpectedly, OPG, RANK, MMP-2 and MMP-9 expression was not altered in HFHS groups (Western blot analysis). In conclusion, the expression of RANKL/RANK/OPG system proteins and MMPs was not influenced by diet-induced obesity and diabetes in the kidney of male C57BL/6 mice, although some adverse histopathological remodeling is noticed in the renal tissue.
Immune state is associated with natural dietary variation in wild mice Mus musculus domesticus
Authors: Taylor Christopher H. , Young Stuart , Fenn Jonathan , Lamb Angela L. , Lowe Ann E. , Poulin Benoit , MacColl Andrew D. C. , Bradley Janette E. 
Published: April 2019

Abstract

The ability, propensity and need to mount an immune response vary both among individuals and within a single individual over time.

A wide array of parameters has been found to influence immune state in carefully controlled experiments, but we understand much less about which of these parameters are important in determining immune state in wild populations.

Diet can influence immune responses, for example when nutrient availability is limited. We therefore predict that natural dietary variation will play a role in modulating immune state, but this has never been tested.

We measured carbon and nitrogen stable isotope ratios in an island population of house mice Mus musculus domesticus as an indication of dietary variation, and the expression of a range of immune‐related genes to represent immune state.

After accounting for potential confounding influences such as age, sex and helminth load, we found a significant association between carbon isotope ratio and levels of immune activity in the mesenteric lymph nodes, particularly in relation to the inflammatory response.

This association demonstrates the important interplay between diet and an animal's response to immune challenges, and therefore potentially its susceptibility to disease.

A plain language summary is available for this article.
Research note: deblended‐data reconstruction using generalized blending and deblending models
Authors: Ishiyama Tomohide , Ali Mohammed Y. , Ishikawa Satoshi , Blacquiere Gerrit , Nakayama Shotaro 
Published: April 2019

ABSTRACTWe introduce a concept of generalized blending and deblending, develop its models and accordingly establish a method of deblended‐data reconstruction using these models. The generalized models can handle real situations by including random encoding into the generalized operators both in the space and time domain, and both at the source and receiver side. We consider an iterative optimization scheme using a closed‐loop approach with the generalized blending and deblending models, in which the former works for the forward modelling and the latter for the inverse modelling in the closed loop. We applied our method to existing real data acquired in Abu Dhabi. The results show that our method succeeded to fully reconstruct deblended data even from the fully generalized, thus quite complicated blended data. We discuss the complexity of blending properties on the deblending performance. In addition, we discuss the applicability to time‐lapse seismic monitoring as it ensures high repeatability of the surveys. Conclusively, we should acquire blended data and reconstruct deblended data without serious problems but with the benefit of blended acquisition.
Pharmacogenomics guidelines: Current status and future development
Authors: Guo Chengxian , Xie Xiaoxue , Li Jingao , Huang Lihua , Chen Shaojun , Li Xi , Yi Xin , Wu Qin , Yang Guoping , Zhou Honghao , Liu Jun‐Ping , Chen Xiang 
Published: April 2019

AbstractGenetic polymorphisms impact biological responses to drugs. Current pharmacogenomics guidelines formulated by different countries, such as the Clinical Pharmacogenetics Implementation Consortium, the Dutch Pharmacogenetics Working Group, the Canadian Pharmacogenomics Network for Drug Safety, and the French National Network (Réseau) of Pharmacogenetics, play important roles in clinical practices. However, the standards for these guidelines vary significantly, resulting in differences in recommendations. The present article discusses these differences by head‐to‐head comparison of the existing pharmacogenomics guidelines and proposes new strategies for their future development.
The Common Agricultural Policy's New Delivery Model Post‐2020: National Administration Perspective
Authors: Carey Mary 
Published: April 2019

SummaryThis article assesses the June 2018 European Commission's legislative proposals for the Common Agricultural Policy (CAP) post‐2020. It does not consider the positions of the co‐legislators – the Council of Ministers and the European Parliament. The article considers the European Commission's New Delivery Model (NDM), the enhanced environmental and climate ambition, and the new performance framework from the perspective of a national administration. The enhanced focus on performance is the cornerstone of the NDM. However, the article highlights the complexity associated with enhanced reporting requirements of the NDM and asserts that the reporting requirements will need to be simplified and streamlined to ensure a simplified CAP for all involved; and to encourage the enhanced environmental and climate ambition foreseen in the European Commission's proposal. The move from compliance‐based to performance‐based oversight is welcomed from the perspective of the national administration. The single audit approach, whereby multiple audits and inspections are avoided, should result in simplification for the CAP beneficiaries and for the national administrations. The proposed NDM is very different to what the European Commission, national administrations and beneficiaries are used to – it will take time to bed down.
The Future of US Farm Policy
Authors: Smith Vincent H. , Glauber Joseph W. 
Published: April 2019

SummaryThe farm bill is the primary legislative vehicle for federal food and agricultural policies in the United States that is renewed roughly once every five years. Most current farm bill subsidy and other domestic support programmes for agriculture have their origins in legislation introduced in the 1930s to alleviate poverty among farm households during the Great Depression. Although US farm households have enjoyed higher incomes and wealth than the average US family for many years, legislation to support agricultural commodity prices and to increase farm incomes has persisted. A new farm bill offers the US Congress an opportunity to reform agricultural subsidy policies. But if recent history is a guide, what will emerge is likely to resemble much of what was in the 2014 bill. As was the case with that bill, maintaining the status quo will represent a missed opportunity to cut farm subsidies and make agricultural programmes more market oriented, and be unlikely to improve trade relations for the United States in the context of its commitments under current World Trade Organization agreements. In many ways, agricultural policy in the United States seems to be firmly marching back to the past rather than looking to the future.
Generation of a highly attenuated strain of Pseudomonas aeruginosa for commercial production of alginate
Authors: Valentine Meagan E. , Kirby Brandon D. , Withers Thomas R. , Johnson Shannon L. , Long Timothy E. , Hao Youai , Lam Joseph S. , Niles Richard M. , Yu Hongwei D. 
Published: April 2019

SummaryAlginate is an important polysaccharide that is commonly used as a gelling agent in foods, cosmetics and healthcare products. Currently, all alginate used commercially is extracted from brown seaweed. However, with environmental changes such as increasing ocean temperature and the increasing number of biotechnological uses of alginates with specific properties, there is an emerging need for more reliable and customizable sources of alginate. An alternative to seaweed for alginate production is Pseudomonas aeruginosa, a common Gram‐negative bacterium that can form alginate‐containing biofilms. However, P. aeruginosa is an opportunistic pathogen that can cause life‐threatening infections in immunocompromised patients. Therefore, we sought to engineer a non‐pathogenic P. aeruginosa strain that is safe for commercial production of alginate. Using a homologous recombination strategy, we sequentially deleted five key pathogenicity genes from the P. aeruginosa chromosome, resulting in the marker‐free strain PGN5. Intraperitoneal injection of mice with PGN5 resulted in 0% mortality, while injection with wild‐type P. aeruginosa resulted in 95% mortality, providing evidence that the systemic virulence of PGN5 is highly attenuated. Importantly, PGN5 produces large amounts of alginate in response to overexpression of MucE, an activator of alginate biosynthesis. The alginate produced by PGN5 is structurally identical to alginate produced by wild‐type P. aeruginosa, indicating that the alginate biosynthetic pathway remains functional in this modified strain. The genetic versatility of P. aeruginosa will allow us to further engineer PGN5 to produce alginates with specific chemical compositions and physical properties to meet different industrial and biomedical needs.
Hydroclimatology of the Mississippi River Basin
Authors: McCabe Gregory J. , Wolock David M. 
Published: April 2019

AbstractModel estimated monthly water balance (WB) components (i.e., potential evapotranspiration, actual evapotranspiration, and runoff [R]) for 848 United States (U.S.) Geological Survey 8‐digit hydrologic units located in the Mississippi River Basin (MRB) are used to examine the temporal and spatial variability of the MRB WB for water years 1901 through 2014. Results indicate the MRB can be divided into nine subregions with similar temporal variability in R. The WB analyses indicated ~79% of total water‐year MRB runoff is generated by four of the nine subregions and most of the R in the basin is derived from surplus (S) water during the months of December through May. Furthermore, the analyses showed temporal variability in S is largely controlled by the occurrence of negative atmospheric pressure anomalies over the western U.S. and positive atmospheric pressure anomalies over the eastern U.S. coast. This combination of atmospheric pressure anomalies results in an anomalous flow of moist air from the Gulf of Mexico into the MRB. In the context of paleo‐climate reconstructions of the Palmer Drought Severity Index, since about 1900 the MRB has experienced wetter conditions than were experienced during the previous 500 years.