bluuebunny/crossref_metadata_2025_split huggingface dataset:
Efficacy of aldose reductase inhibitors is affected by oxidative stress induced under X-ray irradiation
Authors: Castellví Albert , Crespo Isidro , Crosas Eva , Cámara-Artigas Ana , Gavira José A. , Aranda Miguel A. G. , Parés Xavier , Farrés Jaume , Juanhuix Judith 
Published: February 2019

AbstractHuman aldose reductase (hAR, AKR1B1) has been explored as drug target since the 1980s for its implication in diabetic complications. An activated form of hAR was found in cells from diabetic patients, showing a reduced sensitivity to inhibitors in clinical trials, which may prevent its pharmacological use. Here we report the conversion of native hAR to its activated form by X-ray irradiation simulating oxidative stress conditions. Upon irradiation, the enzyme activity increases moderately and the potency of several hAR inhibitors decay before global protein radiation damage appears. The catalytic behavior of activated hAR is also reproduced as the KM increases dramatically while the kcat is not much affected. Consistently, the catalytic tetrad is not showing any modification. The only catalytically-relevant structural difference observed is the conversion of residue Cys298 to serine and alanine. A mechanism involving electron capture is suggested for the hAR activation. We propose that hAR inhibitors should not be designed against the native protein but against the activated form as obtained from X-ray irradiation. Furthermore, since the reactive species produced under irradiation conditions are the same as those produced under oxidative stress, the described irradiation method can be applied to other relevant proteins under oxidative stress environments.
Environmental structure drives resistance to phages and antibiotics during phage therapy and to invading lysogens during colonisation
Authors: Sousa Jorge A. Moura de , Rocha Eduardo P. C. 
Published: February 2019

AbstractMicrobial communities are shaped by bacteriophages through predation and lysogeny. A better understanding of the interactions between these processes across different types of environments is key to elucidate how phages mediate microbial competition and to design efficient phage therapies. We introduce an individual-based model (eVIVALDI) to investigate the role of environmental structure in the elimination of a population with a combined treatment of antibiotics and virulent phages, and in the invasion of a population of phage-sensitive bacteria by lysogens. We show that structured environments facilitate the emergence of double resistance, to antibiotics and phages, due to limited diffusion of phage particles and increased nutrient availability from dead cells. They also hinder phage amplification, thus decreasing the generation of phage genetic diversity and increasing the unpredictability of phage-bacteria arms-races. We used a machine learning approach to determine the variables most important for the invasion of sensitive populations by lysogens. They revealed that phage-associated traits and environmental structure are the key drivers of the process. Structured environments hinder invasions, and accounting for their existence improves the fit of the model to publishedin vivoexperimental data. Our results underline environmental structure as key to understandin vivophage-bacteria interactions.
Isolation of photoprotective signal transduction mutants by systematic bioluminescence screening in Chlamydomonas reinhardtii
Authors: Tokutsu Ryutaro , Fujimura-Kamada Konomi , Yamasaki Tomohito , Matsuo Takuya , Minagawa Jun 
Published: February 2019

AbstractIn photosynthetic organisms, photoprotection to avoid overexcitation of photosystems is a prerequisite for survival. Green algae have evolved light-inducible photoprotective mechanisms mediated by genes such as light-harvesting complex stress-related (LHCSR). Studies on the light-dependent regulation of LHCSR expression in the green alga Chlamydomonas reinhardtii have revealed that photoreceptors for blue light (phototropin) and ultraviolet light perception (UVR8) play key roles in initiating photoprotective signal transduction. Although initial light perception via phototropin or UVR8 is known to result in increased LHCSR3 and LHCSR1 gene expression, respectively, the mechanisms of signal transduction from the input (light perception) to the output (gene expression) remain unclear. In this study, to further elucidate the signal transduction pathway of the photoprotective response of green algae, we established a systematic screening protocol for UV-inducible LHCSR1 gene expression mutants using a bioluminescence reporter assay. Following random mutagenesis screening, we succeeded in isolating mutants deficient in LHCSR1 gene and protein expression after UV illumination. Further characterization revealed that the obtained mutants could be separated into 3 different phenotype groups, the “UV-specific”, “LHCSR1-promoter/transcript-specific” and “general photoprotective” mutant groups, which provided further insight into photoprotective signal transduction in C. reinhardtii.
A genome-wide analysis of desferrioxamine mediated iron uptake in Erwinia spp. reveals genes exclusive of the Rosaceae infecting strains
Authors: Polsinelli Ivan , Borruso Luigimaria , Caliandro Rosanna , Triboli Luca , Esposito Alfonso , Benini Stefano 
Published: February 2019

AbstractErwinia amylovora is the etiological agent of fire blight, a devastating disease which is a global threat to commercial apple and pear production. The Erwinia genus includes a wide range of different species belonging to plant pathogens, epiphytes and even opportunistic human pathogens. The aim of the present study is to understand, within the Erwinia genus, the genetic differences between phytopathogenic strains and those strains not reported to be phytopathogenic. The genes related to the hydroxamate siderophores iron uptake have been considered due to their potential druggability. In E. amylovora siderophore-mediated iron acquisition plays a relevant role in the progression of Fire blight. Here we analyzed the taxonomic relations within Erwinia genus and the relevance of the genes related to the siderophore-mediated iron uptake pathway. The results of this study highlight the presence of a well-defined sub-group of Rosaceae infecting species taxonomically and genetically related with a high number of conserved core genes. The analysis of the complete ferrioxamine transport system has led to the identification of two genes exclusively present in the Rosaceae infecting strains.
Automatic Choroid Layer Segmentation from Optical Coherence Tomography Images Using Deep Learning
Authors: Masood Saleha , Fang Ruogu , Li Ping , Li Huating , Sheng Bin , Mathavan Akash , Wang Xiangning , Yang Po , Wu Qiang , Qin Jing , Jia Weiping 
Published: February 2019

AbstractThe choroid layer is a vascular layer in human retina and its main function is to provide oxygen and support to the retina. Various studies have shown that the thickness of the choroid layer is correlated with the diagnosis of several ophthalmic diseases. For example, diabetic macular edema (DME) is a leading cause of vision loss in patients with diabetes. Despite contemporary advances, automatic segmentation of the choroid layer remains a challenging task due to low contrast, inhomogeneous intensity, inconsistent texture and ambiguous boundaries between the choroid and sclera in Optical Coherence Tomography (OCT) images. The majority of currently implemented methods manually or semi-automatically segment out the region of interest. While many fully automatic methods exist in the context of choroid layer segmentation, more effective and accurate automatic methods are required in order to employ these methods in the clinical sector. This paper proposed and implemented an automatic method for choroid layer segmentation in OCT images using deep learning and a series of morphological operations. The aim of this research was to segment out Bruch’s Membrane (BM) and choroid layer to calculate the thickness map. BM was segmented using a series of morphological operations, whereas the choroid layer was segmented using a deep learning approach as more image statistics were required to segment accurately. Several evaluation metrics were used to test and compare the proposed method against other existing methodologies. Experimental results showed that the proposed method greatly reduced the error rate when compared with the other state-of-the-art methods.
Weight change after smoking cessation and incident metabolic syndrome in middle-aged Korean men: an observational study
Authors: Kim Kyuwoong , Choi Seulggie , Lee Jong-Koo , Choi Ji-Yeob , Shin Aesun , Park Sue Kyung , Kang Daehee , Park Sang Min 
Published: February 2019

AbstractWe aimed to examine the effect of weight change attributable to cessation of cigarette smoking on newly diagnosed metabolic syndrome (MetS). We prospectively followed 5,809 men aged between 40 to 69 years without MetS at baseline in the Health Examinees-Gem (HEXA-G) study up to 4 years. The participants were grouped into continual smokers, quitters with weight gain, quitters without weight change, quitters with weight loss, and never smokers. We constructed multivariable logistic regression models adjusted for sociodemographic factors, health status, and health conditions to estimate the odds of newly diagnosed MetS. During the follow-up, there were 609 cases of newly diagnosed MetS in 5,809 men of the HEXA-G study. After adjustment for potential confounders, the odd ratios (OR) and 95% confidence intervals (95% CI) for MetS were 1.90 (95% CI: 1.43–2.52) in quitters with weight gain, 0.77 (95% CI: 0.60–1.00) in quitters without weight change, and 0.40 (95% CI: 0.28–0.57) in quitters with weight loss compared with continual smokers. Never smokers also had lower odds of MetS (OR = 0.54; 95% CI: 0.42–0.71) compared to continual smokers. Weight management program following smoking cessation may be necessary in clinical practice to reduce worsening of cardiometabolic risk factors related to post-cessation weight gain.
Body-limb coordination mechanism underlying speed-dependent gait transitions in sea roaches
Authors: Kano Takeshi , Ikeshita Yoshihito , Fukuhara Akira , Ishiguro Akio 
Published: February 2019

AbstractThe sea roach is an isopod with 14 legs; owing to its many degrees of freedom and coordination thereof, it can walk rapidly on rough terrain. Although there likely exists a remarkable decentralized control mechanism that facilitates fast and adaptive locomotion of sea roaches, it still remains elusive. To address this issue, we performed behavioural experiments and revealed that sea roaches often change their gait patterns depending on the locomotion speed. We suggest that the bending of the body trunk in the pitch direction is essential for the gait transitions, and we propose a decentralized control mechanism for body-limb coordination. We demonstrate this with a sea-roach-like robot whose gait transition is achieved by the proposed mechanism. This mechanism has some points in common with control mechanisms proposed for other legged animals. Thus, our findings will help unveil the common principle of legged locomotion and aid the design of multi-legged robots that move like animals.
ENLIVE: An Efficient Nonlinear Method for Calibrationless and Robust Parallel Imaging
Authors: Holme H. Christian M. , Rosenzweig Sebastian , Ong Frank , Wilke Robin N. , Lustig Michael , Uecker Martin 
Published: February 2019

AbstractRobustness against data inconsistencies, imaging artifacts and acquisition speed are crucial factors limiting the possible range of applications for magnetic resonance imaging (MRI). Therefore, we report a novel calibrationless parallel imaging technique which simultaneously estimates coil profiles and image content in a relaxed forward model. Our method is robust against a wide class of data inconsistencies, minimizes imaging artifacts and is comparably fast, combining important advantages of many conceptually different state-of-the-art parallel imaging approaches. Depending on the experimental setting, data can be undersampled well below the Nyquist limit. Here, even high acceleration factors yield excellent imaging results while being robust to noise and the occurrence of phase singularities in the image domain, as we show on different data. Moreover, our method successfully reconstructs acquisitions with insufficient field-of-view. We further compare our approach to ESPIRiT and SAKE using spin-echo and gradient echo MRI data from the human head and knee. In addition, we show its applicability to non-Cartesian imaging on radial FLASH cardiac MRI data. Using theoretical considerations, we show that ENLIVE can be related to a low-rank formulation of blind multi-channel deconvolution, explaining why it inherently promotes low-rank solutions.
Anopheline antiplatelet protein from mosquito saliva regulates blood feeding behavior
Authors: Islam Ashekul , Emran Talha Bin , Yamamoto Daisuke S. , Iyori Mitsuhiro , Amelia Fitri , Yusuf Yenni , Yamaguchi Ririka , Alam Md. Shah , Silveira Henrique , Yoshida Shigeto 
Published: February 2019

AbstractThe saliva of hematophagous arthropods is enriched with a complex mixture of antihemostatic molecules, the biological functions of which are largely unknown. Anopheline antiplatelet protein (AAPP) from malaria vector mosquito exhibits strong antiplatelet activity when bound directly to host collagen by its C-terminus and through its N-terminus with Ca2+-binding activity. To investigate the biological functions of AAPP in blood feeding behavior and malaria transmission, we generated transgenic Anopheles stephensi mosquito lines expressing anti-AAPP antibody single-chain fragment (scFv) in their salivary glands. The AAPP-specific collagen-binding activity was completely abolished by AAPP-scFv complex formation in the saliva. Probing and prediuresis time, feeding success, blood meal size, and fecundity, which are all fitness characteristics, were significantly reduced in the transgenic mosquitoes. However, oocysts number in these mosquitoes were not significantly reduced following blood meal intake from Plasmodium berghei-infected mice. These results show that although AAPP plays an important role in mosquito blood feeding, its neutralizing activity did not affect sporogonic development in our laboratory model, but its high fitness cost would pose a survival risk for parasite-infected mosquitoes in nature.
Identification of P2Y receptors involved in oleamide-suppressing inflammatory responses in murine microglia and human dendritic cells
Authors: Kita Masahiro , Ano Yasuhisa , Inoue Asuka , Aoki Junken 
Published: February 2019

AbstractMicroglia, a type of immune cell in the central nervous system, are involved in inflammation leading to neurodegenerative diseases. We previously identified oleamide from fermented dairy products as a neuroprotective compound suppressing microglial inflammation. Oleamide is an endocannabinoid and displays anti-inflammatory activity via the cannabinoid-2 (CB2) receptor; however, the mechanism underlying this anti-inflammatory activity has not been fully elucidated. Here, we found that the suppressive effect of oleamide on microglial tumor necrosis factor-α (TNF-α) production was canceled by inhibitors of G-protein-coupled receptor (GPCR) downstream signaling but not by a CB2 antagonist, suggesting that GPCRs other than CB2 are involved in the anti-inflammatory effects of oleamide. An extensive screen for GPCRs using a transforming growth factor-α shedding assay system identified P2Y1, P2Y4, P2Y6, P2Y10, and P2Y11 as candidates for the oleamide target. P2Y1 and P2Y10 agonists suppressed microglial TNF-α production, while a pan P2 receptor antagonist canceled the suppressive effect. Furthermore, we observed a relationship between the P2Y1 agonistic activities and the suppressive activities of oleamide and its analogs. Taken together, our results suggest that, in addition to CB2, P2Y type receptors are the potential targets of oleamide, and P2Y1 plays a role in the suppression of microglial inflammatory responses by oleamide. (200/200 words)
Poly-stable energy harvesting based on synergetic multistable vibration
Authors: Deng Huaxia , Du Yu , Wang Zhemin , Ye Jingchang , Zhang Jin , Ma Mengchao , Zhong Xiang 
Published: February 2019

AbstractDistributed energy sources, for example the ambient broadband vibrations, are of great importance for the development of the Internet of Things. However, for multistable vibrational energy harvesters, increasing the number of stable equilibrium states to broaden working frequency bands is very difficult. Here we present a poly-stable vibrational energy harvesting approach capable of achieving an exponentially growing maximum number of stable equilibrium states. Unlike the traditional multistable harvesters relying on an external static magnetic field, the nonlinear dynamical behaviours achieved by the proposed approach are synergetic poly-stable motions without the need of external magnets. Comparison experiments in contrast with a linear harvester demonstrate the working bandwidth widened by a factor of 41.0, the power density increased to 760% and the electricity generation raised to 178%. This demonstration of new multistable energy harvester expands the approach to achieving multistable motion and provides a new design philosophy for nonlinear vibrational energy harvesters.
Map of physical interactions between extracellular domains of Arabidopsis leucine-rich repeat receptor kinases
Authors: Mott G. Adam , Smakowska-Luzan Elwira , Pasha Asher , Parys Katarzyna , Howton Timothy C. , Neuhold Jana , Lehner Anita , Grünwald Karin , Stolt-Bergner Peggy , Provart Nicholas J. , Mukhtar M. Shahid , Desveaux Darrell , Guttman David S. , Belkhadir Youssef 
Published: February 2019

AbstractPlants use surface receptors to perceive information about many aspects of their local environment. These receptors physically interact to form both steady state and signalling competent complexes. The signalling events downstream of receptor activation impact both plant developmental and immune responses. Here, we present a comprehensive study of the physical interactions between the extracellular domains of leucine-rich repeat receptor kinases (LRR-RKs) in Arabidopsis. Using a sensitized assay, we tested reciprocal interactions among 200 of the 225 Arabidopsis LRR-RKs for a total search space of 40,000 interactions. Applying a stringent statistical cut-off and requiring that interactions performed well in both bait-prey and prey-bait orientations resulted in a high-confidence set of 567 bidirectional interactions. Additionally, we identified a total of 2,586 unidirectional interactions, which passed our stringent statistical cut-off in only one orientation. These datasets will guide further investigation into the regulatory roles of LRR-RKs in plant developmental and immune signalling decisions.
Assessing data availability and research reproducibility in hydrology and water resources
Authors: Stagge James H. , Rosenberg David E. , Abdallah Adel M. , Akbar Hadia , Attallah Nour A. , James Ryan 
Published: February 2019

AbstractThere is broad interest to improve the reproducibility of published research. We developed a survey tool to assess the availability of digital research artifacts published alongside peer-reviewed journal articles (e.g. data, models, code, directions for use) and reproducibility of article results. We used the tool to assess 360 of the 1,989 articles published by six hydrology and water resources journals in 2017. Like studies from other fields, we reproduced results for only a small fraction of articles (1.6% of tested articles) using their available artifacts. We estimated, with 95% confidence, that results might be reproduced for only 0.6% to 6.8% of all 1,989 articles. Unlike prior studies, the survey tool identified key bottlenecks to making work more reproducible. Bottlenecks include: only some digital artifacts available (44% of articles), no directions (89%), or all artifacts available but results not reproducible (5%). The tool (or extensions) can help authors, journals, funders, and institutions to self-assess manuscripts, provide feedback to improve reproducibility, and recognize and reward reproducible articles as examples for others.
Single-cell RNA-seq of cultured human adipose-derived mesenchymal stem cells
Authors: Liu Xuanyu , Xiang Qinqin , Xu Fen , Huang Jiuzuo , Yu Nanze , Zhang Qixu , Long Xiao , Zhou Zhou 
Published: February 2019

AbstractAdipose-derived mesenchymal stem cells (ADSCs) show considerable promise for clinical applications in regenerative medicine. We performed a large-scale single-cell transcriptomic sequencing of 24,358 cultured human ADSCs from three donors. We provide a high-quality dataset, which would be a valuable resource for dissecting the intrapopulation heterogeneity of cultured ADSCs as well as interrogating lineage priming patterns for any interested lineages at single-cell resolution.
A 1980–2018 global fire danger re-analysis dataset for the Canadian Fire Weather Indices
Authors: Vitolo Claudia , Di Giuseppe Francesca , Krzeminski Blazej , San-Miguel-Ayanz Jesus 
Published: February 2019

AbstractThis data descriptor documents a dataset containing over 38 years of global reanalysis of wildfire danger. It consists of seven fields to assess fuel moisture as well as fire behavior. The methodology employed to generate these data is based on the Canadian Forest Fire Weather Danger Rating and utilizes weather forcing from ERA-Interim, a global reanalysis dataset produced by the European Centre for Medium-range Weather Forecasts. Global fire danger reanalysis data are used to quantify the climatological expectation of fire danger at a certain time of the year and for any location on the globe. It can be regarded as a complementary product to the fire danger forecasts issued daily by the Global Wildfire Information System (GWIS) under the umbrella of the European Copernicus program.
Mucosal immune responses induced by oral administration recombinantBacillus subtilisexpressing the COE antigen of PEDV in newborn piglets
Authors: Wang Jialu , Huang Lulu , Mou Chunxiao , Zhang En , Wang Yongheng , Cao Yanan , Yang Qian 
Published: February 2019

AbstractPorcine epidemic diarrhea (PED) is a highly contagious disease in newborn piglets and causes substantial economic losses in the world. PED virus (PEDV) spreads by fecal–oral contact and can be prevented by oral immunization. Therefore, it is necessary to develop an effective oral vaccine against PEDV infection. Currently, Bacillus subtilis as recombinant vaccine carrier has been used for antigen delivery and proved well in immune effect and safety. The present study evaluated the immunogenicity of recombinant Bacillus subtilis (B. subtilis-RC) in piglets via oral administration. After oral immunization in piglets, B. subtilis-RC significantly increased the local mucosal immune responses. Oral administration with B. subtilis-RC significantly improved the level of specific mucosal immunoglobulin A (IgA) antibodies against PEDV infection, through enlarging the area of Peyer’s patches (PPs) and increasing the number of ileum IgA+ secreting (SIgA) cells. In the meantime, B. subtilis-RC remarkably increased the number of intraepithelial lymphocytes (IELs). We also observed that oral administration of B. subtilis-RC significantly increased CD3+T lymphocytes’ numbers and up-regulated the ratio of CD4+/CD8+ T cells. Furthermore, high titers of specific serum immunoglobulin G (IgG) revealed satisfactory systemic immune response against PEDV infection. In summary, our study demonstrated that oral administration of B. subtilis-RC could trigger a high level of local and systemic immune responses and would be a promising candidate vaccine against PEDV infection in piglets.