bluuebunny/crossref_metadata_2025_split huggingface dataset:
Nickel chelation therapy as an approach to combat multi-drug resistant enteric pathogens
Authors: Benoit Stéphane L. , Schmalstig Alan A. , Glushka John , Maier Susan E. , Edison Arthur S. , Maier Robert J. 
Published: September 2019

AbstractThe nickel (Ni)-specific chelator dimethylglyoxime (DMG) has been used for many years to detect, quantitate or decrease Ni levels in various environments. Addition of DMG at millimolar levels has a bacteriostatic effect on some enteric pathogens, including multidrug resistant (MDR) strains of Salmonella Typhimurium and Klebsiella pneumoniae. DMG inhibited activity of two Ni-containing enzymes, Salmonella hydrogenase and Klebsiella urease. Oral delivery of nontoxic levels of DMG to mice previously inoculated with S. Typhimurium led to a 50% survival rate, while 100% of infected mice in the no-DMG control group succumbed to salmonellosis. Pathogen colonization numbers from livers and spleens of mice were 10- fold reduced by DMG treatment of the Salmonella-infected mice. Using Nuclear Magnetic Resonance, we were able to detect DMG in the livers of DMG-(orally) treated mice. Inoculation of Galleria mellonella (wax moth) larvae with DMG prior to injection of either MDR K. pneumoniae or MDR S. Typhimurium led to 40% and 60% survival, respectively, compared to 100% mortality of larvae infected with either pathogen, but without prior DMG administration. Our results suggest that DMG-mediated Ni-chelation could provide a novel approach to combat enteric pathogens, including recalcitrant multi-drug resistant strains.
Cold Preflush of Porcine Kidney Grafts Prior to Normothermic Machine Perfusion Aggravates Ischemia Reperfusion Injury
Authors: Fabry Gregor , Doorschodt Benedict M. , Grzanna Tim , Boor Peter , Elliott Aaron , Stollenwerk André , Tolba René H. , Rossaint Rolf , Bleilevens Christian 
Published: September 2019

AbstractNormothermic machine perfusion (NMP) of kidney grafts is a promising new preservation method to improve graft quality and clinical outcome. Routinely, kidneys are washed out of blood remnants and cooled using organ preservation solutions prior to NMP. Here we assessed the effect of cold preflush compared to direct NMP. After 30 min of warm ischemia, porcine kidneys were either preflushed with cold histidine-tryptophan-ketoglutarate solution (PFNMP group) prior to NMP or directly subjected to NMP (DNMP group) using a blood/buffer solution. NMP was performed at a perfusion pressure of 75 mmHg for 6 h. Functional parameters were assessed as well as histopathological and biochemical analyses. Renal function as expressed by creatinine clearance, fractional excretion of sodium and total output of urine was inferior in PFNMP. Urine protein and neutrophil gelatinase-associated lipocalin (NGAL) concentrations as markers for kidney damage were significantly higher in the PFNMP group. Additionally, increased osmotic nephropathy was found after PFNMP. This study demonstrated that cold preflush prior to NMP aggravates ischemia reperfusion injury in comparison to direct NMP of warm ischemia-damaged kidney grafts. With increasing use of NMP systems for kidneys and other organs, further research into graft flushing during retrieval is warranted.
The role of FRIGIDA and FLOWERING LOCUS C genes in flowering time of Brassica rapa leafy vegetables
Authors: Takada Satoko , Akter Ayasha , Itabashi Etsuko , Nishida Namiko , Shea Daniel J. , Miyaji Naomi , Mehraj Hasan , Osabe Kenji , Shimizu Motoki , Takasaki-Yasuda Takeshi , Kakizaki Tomohiro , Okazaki Keiichi , Dennis Elizabeth S. , Fujimoto Ryo 
Published: September 2019

AbstractThere is a wide variation of flowering time among lines of Brassica rapa L. Most B. rapa leafy (Chinese cabbage etc.) or root (turnip) vegetables require prolonged cold exposure for flowering, known as vernalization. Premature bolting caused by low temperature leads to a reduction in the yield/quality of these B. rapa vegetables. Therefore, high bolting resistance is an important breeding trait, and understanding the molecular mechanism of vernalization is necessary to achieve this goal. In this study, we demonstrated that BrFRIb functions as an activator of BrFLC in B. rapa. We showed a positive correlation between the steady state expression levels of the sum of the BrFLC paralogs and the days to flowering after four weeks of cold treatment, suggesting that this is an indicator of the vernalization requirement. We indicate that BrFLCs are repressed by the accumulation of H3K27me3 and that the spreading of H3K27me3 promotes stable FLC repression. However, there was no clear relationship between the level of H3K27me3 in the BrFLC and the vernalization requirement. We also showed that if there was a high vernalization requirement, the rate of repression of BrFLC1 expression following prolonged cold treatments was lower.
Chemical Profiling of Volatile Organic Compounds in the Headspace of Algal Cultures as Early Biomarkers of Algal Pond Crashes
Authors: Reese Kristen L. , Fisher Carolyn L. , Lane Pamela D. , Jaryenneh James D. , Moorman Matthew W. , Jones A. Daniel , Frank Matthias , Lane Todd W. 
Published: September 2019

AbstractAlgae ponds used in industrial biomass production are susceptible to pathogen or grazer infestation, resulting in pond crashes with high economic costs. Current methods to monitor and mitigate unhealthy ponds are hindered by a lack of early indicators that precede culture crash. We used solid-phase microextraction (SPME) coupled with gas chromatography-mass spectrometry (GC-MS) to identify volatiles emitted from healthy and rotifer infested cultures of Microchloropsis salina. After 48 hours of algal growth, marine rotifers, Brachionus plicatilis, were added to the algae cultures and volatile organic compounds (VOC) were sampled from the headspace using SPME fibers. A GC-MS approach was used in an untargeted analysis of VOCs, followed by preliminary identification. The addition of B. plicatilis to healthy cultures of M. salina resulted in decreased algal cell numbers, relative to uninfected controls, and generated trans-β-ionone and β-cyclocitral, which were attributed to carotenoid degradation. The abundances of the carotenoid-derived VOCs increased with rotifer consumption of algae. Our results indicate that specific VOCs released by infected algae cultures may be early indicators for impending pond crashes, providing a useful tool to monitor algal biomass production and pond crash prevention.
The soil bacterial and fungal diversity were determined by the stoichiometric ratios of litter inputs: evidence from a constructed wetland
Authors: Ping Yunmei , Pan Xu , Li Wei , Wang Jinzhi , Cui Lijuan 
Published: September 2019

AbstractPlant litter is an important component in wetland ecosystems, and the role of plant litter decomposition is considered to be important for wetland ecosystem functions and services. However, the consequences of litter inputs have seldom been experimentally tested in real ecosystems such as constructed wetlands (CWs). The enriched nutrients in CWs might weaken the role of litter inputs on soil carbon and nitrogen cycling. Here, we conducted a two-month field experiment to examine the effects of litter inputs on the soils in CWs. Our results showed that litter inputs significantly affected soil microbial (bacterial and fungi) diversities and properties (soil total nitrogen and nitrogen isotopes), and litter species with higher stoichiometry ratios, i.e. C/N, C/P and N/P led to higher microbial diversities. However, litter species had no or weak effects on microbial activities (CO2and CH4flux) or on the relative abundance of microbial communities, indicating that other environmental factors in such a CW might have stronger effects on those factors than litter inputs. These results highlighted the importance of submerged plant litter in nutrient-rich wetland ecosystems and provide potential tools for managers to improve the ecosystem functions and/or services via altering microbial diversities.
RETRACTED ARTICLE: Discrimination of urinary exosomes from microvesicles by lipidomics using thin layer liquid chromatography (TLC) coupled with MALDI-TOF mass spectrometry
Authors: Singhto Nilubon , Vinaiphat Arada , Thongboonkerd Visith 
Published: September 2019

AbstractUrinary extracellular vesicles (EVs), including microvesicles and exosomes, play several important roles in cell biology and serve as potential biomarkers in various kidney diseases. Although they have differential biophysical properties, specific biomarkers are required to discriminate these EVs during isolation/purification. The present study aimed to define differential lipidome profiles of urinary microvesicles vs. exosomes. Urine samples collected from eight healthy individuals were pooled and underwent lipid extraction using 2:1(v/v) chloroform/methanol. The recovered lipids were resolved by thin layer liquid chromatography (TLC) and analyzed by MALDI-TOF MS. From three and five TLC bands observed in microvesicles and exosomes, respectively, several fatty acids, glycerolipids and phospholipids were identified from both EVs without clear differential patterns. However, their sphingolipid profiles were unique. Ceramide phosphates (CerP), hexosyl sphingoid bases (HexSph), lactosyl ceramides (LacCer), mannosyl di-PI-ceramides (M(IP)2 C), sulfatides hexosyl ceramide (SHexCer) and sulfatides hexoxyl sphingoid bases (SHexSph) were detectable only in urinary exosomes, whereas phosphatidylinositol ceramides (PI-Cer) were detectable only in urinary microvesicles. The presence of CerP only in urinary exosomes was successfully validated by dot blot analysis. Our extensive lipidome analyses of urinary microvesicles vs. exosomes provide potential lipidome markers to discriminate exosomes from microvesicles and may lead to better understanding of EVs biogenesis.
Characteristics and Evolution of sill-driven off-axis hydrothermalism in Guaymas Basin – the Ringvent site
Authors: Teske Andreas , McKay Luke J. , Ravelo Ana Christina , Aiello Ivano , Mortera Carlos , Núñez-Useche Fernando , Canet Carles , Chanton Jeffrey P. , Brunner Benjamin , Hensen Christian , Ramírez Gustavo A. , Sibert Ryan J. , Turner Tiffany , White Dylan , Chambers Christopher R. , Buckley Andrew , Joye Samantha B. , Soule S. Adam , Lizarralde Daniel 
Published: September 2019

AbstractThe Guaymas Basin spreading center, at 2000 m depth in the Gulf of California, is overlain by a thick sedimentary cover. Across the basin, localized temperature anomalies, with active methane venting and seep fauna exist in response to magma emplacement into sediments. These sites evolve over thousands of years as magma freezes into doleritic sills and the system cools. Although several cool sites resembling cold seeps have been characterized, the hydrothermally active stage of an off-axis site was lacking good examples. Here, we present a multidisciplinary characterization of Ringvent, an ~1 km wide circular mound where hydrothermal activity persists ~28 km northwest of the spreading center. Ringvent provides a new type of intermediate-stage hydrothermal system where off-axis hydrothermal activity has attenuated since its formation, but remains evident in thermal anomalies, hydrothermal biota coexisting with seep fauna, and porewater biogeochemical signatures indicative of hydrothermal circulation. Due to their broad potential distribution, small size and limited life span, such sites are hard to find and characterize, but they provide critical missing links to understand the complex evolution of hydrothermal systems.
Persistent homology of unweighted complex networks via discrete Morse theory
Authors: Kannan Harish , Saucan Emil , Roy Indrava , Samal Areejit 
Published: September 2019

AbstractTopological data analysis can reveal higher-order structure beyond pairwise connections between vertices in complex networks. We present a new method based on discrete Morse theory to study topological properties of unweighted and undirected networks using persistent homology. Leveraging on the features of discrete Morse theory, our method not only captures the topology of the clique complex of such graphs via the concept of critical simplices, but also achieves close to the theoretical minimum number of critical simplices in several analyzed model and real networks. This leads to a reduced filtration scheme based on the subsequence of the corresponding critical weights, thereby leading to a significant increase in computational efficiency. We have employed our filtration scheme to explore the persistent homology of several model and real-world networks. In particular, we show that our method can detect differences in the higher-order structure of networks, and the corresponding persistence diagrams can be used to distinguish between different model networks. In summary, our method based on discrete Morse theory further increases the applicability of persistent homology to investigate the global topology of complex networks.
Plasma metabolites associated with homeostatic model assessment of insulin resistance: metabolite-model design and external validation
Authors: Hernández-Alonso Pablo , García-Gavilán Jesús , Camacho-Barcia Lucía , Sjödin Anders , Hansen Thea T. , Harrold Jo , Salas-Salvadó Jordi , Halford Jason C. G. , Canudas Silvia , Bulló Mònica 
Published: September 2019

AbstractDifferent plasma metabolites have been related to insulin resistance (IR). However, there is a lack of metabolite models predicting IR with external validation. The aim of this study is to identify a multi-metabolite model associated to the homeostatic model assessment (HOMA)-IR values. We performed a cross-sectional metabolomics analysis of samples collected from overweight and obese subjects from two independent studies. The training step was performed in 236 subjects from the SATIN study and validated in 102 subjects from the GLYNDIET study. Plasma metabolomics profile was analyzed using three different approaches: GC/quadrupole-TOF, LC/quadrupole-TOF, and nuclear magnetic resonance (NMR). Associations between metabolites and HOMA-IR were assessed using elastic net regression analysis with a leave-one-out cross validation (CV) and 100 CV runs. HOMA-IR was analyzed both as linear and categorical (median or lower versus higher than the median). Receiver operating characteristic curves were constructed based on metabolites’ weighted models. A set of 30 metabolites discriminating extremes of HOMA-IR were consistently selected. These metabolites comprised some amino acids, lipid species and different organic acids. The area under the curve (AUC) for the discrimination between HOMA-IR extreme categories was 0.82 (95% CI: 0.74–0.90), based on the multi-metabolite model weighted with the regression coefficients of metabolites in the validation dataset. We identified a set of metabolites discriminating between extremes of HOMA-IR and able to predict HOMA-IR with high accuracy.
A multicentre clinical validation of AminoIndex Cancer Screening (AICS)
Authors: Mikami Haruo , Kimura Osamu , Yamamoto Hiroshi , Kikuchi Shinya , Nakamura Yohko , Ando Toshihiko , Yamakado Minoru 
Published: September 2019

AbstractAminoIndex Cancer Screening (AICS) is a novel cancer screening test based on plasma free amino acid (PFAA) levels. This system categorises subjects as rank A, B, or C in order of increasing probability of each cancer incidence. The current study aimed to validate the potential of AICS for cancer detection. AICS values were determined from the PFAA levels in subjects examined at Chiba Cancer Center Cohort, Mitsui Memorial Hospital, and Saihaku Hospital, and the cancer incidence was investigated. The sensitivities of rank C for cancer diagnosis within 1 year after AICS examination were 83.3% (10/12) for gastric, 50.0% (2/4) for lung, 46.2% (6/13) for colorectal, 50.0% (8/16) for prostate, 43.8% (7/16) for breast, and 50.0% (1/2) for uterine/ovarian cancer. The total cancer detection rate via AICS was 0.33% (34/10,245). The sensitivities during the maximum follow-up period of 6.2 years were 51.7% (15/29) for gastric, 18.2% (2/11) for lung, 28.6% (8/28) for colorectal, 36.4% (8/22) for prostate, 29.0% (9/31) for breast, and 33.3% (2/6) for uterine/ovarian cancers. In conclusion, AICS is a more useful method for evaluating the probability of cancer incidence than for predicting onset, suggesting that annual AICS should be recommended to detect any malignancy.
Sensory sensitivity as a link between concussive traumatic brain injury and PTSD
Authors: Hoffman Ann N. , Lam Jamie , Hovda David A. , Giza Christopher C. , Fanselow Michael S. 
Published: September 2019

AbstractTraumatic brain injury (TBI) is one of the most common injuries to military personnel, a population often exposed to stressful stimuli and emotional trauma. Changes in sensory processing after TBI might contribute to TBI-post traumatic stress disorder (PTSD) comorbidity. Combining an animal model of TBI with an animal model of emotional trauma, we reveal an interaction between auditory sensitivity after TBI and fear conditioning where 75 dB white noise alone evokes a phonophobia-like phenotype and when paired with footshocks, fear is robustly enhanced. TBI reduced neuronal activity in the hippocampus but increased activity in the ipsilateral lateral amygdala (LA) when exposed to white noise. The white noise effect in LA was driven by increased activity in neurons projecting from ipsilateral auditory thalamus (medial geniculate nucleus). These data suggest that altered sensory processing within subcortical sensory-emotional circuitry after TBI results in neutral stimuli adopting aversive properties with a corresponding impact on facilitating trauma memories and may contribute to TBI-PTSD comorbidity.
Legumes display common and host-specific responses to the rhizobial cellulase CelC2 during primary symbiotic infection
Authors: Menéndez E. , Robledo M. , Jiménez-Zurdo J. I. , Velázquez E. , Rivas R. , Murray J. D. , Mateos P. F. 
Published: September 2019

AbstractPrimary infection of legumes by rhizobia involves the controlled localized enzymatic breakdown of cell walls at root hair tips. Previous studies determined the role of rhizobial CelC2 cellulase in different steps of the symbiotic interaction Rhizobium leguminosarum-Trifolium repens. Recent findings also showed that CelC2 influences early signalling events in the Ensifer meliloti-Medicago truncatula interaction. Here, we have monitored the root hair phenotypes of two legume plants, T. repens and M. sativa, upon inoculation with strains of their cognate and non-cognate rhizobial species, R. leguminosarum bv trifolii and E. meliloti, (over)expressing the CelC2 coding gene, celC. Regardless of the host, CelC2 specifically elicited ‘hole-on-the-tip’ events (Hot phenotype) in the root hair apex, consistent with the role of this endoglucanase in eroding the noncrystalline cellulose found in polarly growing cell walls. Overproduction of CelC2 also increased root hair tip redirections (RaT phenotype) events in both cognate and non-cognate hosts. Interestingly, heterologous celC expression also induced non-canonical alterations in ROS (Reactive Oxygen Species) homeostasis at root hair tips of Trifolium and Medicago. These results suggest the concurrence of shared unspecific and host-related plant responses to CelC2 during early steps of symbiotic rhizobial infection. Our data thus identify CelC2 cellulase as an important determinant of events underlying early infection of the legume host by rhizobia.
Widespread distribution of supraglacial lakes around the margin of the East Antarctic Ice Sheet
Authors: Stokes Chris R. , Sanderson Jack E. , Miles Bertie W. J. , Jamieson Stewart S. R. , Leeson Amber A. 
Published: September 2019

AbstractSupraglacial lakes are important to ice sheet mass balance because their development and drainage has been linked to changes in ice flow velocity and ice shelf disintegration. However, little is known about their distribution on the world’s largest ice sheet in East Antarctica. Here, we use ~5 million km2 of high-resolution satellite imagery to identify >65,000 lakes (>1,300 km2) that formed around the peak of the melt season in January 2017. Lakes occur in most marginal areas where they typically develop at low elevations (<100 m) and on low surface slopes (<1°), but they can exist 500 km inland and at elevations >1500 m. We find that lakes often cluster a few kilometres down-ice from grounding lines and ~60% (>80% by area) develop on ice shelves, including some potentially vulnerable to collapse driven by lake-induced hydro-fracturing. This suggests that parts of the ice sheet may be highly sensitive to climate warming.
NRF2-dependent gene expression promotes ciliogenesis and Hedgehog signaling
Authors: Martin-Hurtado Ana , Martin-Morales Raquel , Robledinos-Antón Natalia , Blanco Ruth , Palacios-Blanco Ines , Lastres-Becker Isabel , Cuadrado Antonio , Garcia-Gonzalo Francesc R. 
Published: September 2019

AbstractThe transcription factor NRF2 is a master regulator of cellular antioxidant and detoxification responses, but it also regulates other processes such as autophagy and pluripotency. In human embryonic stem cells (hESCs), NRF2 antagonizes neuroectoderm differentiation, which only occurs after NRF2 is repressed via a Primary Cilia-Autophagy-NRF2 (PAN) axis. However, the functional connections between NRF2 and primary cilia, microtubule-based plasma membrane protrusions that function as cellular antennae, remain poorly understood. For instance, nothing is known about whether NRF2 affects cilia, or whether cilia regulation of NRF2 extends beyond hESCs. Here, we show that NRF2 and primary cilia reciprocally regulate each other. First, we demonstrate that fibroblasts lacking primary cilia have higher NRF2 activity, which is rescued by autophagy-activating mTOR inhibitors, indicating that the PAN axis also operates in differentiated cells. Furthermore, NRF2 controls cilia formation and function. NRF2-null cells grow fewer and shorter cilia and display impaired Hedgehog signaling, a cilia-dependent pathway. These defects are not due to increased oxidative stress or ciliophagy, but rather to NRF2 promoting expression of multiple ciliogenic and Hedgehog pathway genes. Among these, we focused on GLI2 and GLI3, the transcription factors controlling Hh pathway output. Both their mRNA and protein levels are reduced in NRF2-null cells, consistent with their gene promoters containing consensus ARE sequences predicted to bind NRF2. Moreover, GLI2 and GLI3 fail to accumulate at the ciliary tip of NRF2-null cells upon Hh pathway activation. Given the importance of NRF2 and ciliary signaling in human disease, our data may have important biomedical implications.