bluuebunny/crossref_metadata_2025_split huggingface dataset:
Long noncoding RNAs in Brassica rapa L. following vernalization
Authors: Shea Daniel J. , Nishida Namiko , Takada Satoko , Itabashi Etsuko , Takahashi Satoshi , Akter Ayasha , Miyaji Naomi , Osabe Kenji , Mehraj Hasan , Shimizu Motoki , Seki Motoaki , Kakizaki Tomohiro , Okazaki Keiichi , Dennis Elizabeth S. , Fujimoto Ryo 
Published: June 2019

AbstractBrassica rapa L. is an important agricultural crop that requires a period of prolonged cold for flowering. This process is known as vernalization. Studies have shown that long noncoding RNAs (lncRNAs) play important roles in abiotic stress responses and several cold-responsive noncoding RNAs have been suggested to be involved in vernalization. We examined the transcriptome of the Chinese cabbage inbred line (B. rapa L. var. pekinensis) RJKB-T24, and identified 1,444 long intergenic noncoding RNAs (lincRNAs), 551 natural antisense transcripts (NATs), and 93 intronic noncoding RNAs (incRNAs); 549 of the 2,088 lncRNAs significantly altered their expression in response to four weeks of cold treatment. Most differentially expressed lncRNAs did not lead to a change of expression levels in mRNAs covering or near lncRNAs, suggesting that the transcriptional responses to four weeks of cold treatment in lncRNA and mRNA are independent. However, some differentially expressed mRNAs had NATs with expression altered in the same direction. These genes were categorized as having an abiotic stress response, suggesting that the paired-expression may play a role in the transcriptional response to vernalization or cold treatment. We also identified short-term cold treatment induced NATs in BrFLC and BrMAF genes, which are involved in vernalization. The lncRNAs we identified differed from those reported in Arabidopsis thaliana, suggesting the role of lncRNAs in vernalization differ between these two species.
A preliminary examination of bacterial, archaeal, and fungal communities inhabiting different rhizocompartments of tomato plants under real-world environments
Authors: Lee Shin Ae , Kim Yiseul , Kim Jeong Myeong , Chu Bora , Joa Jae-Ho , Sang Mee Kyung , Song Jaekyeong , Weon Hang-Yeon 
Published: June 2019

AbstractPlant microbiota is a key determinant of plant health and productivity. The composition and structure of plant microbiota varies according to plant tissue and compartment, which are specific habitats for microbial colonization. To investigate the structural composition of the microbiome associated with tomato roots under natural systems, we characterized the bacterial, archaeal, and fungal communities of three belowground compartments (rhizosphere, endosphere, and bulk soil) of tomato plants collected from 23 greenhouses in 7 geographic locations of South Korea. The microbial diversity and structure varied by rhizocompartment, with the most distinctive community features found in the endosphere. The bacterial and fungal communities in the bulk soil and rhizosphere were correlated with soil physicochemical properties, such as pH, electrical conductivity, and exchangeable cation levels, while this trend was not evident in the endosphere samples. A small number of core bacterial operational taxonomic units (OTUs) present in all samples from the rhizosphere and endosphere represented more than 60% of the total relative abundance. Among these core microbes, OTUs belonging to the genera Acidovorax, Enterobacter, Pseudomonas, Rhizobium, Streptomyces, and Variovorax, members of which are known to have beneficial effects on plant growth, were more relatively abundant in the endosphere samples. A co-occurrence network analysis indicated that the microbial community in the rhizosphere had a larger and more complex network than those in the bulk soil and endosphere. The analysis also identified keystone taxa that might play important roles in microbe-microbe interactions in the community. Additionally, profiling of predicted gene functions identified many genes associated with membrane transport in the endospheric and rhizospheric communities. Overall, the data presented here provide preliminary insight into bacterial, archaeal, and fungal phylogeny, functionality, and interactions in the rhizocompartments of tomato roots under real-world environments.
Recent morphologic evolution of the German Wadden Sea
Authors: Benninghoff Markus , Winter Christian 
Published: June 2019

AbstractThe Wadden Sea is a unique and important intertidal coastal zone under the pressure of changing driving forces (i.e. sea level rise, storm surges and increasing tidal range). In this study, we characterize the recent morphologic evolution of the German part of the Wadden Sea for the time period 1998 to 2016 based on a large dataset of available digital elevation models. A sediment budget analysis reveals that the Wadden Sea is accumulating sediment. Changes in the ratio of intertidal to subtidal surface area indicate an extension of the intertidal zone. Most of the intertidal flats accumulate sediments with rates higher than the observed mean sea level rise in the German Bight, while simultaneously the subtidal mean depth increases. For the period of investigation this Wadden Sea steepening is quantified to averaged values of +7.9 mm/yr for the tidal flats and −20.0 mm/yr for the channels.
Utility of the Z-score of log-transformed A Body Shape Index (LBSIZ) in the assessment for sarcopenic obesity and cardiovascular disease risk in the United States
Authors: Chung Wankyo , Park Jung Hwan , Chung Hye Soo , Yu Jae Myung , Kim Dong Sun , Moon Shinje 
Published: June 2019

AbstractBody mass index (BMI) has limited accuracy for predicting cardiovascular diseases (CVD) and is not capable of identifying sarcopenic obesity, the combination of sarcopenia (an age-associated decline in muscle mass and physical function) and obesity. To overcome this, the z-score of the log-transformed A Body Shape Index (LBSIZ) was recently introduced as a measure of obesity using waist circumference, height, and weight. We aimed to investigate the association of LBSIZ with sarcopenic obesity and CVD, and propose appropriate cut-off values using the National Health and Nutrition Examination Survey 1999–2016 data. Of 92,062 participants, 40,468 adults (≥20 years) were included. Overall area under curve (AUC) of LBSIZ was 0.735 (95% confidence interval [CI]: 0.716–0.754) for sarcopenic obesity, and 0.695 (95% CI: 0.687–0.703) for CVD. The subgroup analysis of ethnicity/race showed similar results. Waist circumference (WC), BMI, conicity index, body roundness index (BRI), Clinica Universidad de Navarra-Body Adiposity Estimator (CUN-BAE), new BMI, and waist to height ratio (WHtR) showed a negative association with sarcopenic obesity, while LBSIZ and conicity index showed a positive association. The AUC of LBSIZ was significantly higher for sarcopenic obesity than that of conicity index (p < 0.001). The AUC of LBSIZ was significantly higher for CVD than those of parameters including WC, BMI, BRI, CUN-BAE, new BMI, and WHtR (p < 0.001). The AUC for conicity index alone was comparable to that of LBSIZ for CVD. Overall LBSIZ cut-off was 0.35 for both sarcopenic obesity (sensitivity, 65.3%; specificity, 71.5%) and CVD (sensitivity, 63.3%; specificity, 66.6%). These results may be useful not only to identify sarcopenic obesity, but also to conduct CVD risk assessment in the clinical setting.
Piezoelectric needle sensor reveals mechanical heterogeneity in human thyroid tissue lesions
Authors: Sharma Shivani , Aguilera Renato , Rao JianYu , Gimzewski James K. 
Published: June 2019

AbstractPalpable thyroid lesions are common, and although mostly benign, lethal malignant nodules do occur and may be difficult to differentiate. Here, we introduce the use of a piezoelectric system called Smart-touch fine needle (or STFN) mounted directly onto conventional biopsy needles, to evaluate abnormal tissues, through quantitative real-time measurements of variations in tissue stiffness as the needle penetrates tissue. Using well-characterized biomaterials of known stiffness and explanted animal tissue models, we first established experimental protocols for STFN measures on biological tissues, as well as optimized device design for high signal-to-noise ratio. Freshly excised patient thyroids with varying fibrotic and malignant potential revealed discrete variations in STFN based tissue stiffness/stiffness heterogeneity and correlated well with final histopathology. Our piezoelectric needle sensor reveals mechanical heterogeneity in thyroid tissue lesions and provides a foundation for the design of hand-held tools for the rapid, mechano-profiling of malignant lesions in vivo while performing fine needle aspiration (FNA).
Myocardial death and dysfunction after ischemia-reperfusion injury require CaMKIIδ oxidation
Authors: Wu Yuejin , Wang Qinchuan , Feng Ning , Granger Jonathan M. , Anderson Mark E. 
Published: June 2019

AbstractReactive oxygen species (ROS) contribute to myocardial death during ischemia-reperfusion (I/R) injury, but detailed knowledge of molecular pathways connecting ROS to cardiac injury is lacking. Activation of the Ca2+/calmodulin-dependent protein kinase II (CaMKIIδ) is implicated in myocardial death, and CaMKII can be activated by ROS (ox-CaMKII) through oxidation of regulatory domain methionines (Met281/282). We examined I/R injury in mice where CaMKIIδ was made resistant to ROS activation by knock-in replacement of regulatory domain methionines with valines (MMVV). We found reduced myocardial death, and improved left ventricular function 24 hours after I/R injury in MMVV in vivo and in vitro compared to WT controls. Loss of ATP sensitive K+ channel (KATP) current contributes to I/R injury, and CaMKII promotes sequestration of KATP from myocardial cell membranes. KATP current density was significantly reduced by H2O2 in WT ventricular myocytes, but not in MMVV, showing ox-CaMKII decreases KATP availability. Taken together, these findings support a view that ox-CaMKII and KATP are components of a signaling axis promoting I/R injury by ROS.
Simple method to detect triclofos and its metabolites in plasma of children by combined use of liquid chromatography tandem-mass spectrometry and gas chromatography-mass spectrometry
Authors: Sato Hirotaka , Ito Yuki , Inoue Miho , Nakahira Yuki , Hashimoto Satoru , Nakajima Tamie , Kamijima Michihiro 
Published: June 2019

AbstractTriclofos sodium (TCS) and chloral hydrate (CH) are widely used as sedatives for children, but no analytical method to simultaneously monitor concentrations of blood TCS, CH and their metabolites, trichloroacetic acid (TCA) and trichloroethanol (TCEOH), has been reported. The present study aimed to develop a simple analytical method for TCS and its metabolites (TCA, TCEOH and CH) in small-volume plasma from children. After acidification of specimens, TCS formic acid adduct or the metabolites derivatized using water/sulfuric acid/methanol (6:5:1, v/v) were measured by combined use of liquid chromatography tandem-mass spectrometry and gas chromatography mass-spectrometry. The limits of detection and quantification levels (µg/ml) were 0.10 and 0.29 for TCS, 0.24 and 0.72 for TCA, 0.10 and 0.31 for TCEOH, and 0.25 and 0.76 for CH, respectively. The mean recoveries were 82.8–107% for TCS, 85.4–101% for TCA, 91.6–107% for TCEOH, and 88.9–109% for CH. Within-run and between-run precision (percent of relative standard deviation, %RSD) using this method ranged from 1.1 to 15.7% and 3.6 to 13.5%, respectively, for TCS and all of its metabolites. The calibration curves were obtained with standard spiked plasma, and all of the coefficients of determination were more than 0.975. Subsequently, we applied the present method to plasma taken from five children after sedation induced by CH and TCS. In addition to TCS and CH, elevated TCA and TCEOH concentrations were detected. This new method can be applied for the pharmacokinetic analysis of TCS and its metabolites and the determination of the optimal TCS dosage in children.
Modulation of osteogenic and myogenic differentiation by a phytoestrogen formononetin via p38MAPK-dependent JAK-STAT and Smad-1/5/8 signaling pathways in mouse myogenic progenitor cells
Authors: Soundharrajan Ilavenil , Kim Da Hye , Kuppusamy Palaniselvam , Choi Ki Choon 
Published: June 2019

AbstractFormononetin (FN), a typical phytoestrogen has attracted substantial attention as a novel agent because of its diverse biological activities including, osteogenic differentiation. However, the molecular mechanisms underlying osteogenic and myogenic differentiation by FN in C2C12 progenitor cells remain unknown. Therefore the objective of the current study was to investigate the action of FN on myogenic and osteogenic differentiation and its impact on signaling pathways in C2C12 cells. FN significantly increased myogenic markers such as Myogenin, myosin heavy chains, and myogenic differentiation 1 (MyoD). In addition, the expression of osteogenic specific genes alkaline phosphatase (ALP), Run-related transcription factor 2(RUNX2), and osteocalcin (OCN) were up-regulated by FN treatment. Moreover, FN enhanced the ALP level, calcium deposition and the expression of bone morphogenetic protein isoform (BMPs). Signal transduction pathways mediated by p38 mitogen-activated protein kinase (p38MAPK), extracellular signal-related kinases (ERKs), protein kinase B (Akt), Janus kinases (JAKs), and signal transducer activator of transcription proteins (STATs) in myogenic and osteogenic differentiation after FN treatment were also examined. FN treatment activates myogenic differentiation by increasing p38MAPK and decreasing JAK1-STAT1 phosphorylation levels, while osteogenic induction was enhanced by p38MAPK dependent Smad, 1/5/8 signaling pathways in C2C12 progenitor cells.
Latitudinal and bathymetrical species richness patterns in the NW Pacific and adjacent Arctic Ocean
Authors: Saeedi Hanieh , Costello Mark J. , Warren Dan , Brandt Angelika 
Published: June 2019

AbstractGlobal scale analyses have recently revealed that the latitudinal gradient in marine species richness is bimodal, peaking at low-mid latitudes but with a dip at the equator; and that marine species richness decreases with depth in many taxa. However, these overall and independently studied patterns may conceal regional differences that help support or qualify the causes in these gradients. Here, we analysed both latitudinal and depth gradients of species richness in the NW Pacific and its adjacent Arctic Ocean. We analysed 324,916 distribution records of 17,414 species from 0 to 10,900 m depth, latitude 0 to 90°N, and longitude 100 to 180°N. Species richness per c. 50 000 km2 hexagonal cells was calculated as alpha (local average), gamma (regional total) and ES50 (estimated species for 50 records) per latitudinal band and depth interval. We found that average ES50 and gamma species richness decreased per 5° latitudinal bands and 100 m depth intervals. However, average ES50 per hexagon showed that the highest species richness peaked around depth 2,000 m where the highest total number of species recorded. Most (83%) species occurred in shallow depths (0 to 500 m). The area around Bohol Island in the Philippines had the highest alpha species richness (more than 8,000 species per 50,000 km2). Both alpha and gamma diversity trends increased from the equator to latitude 10°N, then further decreased, but reached another peak at higher latitudes. The latitudes 60–70°N had the lowest gamma and alpha diversity where there is almost no ocean in our study area. Model selection on Generalized Additive Models (GAMs) showed that the combined effects of all environmental predictors produced the best model driving species richness in both shallow and deep sea. The results thus support recent hypotheses that biodiversity, while highest in the tropics and coastal depths, is decreasing at the equator and decreases with depth below ~2000 m. While we do find the declines of species richness with latitude and depth that reflect temperature gradients, local scale richness proved poorly correlated with many environmental variables. This demonstrates that while regional scale patterns in species richness may be related to temperature, that local scale richness depends on a greater variety of variables.
Erosion and deposition beneath the Subantarctic Front since the Early Oligocene
Authors: Nicholson Uisdean , Stow Dorrik 
Published: June 2019

AbstractThe Antarctic Circumpolar Current (ACC) spills across the Falkland Plateau into the South Atlantic as a series of high-velocity jets. These currents are a driving force for global overturning circulation, and affect climate by modulating CO2 exchange between the atmosphere and ocean, but their timing of onset remains controversial. We present new evidence of strong currents associated with the Subantarctic Front (SAF) jet since the earliest Oligocene (~34 Ma) based on a widespread erosional surface on the Falkland Plateau, preserved below a 30,000 km2 contourite sand deposit. This is the largest such feature ever to be recognized, and provides the most robust constraint of the initiation of the SAF to date. By contrast, the South Falkland Slope Drift is dominated by contourite mud of Pleistocene-Recent age, substantially younger than previous estimates, indicating a significant decrease in long-term current strength at that time. As ACC strength is primarily a function of the position of the South-Westerly Winds, our data indicates that associated currents are likely to increase substantially in a warming world. Likely implications include increased upwelling and associated carbon flux from the deep ocean to the atmosphere, a positive feedback loop not included in most future projections of atmospheric CO2.
The use of photoplethysmography for assessing hypertension
Authors: Elgendi Mohamed , Fletcher Richard , Liang Yongbo , Howard Newton , Lovell Nigel H. , Abbott Derek , Lim Kenneth , Ward Rabab 
Published: June 2019

AbstractThe measurement of blood pressure (BP) is critical to the treatment and management of many medical conditions. High blood pressure is associated with many chronic disease conditions, and is a major source of mortality and morbidity around the world. For outpatient care as well as general health monitoring, there is great interest in being able to accurately and frequently measure BP outside of a clinical setting, using mobile or wearable devices. One possible solution is photoplethysmography (PPG), which is most commonly used in pulse oximetry in clinical settings for measuring oxygen saturation. PPG technology is becoming more readily available, inexpensive, convenient, and easily integrated into portable devices. Recent advances include the development of smartphones and wearable devices that collect pulse oximeter signals. In this article, we review (i) the state-of-the-art and the literature related to PPG signals collected by pulse oximeters, (ii) various theoretical approaches that have been adopted in PPG BP measurement studies, and (iii) the potential of PPG measurement devices as a wearable application. Past studies on changes in PPG signals and BP are highlighted, and the correlation between PPG signals and BP are discussed. We also review the combined use of features extracted from PPG and other physiological signals in estimating BP. Although the technology is not yet mature, it is anticipated that in the near future, accurate, continuous BP measurements may be available from mobile and wearable devices given their vast potential.
An influenza-derived membrane tension-modulating peptide regulates cell movement and morphology via actin remodeling
Authors: Masuda Toshihiro , Baba Kentarou , Nomura Takeshi , Tsujita Kazuya , Murayama Tomo , Itoh Toshiki , Takatani-Nakase Tomoka , Sokabe Masahiro , Inagaki Naoyuki , Futaki Shiroh 
Published: June 2019

AbstractTension in cell membranes is closely related to various cellular events, including cell movement and morphogenesis. Therefore, modulation of membrane tension can be a new approach for manipulating cellular events. Here, we show that an amphipathic peptide derived from the influenza M2 protein (M2[45–62]) yields lamellipodia at multiple sites in the cell. Effect of M2[45–62] on cell membrane tension was evaluated by optical tweezer. The membrane tension sensor protein FBP17 was involved in M2[45–62]-driven lamellipodium formation. Lysine-to-arginine substitution in M2[45–62] further enhanced its activity of lamellipodium formation. M2[45–62] had an ability to reduce cell motility, evaluated by scratch wound migration and transwell migration assays. An increase in neurite outgrowth was also observed after treatment with M2[45–62]. The above results suggest the potential of M2[45–62] to modulate cell movement and morphology by modulating cell membrane tension.
Measurement of the α1-proteinase inhibitor (α1-antitrypsin) of common marmoset and intestinal protein loss in wasting syndrome
Authors: Niimi Kimie , Morishita Hiromasa , Usui Masaya , Ito Reiko , Kurata Shino , Mataga Nobuko , Takahashi Eiki 
Published: June 2019

AbstractAlthough wasting marmoset syndrome (WMS) is one of the biggest problems facing captive marmoset colonies, the mechanisms underlying its pathogenesis remain unclear. In our clinical experience, it is difficult to cure WMS-affected marmosets with severe hypoalbuminemia. Thus, the mechanisms underlying hypoalbuminemia in WMS must be understood. In the present study, we investigated whether intestinal protein loss, a known reason for hypoalbuminemia, occurs in this disease. Fecal α1-proteinase inhibitor (α1-PI, also known as α1-antitrypsin) has been used to diagnose intestinal protein loss in other species. To develop an assay system for this protein, marmoset α1-PI was purified from plasma and antibodies against it were developed using the purified protein. Using the antibodies, a sandwich enzyme-linked immunosorbent assay (ELISA) to measure marmoset α1-PI was developed, and its detection sensitivity for fecal samples was ∼20-fold higher than that of a commercial kit for human α1-PI. From this ELISA, the reference intervals for serum and feces of healthy marmosets were 0.87–1.85 mg/ml and 0.53–395.58 μg/g, respectively. The average concentrations of α1-PI in serum and feces of seven WMS-affected marmosets were 1.17 mg/ml and 1357.58 μg/g, respectively. Although there were no significant differences in the serum concentrations between healthy and WMS-affected marmosets, the fecal concentrations were significantly higher in WMS-affected marmosets than in healthy individuals, suggesting that intestinal protein loss occurs in WMS. Intestinal protein loss of WMS-affected marmosets was significantly attenuated with treatment, suggesting that it is one of the mechanisms involved in the hypoalbuminemia observed in WMS.