bluuebunny/crossref_metadata_2025_split huggingface dataset:
Microsatellite analysis for differentiating the origin of renal angiomyolipoma and involved regional lymph node
Authors: Tan Ping , Xu Huan , Jiang Yong , Yang Lu , Zou Yan , Liu Liangren , Liu Nian , Cao Dehong , Fan Yu , Li Qiyuan , Wei Qiang 
Published: March 2017

AbstractRenal angiomyolipoma (AML) with the regional lymph node (LN) involved leads to a question of metastasis versus multicentric origin when their histology are similar. As the genomic instability is a common feature of cancer, we hypothesized that independently arising neoplasms in an individual patient would exhibit measurable genomic variation, facilitating the discrimination of tumor lineage and relatedness. Our study enrolled 12 patients who were diagnosed with nodal-involved renal AML at West China Hospital. Genomic DNA from kidney and lymph node lesion from individuals was analyzed through PCR-based analysis which using six microsatellite markers to identify discordant allelic variation. The results showed all 12 patients underwent surgical treatment and none suffered local recurrence or distant metastasis during the follow-up. Ten patients of the included cases showed a consistent trend that all corresponding to six microsatellite markers were detected in DNA from renal AMLs but were reduced or not observed in DNA from the paired LN. With this technique, a possible lineage relationship cannot be excluded between renal AMLs and LN. Thus when enlarged LN were found in images, active surveillance should be taken into consider; if enlarged LN were found intraoperatively, LN resection might be necessary to demonstrate their pathological nature.
Dual regulation of water retention and cell growth by a stress-associated protein (SAP) gene in Prunus
Authors: Lloret Alba , Conejero Ana , Leida Carmen , Petri César , Gil-Muñoz Francisco , Burgos Lorenzo , Badenes María Luisa , Ríos Gabino 
Published: March 2017

AbstractWe have identified a gene (PpSAP1) of Prunus persica coding for a stress-associated protein (SAP) containing Zn-finger domains A20 and AN1. SAPs have been described as regulators of the abiotic stress response in plant species, emerging as potential candidates for improvement of stress tolerance in plants. PpSAP1 was highly expressed in leaves and dormant buds, being down-regulated before bud dormancy release. PpSAP1 expression was moderately induced by water stresses and heat in buds. In addition, it was found that PpSAP1 strongly interacts with polyubiquitin proteins in the yeast two-hybrid system. The overexpression of PpSAP1 in transgenic plum plants led to alterations in leaf shape and an increase of water retention under drought stress. Moreover, we established that leaf morphological alterations were concomitant with a reduced cell size and down-regulation of genes involved in cell growth, such as GROWTH-REGULATING FACTOR (GRF)1-like, TONOPLAST INTRINSIC PROTEIN (TIP)-like, and TARGET OF RAPAMYCIN (TOR)-like. Especially, the inverse expression pattern of PpSAP1 and TOR-like in transgenic plum and peach buds suggests a role of PpSAP1 in cell expansion through the regulation of TOR pathway.
Microbial community composition is related to soil biological and chemical properties and bacterial wilt outbreak
Authors: Wang Rui , Zhang Hongchun , Sun Liguang , Qi Gaofu , Chen Shu , Zhao Xiuyun 
Published: March 2017

AbstractSoil microbes play important roles in plant growth and health. Little is known about the differences of soil microbes between healthy and bacterial wilt infected soils with Ralstonia solanacearum. By Illumina-MiSeq sequencing of 16S rRNA and 18S rRNA gene amplicons, we found the soil microbial composition and diversity were distinct between healthy and bacterial wilt infected soils. Soil microbial community varied at different plant growth stages due to changes of root exudates composition and soil pH. Healthy soils exhibited higher microbial diversity than the bacterial wilt infected soils. More abundant beneficial microbes including Bacillus, Agromyces, Micromonospora, Pseudonocardia, Acremonium, Lysobacter, Mesorhizobium, Microvirga, Bradyrhizobium, Acremonium and Chaetomium were found in the healthy soils rather than the bacterial wilt infected soils. Compared to bacterial wilt infected soils, the activities of catalase, invertase and urease, as well as soil pH, available phosphorous and potassium content, were all significantly increased in the healthy soils. In a conclusion, the higher abundance of beneficial microbes are positively related the higher soil quality, including better plant growth, lower disease incidence, and higher nutrient contents, soil enzyme activities and soil pH.
Integrative analysis of multi-omics data reveals distinct impacts of DDB1-CUL4 associated factors in human lung adenocarcinomas
Authors: Yan Hong , Bi Lei , Wang Yunshan , Zhang Xia , Hou Zhibo , Wang Qian , Snijders Antoine M. , Mao Jian-Hua 
Published: March 2017

AbstractMany DDB1-CUL4 associated factors (DCAFs) have been identified and serve as substrate receptors. Although the oncogenic role of CUL4A has been well established, specific DCAFs involved in cancer development remain largely unknown. Here we infer the potential impact of 19 well-defined DCAFs in human lung adenocarcinomas (LuADCs) using integrative omics analyses, and discover that mRNA levels of DTL, DCAF4, 12 and 13 are consistently elevated whereas VBRBP is reduced in LuADCs compared to normal lung tissues. The transcriptional levels of DCAFs are significantly correlated with their gene copy number variations. SKIP2, DTL, DCAF6, 7, 8, 13 and 17 are frequently gained whereas VPRBP, PHIP, DCAF10, 12 and 15 are frequently lost. We find that only transcriptional level of DTL is robustly, significantly and negatively correlated with overall survival across independent datasets. Moreover, DTL-correlated genes are enriched in cell cycle and DNA repair pathways. We also identified that the levels of 25 proteins were significantly associated with DTL overexpression in LuADCs, which include significant decreases in protein level of the tumor supressor genes such as PDCD4, NKX2-1 and PRKAA1. Our results suggest that different CUL4-DCAF axis plays the distinct roles in LuADC development with possible relevance for therapeutic target development.
Sprint Interval Training Induces A Sexual Dimorphism but does not Improve Peak Bone Mass in Young and Healthy Mice
Authors: Koenen Kathrin , Knepper Isabell , Klodt Madlen , Osterberg Anja , Stratos Ioannis , Mittlmeier Thomas , Histing Tina , Menger Michael D. , Vollmar Brigitte , Bruhn Sven , Müller-Hilke Brigitte 
Published: March 2017

AbstractElevated peak bone mass in early adulthood reduces the risk for osteoporotic fractures at old age. As sports participation has been correlated with elevated peak bone masses, we aimed to establish a training program that would efficiently stimulate bone accrual in healthy young mice. We combined voluntary treadmill running with sprint interval training modalities that were tailored to the individual performance limits and were of either high or intermediate intensity. Adolescent male and female STR/ort mice underwent 8 weeks of training before the hind legs were analyzed for cortical and trabecular bone parameters and biomechanical strength. Sprint interval training led to increased running speeds, confirming an efficient training. However, males and females responded differently. The males improved their running speeds in response to intermediate intensities only and accrued cortical bone at the expense of mechanical strength. High training intensities induced a significant loss of trabecular bone. The female bones showed neither adverse nor beneficial effects in response to either training intensities. Speculations about the failure to improve geometric alongside mechanical bone properties include the possibility that our training lacked sufficient axial loading, that high cardio-vascular strains adversely affect bone growth and that there are physiological limits to bone accrual.
Automated Protein Biomarker Analysis: on-line extraction of clinical samples by Molecularly Imprinted Polymers
Authors: Rossetti Cecilia , Świtnicka-Plak Magdalena A. , Grønhaug Halvorsen Trine , Cormack Peter A.G. , Sellergren Börje , Reubsaet Léon 
Published: March 2017

AbstractRobust biomarker quantification is essential for the accurate diagnosis of diseases and is of great value in cancer management. In this paper, an innovative diagnostic platform is presented which provides automated molecularly imprinted solid-phase extraction (MISPE) followed by liquid chromatography-mass spectrometry (LC-MS) for biomarker determination using ProGastrin Releasing Peptide (ProGRP), a highly sensitive biomarker for Small Cell Lung Cancer, as a model. Molecularly imprinted polymer microspheres were synthesized by precipitation polymerization and analytical optimization of the most promising material led to the development of an automated quantification method for ProGRP. The method enabled analysis of patient serum samples with elevated ProGRP levels. Particularly low sample volumes were permitted using the automated extraction within a method which was time-efficient, thereby demonstrating the potential of such a strategy in a clinical setting.
Increased chemical weathering during the deglacial to mid-Holocene summer monsoon intensification
Authors: Miriyala Pavan , Sukumaran N. P. , Nath B. Nagender , Ramamurty P. B. , Sijinkumar A. V. , Vijayagopal B. , Ramaswamy V. , Sebastian Tyson 
Published: March 2017

AbstractChemical weathering and the ensuing atmospheric carbon dioxide consumption has long been considered to work on geological time periods until recently when some modelling and natural records have shown that the weathering-related CO2 consumption can change at century to glacial-interglacial time scale. Last glacial to interglacial transition period is a best test case to understand the interplay between Pco2-temperature-chemical weathering when a pulse of rapid chemical weathering was initiated. Here we show, from a high resolution 54 ka record from the Andaman Sea in the northern Indian Ocean, that the chemical weathering responds to deglacial to mid-Holocene summer monsoon intensification in the Myanmar watersheds. The multi-proxy data (Al/K, CIA, Rb/Sr, 87Sr/86Sr for degree of weathering and 143Nd/144Nd for provenance) reveal an increase in silicate weathering with initiation of interglacial warm climate at ~17.7 ka followed by a major change at 15.5 ka. Inferred changes in chemical weathering have varied in tandem with the regional monsoonal proxies (δ18Osw-salinity changes of Northern Indian Ocean, effective Asian moisture content and δ18O records of Chinese caves) and are synchronous with changes in summer insolation at 30°N and δ18O of GISP2 implying that chemical weathering was not a later amplifier but worked in tandem with global climate change.
Collection and characterization of grapevine genetic resources (Vitis vinifera) in the Holy Land, towards the renewal of ancient winemaking practices
Authors: Drori Elyashiv , Rahimi Oshrit , Marrano Annarita , Henig Yakov , Brauner Hodaya , Salmon-Divon Mali , Netzer Yishay , Prazzoli Maria Lucia , Stanevsky Maria , Failla Osvaldo , Weiss Ehud , Grando Maria Stella 
Published: March 2017

AbstractThe importance and extent of wine consumption in all life aspects at the Holy Land is well documented. The Muslim influence in this region led to the abandonment of winemaking practices, and possible loss of indigenous wine varieties. Here we present a country wide collection of the local grapevine population including wild and cultivated forms, and its characterization by genetic, ampelographic and enological methods. The ampelographic analysis shows clear differences between Sativa and Sylvestris groups in flower, leaf and cluster parameters, and that most Sativa belong to proles orientalis. Genetic population analysis was conducted by analyzing 22 common SSR markers, determining first the unique genotypes, and internally assessing the population’s structure, showing the existence of two distinct Sativa and Sylvestris populations, and a third mixed one. Likewise, the relationship between the Israeli grapevine population and grapevine populations in Europe and parts of Asia was investigated, showing that the Israeli Sativa and Sylvestris populations cluster closely together, suggesting a common genetic source. Lastly, the enological characteristics of selected Sativa and Sylvestris genotypes are presented, demonstrating their potential for quality wine production. This research significantly contributes toward the re-establishment of indigenous and traditional local grapevine varieties into the modern international wine industry.
Structural Analysis of Human Cofilin 2/Filamentous Actin Assemblies: Atomic-Resolution Insights from Magic Angle Spinning NMR Spectroscopy
Authors: Yehl Jenna , Kudryashova Elena , Reisler Emil , Kudryashov Dmitri , Polenova Tatyana 
Published: March 2017

AbstractCellular actin dynamics is an essential element of numerous cellular processes, such as cell motility, cell division and endocytosis. Actin’s involvement in these processes is mediated by many actin-binding proteins, among which the cofilin family plays unique and essential role in accelerating actin treadmilling in filamentous actin (F-actin) in a nucleotide-state dependent manner. Cofilin preferentially interacts with older filaments by recognizing time-dependent changes in F-actin structure associated with the hydrolysis of ATP and release of inorganic phosphate (Pi) from the nucleotide cleft of actin. The structure of cofilin on F-actin and the details of the intermolecular interface remain poorly understood at atomic resolution. Here we report atomic-level characterization by magic angle spinning (MAS) NMR of the muscle isoform of human cofilin 2 (CFL2) bound to F-actin. We demonstrate that resonance assignments for the majority of atoms are readily accomplished and we derive the intermolecular interface between CFL2 and F-actin. The MAS NMR approach reported here establishes the foundation for atomic-resolution characterization of a broad range of actin-associated proteins bound to F-actin.
Identification of the metabolic alterations associated with the multidrug resistant phenotype in cancer and their intercellular transfer mediated by extracellular vesicles
Authors: Lopes-Rodrigues Vanessa , Di Luca Alessio , Mleczko Justyna , Meleady Paula , Henry Michael , Pesic Milica , Cabrera Diana , van Liempd Sebastiaan , Lima Raquel T. , O’Connor Robert , Falcon-Perez Juan M. , Vasconcelos M. Helena 
Published: March 2017

AbstractMultidrug resistance (MDR) is a serious obstacle to efficient cancer treatment. Overexpression of P-glycoprotein (P-gp) plays a significant role in MDR. Recent studies proved that targeting cellular metabolism could sensitize MDR cells. In addition, metabolic alterations could affect the extracellular vesicles (EVs) cargo and release. This study aimed to: i) identify metabolic alterations in P-gp overexpressing cells that could be involved in the development of MDR and, ii) identify a potential role for the EVs in the acquisition of the MDR. Two different pairs of MDR and their drug-sensitive counterpart cancer cell lines were used. Our results showed that MDR (P-gp overexpressing) cells have a different metabolic profile from their drug-sensitive counterparts, demonstrating decreases in the pentose phosphate pathway and oxidative phosphorylation rate; increases in glutathione metabolism and glycolysis; and alterations in the methionine/S-adenosylmethionine pathway. Remarkably, EVs from MDR cells were capable of stimulating a metabolic switch in the drug-sensitive cancer cells, towards a MDR phenotype. In conclusion, obtained results contribute to the growing knowledge about metabolic alterations in MDR cells and the role of EVs in the intercellular transfer of MDR. The specific metabolic alterations identified in this study may be further developed as targets for overcoming MDR.
Redox-sensing regulator Rex regulates aerobic metabolism, morphological differentiation, and avermectin production in Streptomyces avermitilis
Authors: Liu Xingchao , Cheng Yaqing , Lyu Mengya , Wen Ying , Song Yuan , Chen Zhi , Li Jilun 
Published: March 2017

AbstractThe regulatory role of redox-sensing regulator Rex was investigated in Streptomyces avermitilis. Eleven genes/operons were demonstrated to be directly regulated by Rex; these genes/operons are involved in aerobic metabolism, morphological differentiation, and secondary metabolism. Rex represses transcription of target genes/operons by binding to Rex operator (ROP) sequences in the promoter regions. NADH reduces DNA-binding activity of Rex to target promoters, while NAD+ competitively binds to Rex and modulates its DNA-binding activity. Rex plays an essential regulatory role in aerobic metabolism by controlling expression of the respiratory genes atpIBEFHAGDC, cydA1B1CD, nuoA1-N1, rex-hemAC1DB, hppA, and ndh2. Rex also regulates morphological differentiation by repressing expression of wblE, which encodes a putative WhiB-family transcriptional regulator. A rex-deletion mutant (Drex) showed higher avermectin production than the wild-type strain ATCC31267, and was more tolerant of oxygen limitation conditions in regard to avermectin production.
Relationships between strength and endurance parameters and air depletion rates in professional firefighters
Authors: Windisch Stephanie , Seiberl Wolfgang , Schwirtz Ansgar , Hahn Daniel 
Published: March 2017

AbstractThe aim of this study was to quantify the physical demands of a simulated firefighting circuit and to establish the relationship between job performance and endurance and strength fitness measurements. On four separate days 41 professional firefighters (39 ± 9 yr, 179.6 ± 2.3 cm, 84.4 ± 9.2 kg, BMI 26.1 ± 2.8 kg/m2) performed treadmill testing, fitness testing (strength, balance and flexibility) and a simulated firefighting exercise. The firefighting exercise included ladder climbing (20 m), treadmill walking (200 m), pulling a wire rope hoist (15 times) and crawling an orientation section (50 m). Firefighting performance during the simulated exercise was evaluated by a simple time-strain-air depletion model (TSA) taking the sum of z-transformed parameters of time to finish the exercise, strain in terms of mean heart rate, and air depletion from the breathing apparatus. Multiple regression analysis based on the TSA-model served for the identification of the physiological determinants most relevant for professional firefighting. Three main factors with great influence on firefighting performance were identified (70.1% of total explained variance): VO2peak, the time firefighter exercised below their individual ventilatory threshold and mean breathing frequency. Based on the identified main factors influencing firefighting performance we recommend a periodic preventive health screening for incumbents to monitor peak VO2 and individual ventilatory threshold.
Characterization of the polyphenol oxidase gene family reveals a novel microRNA involved in posttranscriptional regulation of PPOs in Salvia miltiorrhiza
Authors: Li Caili , Li Dongqiao , Li Jiang , Shao Fenjuan , Lu Shanfa 
Published: March 2017

AbstractSalvia miltiorrhiza is a well-known material of traditional Chinese medicine. Understanding the regulatory mechanisms of phenolic acid biosynthesis and metabolism are important for S. miltiorrhiza quality improvement. We report here that S. miltiorrhiza contains 19 polyphenol oxidases (PPOs), forming the largest PPO gene family in plant species to our knowledge. Analysis of gene structures and sequence features revealed the conservation and divergence of SmPPOs. SmPPOs were differentially expressed in plant tissues and eight of them were predominantly expressed in phloem and xylem, indicating that some SmPPOs are functionally redundant, whereas the others are associated with different physiological processes. Expression patterns of eighteen SmPPOs were significantly altered under MeJA treatment, and twelve were yeast extract and Ag+-responsive, suggesting the majority of SmPPOs are stress-responsive. Analysis of high-throughput small RNA sequences and degradome data showed that miR1444-mediated regulation of PPOs existing in P. trichocarpa is absent from S. miltiorrhiza. Instead, a subset of SmPPOs was posttranscriptionally regulated by a novel miRNA, termed Smi-miR12112. It indicates the specificity and significance of miRNA-mediated regulation of PPOs. The results shed light on the regulation of SmPPO expression and suggest the complexity of SmPPO-associated phenolic acid biosynthesis and metabolism.
Continuous transport of Pacific-derived anthropogenic radionuclides towards the Indian Ocean
Authors: Pittauer Daniela , Tims Stephen G. , Froehlich Michaela B. , Fifield L. Keith , Wallner Anton , McNeil Steven D. , Fischer Helmut W. 
Published: March 2017

AbstractUnusually high concentrations of americium and plutonium have been observed in a sediment core collected from the eastern Lombok Basin between Sumba and Sumbawa Islands in the Indonesian Archipelago. Gamma spectrometry and accelerator mass spectrometry data together with radiometric dating of the core provide a high-resolution record of ongoing deposition of anthropogenic radionuclides. A plutonium signature characteristic of the Pacific Proving Grounds (PPG) dominates in the first two decades after the start of the high yield atmospheric tests in 1950’s. Approximately 40–70% of plutonium at this site in the post 1970 period originates from the PPG. This sediment record of transuranic isotopes deposition over the last 55 years provides evidence for the continuous long-distance transport of particle-reactive radionuclides from the Pacific Ocean towards the Indian Ocean.
Experimental investigation on the coupled effect of effective stress and gas slippage on the permeability of shale
Authors: Yang Diansen , Wang Wei , Chen Weizhong , Wang Shugang , Wang Xiaoqiong 
Published: March 2017

AbstractPermeability is one of the most important parameters to evaluate gas production in shale reservoirs. Because shale permeability is extremely low, gas is often used in the laboratory to measure permeability. However, the measured apparent gas permeability is higher than the intrinsic permeability due to the gas slippage effect, which could be even more dominant for materials with nanopores. Increasing gas pressure during tests reduces gas slippage effect, but it also decreases the effective stress which in turn influences the permeability. The coupled effect of gas slippage and effective stress on shale permeability remains unclear. Here we perform laboratory experiments on Longmaxi shale specimens to explore the coupled effect. We use the pressure transient method to measure permeability under different stress and pressure conditions. Our results reveal that the apparent measured permeability is controlled by these two competing effects. With increasing gas pressure, there exists a pressure threshold at which the dominant effect on permeability switches from gas slippage to effective stress. Based on the Klinkenberg model, we propose a new conceptual model that incorporates both competing effects. Combining microstructure analysis, we further discuss the roles of stress, gas pressure and water contents on gas permeability of shale.